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Jin S, Huang J, Wang Y, Zou H. SRSF10 regulates isoform expression of transcripts associated with proliferative diabetes retinopathy in ARPE-19 cells based on long-read RNA and immunoprecipitation sequencing. Gene 2025; 957:149412. [PMID: 40090530 DOI: 10.1016/j.gene.2025.149412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2024] [Revised: 03/01/2025] [Accepted: 03/09/2025] [Indexed: 03/18/2025]
Abstract
BACKGROUND Following injury and disruption of the retinal barrier, retinal pigment epithelium can differentiate into a fibroblastic phenotype, leading to proliferation and migration, thereby resulting in pathological conditions such as proliferative vitreoretinopathy and diabetic retinopathy. Previous studies have detected the specific expression of serine/arginine-rich splicing factor 10 (SRSF10) in the retina; however, its specific function has not been thoroughly studied. SRSF10 has been hypothesized to play an important role in retinal function. METHODS We used Oxford Nanopore Technologies (ONT) full-length transcriptome sequencing and Illumina next-generation transcriptome sequencing platforms to detect splice isoforms affected by SRSF10 and employed improved RNA immunoprecipitation sequencing (iRIP-seq) in human retinal pigment epithelial cells to detect RNA binding with SRSF10. RESULTS ARPE-19 cells overexpressing SRSF10 showed significant transcriptional differences in the sequencing data obtained from the ONT and Illumina sequencing platforms. Notably, ONT sequencing was more sensitive in detecting new transcripts compared to Illumina. ONT and Illumina sequencing platforms revealed characteristics of alternative splicing events regulated by SRSF10. ONT data showed a primary impact on overlapping exons (olp) events followed by alternative 3' splice site (alt3p) and alt5p, aligning with SRSF10's known functions in exon skipping and inclusion. ONT long-read transcriptome sequencing analysis identified polyadenylation sites (PASs) affected by SRSF10, indicating its role in the dysregulation of polyadenylation in key metabolic genes. In addition, SRSF10 regulates autophagy in cells by influencing the polyadenylation of DEAD-box helicase 58 (DDX58), thereby affecting cell apoptosis. CONCLUSIONS The study establishes SRSF10 as a significant splicing factor regulating the alternative splicing of multiple genes and interacting with splicing factors. It plays a pivotal role in cell proliferation, apoptosis, and possibly in the epithelial-mesenchymal transition (EMT) of ARPE-19 cells.
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Affiliation(s)
- Siyan Jin
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun 130000 Jilin, China
| | - Ju Huang
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun 130000 Jilin, China
| | - Yu Wang
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun 130000 Jilin, China
| | - He Zou
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun 130000 Jilin, China.
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2
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Lei Z, Luo Y, Fu Q, Lu J, Wang C, Zhang L, Zhang Z. Ribosomal protein L6 suppresses hepatocellular carcinoma by modulating FBXO22-mediated p53 degradation. Cell Signal 2025; 127:111612. [PMID: 39842528 DOI: 10.1016/j.cellsig.2025.111612] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2024] [Revised: 12/30/2024] [Accepted: 01/17/2025] [Indexed: 01/24/2025]
Abstract
The ribosomal protein L6 (RPL6) is significant in the progression of different cancer types. However, its precise role in hepatocellular carcinoma (HCC) remains unclear. This research demonstrated that the expression levels of RPL6 are notably decreased in HCC tissues. The decreased expression of RPL6 is strongly linked to tumor size, the presence of vascular invasion, and a worse prognosis. Functional experiments revealed that the expression of RPL6 impedes the proliferation of HCC cells and the advancement of xenograft tumors. Mechanistically, we found that RPL6 binds to and is degraded by the E3 ubiquitin ligase FBXO22, thereby inhibiting the polyubiquitination and subsequent degradation of p53 by FBXO22. The enhanced activity of p53 further contributes to cell growth inhibition. In contrast, the levels of p53 decreased significantly following RPL6 depletion, indicating that RPL6 is essential for the stabilization of p53. In summary, RPL6 inhibits the proliferation of HCC cells via the FBXO22/p53 signaling pathway, suggesting its potential as a biomarker and a therapeutic target for HCC.
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Affiliation(s)
- Zhen Lei
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Clinical Medicine Research Center for Hepatic Surgery of Hubei Province, Key Laboratory of Organ Transplantation, Ministry of Education, NHC Key Laboratory of Organ Transplantation, Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, Hubei 430030, PR China; Department of Hepatobiliary Surgery, The First Affiliated Hospital of Shihezi University, Shihezi, Xinjiang 832008, PR China
| | - Yiming Luo
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Clinical Medicine Research Center for Hepatic Surgery of Hubei Province, Key Laboratory of Organ Transplantation, Ministry of Education, NHC Key Laboratory of Organ Transplantation, Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, Hubei 430030, PR China
| | - Qinggang Fu
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Clinical Medicine Research Center for Hepatic Surgery of Hubei Province, Key Laboratory of Organ Transplantation, Ministry of Education, NHC Key Laboratory of Organ Transplantation, Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, Hubei 430030, PR China
| | - Junli Lu
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Clinical Medicine Research Center for Hepatic Surgery of Hubei Province, Key Laboratory of Organ Transplantation, Ministry of Education, NHC Key Laboratory of Organ Transplantation, Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, Hubei 430030, PR China
| | - Chao Wang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Clinical Medicine Research Center for Hepatic Surgery of Hubei Province, Key Laboratory of Organ Transplantation, Ministry of Education, NHC Key Laboratory of Organ Transplantation, Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, Hubei 430030, PR China
| | - Long Zhang
- Department of Hepatopancreatobiliary Surgery, Ganzhou People's Hospital of Jiangxi Province (Ganzhou Hospital Afffliated to Nanchang University), Ganzhou 341000, PR China.
| | - Zhiwei Zhang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Clinical Medicine Research Center for Hepatic Surgery of Hubei Province, Key Laboratory of Organ Transplantation, Ministry of Education, NHC Key Laboratory of Organ Transplantation, Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, Hubei 430030, PR China.
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Sojoudi K, Solaimani M, Azizi H. Exosomal insights into ovarian cancer stem cells: revealing the molecular hubs. J Ovarian Res 2025; 18:20. [PMID: 39891297 PMCID: PMC11784003 DOI: 10.1186/s13048-025-01597-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2024] [Accepted: 01/10/2025] [Indexed: 02/03/2025] Open
Abstract
Ovarian cancer is a deadly disease, often diagnosed at advanced stages due to a lack of reliable biomarkers. Exosomes, which carry a variety of molecules such as proteins, lipids, DNA, and non-coding RNAs, have recently emerged as promising tools for early cancer detection. While exosomes have been studied in various cancer types, comprehensive network analyses of exosome proteins in ovarian cancer remain limited. In this study, we used a protein-protein interaction (PPI) network. Using the Clustermaker2 app and the MCODE algorithm, we identified six significant clusters within the network, highlighting regions involved in functional pathways. A four-fold algorithmic approach, including MCC, DMNC, Degree, and EPC, identified 12 common hub genes. STRING analysis and visualization techniques provided a detailed understanding of the biological processes associated with these hub genes. Notably, 91.7% of the identified hub genes were involved in translational processes, showing an important role in protein synthesis regulation in ovarian cancer. In addition, we identified the miRNAs and LncRNAs carried by ovarian cancer exosomes. These findings highlight potential biomarkers for early detection and therapeutic targets.
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Affiliation(s)
- Kiana Sojoudi
- Department of Biology, Faculty of Sciences, University of Guilan, Rasht, Iran
- Faculty of Biotechnology, Amol University of Special Modern Technologies, Amol, 49767, Iran
| | - Maryam Solaimani
- Faculty of Biotechnology, Amol University of Special Modern Technologies, Amol, 49767, Iran
| | - Hossein Azizi
- Faculty of Biotechnology, Amol University of Special Modern Technologies, Amol, 49767, Iran.
