Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
8.3
5.5
Journals
Biomolecules
Special Issues
Recent Advances in Proteogenomics
share announcement

Recent Advances in Proteogenomics

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

Deadline for manuscript submissions: closed (31 March 2024) | Viewed by 2915

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,

Proteogenomics is a newly emerging field that aims to understand biological systems through the comprehensive annotation of translated products based on the integration of proteomics, genomics, and transcriptomics technologies. Accumulating DNA/RNA sequence data regarding a variety of biological species, in combination with the transcriptome-wide determination of potentially translatable regions by ribosome profiling has successfully unveiled the widespread existence of non-canonical open reading frames (ORFs) besides the already defined protein-coding regions on a proteomic scale. In this Special Issue, we would like to highlight the diversified impact of advanced proteomic technologies towards the systematic annotation of novel ORFs encoded in each biological or clinical context. Research articles, review articles, and short communications in relation to proteogenomics 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

  • proteogenomics
  • mass spectrometry
  • ribosome profiling
  • open reading frame
  • translational regulation

Published Papers (1 paper)

Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Research

11 pages, 1789 KiB  
Communication
Real-Time Search-Assisted Multiplexed Quantitative Proteomics Reveals System-Wide Translational Regulation of Non-Canonical Short Open Reading Frames
by Hiroko Kozuka-Hata, Tomoko Hiroki, Naoaki Miyamura, Aya Kitamura, Kouhei Tsumoto, Jun-ichiro Inoue and Masaaki Oyama
Biomolecules 2023, 13(6), 979; https://doi.org/10.3390/biom13060979 - 12 Jun 2023
Viewed by 2299
Abstract
Abnormal expression of histone deacetylases (HDACs) is reported to be associated with angiogenesis, metastasis and chemotherapy resistance regarding cancer in a wide range of previous studies. Suberoylanilide hydroxamic acid (SAHA) is well known to function as a pan-inhibitor for HDACs and recognized as [...] Read more.
Abnormal expression of histone deacetylases (HDACs) is reported to be associated with angiogenesis, metastasis and chemotherapy resistance regarding cancer in a wide range of previous studies. Suberoylanilide hydroxamic acid (SAHA) is well known to function as a pan-inhibitor for HDACs and recognized as one of the therapeutic drug candidates to epigenetically coordinate cancer cell fate regulation on a genomic scale. Here, we established a Real-Time Search (RTS)-assisted mass spectrometric platform for system-wide quantification of translated products encoded by non-canonical short open reading frames (ORFs) as well as already annotated protein coding sequences (CDSs) on the human transciptome and applied this methodology to quantitative proteomic analyses of suberoylanilide hydroxamic acid (SAHA)-treated human HeLa cells to evaluate proteome-wide regulation in response to drug perturbation. Very intriguingly, our RTS-based in-depth proteomic analysis enabled us to identify approximately 5000 novel peptides from the ribosome profiling-based short ORFs encoded in the diversified regions on presumed ‘non-coding’ nucleotide sequences of mRNAs as well as lncRNAs and nonsense mediated decay (NMD) transcripts. Furthermore, TMT-based multiplex large-scale quantification of the whole proteome changes upon differential SAHA treatment unveiled dose-dependent selective translational regulation of a limited fraction of the non-canonical short ORFs in addition to key cell cycle/proliferation-related molecules such as UBE2C, CENPF and PRC1. Our study provided the first system-wide landscape of drug-perturbed translational modulation on both canonical and non-canonical proteome dynamics in human cancer cells. Full article
(This article belongs to the Special Issue Recent Advances in Proteogenomics)
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-1
Back to TopTop