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Genome Organization and Regulation of Its Activity in Cancer

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: closed (30 November 2022) | Viewed by 6459

Special Issue Editors


E-Mail Website1 Website2
Guest Editor
Institute of Computer Science, Polish Academy of Sciences, 01-248 Warsaw, Poland
Interests: epigenetic marks; transcriptomic regulation; DNA methylation; cancer; glioma; population genetics

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Guest Editor
Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
Interests: molecular oncology; transcriptomics; genomics and epigenomics

Special Issue Information

Dear Colleagues, 

Understanding genome organization and its activity is vital for discovering the disorders in signalling pathways and biological mechanisms that lead to human diseases, including cancer development. The tightly regulated process of transcription is very often highly dysregulated in oncogenic processes. Changes in chromatin organization, activity and accessibility can lead to tremendous modifications in transcriptomic profiles. Direct alterations in DNA activity caused by abnormally methylated DNA are recognized as early oncogenic changes that have already been reported for many human cancer types. Changes in chromatin activity introduced by histone modifications or alterations in DNA methylation affect the transcription factor binding affinity to DNA sequences, which results in either the inhibition or activation of the target genes. The last decade brought a breakthrough in technological and computational advances that led to the collection of petabytes of data that were created in order to decipher the associations between elements of genome regulatory machinery and human disease development. In this Special Issue, we aim to summarize a variety of aspects of these transcription regulatory layers and present the new nature of genomic complexity and/or new methods to study genomic organization.

Dr. Michal J. Dabrowski
Dr. Bartosz Wojtas
Guest Editors

Manuscript Submission Information

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Keywords

  • cancer
  • chromatin organization
  • computational biology
  • DNA methylation
  • epigenomics
  • genome
  • histone modifications
  • molecular oncology
  • transcription factors
  • transcriptomics

Published Papers (2 papers)

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Research

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16 pages, 6171 KiB  
Article
Pancancer Analysis of the Oncogenic and Prognostic Role of NOL7: A Potential Target for Carcinogenesis and Survival
by Qiaojun Liu, Renjian Xie and Yumei Li
Int. J. Mol. Sci. 2022, 23(17), 9611; https://doi.org/10.3390/ijms23179611 - 25 Aug 2022
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Abstract
Despite growing evidence suggesting the critical function of NOL7 in cancer initiation and development, a systematic pancancer analysis of NOL7 is lacking. Herein, we present a comprehensive study of NOL7 which aimed to explore its potential role and detailed mechanisms across 33 human [...] Read more.
Despite growing evidence suggesting the critical function of NOL7 in cancer initiation and development, a systematic pancancer analysis of NOL7 is lacking. Herein, we present a comprehensive study of NOL7 which aimed to explore its potential role and detailed mechanisms across 33 human tumors based on The Cancer Genome Atlas (TCGA) and Clinical Proteomic Tumor Analysis Consortium (CATPAC) databases. As a result, both gene and protein levels of NOL7 were found to be increased in various tumor tissues, including breast invasive carcinoma (BRCA), colon adenocarcinoma (COAD), hepatocellular carcinoma (LIHC), lung adenocarcinoma (LUAD), and head and neck squamous cell carcinoma (HNSC) as compared with corresponding normal tissues. Meanwhile, dysregulated NOL7 expression was found to be closely related to pathological stage and prognosis in several cancers, including LIHC, ovarian serous cystadenocarcinoma (OV), and bladder urothelial carcinoma (BLCA). The DNA methylation level of NOL7 was found to be decreased in most cancers and to be negatively associated with NOL7 expression. Furthermore, NOL7 expression was determined to be significantly associated with levels of infiltrating cells and immune checkpoint genes, including HMGB1. Analysis of NOL7-related genes revealed that RNA metabolism pathways, including “ribosome biogenesis”, “spliceosome”, and “RNA transport”, were mainly involved in the functional mechanism of NOL7 in human cancers. In summary, this pancancer study characterized the relationship between NOL7 expression and clinicopathologic features in multiple cancer types and further showed its potential regulatory network in human cancers. It represents a systemic analysis for further functional and therapeutic studies of NOL7 and highlights its predictive value with respect to the carcinogenesis and prognosis of various cancers, especially LIHC. Full article
(This article belongs to the Special Issue Genome Organization and Regulation of Its Activity in Cancer)
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Review

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19 pages, 1838 KiB  
Review
An Insight into Molecular Targets of Breast Cancer Brain Metastasis
by Mohammed Kaleem, Mahmood Hassan Dalhat, Lubna Azmi, Turky Omar Asar, Wasim Ahmad, Maimonah Alghanmi, Amal Almostadi, Torki A. Zughaibi and Shams Tabrez
Int. J. Mol. Sci. 2022, 23(19), 11687; https://doi.org/10.3390/ijms231911687 - 2 Oct 2022
Cited by 5 | Viewed by 3164
Abstract
Brain metastasis is one of the major reasons of death in breast cancer (BC) patients, significantly affecting the quality of life, physical activity, and interdependence on several individuals. There is no clear evidence in scientific literature that depicts an exact mechanism relating to [...] Read more.
Brain metastasis is one of the major reasons of death in breast cancer (BC) patients, significantly affecting the quality of life, physical activity, and interdependence on several individuals. There is no clear evidence in scientific literature that depicts an exact mechanism relating to brain metastasis in BC patients. The tendency to develop breast cancer brain metastases (BCBMs) differs by the BC subtype, varying from almost half with triple-negative breast cancer (TNBC) (HER2 ER PR), one-third with HER2+ (human epidermal growth factor receptor 2-positive, and around one-tenth with luminal subclass (ER+ (estrogen positive) or PR+ (progesterone positive)) breast cancer. This review focuses on the molecular pathways as possible therapeutic targets of BCBMs and their potent drugs under different stages of clinical trial. In view of increased numbers of clinical trials and systemic studies, the scientific community is hopeful of unraveling the underlying mechanisms of BCBMs that will help in designing an effective treatment regimen with multiple molecular targets. Full article
(This article belongs to the Special Issue Genome Organization and Regulation of Its Activity in Cancer)
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