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4
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Kulkarni R, Goda C, Rudich A, Karunasiri M, Urs AP, Bustos Y, Balcioglu O, Li W, Chidester S, Rodgers KA, Garfinkle EA, Patel A, Miller KE, Popovich PG, Elf S, Garzon R, Dorrance AM. Regulation of hematopoietic stem cell (HSC) proliferation by Epithelial Growth Factor Like-7 (EGFL7). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.21.634107. [PMID: 39896615 PMCID: PMC11785128 DOI: 10.1101/2025.01.21.634107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2025]
Abstract
Understanding the pathways regulating normal and malignant hematopoietic stem cell (HSC) biology is important for improving outcomes for patients with hematologic disorders. Epithelial Growth Factor Like-7 (EGFL7 ) is ∼30 kDa secreted protein that is highly expressed in adult HSCs. Using Egfl7 genetic knock-out ( Egfl7 KO) mice and recombinant EGFL7 (rEGFL7) protein, we examined the role of Egfl7 in regulating normal hematopoiesis. We found that Egfl7 KO mice had decreases in overall BM cellularity resulting in significant reduction in the number of hematopoietic stem and progenitor cells (HSPCs), which was due to dysregulation of normal cell-cycle progression along with a corresponding increase in quiescence. rEGFL7 treatment rescued our observed hematopoietic defects of Egfl7 KO mice and enhanced HSC expansion after genotoxic stress such as 5-FU and irradiation. Furthermore, treatment of WT mice with recombinant EGFL7 (rEGFL7) protein expands functional HSCs evidenced by an increase in transplantation potential. Overall, our data demonstrates a role for EGFL7 in HSC expansion and survival and represents a potential strategy for improving transplant engraftment or recovering bone marrow function after stress.
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5
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Shishkin SS. Moonlighting Proteins of Human and Some Other Eukaryotes. Evolutionary Aspects. BIOCHEMISTRY. BIOKHIMIIA 2025; 90:S36-S59. [PMID: 40164152 DOI: 10.1134/s0006297924602855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 03/27/2024] [Accepted: 04/02/2024] [Indexed: 04/02/2025]
Abstract
This review presents materials on formation of the concept of moonlighting proteins and general characteristics of different similar proteins. It is noted that the concept under consideration is based on the data on the existence in different organisms of individual genes, protein products of which have not one, but at least two fundamentally different functions, for example, depending on cellular or extracellular location. An important feature of these proteins is that their functions can be switched. As a result, in different cellular compartments or outside the cells, as well as under a number of other circumstances, one of the possible functions can be carried out, and under other conditions, another. It is emphasized that the significant interest in moonlighting proteins is due to the fact that information is currently accumulating about their involvement in many vital molecular processes (glycolysis, translation, transcription, replication, etc.). Alternative hypotheses on the evolutionary origin of moonlighting proteins are discussed.
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Affiliation(s)
- Sergei S Shishkin
- Federal Research Center "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, 119071, Russia.
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6
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Zhao Z, Ruan S, Li Y, Qi T, Qi Y, Huang Y, Liu Z, Ruan Q, Ma Y. The Influence of Extra-Ribosomal Functions of Eukaryotic Ribosomal Proteins on Viral Infection. Biomolecules 2024; 14:1565. [PMID: 39766272 PMCID: PMC11674327 DOI: 10.3390/biom14121565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2024] [Revised: 11/25/2024] [Accepted: 12/06/2024] [Indexed: 01/11/2025] Open
Abstract
The eukaryotic ribosome is a large ribonucleoprotein complex consisting of four types of ribosomal RNA (rRNA) and approximately 80 ribosomal proteins (RPs), forming the 40S and 60S subunits. In all living cells, its primary function is to produce proteins by converting messenger RNA (mRNA) into polypeptides. In addition to their canonical role in protein synthesis, RPs are crucial in controlling vital cellular processes such as cell cycle progression, cellular proliferation, differentiation, DNA damage repair, genome structure maintenance, and the cellular stress response. Viruses, as obligate intracellular parasites, depend completely on the machinery of the host cell for their replication and survival. During viral infection, RPs have been demonstrated to perform a variety of extra-ribosomal activities, which are especially important in viral disease processes. These functions cover a wide range of activities, ranging from controlling inflammatory responses and antiviral immunity to promoting viral replication and increasing viral pathogenicity. Deciphering the regulatory mechanisms used by RPs in response to viral infections has greatly expanded our understanding of their functions outside of the ribosome. Furthermore, these findings highlight the promising role of RPs as targets for the advancement of antiviral therapies and the development of novel antiviral approaches. This review comprehensively examines the many functions of RPs outside of the ribosome during viral infections and provides a foundation for future research on the host-virus interaction.
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Affiliation(s)
- Zhongwei Zhao
- Virology Laboratory, Shengjing Hospital of China Medical University, Shenyang 110004, China; (Z.Z.); (T.Q.); (Y.Q.); (Y.H.); (Z.L.)
| | - Shan Ruan
- Department of Gerontology, and Geriatrics, Shengjing Hospital of China Medical University, Shenyang 110004, China;
| | - Yang Li
- Department of Blood Transfusion, Shengjing Hospital of China Medical University, Shenyang 110004, China;
| | - Te Qi
- Virology Laboratory, Shengjing Hospital of China Medical University, Shenyang 110004, China; (Z.Z.); (T.Q.); (Y.Q.); (Y.H.); (Z.L.)
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang 110004, China
- Departments of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Ying Qi
- Virology Laboratory, Shengjing Hospital of China Medical University, Shenyang 110004, China; (Z.Z.); (T.Q.); (Y.Q.); (Y.H.); (Z.L.)
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang 110004, China
- Departments of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Yujing Huang
- Virology Laboratory, Shengjing Hospital of China Medical University, Shenyang 110004, China; (Z.Z.); (T.Q.); (Y.Q.); (Y.H.); (Z.L.)
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang 110004, China
- Departments of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Zhongyang Liu
- Virology Laboratory, Shengjing Hospital of China Medical University, Shenyang 110004, China; (Z.Z.); (T.Q.); (Y.Q.); (Y.H.); (Z.L.)
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang 110004, China
- Departments of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Qiang Ruan
- Virology Laboratory, Shengjing Hospital of China Medical University, Shenyang 110004, China; (Z.Z.); (T.Q.); (Y.Q.); (Y.H.); (Z.L.)
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang 110004, China
- Departments of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Yanping Ma
- Virology Laboratory, Shengjing Hospital of China Medical University, Shenyang 110004, China; (Z.Z.); (T.Q.); (Y.Q.); (Y.H.); (Z.L.)
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang 110004, China
- Departments of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang 110004, China
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7
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Wang X, Ji D, Ma J, Chi W. Function of plastid translation in plant temperature acclimation: Retrograde signalling or extraribosomal 'moonlighting' functions? PLANT, CELL & ENVIRONMENT 2024; 47:4908-4916. [PMID: 39101459 DOI: 10.1111/pce.15074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 07/06/2024] [Accepted: 07/25/2024] [Indexed: 08/06/2024]
Abstract
Summary StatementSpecific components of the plastid ribosome could act as pivotal limiting factors in plant temperature acclimation. We endeavour to elucidate the molecular nexus between plastid translation and temperature acclimation by incorporating the concept of extraribosomal ‘moonlighting’ functions of plastid ribosome proteins.
