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Application of Bioinformatics to Unravel the Molecular Mechanisms of Cancer...
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Application of Bioinformatics to Unravel the Molecular Mechanisms of Cancer Biology

A special issue of Biology (ISSN 2079-7737). This special issue belongs to the section "Biochemistry and Molecular Biology".

Deadline for manuscript submissions: 31 May 2025 | Viewed by 5900

Special Issue Editor

Dr. Yuanyan Xiong

E-Mail Website
Guest Editor
Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, China
Interests: cancer biology; bioinformatics; genetics; epigenetics; transcriptomics; tumorigenesis
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Cancer is a heterogeneous group of diseases characterized by uncontrolled cell growth, metastasis, and invasiveness. Although significant progress has been made in cancer biology research, the underlying mechanisms of carcinogenesis remain incompletely understood. Bioinformatics can accelerate the elucidation of key molecular pathways and networks driving cancer progression. This Special Issue aims to focus on the application of bioinformatics in unraveling the genetic and epigenetic mechanisms underlying cancer initiation and advancement. We invite submissions of original research papers covering integrative analyses of cancer genomics, transcriptomics, and epigenomics data to gain deeper insights into the molecular mechanisms of cancer and facilitate the discovery of cancer biomarkers and novel drug targets.

Dr. Yuanyan Xiong
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. Biology 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 2700 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

  • cancer biology
  • bioinformatics
  • genetics
  • epigenetics
  • transcriptomics

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Published Papers (4 papers)

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Research

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21 pages, 3703 KiB  
Article
Multi-Omics Profiling Unveils the Complexity and Dynamics of Immune Infiltrates in Intrahepatic Cholangiocarcinoma
by Xuan Li, Yan Wang, Renchu Guan, Nan Sheng and Shuangquan Zhang
Biology 2024, 13(10), 816; https://doi.org/10.3390/biology13100816 - 11 Oct 2024
Cited by 1 | Viewed by 1331
Abstract
Intrahepatic cholangiocarcinoma (ICC) is a highly heterogeneous malignancy. The reasons behind the global rise in the incidence of ICC remain unclear, and there exists limited knowledge regarding the immune cells within the tumor microenvironment (TME). In this study, a more comprehensive analysis of [...] Read more.
Intrahepatic cholangiocarcinoma (ICC) is a highly heterogeneous malignancy. The reasons behind the global rise in the incidence of ICC remain unclear, and there exists limited knowledge regarding the immune cells within the tumor microenvironment (TME). In this study, a more comprehensive analysis of multi-omics data was performed using machine learning methods. The study found that the immunoactivity of B cells, macrophages, and T cells in the infiltrating immune cells of ICC exhibits a significantly higher level of immunoactivity in comparison to other immune cells. During the immune sensing and response, the effect of antigen-presenting cells (APCs) such as B cells and macrophages on activating NK cells was weakened, while the effect of activating T cells became stronger. Simultaneously, four distinct subpopulations, namely BLp, MacrophagesLp, BHn, and THn, have been identified from the infiltrating immune cells, and their corresponding immune-related marker genes have been identified. The immune sensing and response model of ICC has been revised and constructed based on our current comprehension. This study not only helps to deepen the understanding the heterogeneity of infiltrating immune cells in ICC, but also may provide valuable insights into the diagnosis, evaluation, treatment, and prognosis of ICC. Full article
(This article belongs to the Special Issue Application of Bioinformatics to Unravel the Molecular Mechanisms of Cancer Biology)
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14 pages, 1700 KiB  
Article
Cell Migration–Proliferation Dichotomy in Cancer: Biological Fact or Experimental Artefact?
by Abdulaziz Alfahed
Biology 2024, 13(10), 753; https://doi.org/10.3390/biology13100753 - 24 Sep 2024
Cited by 1 | Viewed by 1658
Abstract
The migration–proliferation dichotomy (MPD) has long been observed in cultured cancer cells. This phenomenon is not only relevant to tumour progression but may also have therapeutic significance in clinical cancer. However, MPD has rarely been investigated in primary cancer. This study aimed to [...] Read more.
The migration–proliferation dichotomy (MPD) has long been observed in cultured cancer cells. This phenomenon is not only relevant to tumour progression but may also have therapeutic significance in clinical cancer. However, MPD has rarely been investigated in primary cancer. This study aimed to either confirm or disprove the existence of MPD in primary cancer. Using primary gastric, colorectal and prostate cancer (GC, CRC and PCa) cohorts from the Cancer Genome Atlas and Memorial Sloan Kettering Cancer Center, this study interrogated the MPD phenomenon by utilising RNA–Seq-based proliferation (CIN70 signature) and migration (epithelial-mesenchymal transition) indices, as well as gene set enrichment analyses (GSEA). Alternative hypothetical migration–proliferation models—The simultaneous migration–proliferation (SMP) and phenotype–refractory (PR) models—were compared to the MPD model by probing the migration–proliferation relationships within cancer stages and between early- and late-stage diseases using chi-square and independent T tests, z-score statistics and GSEA. The results revealed an inverse relationship between migration and proliferation signatures overall in the GC, CRC and PCa cohorts, as well as in early- and late-stage diseases. Additionally, a shift in proliferation- to migration dominance was observed from early- to late-stage diseases in the GC and CRC cohorts but not in the PCa cohorts, which showed enhanced proliferation dominance in metastatic tumours compared to primary cancers. The above features exhibited by the cancer cohorts are in keeping with the MPD model of the migration–proliferation relationship at the cellular level and exclude the SMP and PR migration–proliferation models. Full article
(This article belongs to the Special Issue Application of Bioinformatics to Unravel the Molecular Mechanisms of Cancer Biology)
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15 pages, 5753 KiB  
Article
Identification and Validation of eRNA as a Prognostic Indicator for Cervical Cancer
by Lijing Huang, Jingkai Zhang, Zhou Songyang and Yuanyan Xiong
Biology 2024, 13(4), 227; https://doi.org/10.3390/biology13040227 - 29 Mar 2024
Viewed by 1744
Abstract
The survival of CESC patients is closely related to the expression of enhancer RNA (eRNA). In this work, we downloaded eRNA expression, clinical, and gene expression data from the TCeA and TCGA portals. A total of 7936 differentially expressed eRNAs were discovered by [...] Read more.
The survival of CESC patients is closely related to the expression of enhancer RNA (eRNA). In this work, we downloaded eRNA expression, clinical, and gene expression data from the TCeA and TCGA portals. A total of 7936 differentially expressed eRNAs were discovered by limma analysis, and the relationship between these eRNAs and survival was analyzed by univariate Cox hazard analysis, LASSO regression, and multivariate Cox hazard analysis to obtain an 8-eRNA model. Risk score heat maps, KM curves, ROC analysis, robustness analysis, and nomograms further indicate that this 8-eRNA model is a novel indicator with high prognostic performance independent of clinicopathological classification. The model divided patients into high-risk and low-risk groups, compared pathway diversity between the two groups through GSEA analysis, and provided potential therapeutic agents for high-risk patients. Full article
(This article belongs to the Special Issue Application of Bioinformatics to Unravel the Molecular Mechanisms of Cancer Biology)
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Review

