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Recent Developments in Omics Technologies Applied to Oncology Research

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

Deadline for manuscript submissions: 30 September 2024 | Viewed by 822

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Preclinical Models and New Therapeutic Agents Unit, Translational Research Functional Departmental Area, Research, Advanced Diagnostics and Technological Innovation Department, Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144 Rome, Italy
Interests: cancer research; melanoma; personalized precision medicine; pathway-targeted drugs; bcl-2 family protein; cancer biomarkers; microRNA; proteomics
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Special Issue Information

Dear Colleagues,

Intra-tumour heterogeneity is likely to have implications for cancer therapeutics and biomarker discovery, particularly in the era of targeted treatment, and evidence for a relationship between intra-tumoural heterogeneity and clinical outcome is emerging. Moreover, the composition of the tumor microenvironment, including immune cells, stromal cells, blood vessels, and extracellular matrix, also has a role in tumor aggressiveness and response to therapy. In particular, immune cells in the tumor microenvironment are relevant in determining tumor growth and response to immunotherapy. Thus, there is a need to characterize intra-tumour heterogeneity. Various techniques have been developed to characterize tumor heterogeneity and immune infiltrate composition in recent years. This Special Issue will focus on recent developments in spatial analysis (also at single cell level) of genomic, transcriptomic, proteomic, or metabolomic information obtainable from samples (tissues or fluids) derived from cancer patients. Authors are encouraged to submit original research manuscripts but can also provide suggestions for review articles.

Suitable topics include, but are not limited to:

  • Single‑cell genome sequencing;
  • Single‑cell epigenome sequencing;
  • Single‑cell CRISPR sequencing;
  • Imaging mass cytometry;
  • RNAscope;
  • Digital spatial profiling;
  • Multiplex IHC;
  • Multiplex IF.

Dr. Simona D’Aguanno
Guest Editor

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Keywords

  • single‑cell genome sequencing
  • single‑cell epigenome sequencing
  • single‑cell CRISPR sequencing
  • imaging mass cytometry
  • RNAscope
  • digital spatial profiling
  • multiplex IHC
  • multiplex IF
  • omics technologies

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Published Papers (1 paper)

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Research

17 pages, 3117 KiB  
Article
Comparative Analysis of Breast Cancer Metabolomes Highlights Fascin’s Central Role in Regulating Key Pathways Related to Disease Progression
by Reem H. AlMalki, Huda K. Al-Nasrallah, Alanoud Aldossry, Rayanah Barnawi, Samiyah Al-Khaldi, Sheema Almozyan, Mysoon M. Al-Ansari, Hazem Ghebeh, Anas M. Abdel Rahman and Monther Al-Alwan
Int. J. Mol. Sci. 2024, 25(14), 7891; https://doi.org/10.3390/ijms25147891 - 18 Jul 2024
Viewed by 579
Abstract
Omics technologies provide useful tools for the identification of novel biomarkers in many diseases, including breast cancer, which is the most diagnosed cancer in women worldwide. We and others have reported a central role for the actin-bundling protein (fascin) in regulating breast cancer [...] Read more.
Omics technologies provide useful tools for the identification of novel biomarkers in many diseases, including breast cancer, which is the most diagnosed cancer in women worldwide. We and others have reported a central role for the actin-bundling protein (fascin) in regulating breast cancer disease progression at different levels. However, whether fascin expression promotes metabolic molecules that could predict disease progression has not been fully elucidated. Here, fascin expression was manipulated via knockdown (fascinKD+NORF) and rescue (fascinKD+FORF) in the naturally fascin-positive (fascinpos+NORF) MDA-MB-231 breast cancer cells. Whether fascin dysregulates metabolic profiles that are associated with disease progression was assessed using untargeted metabolomics analyses via liquid chromatography–mass spectrometry. Overall, 12,226 metabolic features were detected in the tested cell pellets. Fascinpos+NORF cell pellets showed 2510 and 3804 significantly dysregulated metabolites compared to their fascinKD+NORF counterparts. Fascin rescue (fascinKD+FORF) revealed 2710 significantly dysregulated cellular metabolites compared to fascinKD+NORF counterparts. A total of 101 overlapped cellular metabolites between fascinKD+FORF and fascinpos+NORF were significantly dysregulated in the fascinKD+NORF cells. Analysis of the significantly dysregulated metabolites by fascin expression revealed their involvement in the metabolism of sphingolipid, phenylalanine, tyrosine, and tryptophan biosynthesis, and pantothenate and CoA biosynthesis, which are critical pathways for breast cancer progression. Our findings of fascin-mediated alteration of metabolic pathways could be used as putative poor prognostic biomarkers and highlight other underlying mechanisms of fascin contribution to breast cancer progression. Full article
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