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Article ; Online: Circulating nucleosomes as potential biomarkers for cancer diagnosis and treatment monitoring.

Wang, Huawei / Wang, Yin / Zhang, Dejiu / Li, Peifeng

International journal of biological macromolecules

2024 Volume 262, Issue Pt 1, Page(s) 130005

Abstract: Nucleosomes play a crucial role in regulating gene expression through their composition and post-translational modifications. When cells die, intracellular endonucleases are activated and cleave chromatin into oligo- and mono-nucleosomes, which are then ... ...

Abstract	Nucleosomes play a crucial role in regulating gene expression through their composition and post-translational modifications. When cells die, intracellular endonucleases are activated and cleave chromatin into oligo- and mono-nucleosomes, which are then released into the body fluids. Studies have shown that the levels of nucleosomes are increased in serum and plasma in various cancer types, suggesting that analysis of circulating nucleosomes can provide an initial assessment of carcinogenesis. However, it should be noted that elevated serum nucleosome levels may not accurately diagnose certain tumor types, as increased cell death may occur in different pathological conditions. Nevertheless, detection of circulating nucleosomes and their histone modifications, along with specific tumor markers, can help diagnose certain types of cancer. Furthermore, monitoring changes in circulating nucleosome levels during chemotherapy or radiotherapy in patients with malignancies can provide valuable insights into clinical outcomes and therapeutic efficacy. The utilization of circulating nucleosomes as biomarkers is an exciting and emerging area of research, with the potential for early detection of various diseases and monitoring of treatment response. Integrating nucleosome-based biomarkers with existing ones may improve the specificity and sensitivity of current assays, offering the possibility of personalized precision medical treatment for patients.
MeSH term(s)	Humans ; Nucleosomes ; Neoplasms/diagnosis ; Neoplasms/drug therapy ; Neoplasms/genetics ; Biomarkers, Tumor ; Chromatin
Chemical Substances	Nucleosomes ; Biomarkers, Tumor ; Chromatin
Language	English
Publishing date	2024-02-06
Publishing country	Netherlands
Document type	Journal Article ; Review
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2024.130005
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Article ; Online: Advances and opportunities in methods to study protein translation - A review.

Zhang, Dejiu / Gao, Yanyan / Zhu, Lei / Wang, Yin / Li, Peifeng

International journal of biological macromolecules

2024 Volume 259, Issue Pt 1, Page(s) 129150

Abstract: It is generally believed that the regulation of gene expression involves protein translation occurring before RNA transcription. Therefore, it is crucial to investigate protein translation and its regulation. Recent advancements in biological sciences, ... ...

Abstract	It is generally believed that the regulation of gene expression involves protein translation occurring before RNA transcription. Therefore, it is crucial to investigate protein translation and its regulation. Recent advancements in biological sciences, particularly in the field of omics, have revolutionized protein translation research. These studies not only help characterize changes in protein translation during specific biological or pathological processes but also have significant implications in disease prevention and treatment. In this review, we summarize the latest methods in ribosome-based translation omics. We specifically focus on the application of fluorescence imaging technology and omics technology in studying overall protein translation. Additionally, we analyze the advantages, disadvantages, and application of these experimental methods, aiming to provide valuable insights and references to researchers studying translation.
MeSH term(s)	Protein Biosynthesis ; RNA, Messenger/genetics ; Ribosomes/genetics ; Ribosomes/metabolism
Chemical Substances	RNA, Messenger
Language	English
Publishing date	2024-01-01
Publishing country	Netherlands
Document type	Journal Article ; Review
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2023.129150
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Article: RNA editing enzymes: structure, biological functions and applications.

Zhang, Dejiu / Zhu, Lei / Gao, Yanyan / Wang, Yin / Li, Peifeng

Cell & bioscience

2024 Volume 14, Issue 1, Page(s) 34

Abstract: With the advancement of sequencing technologies and bioinformatics, over than 170 different RNA modifications have been identified. However, only a few of these modifications can lead to base pair changes, which are called RNA editing. RNA editing is a ... ...

