Multi-omics inference of differential breast cancer-related transcriptional regulatory network gene hubs between young Black and White patients

Aguilar, Boris; Abdilleh, Kawther; Acquaah‐Mensah, George

doi:10.1016/j.cancergen.2022.11.001

Cited by 6 publications

(2 citation statements)

References 48 publications

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“…BC is characterized by a high genomic instability expressed in somatic gene mutations, copy number alterations (CNAs), and chromosome structural rearrangements caused by defects in DNA damage repair (DDR), transcription, DNA replication, telomere maintenance and mitotic chromosome segregation [33,34]. Multi-omics analyses, including genomics, transcriptomics, proteomics, and even single-cell molecular profiling, are essential to characterize the molecular mechanisms of multi-omics regulation in BC [35], or to identify -omics differences in BC-related transcriptional regulatory network gene hubs between certain ethnic groups [36].…”

Section: Bc Is a Genomic Diseasementioning

confidence: 99%

Onco-Breastomics: An Eco-Evo-Devo Holistic Approach

Neagu,

Whitham,

Bruno

et al. 2024

IJMS

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Known as a diverse collection of neoplastic diseases, breast cancer (BC) can be hyperbolically characterized as a dynamic pseudo-organ, a living organism able to build a complex, open, hierarchically organized, self-sustainable, and self-renewable tumor system, a population, a species, a local community, a biocenosis, or an evolving dynamical ecosystem (i.e., immune or metabolic ecosystem) that emphasizes both developmental continuity and spatio-temporal change. Moreover, a cancer cell community, also known as an oncobiota, has been described as non-sexually reproducing species, as well as a migratory or invasive species that expresses intelligent behavior, or an endangered or parasite species that fights to survive, to optimize its features inside the host’s ecosystem, or that is able to exploit or to disrupt its host circadian cycle for improving the own proliferation and spreading. BC tumorigenesis has also been compared with the early embryo and placenta development that may suggest new strategies for research and therapy. Furthermore, BC has also been characterized as an environmental disease or as an ecological disorder. Many mechanisms of cancer progression have been explained by principles of ecology, developmental biology, and evolutionary paradigms. Many authors have discussed ecological, developmental, and evolutionary strategies for more successful anti-cancer therapies, or for understanding the ecological, developmental, and evolutionary bases of BC exploitable vulnerabilities. Herein, we used the integrated framework of three well known ecological theories: the Bronfenbrenner’s theory of human development, the Vannote’s River Continuum Concept (RCC), and the Ecological Evolutionary Developmental Biology (Eco-Evo-Devo) theory, to explain and understand several eco-evo-devo-based principles that govern BC progression. Multi-omics fields, taken together as onco-breastomics, offer better opportunities to integrate, analyze, and interpret large amounts of complex heterogeneous data, such as various and big-omics data obtained by multiple investigative modalities, for understanding the eco-evo-devo-based principles that drive BC progression and treatment. These integrative eco-evo-devo theories can help clinicians better diagnose and treat BC, for example, by using non-invasive biomarkers in liquid-biopsies that have emerged from integrated omics-based data that accurately reflect the biomolecular landscape of the primary tumor in order to avoid mutilating preventive surgery, like bilateral mastectomy. From the perspective of preventive, personalized, and participatory medicine, these hypotheses may help patients to think about this disease as a process governed by natural rules, to understand the possible causes of the disease, and to gain control on their own health.

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Section: Bc Is a Genomic Diseasementioning

confidence: 99%

Onco-Breastomics: An Eco-Evo-Devo Holistic Approach

Neagu,

Whitham,

Bruno

et al. 2024

IJMS

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“…Employing RNA-seq, genes that are expressed at extremely high and low levels can be identified [ 45 , 46 ]. For example, dysregulated genes such as TP53 , GAPDH , cyclin D1 , HRAS , CDK1, CDC6 and PCNA , and the activation of ERBB2 , FOXM1 , ESR1 and IGFBP2 networks, have been reported in BC tissue compared to control tissue [ 47 ].…”

Section: Omics Approaches To Uncover Bc Alterationsmentioning

confidence: 99%

Omics Technologies Improving Breast Cancer Research and Diagnostics

Orsini

Diquigiovanni

Bonora

2023

IJMS

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Breast cancer (BC) has yielded approximately 2.26 million new cases and has caused nearly 685,000 deaths worldwide in the last two years, making it the most common diagnosed cancer type in the world. BC is an intricate ecosystem formed by both the tumor microenvironment and malignant cells, and its heterogeneity impacts the response to treatment. Biomedical research has entered the era of massive omics data thanks to the high-throughput sequencing revolution, quick progress and widespread adoption. These technologies—liquid biopsy, transcriptomics, epigenomics, proteomics, metabolomics, pharmaco-omics and artificial intelligence imaging—could help researchers and clinicians to better understand the formation and evolution of BC. This review focuses on the findings of recent multi-omics-based research that has been applied to BC research, with an introduction to every omics technique and their applications for the different BC phenotypes, biomarkers, target therapies, diagnosis, treatment and prognosis, to provide a comprehensive overview of the possibilities of BC research.

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