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Biomolecules
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Integrative Analysis of Cancer Cell Signaling Networks by Proteomics and...
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Integrative Analysis of Cancer Cell Signaling Networks by Proteomics and Systems Biology

A special issue of Biomolecules (ISSN 2218-273X). This special issue belongs to the section "Molecular Biology".

Deadline for manuscript submissions: closed (31 October 2021) | Viewed by 15113

Special Issue Editor

Prof. Dr. Masaaki Oyama

E-Mail Website
Guest Editor
The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
Interests: proteomics; systems biology; cancer; signal transduction; translation
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Signal transduction is known to play a crucial role in regulating complex biological events such as proliferation, differentiation, and apoptosis. Post-translational modifications (PTMs), including phosphorylation, ubiquitination, and acetylation, are widely involved in the regulation of cellular signaling through extensive diversification of each protein function at the network level. Previous functional analysis of cancer cell signaling under a variety of experimental conditions unveiled many of the key protein molecules and their associated PTMs in relation to each type of cancer. Recent technological advances in mass-spectrometry-based proteomics have enabled us to perform comprehensive identification and quantification of protein PTM dynamics and analyze their network-wide regulation from statistical and mathematical points of view. In this Special Issue, we would like to highlight the potential impact of computational network dissection based on large-scale PTM proteomic data towards systematic understanding of cellular signaling principles. Research articles, review articles, and short communications using advanced proteomics and/or bioinformatics technologies are welcome from any relevant fields.

Prof. Dr. Masaaki Oyama
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. Biomolecules is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). 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

  • proteomics
  • systems biology
  • cancer
  • cell signaling
  • post-translational modification

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Published Papers (3 papers)

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Research

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13 pages, 2530 KiB  
Communication
RNA-seq Characterization of Melanoma Phenotype Switch in 3D Collagen after p38 MAPK Inhibitor Treatment
by Vladimír Čermák, Aneta Škarková, Ladislav Merta, Veronika Kolomazníková, Veronika Palušová, Stjepan Uldrijan, Daniel Rösel and Jan Brábek
Biomolecules 2021, 11(3), 449; https://doi.org/10.3390/biom11030449 - 17 Mar 2021
Cited by 2 | Viewed by 3270
Abstract
Melanoma phenotype plasticity underlies tumour dissemination and resistance to therapy, yet its regulation is incompletely understood. In vivo switching between a more differentiated, proliferative phenotype and a dedifferentiated, invasive phenotype is directed by the tumour microenvironment. We found that treatment of partially dedifferentiated, [...] Read more.
Melanoma phenotype plasticity underlies tumour dissemination and resistance to therapy, yet its regulation is incompletely understood. In vivo switching between a more differentiated, proliferative phenotype and a dedifferentiated, invasive phenotype is directed by the tumour microenvironment. We found that treatment of partially dedifferentiated, invasive A375M2 cells with two structurally unrelated p38 MAPK inhibitors, SB2021920 and BIRB796, induces a phenotype switch in 3D collagen, as documented by increased expression of melanocyte differentiation markers and a loss of invasive phenotype markers. The phenotype is accompanied by morphological change corresponding to amoeboid–mesenchymal transition. We performed RNA sequencing with an Illumina HiSeq platform to fully characterise transcriptome changes underlying the switch. Gene expression results obtained with RNA-seq were validated by comparing them with RT-qPCR. Transcriptomic data generated in the study will extend the present understanding of phenotype plasticity in melanoma and its contribution to invasion and metastasis. Full article
(This article belongs to the Special Issue Integrative Analysis of Cancer Cell Signaling Networks by Proteomics and Systems Biology)
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8 pages, 1606 KiB  
Article
System-Wide Analysis of Protein Acetylation and Ubiquitination Reveals a Diversified Regulation in Human Cancer Cells
by Hiroko Kozuka-Hata, Aya Kitamura, Tomoko Hiroki, Aiko Aizawa, Kouhei Tsumoto, Jun-ichiro Inoue and Masaaki Oyama
Biomolecules 2020, 10(3), 411; https://doi.org/10.3390/biom10030411 - 6 Mar 2020
Cited by 8 | Viewed by 3823
Abstract
Post-translational modifications are known to be widely involved in the regulation of various biological processes, through the extensive diversification of each protein function at the cellular network level. In order to unveil the system-wide function of the protein lysine modification in cancer cell [...] Read more.
Post-translational modifications are known to be widely involved in the regulation of various biological processes, through the extensive diversification of each protein function at the cellular network level. In order to unveil the system-wide function of the protein lysine modification in cancer cell signaling, we performed global acetylation and ubiquitination proteome analyses of human cancer cells, based on high-resolution nanoflow liquid chromatography–tandem mass spectrometry, in combination with the efficient biochemical enrichment of target modified peptides. Our large-scale proteomic analysis enabled us to identify more than 5000 kinds of ubiquitinated sites and 1600 kinds of acetylated sites, from representative human cancer cell lines, leading to the identification of approximately 900 novel lysine modification sites in total. Very interestingly, 236 lysine residues derived from 141 proteins were found to be modified with both ubiquitination and acetylation. As a consequence of the subsequent motif extraction analyses, glutamic acid (E) was found to be highly enriched at the position (−1) for the lysine acetylation sites, whereas the same amino acid was relatively dispersed along the neighboring residues of the lysine ubiquitination sites. Our pathway analysis also indicated that the protein translational control pathways, such as the eukaryotic initiation factor 2 (EIF2) and the ubiquitin signaling pathways, were highly enriched in both of the acetylation and ubiquitination proteome data at the network level. This report provides the first integrative description of the protein acetylation and ubiquitination-oriented systematic regulation in human cancer cells. Full article
(This article belongs to the Special Issue Integrative Analysis of Cancer Cell Signaling Networks by Proteomics and Systems Biology)
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Review

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44 pages, 3926 KiB  
Review
Post-Translational Modifications That Drive Prostate Cancer Progression
by Ivana Samaržija
Biomolecules 2021, 11(2), 247; https://doi.org/10.3390/biom11020247 - 9 Feb 2021
Cited by 28 | Viewed by 6895
Abstract
While a protein primary structure is determined by genetic code, its specific functional form is mostly achieved in a dynamic interplay that includes actions of many enzymes involved in post-translational modifications. This versatile repertoire is widely used by cells to direct their response [...] Read more.
While a protein primary structure is determined by genetic code, its specific functional form is mostly achieved in a dynamic interplay that includes actions of many enzymes involved in post-translational modifications. This versatile repertoire is widely used by cells to direct their response to external stimuli, regulate transcription and protein localization and to keep proteostasis. Herein, post-translational modifications with evident potency to drive prostate cancer are explored. A comprehensive list of proteome-wide and single protein post-translational modifications and their involvement in phenotypic outcomes is presented. Specifically, the data on phosphorylation, glycosylation, ubiquitination, SUMOylation, acetylation, and lipidation in prostate cancer and the enzymes involved are collected. This type of knowledge is especially valuable in cases when cancer cells do not differ in the expression or mutational status of a protein, but its differential activity is regulated on the level of post-translational modifications. Since their driving roles in prostate cancer, post-translational modifications are widely studied in attempts to advance prostate cancer treatment. Current strategies that exploit the potential of post-translational modifications in prostate cancer therapy are presented. Full article
(This article belongs to the Special Issue Integrative Analysis of Cancer Cell Signaling Networks by Proteomics and Systems Biology)
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