Abstract	With the advancement of sequencing technologies and bioinformatics, over than 170 different RNA modifications have been identified. However, only a few of these modifications can lead to base pair changes, which are called RNA editing. RNA editing is a ubiquitous modification in mammalian transcriptomes and is an important co/posttranscriptional modification that plays a crucial role in various cellular processes. There are two main types of RNA editing events: adenosine to inosine (A-to-I) editing, catalyzed by ADARs on double-stranded RNA or ADATs on tRNA, and cytosine to uridine (C-to-U) editing catalyzed by APOBECs. This article provides an overview of the structure, function, and applications of RNA editing enzymes. We discuss the structural characteristics of three RNA editing enzyme families and their catalytic mechanisms in RNA editing. We also explain the biological role of RNA editing, particularly in innate immunity, cancer biogenesis, and antiviral activity. Additionally, this article describes RNA editing tools for manipulating RNA to correct disease-causing mutations, as well as the potential applications of RNA editing enzymes in the field of biotechnology and therapy.
Language	English
Publishing date	2024-03-16
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2593367-X
ISSN	2045-3701
ISSN	2045-3701
DOI	10.1186/s13578-024-01216-6
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Article ; Online: Mitochondrial Ca

Zhang, Dejiu / Wang, Fei / Li, Peifeng / Gao, Yanyan

International journal of molecular sciences

2022 Volume 23, Issue 6

Abstract: Mitochondria are the sites of oxidative metabolism in eukaryotes where the metabolites of sugars, fats, and amino acids are oxidized to harvest energy. Notably, mitochondria store ... ...

Abstract	Mitochondria are the sites of oxidative metabolism in eukaryotes where the metabolites of sugars, fats, and amino acids are oxidized to harvest energy. Notably, mitochondria store Ca
MeSH term(s)	Calcium/metabolism ; Calcium Signaling ; Homeostasis ; Humans ; Mitochondria/metabolism ; Ventricular Remodeling
Chemical Substances	Calcium (SY7Q814VUP)
Language	English
Publishing date	2022-03-11
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms23063025
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Article ; Online: Mitochondrial Ca 2+ Homeostasis

Dejiu Zhang / Fei Wang / Peifeng Li / Yanyan Gao

International Journal of Molecular Sciences, Vol 23, Iss 3025, p

Emerging Roles and Clinical Significance in Cardiac Remodeling

2022 Volume 3025

Abstract: Mitochondria are the sites of oxidative metabolism in eukaryotes where the metabolites of sugars, fats, and amino acids are oxidized to harvest energy. Notably, mitochondria store Ca 2+ and work in synergy with organelles such as the endoplasmic ... ...

Abstract	Mitochondria are the sites of oxidative metabolism in eukaryotes where the metabolites of sugars, fats, and amino acids are oxidized to harvest energy. Notably, mitochondria store Ca 2+ and work in synergy with organelles such as the endoplasmic reticulum and extracellular matrix to control the dynamic balance of Ca 2+ concentration in cells. Mitochondria are the vital organelles in heart tissue. Mitochondrial Ca 2+ homeostasis is particularly important for maintaining the physiological and pathological mechanisms of the heart. Mitochondrial Ca 2+ homeostasis plays a key role in the regulation of cardiac energy metabolism, mechanisms of death, oxygen free radical production, and autophagy. The imbalance of mitochondrial Ca 2+ balance is closely associated with cardiac remodeling. The mitochondrial Ca 2+ uniporter (mtCU) protein complex is responsible for the uptake and release of mitochondrial Ca 2+ and regulation of Ca 2+ homeostasis in mitochondria and consequently, in cells. This review summarizes the mechanisms of mitochondrial Ca 2+ homeostasis in physiological and pathological cardiac remodeling and the regulatory effects of the mitochondrial calcium regulatory complex on cardiac energy metabolism, cell death, and autophagy, and also provides the theoretical basis for mitochondrial Ca 2+ as a novel target for the treatment of cardiovascular diseases.
Keywords	mitochondria ; Ca 2+ homeostasis ; cardiac remodeling ; mitochondrial Ca 2+ uniporter protein complex ; cardiovascular diseases ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	333
Language	English
Publishing date	2022-03-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Molecular mechanisms of eukaryotic translation fidelity and their associations with diseases.

Zhang, Dejiu / Zhu, Lei / Wang, Fei / Li, Peifeng / Wang, Yin / Gao, Yanyan

International journal of biological macromolecules

2023 Volume 242, Issue Pt 1, Page(s) 124680

Abstract: Converting genetic information into functional proteins is a complex, multi-step process, with each step being tightly regulated to ensure the accuracy of translation, which is critical to cellular health. In recent years, advances in modern ... ...

