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Systems Biology Approach in Cancer
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Systems Biology Approach in Cancer

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: closed (31 March 2023) | Viewed by 6009

Special Issue Editor

Dr. Peter J. K. Kuppen

E-Mail Website
Guest Editor
Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
Interests: colorectal cancer; tumor-immmune interactions; cancer genetics and epigenetics; immunotherapy; biomarkers
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Biomedical scientists tend to approach cancer in a reductionistic way, aiming at uncovering underlying components that are at the base of cancer development. This was very successful and led to major discoveries; for instance, familial adenomatous polyposis (FAP) could be reduced to a mutation in the APC gene. Additionally, familial breast cancer could be reduced to a mutated BRCA1 or BRCA2 gene. However, a germline mutation in APC is not 1:1 related with colorectal cancer, which also applies to BRACA1 or BRCA2 with breast cancer. A crucial point is that biological systems have properties that cannot be reduced to single components. The outcome of a complex network, such as tumor–immune interaction, depends on the many cell types involved as well as numerous molecules that interact and activate or inhibit pathways. Genomic analyses, considering full genomes or transcriptomes, better enable the consideration of a system and the understanding of biological pathways as well as their outcomes. This systems biology approach is the future of cancer research. Current techniques, such as next-generation sequencing, nano string analysis, multiplex spatial genomics, etc., allow for a much better understanding of tumor development and its consequences.

Authors are invited to submit papers in which cancer is approached from a systems biology viewpoint. Manuscripts of both original research and reviews are welcome.

Dr. Peter J.K. Kuppen
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

  • cancer systems biology
  • cancer genomics
  • next-generation sequencing
  • nano string analysis
  • spatial genomics
  • cancer genetic profiling
  • cancer immune profiling

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Published Papers (2 papers)

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Review

18 pages, 1371 KiB  
Review
Carcino-Evo-Devo, A Theory of the Evolutionary Role of Hereditary Tumors
by Andrei P. Kozlov
Int. J. Mol. Sci. 2023, 24(10), 8611; https://doi.org/10.3390/ijms24108611 - 11 May 2023
Cited by 4 | Viewed by 2786
Abstract
A theory of the evolutionary role of hereditary tumors, or the carcino-evo-devo theory, is being developed. The main hypothesis of the theory, the hypothesis of evolution by tumor neofunctionalization, posits that hereditary tumors provided additional cell masses during the evolution of multicellular organisms [...] Read more.
A theory of the evolutionary role of hereditary tumors, or the carcino-evo-devo theory, is being developed. The main hypothesis of the theory, the hypothesis of evolution by tumor neofunctionalization, posits that hereditary tumors provided additional cell masses during the evolution of multicellular organisms for the expression of evolutionarily novel genes. The carcino-evo-devo theory has formulated several nontrivial predictions that have been confirmed in the laboratory of the author. It also suggests several nontrivial explanations of biological phenomena previously unexplained by the existing theories or incompletely understood. By considering three major types of biological development—individual, evolutionary, and neoplastic development—within one theoretical framework, the carcino-evo-devo theory has the potential to become a unifying biological theory. Full article
(This article belongs to the Special Issue Systems Biology Approach in Cancer)
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14 pages, 1066 KiB  
Review
Integrative Genomic Tests in Clinical Oncology
by Evgeny Imyanitov and Anna Sokolenko
Int. J. Mol. Sci. 2022, 23(21), 13129; https://doi.org/10.3390/ijms232113129 - 28 Oct 2022
Cited by 14 | Viewed by 2597
Abstract
Many clinical decisions in oncology practice rely on the presence or absence of an alteration in a single genetic locus, be it a pathogenic variant in a hereditary cancer gene or activating mutation in a drug target. In addition, there are integrative tests [...] Read more.
Many clinical decisions in oncology practice rely on the presence or absence of an alteration in a single genetic locus, be it a pathogenic variant in a hereditary cancer gene or activating mutation in a drug target. In addition, there are integrative tests that produce continuous variables and evaluate complex characteristics of the entire tumor genome. Microsatellite instability (MSI) analysis identifies tumors with the accumulation of mutations in short repetitive nucleotide sequences. This procedure is utilized in Lynch syndrome diagnostic pipelines and for the selection of patients for immunotherapy. MSI analysis is well-established for colorectal malignancies, but its applications in other cancer types lack standardization and require additional research. Homologous repair deficiency (HRD) indicates tumor sensitivity to PARP inhibitors and some cytotoxic drugs. HRD-related “genomic scars” are manifested by a characteristic pattern of allelic imbalances, accumulation of deletions with flanking homology, and specific mutation signatures. The detection of the genetic consequences of HRD is particularly sophisticated and expensive, as it involves either whole genome sequencing (WGS) or the utilization of large next-generation sequencing (NGS) panels. Tumor mutation burden (TMB) can be determined by whole exome sequencing (WES) or middle-throughput NGS multigene testing. Although TMB is regarded as an agnostic indicator of tumor sensitivity to immunotherapy, the clinical utility of this test is proven only for a few cancer types. Full article
(This article belongs to the Special Issue Systems Biology Approach in Cancer)
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