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20 pages, 5703 KiB  
Review
Factors Contributing to the High Malignancy Level of Cholangiocarcinoma and Its Epidemiology: Literature Review and Data
by Xuan Li, Renchu Guan and Shuangquan Zhang
Biology 2025, 14(4), 351; https://doi.org/10.3390/biology14040351 - 28 Mar 2025
Viewed by 498
Abstract
CCA is a highly desmoplastic malignant cancer and is the second most common primary liver malignancy after hepatocellular carcinoma (HCC), accounting for approximately 15% of all primary liver tumors. CCA has a poor prognosis, with an average five-year survival rate of 9%, which [...] Read more.
CCA is a highly desmoplastic malignant cancer and is the second most common primary liver malignancy after hepatocellular carcinoma (HCC), accounting for approximately 15% of all primary liver tumors. CCA has a poor prognosis, with an average five-year survival rate of 9%, which is lower than that of pancreatic cancer. Although considerable efforts have been invested into the genomics, epigenetics, and risk factors, very little is known about what might have been the key causes for the high malignancy level of CCA. In this review, we analyze the incidence and mortality of CCA in different regions based on data from 1994 to 2022 obtained from the International Agency for Research on Cancer (IARC), discuss the current status of treatment of the disease, and focus on what might be the main factors contributing to the high malignancy level of CCA: alkalosis caused by the Fenton reaction, hypoxia, and the TIME. The review includes studies published from 1979 to 2024, aiming to provide an updated synthesis of basic early classical theoretical knowledge and current knowledge about CCA. By revealing the epidemiological characteristics of CCA, the potential mechanisms of high malignancy, and the current challenges of treatment, this review aims to provide new directions for future cancer research, promote the development of personalized treatment strategies, and facilitate a deeper understanding and the more effective management of CCA worldwide. Full article
(This article belongs to the Special Issue Application of Bioinformatics to Unravel the Molecular Mechanisms of Cancer Biology)
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