Abstract	Converting genetic information into functional proteins is a complex, multi-step process, with each step being tightly regulated to ensure the accuracy of translation, which is critical to cellular health. In recent years, advances in modern biotechnology, especially the development of cryo-electron microscopy and single-molecule techniques, have enabled a clearer understanding of the mechanisms of protein translation fidelity. Although there are many studies on the regulation of protein translation in prokaryotes, and the basic elements of translation are highly conserved in prokaryotes and eukaryotes, there are still great differences in the specific regulatory mechanisms. This review describes how eukaryotic ribosomes and translation factors regulate protein translation and ensure translation accuracy. However, a certain frequency of translation errors does occur in translation, so we describe diseases that arise when the rate of translation errors reaches or exceeds a threshold of cellular tolerance.
MeSH term(s)	Cryoelectron Microscopy ; Ribosomes/genetics ; Ribosomes/metabolism ; Eukaryotic Cells/metabolism ; Eukaryota/genetics ; Eukaryota/metabolism ; Proteins/metabolism ; Protein Biosynthesis
Chemical Substances	Proteins
Language	English
Publishing date	2023-05-02
Publishing country	Netherlands
Document type	Journal Article ; Review
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2023.124680
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Article ; Online: Translational Control of COVID-19 and Its Therapeutic Implication.

Zhang, Dejiu / Zhu, Lei / Wang, Yin / Li, Peifeng / Gao, Yanyan

Frontiers in immunology

2022 Volume 13, Page(s) 857490

Abstract: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of COVID-19, which has broken out worldwide for more than two years. However, due to limited treatment, new cases of infection are still rising. Therefore, there is ... ...

Abstract	The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of COVID-19, which has broken out worldwide for more than two years. However, due to limited treatment, new cases of infection are still rising. Therefore, there is an urgent need to understand the basic molecular biology of SARS-CoV-2 to control this virus. SARS-CoV-2 replication and spread depend on the recruitment of host ribosomes to translate viral messenger RNA (mRNA). To ensure the translation of their own mRNAs, the SARS-CoV-2 has developed multiple strategies to globally inhibit the translation of host mRNAs and block the cellular innate immune response. This review provides a comprehensive picture of recent advancements in our understanding of the molecular basis and complexity of SARS-CoV-2 protein translation. Specifically, we summarize how this viral infection inhibits host mRNA translation to better utilize translation elements for translation of its own mRNA. Finally, we discuss the potential of translational components as targets for therapeutic interventions.
MeSH term(s)	COVID-19 ; Humans ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; RNA, Viral ; Ribosomes/metabolism ; SARS-CoV-2
Chemical Substances	RNA, Messenger ; RNA, Viral
Language	English
Publishing date	2022-03-29
Publishing country	Switzerland
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2022.857490
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Article ; Online: Development of mitochondrial gene-editing strategies and their potential applications in mitochondrial hereditary diseases: a review.

Gao, Yanyan / Guo, Linlin / Wang, Fei / Wang, Yin / Li, Peifeng / Zhang, Dejiu

Cytotherapy

2023 Volume 26, Issue 1, Page(s) 11–24

Abstract: Mitochondrial DNA (mtDNA) is a critical genome contained within the mitochondria of eukaryotic cells, with many copies present in each mitochondrion. Mutations in mtDNA often are inherited and can lead to severe health problems, including various ... ...

Abstract	Mitochondrial DNA (mtDNA) is a critical genome contained within the mitochondria of eukaryotic cells, with many copies present in each mitochondrion. Mutations in mtDNA often are inherited and can lead to severe health problems, including various inherited diseases and premature aging. The lack of efficient repair mechanisms and the susceptibility of mtDNA to damage exacerbate the threat to human health. Heteroplasmy, the presence of different mtDNA genotypes within a single cell, increases the complexity of these diseases and requires an effective editing method for correction. Recently, gene-editing techniques, including programmable nucleases such as restriction endonuclease, zinc finger nuclease, transcription activator-like effector nuclease, clustered regularly interspaced short palindromic repeats/clustered regularly interspaced short palindromic repeats-associated 9 and base editors, have provided new tools for editing mtDNA in mammalian cells. Base editors are particularly promising because of their high efficiency and precision in correcting mtDNA mutations. In this review, we discuss the application of these techniques in mitochondrial gene editing and their limitations. We also explore the potential of base editors for mtDNA modification and discuss the opportunities and challenges associated with their application in mitochondrial gene editing. In conclusion, this review highlights the advancements, limitations and opportunities in current mitochondrial gene-editing technologies and approaches. Our insights aim to stimulate the development of new editing strategies that can ultimately alleviate the adverse effects of mitochondrial hereditary diseases.
MeSH term(s)	Animals ; Humans ; Genes, Mitochondrial ; Gene Editing/methods ; Mitochondria/genetics ; DNA, Mitochondrial/genetics ; Mutation ; Mammals/genetics
Chemical Substances	DNA, Mitochondrial
Language	English
Publishing date	2023-11-06
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2039821-9
ISSN	1477-2566 ; 1465-3249
ISSN (online)	1477-2566
ISSN	1465-3249
DOI	10.1016/j.jcyt.2023.10.004
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Article ; Online: Mitochondrial Protein Translation

