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Real-Time Search-Assisted Multiplexed Quantitative Proteomics Reveals System-Wide Translational Regulation of Non-Canonical Short Open Reading Frames

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 recognize...

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Autores principales: Kozuka-Hata, Hiroko, Hiroki, Tomoko, Miyamura, Naoaki, Kitamura, Aya, Tsumoto, Kouhei, Inoue, Jun-ichiro, Oyama, Masaaki
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10296652/
https://www.ncbi.nlm.nih.gov/pubmed/37371559
http://dx.doi.org/10.3390/biom13060979
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author Kozuka-Hata, Hiroko
Hiroki, Tomoko
Miyamura, Naoaki
Kitamura, Aya
Tsumoto, Kouhei
Inoue, Jun-ichiro
Oyama, Masaaki
author_facet Kozuka-Hata, Hiroko
Hiroki, Tomoko
Miyamura, Naoaki
Kitamura, Aya
Tsumoto, Kouhei
Inoue, Jun-ichiro
Oyama, Masaaki
author_sort Kozuka-Hata, Hiroko
collection PubMed
description 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.
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spelling pubmed-102966522023-06-28 Real-Time Search-Assisted Multiplexed Quantitative Proteomics Reveals System-Wide Translational Regulation of Non-Canonical Short Open Reading Frames Kozuka-Hata, Hiroko Hiroki, Tomoko Miyamura, Naoaki Kitamura, Aya Tsumoto, Kouhei Inoue, Jun-ichiro Oyama, Masaaki Biomolecules Communication 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. MDPI 2023-06-12 /pmc/articles/PMC10296652/ /pubmed/37371559 http://dx.doi.org/10.3390/biom13060979 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Communication
Kozuka-Hata, Hiroko
Hiroki, Tomoko
Miyamura, Naoaki
Kitamura, Aya
Tsumoto, Kouhei
Inoue, Jun-ichiro
Oyama, Masaaki
Real-Time Search-Assisted Multiplexed Quantitative Proteomics Reveals System-Wide Translational Regulation of Non-Canonical Short Open Reading Frames
title Real-Time Search-Assisted Multiplexed Quantitative Proteomics Reveals System-Wide Translational Regulation of Non-Canonical Short Open Reading Frames
title_full Real-Time Search-Assisted Multiplexed Quantitative Proteomics Reveals System-Wide Translational Regulation of Non-Canonical Short Open Reading Frames
title_fullStr Real-Time Search-Assisted Multiplexed Quantitative Proteomics Reveals System-Wide Translational Regulation of Non-Canonical Short Open Reading Frames
title_full_unstemmed Real-Time Search-Assisted Multiplexed Quantitative Proteomics Reveals System-Wide Translational Regulation of Non-Canonical Short Open Reading Frames
title_short Real-Time Search-Assisted Multiplexed Quantitative Proteomics Reveals System-Wide Translational Regulation of Non-Canonical Short Open Reading Frames
title_sort real-time search-assisted multiplexed quantitative proteomics reveals system-wide translational regulation of non-canonical short open reading frames
topic Communication
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10296652/
https://www.ncbi.nlm.nih.gov/pubmed/37371559
http://dx.doi.org/10.3390/biom13060979
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