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Affiliation(s)
- Xiushun Wang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Daili Ji
- Key Laboratory of Photobiology, Photosynthesis Research Center, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Jinfang Ma
- Key Laboratory of Photobiology, Photosynthesis Research Center, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Wei Chi
- College of Life Sciences, Nanjing Normal University, Nanjing, China
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Hussein NA, El-Shershaby AS, Abdel-Moez S, El-Hakim AE, Shahein YE. Mining the secreted and membrane transcriptome of Hyalomma dromedarii ticks for identification of potential protective antigens. Parasit Vectors 2024; 17:462. [PMID: 39529157 PMCID: PMC11555925 DOI: 10.1186/s13071-024-06538-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2024] [Accepted: 10/16/2024] [Indexed: 11/16/2024] Open
Abstract
BACKGROUND Members belonging to the tick genus Hyalomma function as a multi-host reservoir for several pathogens and important parasites infesting large animals, such as camels, goats, cattle and sheep. In Egypt, there is a high risk of pathogen transmission as camels and cattle are imported from Sudan and Ethiopia and shipped to slaughterhouses and animal markets located in populated areas. Hyalomma dromedarii ticks are semi-desert vectors and, similar to other members of the genus Hyalomma, characterized by long-term feeding. During this process, different physiological, biochemical and immunological interactions occur within both the feeding ticks and their hosts. These biological changes affect the different tick developmental phases. The aim of this study was to explore the transcriptome of mixed messenger RNAs (mRNAs) collected from H. dromedarii eggs, larvae, nymphs and fed and unfed adults, using the Gateway cDNA library prepared in pCMV sport6.1 vector METHODS: The clones were sequenced and searched for potential secreted, membrane-associated or transmembrane (SMaT) sequences. The identified SMaT sequences were compared to the National Center for Biotechnology Information (NCBI) non-redundant protein sequence database using Blastx. Annotation and functional classification were achieved by comparison to sequences in the UniProtKB/Swiss-Prot and VectorBase databases and to the publicly available annotated proteomes of six hard tick species (H. asiaticum, Rhipicephalus sanguineus sensu lato, Dermacentor silvarum, Rhipicephalus microplus, Ixodes scapularis and Haemaphysalis longicornis) in addition to the published H. dromedarii sialotranscriptome. For the common sequences, we predicted the physicochemical properties, secondary structures and antigenicity of the fragments similar to matched sequences in the UniProtKB/Swiss-Prot database using three different methods. RESULTS The quality-trimmed sequences from the cDNA library revealed 319 SMaT transcripts among 1248 sequenced clones. Annotation of the SMaT sequences using the UniProtKB/Swiss-Prot database revealed only 232 non-redundant sequences with at least one match. According to the UniProtKB/Swiss-Prot and Vectorbase databases, the SMaT sequences were either secreted (extracellular) (29 sequences) or cellular (transmembrane and membrane-associated) (203 sequences). These were classified into 10 functional classes: biogenesis (49 sequences), defense (9 sequences), development (36 sequences), signal transduction (28 sequences), transport (15 sequences), protein modification (33 sequences), homeostasis (6 sequences), metabolism (45 sequences) and miscellaneous/uncharacterized (11 sequences). A total of 60 sequences were shared between H. dromedarii SMaT, the sialotransciptome and six other hard tick species. The peptide fragments of these sequences that aligned to proteins from the UniProtKB/Swiss-Prot database were predicted to be promising epitopes and mapped to 10 functional classes at different ratios. CONCLUSIONS Our immuno-informatics analysis identified 60 sequences common among hard tick species and encoded by H. dromedarii salivary glands. These annotated SMaT sequences of H. dromedarii will pave the way for the identification and discovery of novel potential protective antigens that are either secreted, membrane-associated or transmembrane.
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Affiliation(s)
- Nahla A Hussein
- Molecular Biology Department, Biotechnology Research Institute, National Research Centre, Cairo, Egypt
| | - Asmaa S El-Shershaby
- Molecular Biology Department, Biotechnology Research Institute, National Research Centre, Cairo, Egypt
| | - Shaimaa Abdel-Moez
- Molecular Biology Department, Biotechnology Research Institute, National Research Centre, Cairo, Egypt
| | - Amr E El-Hakim
- Molecular Biology Department, Biotechnology Research Institute, National Research Centre, Cairo, Egypt
| | - Yasser E Shahein
- Molecular Biology Department, Biotechnology Research Institute, National Research Centre, Cairo, Egypt.
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Yu M, Liu H, Wang Y, Zhou S, Ding X, Xia Z, An M, Wu Y. Synthesis, Anti-TMV Activities, and Action Mechanisms of a Novel Cytidine Peptide Compound. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:20783-20793. [PMID: 39267339 DOI: 10.1021/acs.jafc.4c02767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/17/2024]
Abstract
Cytidine has a broad range of applications in the pharmaceutical field as an intermediate of antitumor or antiviral agent. Here, a series of new cytidine peptide compounds were synthesized using cytidine and Boc group-protected amino acids and analyzed for their antiviral activities against tobacco mosaic virus (TMV). Among these compounds, the structure of an effective antiviral cytidine peptide SN11 was characterized by 1H NMR, 13C NMR, and high-resolution mass spectrometer. The compound SN11 has a molecular formula of C15H22N6O8 and is named 2-amino-N-(2- ((1- (3,4-dihydroxy-5-(hydroxymethyl) tetrahydrofuran-2-yl) -2-oxo-1,2-dihydropyrimidin-4-yl) amino) -2-oxyethyl) amino). The protection, inactivation, and curation activities of SN11 at a concentration of 500 μg/mL against TMV in Nicotiana glutinosa were 82.6%, 84.2%, and 72.8%, respectively. SN11 also effectively suppressed the systemic transportation of a recombinant TMV carrying GFP reporter gene (p35S-30B:GFP) in Nicotiana benthamiana by reducing viral accumulation to 71.3% in the upper uninoculated leaves and inhibited the systemic infection of TMV in Nicotiana tabacum plants. Furthermore, the results of RNA-seq showed that compound SN11 induced differential expression of genes involved in the biogenesis and function of ribosome, plant hormone signal transduction, plant pathogen interaction, and chromatin. These results validate the antiviral mechanisms of the cytidine peptide compound and provide a theoretical basis for their potential application in the management of plant virus diseases.
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Affiliation(s)
- Miao Yu
- College of Plant Protection, Shenyang Agricultural University, No. 120 Dongling, Shenyang 110866, Liaoning, China
| | - He Liu
- College of Plant Protection, Shenyang Agricultural University, No. 120 Dongling, Shenyang 110866, Liaoning, China
- Center for Research and Development of Fine Chemicals of Guizhou University, Guiyang 550025, Guizhou, China
| | - Yan Wang
- College of Plant Protection, Shenyang Agricultural University, No. 120 Dongling, Shenyang 110866, Liaoning, China
| | - Shidong Zhou
- College of Plant Protection, Shenyang Agricultural University, No. 120 Dongling, Shenyang 110866, Liaoning, China
| | - Xiaojie Ding
- College of Plant Protection, Shenyang Agricultural University, No. 120 Dongling, Shenyang 110866, Liaoning, China
| | - Zihao Xia
- College of Plant Protection, Shenyang Agricultural University, No. 120 Dongling, Shenyang 110866, Liaoning, China
| | - Mengnan An
- College of Plant Protection, Shenyang Agricultural University, No. 120 Dongling, Shenyang 110866, Liaoning, China
| | - Yuanhua Wu
- College of Plant Protection, Shenyang Agricultural University, No. 120 Dongling, Shenyang 110866, Liaoning, China
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McLaughlin E, Zavala Martinez MG, Dujeancourt-Henry A, Chaze T, Gianetto QG, Matondo M, Urbaniak MD, Glover L. Phosphoproteomic analysis of the response to DNA damage in Trypanosoma brucei. J Biol Chem 2024; 300:107657. [PMID: 39128729 PMCID: PMC11408851 DOI: 10.1016/j.jbc.2024.107657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 07/29/2024] [Accepted: 07/31/2024] [Indexed: 08/13/2024] Open
Abstract
Damage to the genetic material of the cell poses a universal threat to all forms of life. The DNA damage response is a coordinated cellular response to a DNA break, key to which is the phosphorylation signaling cascade. Identifying which proteins are phosphorylated is therefore crucial to understanding the mechanisms that underlie it. We have used stable isotopic labeling of amino acids in cell culture-based quantitative phosphoproteomics to profile changes in phosphorylation site abundance following double stranded DNA breaks, at two distinct loci in the genome of the single cell eukaryote Trypanosoma brucei. Here, we report on the T. brucei phosphoproteome following a single double-strand break at either a chromosome internal or subtelomeric locus, specifically the bloodstream form expression site. We detected >6500 phosphorylation sites, of which 211 form a core set of double-strand break responsive phosphorylation sites. Along with phosphorylation of canonical DNA damage factors, we have identified two novel phosphorylation events on histone H2A and found that in response to a chromosome internal break, proteins are predominantly phosphorylated, while a greater proportion of proteins dephosphorylated following a DNA break at a subtelomeric bloodstream form expression site. Our data represent the first DNA damage phosphoproteome and provides novel insights into repair at distinct chromosomal contexts in T. brucei.
