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Bioinformatics in Neuro-Oncology: Latest Applications and Future Perspectives
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Bioinformatics in Neuro-Oncology: Latest Applications and Future Perspectives

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

Deadline for manuscript submissions: closed (30 March 2025) | Viewed by 4050

Special Issue Editor

Prof. Dr. Marco M. Fontanella

E-Mail Website
Guest Editor
Division of Neurosurgery, Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, University of Brescia, Piazza Spedali Civili 1, 25123 Brescia, Italy
Interests: cranial neurosurgery; neuro-oncology; vascular neurosurgery; AI; multi-omics; digital health; bioinformatics; molecular biology; biotechnology; genomics

Special Issue Information

Dear Colleagues,

Artificial intelligence (AI) has transformed our lives and revolutionized medicine. Recently, new methods have been developed to support diagnostic and therapeutic approaches. AI has made significant progress in the field of neuro-oncology, gaining the interest of pathologists, neuroradiologists, surgeons and bioengineers. Bioinformatics is now playing a crucial role in enhancing the performance of physicians in their daily work processes.

This Special Issue welcomes articles that focus on bioinformatics applications in neuro-oncology. The potential topics include, but are not limited to, innovative algorithms for liquid biopsy, radiomics and videomics tools applied to pathology and molecular diagnostics. Furthermore, we encourage submissions that introduce novel diagnostic and therapeutic approaches rooted in recent molecular and genetic discoveries. These may involve genes, DNAs, RNAs, proteins and other biomolecules, where their profiles are reflected in diverse omics data types. An important aspect is the integrative analysis of various types of omics data, such as epigenomics, metabolomics, transcriptomics and genomics. By doing so, our Special Issue aims to collect the latest excellent results to significantly enhance the accuracy of diagnosis and prognosis, deepen our functional understanding of disease mechanisms and pave the way for precision medicine.

We encourage a variety of article types, including original articles, clinical trials, systematic reviews and meta-analyses based on recent molecular and genetic discoveries.

This Special Issue is supervised by Prof. Dr. Marco M. Fontanella and assisted by our Topical Advisory Panel Member Dr. Lucio De Maria (Geneva University Hospitals) and Dr. Francesco Ponzio (Politecnico di Torino).

Prof. Dr. Marco M. Fontanella
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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

  • artificial intelligence
  • machine leraning
  • deep learning
  • multiomics
  • neuro-oncology
  • liquid biopsy
  • pathobiology
  • genetics
  • molecular dynamics
  • proteomics

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Further information on MDPI's Special Issue policies can be found here.

Published Papers (2 papers)

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17 pages, 3221 KiB  
Article
Comprehensive Transcriptomic Analysis Reveals Cell-Type-Specific Roles of Human Odorant Receptors in Glioblastoma and the Tumor Microenvironment
by Hee Jin Cho, Dong Jun Yeo, HeeWoong Yang and JaeHyung Koo
Int. J. Mol. Sci. 2024, 25(24), 13382; https://doi.org/10.3390/ijms252413382 - 13 Dec 2024
Viewed by 1205
Abstract
Odorant receptors (ORs), which constitute approximately 50% of all human G protein-coupled receptors, are increasingly recognized for their diverse roles beyond odor perception, including functions in various pathological conditions like brain diseases and cancers. However, the roles of ORs in glioblastoma (GBM), the [...] Read more.
Odorant receptors (ORs), which constitute approximately 50% of all human G protein-coupled receptors, are increasingly recognized for their diverse roles beyond odor perception, including functions in various pathological conditions like brain diseases and cancers. However, the roles of ORs in glioblastoma (GBM), the most aggressive primary brain tumor with a median survival of only 15 months, remain largely unexplored. Here, we performed an integrated transcriptomic analysis combining The Cancer Genome Atlas RNA-seq and single-cell RNA sequencing data from GBM patients to uncover cell-type-specific roles of ORs within the tumor and its microenvironment. Our findings reveal that ORs display distinct expression patterns, with OR51E1 enriched in pericytes linked to vascular remodeling and angiogenesis, OR2B11 associated with tumor-associated macrophages supporting immunosuppressive phenotypes, and OR2L13 correlated with synaptic activity in recurrent tumors, potentially mediating treatment-induced neuronal adaptations. These results highlight ORs as potential therapeutic targets, offering new insights into their regulatory roles in GBM progression, immune modulation, and treatment resistance. Full article
(This article belongs to the Special Issue Bioinformatics in Neuro-Oncology: Latest Applications and Future Perspectives)
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21 pages, 11501 KiB  
Article
Survival-Related Genes on Chromosomes 6 and 17 in Medulloblastoma
by Jerry Vriend and Xiao-Qing Liu
Int. J. Mol. Sci. 2024, 25(14), 7506; https://doi.org/10.3390/ijms25147506 - 9 Jul 2024
Viewed by 1596
Abstract
Survival of Medulloblastoma (MB) depends on various factors, including the gene expression profiles of MB tumor tissues. In this study, we identified 967 MB survival-related genes (SRGs) using a gene expression dataset and the Cox proportional hazards regression model. Notably, the SRGs were [...] Read more.
Survival of Medulloblastoma (MB) depends on various factors, including the gene expression profiles of MB tumor tissues. In this study, we identified 967 MB survival-related genes (SRGs) using a gene expression dataset and the Cox proportional hazards regression model. Notably, the SRGs were over-represented on chromosomes 6 and 17, known for the abnormalities monosomy 6 and isochromosome 17 in MB. The most significant SRG was HMGA1 (high mobility group AT-hook 1) on chromosome 6, which is a known oncogene and a histone H1 competitor. High expression of HMGA1 was associated with worse survival, primarily in the Group 3γ subtype. The high expression of HMGA1 was unrelated to any known somatic copy number alteration. Most SRGs on chromosome 17p were associated with low expression in Group 4β, the MB subtype, with 93% deletion of 17p and 98% copy gain of 17q. GO enrichment analysis showed that both chromosomes 6 and 17 included SRGs related to telomere maintenance and provided a rationale for testing telomerase inhibitors in Group 3 MBs. We conclude that HMGA1, along with other SRGs on chromosomes 6 and 17, warrant further investigation as potential therapeutic targets in selected subgroups or subtypes of MB. Full article
(This article belongs to the Special Issue Bioinformatics in Neuro-Oncology: Latest Applications and Future Perspectives)
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