Fei Wang / Deyu Zhang / Dejiu Zhang / Peifeng Li / Yanyan Gao

Frontiers in Cell and Developmental Biology, Vol

Emerging Roles and Clinical Significance in Disease

2021 Volume 9

Abstract: Mitochondria are one of the most important organelles in cells. Mitochondria are semi-autonomous organelles with their own genetic system, and can independently replicate, transcribe, and translate mitochondrial DNA. Translation initiation, elongation, ... ...

Abstract	Mitochondria are one of the most important organelles in cells. Mitochondria are semi-autonomous organelles with their own genetic system, and can independently replicate, transcribe, and translate mitochondrial DNA. Translation initiation, elongation, termination, and recycling of the ribosome are four stages in the process of mitochondrial protein translation. In this process, mitochondrial protein translation factors and translation activators, mitochondrial RNA, and other regulatory factors regulate mitochondrial protein translation. Mitochondrial protein translation abnormalities are associated with a variety of diseases, including cancer, cardiovascular diseases, and nervous system diseases. Mutation or deletion of various mitochondrial protein translation factors and translation activators leads to abnormal mitochondrial protein translation. Mitochondrial tRNAs and mitochondrial ribosomal proteins are essential players during translation and mutations in genes encoding them represent a large fraction of mitochondrial diseases. Moreover, there is crosstalk between mitochondrial protein translation and cytoplasmic translation, and the imbalance between mitochondrial protein translation and cytoplasmic translation can affect some physiological and pathological processes. This review summarizes the regulation of mitochondrial protein translation factors, mitochondrial ribosomal proteins, mitochondrial tRNAs, and mitochondrial aminoacyl-tRNA synthetases (mt-aaRSs) in the mitochondrial protein translation process and its relationship with diseases. The regulation of mitochondrial protein translation and cytoplasmic translation in multiple diseases is also summarized.
Keywords	mitochondria ; protein translation ; translation factors ; mitochondrial ribosome ; mitoribosome assembly factors ; mitochondrial aminoacyl-tRNA synthetase ; Biology (General) ; QH301-705.5
Language	English
Publishing date	2021-07-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
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Article: Mitochondrial Protein Translation: Emerging Roles and Clinical Significance in Disease.

Wang, Fei / Zhang, Deyu / Zhang, Dejiu / Li, Peifeng / Gao, Yanyan

Frontiers in cell and developmental biology

2021 Volume 9, Page(s) 675465

Abstract	Mitochondria are one of the most important organelles in cells. Mitochondria are semi-autonomous organelles with their own genetic system, and can independently replicate, transcribe, and translate mitochondrial DNA. Translation initiation, elongation, termination, and recycling of the ribosome are four stages in the process of mitochondrial protein translation. In this process, mitochondrial protein translation factors and translation activators, mitochondrial RNA, and other regulatory factors regulate mitochondrial protein translation. Mitochondrial protein translation abnormalities are associated with a variety of diseases, including cancer, cardiovascular diseases, and nervous system diseases. Mutation or deletion of various mitochondrial protein translation factors and translation activators leads to abnormal mitochondrial protein translation. Mitochondrial tRNAs and mitochondrial ribosomal proteins are essential players during translation and mutations in genes encoding them represent a large fraction of mitochondrial diseases. Moreover, there is crosstalk between mitochondrial protein translation and cytoplasmic translation, and the imbalance between mitochondrial protein translation and cytoplasmic translation can affect some physiological and pathological processes. This review summarizes the regulation of mitochondrial protein translation factors, mitochondrial ribosomal proteins, mitochondrial tRNAs, and mitochondrial aminoacyl-tRNA synthetases (mt-aaRSs) in the mitochondrial protein translation process and its relationship with diseases. The regulation of mitochondrial protein translation and cytoplasmic translation in multiple diseases is also summarized.
Language	English
Publishing date	2021-07-01
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2737824-X
ISSN	2296-634X
ISSN	2296-634X
DOI	10.3389/fcell.2021.675465
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