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Affiliation(s)
- Emilia McLaughlin
- Institut Pasteur, Université Paris Cité, Trypanosome Molecular Biology, Department of Parasites and Insect Vectors, Paris, France; Sorbonne Université, Collège doctoral, Paris, France
| | - Monica Gabriela Zavala Martinez
- Institut Pasteur, Université Paris Cité, Trypanosome Molecular Biology, Department of Parasites and Insect Vectors, Paris, France
| | - Annick Dujeancourt-Henry
- Institut Pasteur, Université Paris Cité, Trypanosome Molecular Biology, Department of Parasites and Insect Vectors, Paris, France
| | - Thibault Chaze
- Institut Pasteur, Université Paris Cité, Proteomics Platform, Mass Spectrometry for Biology Unit, Centre National de la Recherche Scientifique, UAR 2024, Paris, France
| | - Quentin Giai Gianetto
- Institut Pasteur, Université Paris Cité, Proteomics Platform, Mass Spectrometry for Biology Unit, Centre National de la Recherche Scientifique, UAR 2024, Paris, France; Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics HUB, Paris, France
| | - Mariette Matondo
- Institut Pasteur, Université Paris Cité, Proteomics Platform, Mass Spectrometry for Biology Unit, Centre National de la Recherche Scientifique, UAR 2024, Paris, France
| | - Michael D Urbaniak
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, UK
| | - Lucy Glover
- Institut Pasteur, Université Paris Cité, Trypanosome Molecular Biology, Department of Parasites and Insect Vectors, Paris, France.
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Huang J, Zhou M, Chen J, Ke C. Molecular Cloning, Characterization, and Function of Insulin-Related Peptide 1 (IRP1) in the Haliotis discus hanna. Genes (Basel) 2024; 15:960. [PMID: 39062739 PMCID: PMC11275868 DOI: 10.3390/genes15070960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 07/17/2024] [Accepted: 07/19/2024] [Indexed: 07/28/2024] Open
Abstract
Abalone is a popular mollusk in the marine aquaculture industry of China. However, existing challenges, like slow growth, individual miniaturization, and the absence of abundant abalone, have emerged as significant obstacles impeding its long-term progress in aquaculture. Studies have demonstrated that insulin-related peptide (IRP) is a crucial factor in the growth of marine organisms. However, limited studies have been conducted on IRP in abalone. This study indicated that the hdh-MIRP1 open reading frame (ORF) was composed of 456 base pairs, which encoded 151 amino acids. Based on the gene expression and immunofluorescence analyses, the cerebral ganglion of Haliotis discus hannai (H. discus hannai) was the primary site of hdh-MIRP1 mRNA expression. Moreover, hdh-MIRP1 expression was observed to be higher in the larger group than in the smaller group abalones. Only single nucleotide polymorphism (SNP) was related to their growth characteristics. However, approximately 82 proteins that may interact with hdh-MIRP1 were identified. The functional enrichment analysis of the 82 genes indicated that hdh-MIRP1 may be involved in the regulation of glucose metabolism and the process of growth. This study established a benchwork for further investigating the role of IRP in the growth of abalone.
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Affiliation(s)
- Jianfang Huang
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, College of Geography and Oceanography, Minjiang University, Fuzhou 350108, China;
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China;
| | - Mingcan Zhou
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China;
| | - Jianming Chen
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, College of Geography and Oceanography, Minjiang University, Fuzhou 350108, China;
| | - Caihuan Ke
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China;
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12
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Leonardi A, Donato A, Rosani U, Di Stefano A, Cavarzeran F, Brun P. Endoplasmic Reticulum Stress and Unfolded Protein Response in Vernal Keratoconjunctivitis. Invest Ophthalmol Vis Sci 2024; 65:23. [PMID: 38597723 PMCID: PMC11008754 DOI: 10.1167/iovs.65.4.23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 03/20/2024] [Indexed: 04/11/2024] Open
Abstract
Purpose Vernal keratoconjunctivitis (VKC) is an ocular allergic disease characterized by a type 2 inflammation, tissue remodeling, and low quality of life for the affected patients. We investigated the involvement of endoplasmic reticulum (ER) stress and unfolded protein response in VKC. Methods Conjunctival imprints from VKC patients and normal subjects (CTs) were collected, and RNA was isolated, reverse transcribed, and analyzed with the Affymetrix microarray. Differentially expressed genes between VKC patients and CTs were evaluated. Genes related to ER stress, apoptosis, and autophagy were further considered. VKC and CT conjunctival biopsies were analyzed by immunohistochemistry (IHC) with specific antibodies against unfolded protein response (UPR), apoptosis, and inflammation. Conjunctival fibroblast and epithelial cell cultures were exposed to the conditioned medium of activated U937 monocytes and analyzed by quantitative PCR for the expression of UPR, apoptosis, autophagy, and inflammatory markers. Results ER chaperones HSPA5 (GRP78/BiP) and HYOU1 (GRP170) were upregulated in VKC patients compared to CTs. Genes encoding for ER transmembrane proteins, PKR-like ER kinase (PERK), activating transcription factor 6 (ATF6), ER-associated degradation (ERAD), and autophagy were upregulated, but not those related to apoptosis. Increased positive reactivity of BiP and ATF6 and unchanged expression of apoptosis markers were confirmed by IHC. Cell cultures in stress conditions showed an overexpression of UPR, proinflammatory, apoptosis, and autophagy markers. Conclusions A significant overexpression of genes encoding for ER stress, UPR, and pro-inflammatory pathway components was reported for VKC. Even though these pathways may lead to ER homeostasis, apoptosis, or inflammation, ER stress in VKC may predominantly contribute to promote inflammation.
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Affiliation(s)
- Andrea Leonardi
- Ophthalmology Unit, Department of Neuroscience, University of Padova, Padova, Italy
| | - Alice Donato
- Histology Unit, Department of Molecular Medicine, University of Padova, Padova, Italy
| | | | - Antonino Di Stefano
- Istituti Clinici Scientifici Maugeri, IRCCS, Istituto Scientifico di Veruno, Veruno, Italy
| | - Fabiano Cavarzeran
- Ophthalmology Unit, Department of Neuroscience, University of Padova, Padova, Italy
| | - Paola Brun
- Histology Unit, Department of Molecular Medicine, University of Padova, Padova, Italy
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13
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Liang C, Zhou J, Wang Y, Sun Y, Zhou J, Shao L, Zhang Z, Yan W, Liu Z, Dong Y. Essential genes analysis reveals small ribosomal subunit protein eS28 may be a prognostic factor and potential vulnerability in osteosarcoma. J Bone Oncol 2024; 44:100517. [PMID: 38204480 PMCID: PMC10776981 DOI: 10.1016/j.jbo.2023.100517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/26/2023] [Accepted: 12/13/2023] [Indexed: 01/12/2024] Open
Abstract
Background Osteosarcoma, the most common primary malignant bone tumor, is currently treated with surgery combined with chemotherapy, but the limited availability of targeted drugs contributes to a poor prognosis. Identifying effective therapeutic targets is crucial for improving the prognosis of osteosarcoma patients. Methods We screened the DepMap database to identify essential genes as potential therapeutic targets for osteosarcoma. Gene Set Enrichment Analysis (GSEA) was employed to elucidate the biological roles of these essential genes. Promising candidates were filtered through univariate and multivariate Cox analyses, as well as Kaplan-Meier survival analyses using the GSE21257-OSA and TARGET-OSA datasets. The functional role of the target gene was assessed through cell experiments. Additionally, an in situ nude mice model was established to observe the gene's function, and RNA sequencing was utilized to explore the underlying molecular mechanism. Results A total of 934 essential genes were identified based on their effects (Chronos) using the DepMap database. These genes were primarily enriched in the ribosome pathway according to GSEA analysis. Among them, 195 genes were associated with the ribosome pathway. Rps28, Rps7, and Rps25 were validated as promising candidates following univariate and multivariate Cox analyses of the TARGET-OSA and GSE21257-OSA datasets. Kaplan-Meier survival analyses indicated Rps28 represented an especially promising target, with high expression correlating with poor prognosis. Knockdown of small ribosomal subunit protein eS28, the protein of Rps28, inhibited proliferation, migration, and invasion in both in vitro and in vivo experiments. Silencing RPS28 affected the MAPK signaling pathway in osteosarcoma. Conclusion In summary, Rps28 has been identified as an essential gene for osteosarcoma cell survival and eS28 may serve as a potential vulnerability in osteosarcoma.
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Affiliation(s)
- Chao Liang
- Department of Musculoskeletal Oncology, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, 200032, PR China
- Department of Orthopedics, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200233, PR China
| | - Juan Zhou
- Department of Pathology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200233, PR China
| | - Yongjie Wang
- Department of Orthopedics, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200072, PR China
| | - Yin Sun
- Department of Orthopedics, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200233, PR China
| | - Jin Zhou
- Department of Orthopedics, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200233, PR China
| | - Lan Shao
- Department of Orthopedics, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200233, PR China
| | - Zhichang Zhang
- Department of Orthopedics, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200233, PR China
| | - Wangjun Yan
- Department of Musculoskeletal Oncology, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, 200032, PR China
| | - Zhiyan Liu
- Department of Pathology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200233, PR China
| | - Yang Dong
- Department of Orthopedics, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200233, PR China
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14
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Gelfo V, Venturi G, Zacchini F, Montanaro L. Decoding Ribosome Heterogeneity: A New Horizon in Cancer Therapy. Biomedicines 2024; 12:155. [PMID: 38255260 PMCID: PMC10813612 DOI: 10.3390/biomedicines12010155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/05/2024] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
The traditional perception of ribosomes as uniform molecular machines has been revolutionized by recent discoveries, revealing a complex landscape of ribosomal heterogeneity. Opposing the conventional belief in interchangeable ribosomal entities, emerging studies underscore the existence of specialized ribosomes, each possessing unique compositions and functions. Factors such as cellular and tissue specificity, developmental and physiological states, and external stimuli, including circadian rhythms, significantly influence ribosome compositions. For instance, muscle cells and neurons are characterized by distinct ribosomal protein sets and dynamic behaviors, respectively. Furthermore, alternative forms of ribosomal RNA (rRNAs) and their post-transcriptional modifications add another dimension to this heterogeneity. These variations, orchestrated by spatial, temporal, and conditional factors, enable the manifestation of a broad spectrum of specialized ribosomes, each tailored for potentially distinct functions. Such specialization not only impacts mRNA translation and gene expression but also holds significant implications for broader biological contexts, notably in the realm of cancer research. As the understanding of ribosomal diversity deepens, it also paves the way for exploring novel avenues in cellular function and offers a fresh perspective on the molecular intricacies of translation.
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Affiliation(s)
- Valerio Gelfo
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy; (V.G.); (G.V.)
- Centre for Applied Biomedical Research (CRBA), Bologna University Hospital Authority St. Orsola-Malpighi Polyclinic, 40138 Bologna, Italy
| | - Giulia Venturi
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy; (V.G.); (G.V.)
- Centre for Applied Biomedical Research (CRBA), Bologna University Hospital Authority St. Orsola-Malpighi Polyclinic, 40138 Bologna, Italy
| | - Federico Zacchini
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy;
| | - Lorenzo Montanaro
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy; (V.G.); (G.V.)
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy;
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15
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Kitamura K, Hoshino T, Okabe A, Fukuyo M, Rahmutulla B, Tanaka N, Kobayashi S, Tanaka T, Shida T, Ueda M, Minamoto T, Matsubara H, Kaneda A, Ishii H, Matsushita K. The Link of mRNA and rRNA Transcription by PUF60/FIR through TFIIH/P62 as a Novel Therapeutic Target for Cancer. Int J Mol Sci 2023; 24:17341. [PMID: 38139171 PMCID: PMC10743661 DOI: 10.3390/ijms242417341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
The interaction between mRNA and ribosomal RNA (rRNA) transcription in cancer remains unclear. RNAP I and II possess a common N-terminal tail (NTT), RNA polymerase subunit RPB6, which interacts with P62 of transcription factor (TF) IIH, and is a common target for the link between mRNA and rRNA transcription. The mRNAs and rRNAs affected by FUBP1-interacting repressor (FIR) were assessed via RNA sequencing and qRT-PCR analysis. An FIR, a c-myc transcriptional repressor, and its splicing form FIRΔexon2 were examined to interact with P62. Protein interaction was investigated via isothermal titration calorimetry measurements. FIR was found to contain a highly conserved region homologous to RPB6 that interacts with P62. FIRΔexon2 competed with FIR for P62 binding and coactivated transcription of mRNAs and rRNAs. Low-molecular-weight chemical compounds that bind to FIR and FIRΔexon2 were screened for cancer treatment. A low-molecular-weight chemical, BK697, which interacts with FIRΔexon2, inhibited tumor cell growth with rRNA suppression. In this study, a novel coactivation pathway for cancer-related mRNA and rRNA transcription through TFIIH/P62 by FIRΔexon2 was proposed. Direct evidence in X-ray crystallography is required in further studies to show the conformational difference between FIR and FIRΔexon2 that affects the P62-RBP6 interaction.
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Affiliation(s)
- Kouichi Kitamura
- Department of Laboratory Medicine, Chiba University Hospital, Chiba 260-8677, Japan; (K.K.); (N.T.); (S.K.)
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan;
| | - Tyuji Hoshino
- Department of Molecular Design, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, Japan;
| | - Atsushi Okabe
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan; (A.O.); (M.F.); (B.R.); (A.K.)
| | - Masaki Fukuyo
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan; (A.O.); (M.F.); (B.R.); (A.K.)
| | - Bahityar Rahmutulla
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan; (A.O.); (M.F.); (B.R.); (A.K.)
| | - Nobuko Tanaka
- Department of Laboratory Medicine, Chiba University Hospital, Chiba 260-8677, Japan; (K.K.); (N.T.); (S.K.)
| | - Sohei Kobayashi
- Department of Laboratory Medicine, Chiba University Hospital, Chiba 260-8677, Japan; (K.K.); (N.T.); (S.K.)
- Department of Medical Technology and Sciences, Health and Sciences, International University of Health and Welfare, Chiba 286-8686, Japan
| | - Tomoaki Tanaka
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan;
| | - Takashi Shida
- Research Team for Promoting Independence and Mental Health, Tokyo Metropolitan Institute for Geriatrics and Gerontology, Tokyo 173-0015, Japan;
| | - Mashiro Ueda
- Master’s Program in Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba 305-8575, Japan;
| | - Toshinari Minamoto
- Division of Translational and Clinical Oncology, Cancer Research Institute, Kanazawa University, Kanazawa 920-1192, Japan;
| | - Hisahiro Matsubara
- Department of Frontier Surgery, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan;
| | - Atsushi Kaneda
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan; (A.O.); (M.F.); (B.R.); (A.K.)
| | - Hideshi Ishii
- Medical Data Science, Center of Medical Innovation and Translational Research (CoMIT), Osaka University, Osaka 565-0871, Japan;
| | - Kazuyuki Matsushita
- Department of Laboratory Medicine, Chiba University Hospital, Chiba 260-8677, Japan; (K.K.); (N.T.); (S.K.)
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16
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Cheng H, Zhang L, Yang S, Ren Q, Chang S, Jin Y, Mou W, Qin H, Yang W, Zhang X, Zhang W, Wang H. Integration of clinical characteristics and molecular signatures of the tumor microenvironment to predict the prognosis of neuroblastoma. J Mol Med (Berl) 2023; 101:1421-1436. [PMID: 37712965 DOI: 10.1007/s00109-023-02372-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 08/26/2023] [Accepted: 09/04/2023] [Indexed: 09/16/2023]
Abstract
This study aimed to analyze the clinical characteristics, cell types, and molecular characteristics of the tumor microenvironment to better predict the prognosis of neuroblastoma (NB). The gene expression data and corresponding clinical information of 498 NB patients were obtained from the Gene Expression Omnibus (GEO: GSE62564) and ArrayExpress (accession: E-MTAB-8248). The relative cell abundances were estimated using single-sample gene set enrichment analysis (ssGSEA) with the R gene set variation analysis (GSVA) package. We performed Cox regression analyses to identify marker genes indicating cell subsets and combined these with prognostically relevant clinical factors to develop a new prognostic model. Data from the E-MTAB-8248 cohort verified the predictive accuracy of the prognostic model. Single-cell RNA-seq data were analyzed by using the R Seurat package. Multivariate survival analysis for each gene, using clinical characteristics as cofactors, identified 34 prognostic genes that showed a significant correlation with both event-free survival (EFS) and overall survival (OS) (log-rank test, P value < 0.05). The pathway enrichment analysis revealed that these prognostic genes were highly enriched in the marker genes of NB cells with mesenchymal features and protein translation. Ultimately, USP39, RPL8, IL1RAPL1, MAST4, CSRP2, ATP5E, International Neuroblastoma Staging System (INSS) stage, age, and MYCN status were selected to build an optimized Cox model for NB risk stratification. These samples were divided into two groups using the median of the risk score as a cutoff. The prognosis of samples in the poor prognosis group (PP) was significantly worse than that of samples in the good prognosis group (GP) (log-rank test, P value < 0.0001, median EFS: 640.5 vs. 2247 days, median OS: 1279.5 vs. 2519 days). The risk model was also regarded as a prognostic indicator independent of MYCN status, age, and stage. Finally, through scRNA-seq data, we found that as an important prognostic marker, USP39 might participate in the regulation of RNA splicing in NB. Our study established a multivariate Cox model based on gene signatures and clinical characteristics to better predict the prognosis of NB and revealed that mesenchymal signature genes of NB cells, especially USP39, were more abundant in patients with a poor prognosis than in those with a good prognosis. KEY MESSAGES: Our study established a multivariate Cox model based on gene signatures and clinical characteristics to better predict the prognosis of NB and revealed that mesenchymal signature genes of NB cells, especially USP39, were more abundant in patients with a poor prognosis than in those with a good prognosis. USP39, RPL8, IL1RAPL1, MAST4, CSRP2, ATP5E, International Neuroblastoma Staging System (INSS) stage, age, and MYCN status were selected to build an optimized Cox model for NB risk stratification. These samples were divided into two groups using the median of the risk score as a cutoff. The prognosis of samples in the poor prognosis group (PP) was significantly worse than that of samples in the good prognosis group (GP). Finally, through scRNA-seq data, we found that as an important prognostic marker, USP39 might participate in the regulation of RNA splicing in NB.
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Affiliation(s)
- Haiyan Cheng
- Department of Surgical Oncology, MOE Key Laboratory of Major Diseases in Children, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, 56 Nanlishi Road, Beijing, 100045, China
| | - Li Zhang
- Shanghai Institute of Precision Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
| | - Shen Yang
- Department of Surgical Oncology, MOE Key Laboratory of Major Diseases in Children, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, 56 Nanlishi Road, Beijing, 100045, China
| | - Qinghua Ren
- Department of Surgical Oncology, MOE Key Laboratory of Major Diseases in Children, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, 56 Nanlishi Road, Beijing, 100045, China
| | - Saishuo Chang
- Department of Surgical Oncology, MOE Key Laboratory of Major Diseases in Children, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, 56 Nanlishi Road, Beijing, 100045, China
| | - Yaqiong Jin
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, MOE Key Laboratory of Major Diseases in Children, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Wenjun Mou
- Laboratory of Tumor Immunology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Hong Qin
- Department of Surgical Oncology, MOE Key Laboratory of Major Diseases in Children, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, 56 Nanlishi Road, Beijing, 100045, China
| | - Wei Yang
- Department of Surgical Oncology, MOE Key Laboratory of Major Diseases in Children, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, 56 Nanlishi Road, Beijing, 100045, China
| | - Xianwei Zhang
- Zhengzhou Key Laboratory of Precise Diagnosis and Treatment of Children's Malignant Tumors, Department of Pediatric Oncology Surgery, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China
| | - Wancun Zhang
- Zhengzhou Key Laboratory of Precise Diagnosis and Treatment of Children's Malignant Tumors, Department of Pediatric Oncology Surgery, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China
| | - Huanmin Wang
- Department of Surgical Oncology, MOE Key Laboratory of Major Diseases in Children, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, 56 Nanlishi Road, Beijing, 100045, China.
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17
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Perez ÉS, Duran BOS, Zanella BTT, Dal-Pai-Silva M. Review: Understanding fish muscle biology in the indeterminate growth species pacu (Piaractus mesopotamicus). Comp Biochem Physiol A Mol Integr Physiol 2023; 285:111502. [PMID: 37572733 DOI: 10.1016/j.cbpa.2023.111502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 08/08/2023] [Accepted: 08/09/2023] [Indexed: 08/14/2023]
Abstract
The muscle phenotype of fish is regulated by numerous factors that, although widely explored, still need to be fully understood. In this context, several studies aimed to unravel how internal and external stimuli affect the muscle growth of these vertebrates. The pacu (Piaractus mesopotamicus) is a species of indeterminate muscular growth that quickly reaches high body weight. For this reason, it adds great importance to the productive sector, along with other round fish. In this context, we aimed to compile studies on fish biology and skeletal muscle growth, focusing on studies by our research group that used pacu as an experimental model along with other species. Based on these studies, new muscle phenotype regulators were identified and explored in vivo, in vitro, and in silico studies, which strongly contribute to advances in understanding muscle growth mechanisms with future applications in the productive sector.
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Affiliation(s)
- Érika Stefani Perez
- Department of Structural and Functional Biology, Institute of Bioscience of Botucatu, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil.
| | - Bruno Oliveira Silva Duran
- Department of Histology, Embryology and Cell Biology, Institute of Biological Sciences, Federal University of Goiás (UFG), Goiânia, Goiás, Brazil.
| | - Bruna Tereza Thomazini Zanella
- Department of Structural and Functional Biology, Institute of Bioscience of Botucatu, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil.
| | - Maeli Dal-Pai-Silva
- Department of Structural and Functional Biology, Institute of Bioscience of Botucatu, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil.
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18
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Mumme H, Thomas BE, Bhasin SS, Krishnan U, Dwivedi B, Perumalla P, Sarkar D, Ulukaya GB, Sabnis HS, Park SI, DeRyckere D, Raikar SS, Pauly M, Summers RJ, Castellino SM, Wechsler DS, Porter CC, Graham DK, Bhasin M. Single-cell analysis reveals altered tumor microenvironments of relapse- and remission-associated pediatric acute myeloid leukemia. Nat Commun 2023; 14:6209. [PMID: 37798266 PMCID: PMC10556066 DOI: 10.1038/s41467-023-41994-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 09/25/2023] [Indexed: 10/07/2023] Open
Abstract
Acute myeloid leukemia (AML) microenvironment exhibits cellular and molecular differences among various subtypes. Here, we utilize single-cell RNA sequencing (scRNA-seq) to analyze pediatric AML bone marrow (BM) samples from diagnosis (Dx), end of induction (EOI), and relapse timepoints. Analysis of Dx, EOI scRNA-seq, and TARGET AML RNA-seq datasets reveals an AML blasts-associated 7-gene signature (CLEC11A, PRAME, AZU1, NREP, ARMH1, C1QBP, TRH), which we validate on independent datasets. The analysis reveals distinct clusters of Dx relapse- and continuous complete remission (CCR)-associated AML-blasts with differential expression of genes associated with survival. At Dx, relapse-associated samples have more exhausted T cells while CCR-associated samples have more inflammatory M1 macrophages. Post-therapy EOI residual blasts overexpress fatty acid oxidation, tumor growth, and stemness genes. Also, a post-therapy T-cell cluster associated with relapse samples exhibits downregulation of MHC Class I and T-cell regulatory genes. Altogether, this study deeply characterizes pediatric AML relapse- and CCR-associated samples to provide insights into the BM microenvironment landscape.
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Affiliation(s)
- Hope Mumme
- Department of Biomedical Informatics, Emory University School of Medicine, Atlanta, GA, USA
| | - Beena E Thomas
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Swati S Bhasin
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Upaasana Krishnan
- Department of Biomedical Informatics, Emory University School of Medicine, Atlanta, GA, USA
- Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Bhakti Dwivedi
- Department of Biostatistics and Bioinformatics Shared Resource, Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - Pruthvi Perumalla
- Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Debasree Sarkar
- Department of Biomedical Informatics, Emory University School of Medicine, Atlanta, GA, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Gulay B Ulukaya
- Department of Biomedical Informatics, Emory University School of Medicine, Atlanta, GA, USA
| | - Himalee S Sabnis
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Sunita I Park
- Department of Pathology, Children's Healthcare of Atlanta, Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Deborah DeRyckere
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Sunil S Raikar
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Melinda Pauly
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Ryan J Summers
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Sharon M Castellino
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Daniel S Wechsler
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Christopher C Porter
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Douglas K Graham
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Manoj Bhasin
- Department of Biomedical Informatics, Emory University School of Medicine, Atlanta, GA, USA.
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA.
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA.
- Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA.
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19
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Arroyo E, Pérez Sayáns M, Bravo SB, de Oliveira Barbeiro C, Paravani Palaçon M, Chamorro Petronacci CM, García Vence M, Chantada Vázquez MDP, Blanco Carrión A, Suárez Peñaranda JM, García García A, Gándara Vila P, Días Almeida J, Veríssimo da Costa GC, Sousa Nogueira FC, Medeiros Evaristo JA, de Abreu Pereira D, Rintala M, Salo T, Rautava J, Padín Iruegas E, Oliveira Alves MG, Morandin Ferrisse T, Albergoni da Silveira H, Esquiche León J, Vilela Silva E, Flores IL, Bufalino A. Identification of Proteomic Biomarkers in Proliferative Verrucous Leukoplakia through Liquid Chromatography With Tandem Mass Spectrometry. J Transl Med 2023; 103:100222. [PMID: 37507024 DOI: 10.1016/j.labinv.2023.100222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 07/13/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023] Open
Abstract
Proliferative verrucous leukoplakia (PVL) is an oral potentially malignant disorder associated with high risk of malignant transformation. Currently, there is no treatment available, and restrictive follow-up of patients is crucial for a better prognosis. Oral leukoplakia (OL) shares some clinical and microscopic features with PVL but exhibits different clinical manifestations and a lower rate of malignant transformation. This study aimed to investigate the proteomic profile of PVL in tissue and saliva samples to identify potential diagnostic biomarkers with therapeutic implications. Tissue and saliva samples obtained from patients with PVL were compared with those from patients with oral OL and controls. Label-free liquid chromatography with tandem mass spectrometry was employed, followed by qualitative and quantitative analyses, to identify differentially expressed proteins. Potential biomarkers were identified and further validated using immunohistochemistry. Staining intensity scan analyses were performed on tissue samples from patients with PVL, patients with OL, and controls from Brazil, Spain, and Finland. The study revealed differences in the immune system, cell cycle, DNA regulation, apoptosis pathways, and the whole proteome of PVL samples. In addition, liquid chromatography with tandem mass spectrometry analyses showed that calreticulin (CALR), receptor of activated protein C kinase 1 (RACK1), and 14-3-3 Tau-protein (YWHAQ) were highly expressed in PVL samples. Immunohistochemistry validation confirmed increased CARL expression in PVL compared with OL. Conversely, RACK1 and YWHA were highly expressed in oral potentially malignant disorder compared to the control group. Furthermore, significant differences in CALR and RACK1 expression were observed in the OL group when comparing samples with and without oral epithelial dysplasia, unlike the PVL. This research provides insights into the molecular mechanisms underlying these conditions and highlights potential targets for future diagnostic and therapeutic approaches.
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Affiliation(s)
- Esteban Arroyo
- Department of Diagnosis and Surgery, Araraquara, School of Dentistry, São Paulo State University (UNESP), Araraquara, São Paulo, Brazil
| | - Mario Pérez Sayáns
- Oral Medicine, Oral Surgery and Implantology Unit (MedOralRes), Faculty of Medicine and Dentistry, University of Santiago de Compostela, Instituto de los materiales de Santiago de Compostela (iMATUS), Santiago, Spain; Instituto de Investigación Sanitaria de Santiago (IDIS) (ORALRES Group), Santiago de Compostela, Spain.
| | - Susana Belen Bravo
- Proteomic Unit, Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain
| | - Camila de Oliveira Barbeiro
- Department of Diagnosis and Surgery, Araraquara, School of Dentistry, São Paulo State University (UNESP), Araraquara, São Paulo, Brazil
| | - Mariana Paravani Palaçon
- Department of Diagnosis and Surgery, Araraquara, School of Dentistry, São Paulo State University (UNESP), Araraquara, São Paulo, Brazil
| | | | - María García Vence
- Proteomic Unit, Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain
| | | | - Andrés Blanco Carrión
- Oral Medicine, Oral Surgery and Implantology Unit (MedOralRes), Faculty of Medicine and Dentistry, University of Santiago de Compostela, Instituto de los materiales de Santiago de Compostela (iMATUS), Santiago, Spain
| | - José M Suárez Peñaranda
- Servicio de Anatomia Patológica, Hospital Clinico Universitario de Santiago, Choupana s/n Santiago de Compostela, Spain
| | - Abel García García
- Oral Medicine, Oral Surgery and Implantology Unit (MedOralRes), Faculty of Medicine and Dentistry, University of Santiago de Compostela, Instituto de los materiales de Santiago de Compostela (iMATUS), Santiago, Spain
| | - Pilar Gándara Vila
- Oral Medicine, Oral Surgery and Implantology Unit (MedOralRes), Faculty of Medicine and Dentistry, University of Santiago de Compostela, Instituto de los materiales de Santiago de Compostela (iMATUS), Santiago, Spain; Instituto de Investigación Sanitaria de Santiago (IDIS) (ORALRES Group), Santiago de Compostela, Spain
| | - Janete Días Almeida
- Department of Bioscience and Buccal Diagnosis, São José dos Campos, Science and Technologies Institute, São Paulo State University (Unesp), São José dos Campos, São Paulo, Brazil
| | - Giovani Carlo Veríssimo da Costa
- Department of Basic Sciences, Nova Friburgo Health Institute, Univ. Federal Fluminense, Nova Friburgo, Rio de Janeiro, Brazil; Laboratory of Proteomics, Technological Development Support Laboratory (LADETEC), Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fábio César Sousa Nogueira
- Laboratory of Proteomics, Technological Development Support Laboratory (LADETEC), Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Joseph Albert Medeiros Evaristo
- Laboratory of Proteomics, Technological Development Support Laboratory (LADETEC), Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Denise de Abreu Pereira
- Program on Cellular and Molecular Oncobiology, Research Coordination, National Institute of Cancer (INCA), Rio de Janeiro, Brazil
| | - Mirjami Rintala
- Department of Oral Pathology, University of Turku, Turku, Finland
| | - Tuula Salo
- Department of Oral and Maxillofacial Diseases, Clinicum, University of Helsinki, Helsinki, Finland; Department of Pathology, HUSLAB, Helsinki, Finland; Department of Cancer and Translational Research Unit, University of Oulu, Oulu, Finland; Medical Research Center Oulu, Oulu, Finland
| | - Jaana Rautava
- Department of Oral Pathology, University of Turku, Turku, Finland; Department of Oral and Maxillofacial Diseases, Clinicum, University of Helsinki, Helsinki, Finland; Department of Pathology, HUSLAB, Helsinki, Finland
| | - Elena Padín Iruegas
- Human Anatomy and Embryology Area, Faculty of Physiotherapy, Department of Functional Biology and Health Sciences, Pontevedra, Spain
| | | | - Túlio Morandin Ferrisse
- Department of Dental Materials and Prosthodontics, São Paulo State University (UNESP), School of Dentistry, Araraquara, Brazil
| | - Heitor Albergoni da Silveira
- Department of Diagnosis and Surgery, Araraquara, School of Dentistry, São Paulo State University (UNESP), Araraquara, São Paulo, Brazil
| | - Jorge Esquiche León
- Oral Pathology, Department of Stomatology, Public Oral Health, and Forensic Dentistry, Ribeirão Preto Dental School (FORP/USP), University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Evânio Vilela Silva
- Department of Diagnosis and Surgery, Araraquara, School of Dentistry, São Paulo State University (UNESP), Araraquara, São Paulo, Brazil
| | - Isadora Luana Flores
- Oral Pathology Area, Conservative Dentistry Department, Dental School, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre/RS, Brazil
| | - Andreia Bufalino
- Department of Diagnosis and Surgery, Araraquara, School of Dentistry, São Paulo State University (UNESP), Araraquara, São Paulo, Brazil
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20
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Zeng T, Liao P, Zheng C, Gao H, Ye X, Zhou C, Zhou Y. The interaction between the lemon ribosomal protein ClRPS9-2 and citrus yellow vein clearing virus coat protein affects viral infection and gene silencing suppressor activity. MOLECULAR PLANT PATHOLOGY 2023; 24:1047-1062. [PMID: 37148475 PMCID: PMC10423326 DOI: 10.1111/mpp.13347] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 04/12/2023] [Accepted: 04/13/2023] [Indexed: 05/08/2023]
Abstract
Citrus yellow vein clearing virus (CYVCV) is an emerging virus that causes serious economic damage to the lemon industry worldwide. The coat protein (CP) of CYVCV is a strong RNA silencing suppressor and is associated with the severity of symptoms in citrus, yet the interaction between CP and host factors remains unknown. In this study, the 40S ribosomal subunit protein S9-2 (ClRPS9-2) was identified as a CP-binding partner using the yeast two-hybrid system from a lemon (cv. Eureka) cDNA library, and the interaction between CP and ClRPS9-2 was demonstrated by in vivo methods. The results suggest that the N-terminal 8-108 amino acid sequence of ClRPS9-2 is crucial for its interaction with CP and may be associated with the nuclear localization of ClRPS9-2. The accumulation and silencing suppressor activity of CP were reduced by transient expression of ClRPS9-2 in Nicotiana benthamiana. Reverse transcription-quantitative PCR analysis showed that the content of CYVCV in ClRPS9-2 transgenic Eureka lemon plants was approximately 50% of that in CYVCV-infected wild-type plants 1 month after inoculation, and mild yellowing and vein clearing symptoms were observed in the transgenic plants. These findings demonstrate that ClRPS9-2 plays a role in host defensive reactions, and the enhanced resistance of transgenic plants to CYVCV may be associated with the up-regulation of salicylic acid-related and R genes.
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Affiliation(s)
- Ting Zeng
- National Citrus Engineering Research CenterCitrus Research Institute, Southwest UniversityChongqingChina
| | - Ping Liao
- National Citrus Engineering Research CenterCitrus Research Institute, Southwest UniversityChongqingChina
| | - Cairong Zheng
- National Citrus Engineering Research CenterCitrus Research Institute, Southwest UniversityChongqingChina
| | - Haixing Gao
- National Citrus Engineering Research CenterCitrus Research Institute, Southwest UniversityChongqingChina
| | - Xiao Ye
- National Citrus Engineering Research CenterCitrus Research Institute, Southwest UniversityChongqingChina
| | - Changyong Zhou
- National Citrus Engineering Research CenterCitrus Research Institute, Southwest UniversityChongqingChina
| | - Yan Zhou
- National Citrus Engineering Research CenterCitrus Research Institute, Southwest UniversityChongqingChina
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21
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Srivastava S, Patil K, Thompson EW, Nakhai SA, Kim YN, Haynes C, Bryant C, Pai SB. Disruption of Glioblastoma Multiforme Cell Circuits with Cinnamaldehyde Highlights Potential Targets with Implications for Novel Therapeutic Strategies. Cells 2023; 12:cells12091277. [PMID: 37174677 PMCID: PMC10177046 DOI: 10.3390/cells12091277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
Glioblastoma multiforme (GBM) is a major aggressive primary brain tumor with dismal survival outcome and few therapeutic options. Although Temozolomide (TMZ) is a part of the standard therapy, over time, it can cause DNA damage leading to deleterious effects, necessitating the discovery of drugs with minimal side effects. To this end, we investigated the effect of cinnamaldehyde (CA), a highly purified, single ingredient from cinnamon, on the GBM cell lines U87 and U251 and the neuroglioma cell line H4. On observing similar impact on the viability in all the three cell lines, detailed studies were conducted with CA and its isomer/analog, trans-CA (TCA), and methoxy-CA (MCA) on U87 cells. The compounds exhibited equal potency when assessed at the cellular level in inhibiting U87 cells as well as at the molecular level, resulting in an increase in reactive oxygen species (ROS) and an increase in the apoptotic and multicaspase cell populations. To further characterize the key entities, protein profiling was performed with CA. The studies revealed differential regulation of entities that could be key to glioblastoma cell circuits such as downregulation of pyruvate kinase-PKM2, the key enzyme of the glycolytic pathway that is central to the Warburg effect. This allows for monitoring the levels of PKM2 after therapy using recently developed noninvasive technology employing PET [18F] DASA-23. Additionally, the observation of downregulation of phosphomevalonate kinase is significant as the brain tumor initiating cells (BTIC) are maintained by the metabolism occurring via the mevalonate pathway. Results from the current study, if translated in vivo, could provide additional efficacious treatment options for glioblastoma with minimal side effects.
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Affiliation(s)
- Shraddha Srivastava
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313 Ferst Drive, Atlanta, GA 30332, USA
| | - Ketki Patil
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313 Ferst Drive, Atlanta, GA 30332, USA
| | - Elizabeth W Thompson
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313 Ferst Drive, Atlanta, GA 30332, USA
| | - Shadi A Nakhai
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313 Ferst Drive, Atlanta, GA 30332, USA
| | - Yoo Na Kim
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313 Ferst Drive, Atlanta, GA 30332, USA
| | - Casey Haynes
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313 Ferst Drive, Atlanta, GA 30332, USA
| | - Crystal Bryant
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313 Ferst Drive, Atlanta, GA 30332, USA
| | - S Balakrishna Pai
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313 Ferst Drive, Atlanta, GA 30332, USA
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22
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Zhu J, Long T, Gao L, Zhong Y, Wang P, Wang X, Li Z, Hu Z. RPL21 interacts with LAMP3 to promote colorectal cancer invasion and metastasis by regulating focal adhesion formation. Cell Mol Biol Lett 2023; 28:31. [PMID: 37062845 PMCID: PMC10108486 DOI: 10.1186/s11658-023-00443-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 03/28/2023] [Indexed: 04/18/2023] Open
Abstract
BACKGROUND Metastasis is the leading cause of death among patients with colorectal cancer (CRC). Therefore, it is important to explore the molecular mechanisms of metastasis to develop effective therapeutic targets for CRC. In the present study, ribosomal protein L21 (RPL21) was considered as being involved in promoting CRC metastasis, yet the underlying mechanism requires further investigation. METHODS Immunohistochemistry, western blotting, and quantitative reverse transcription polymerase chain reaction were performed to measure the expression of RPL21 and lysosome-associated membrane protein 3 (LAMP3) in CRC tissues and cells. Wound healing, transwell migration, and invasion assays were performed to study the migration and invasion of cultured CRC cells. An orthotopic CRC mouse model was developed to investigate the metastatic ability of CRC. Transcriptome sequencing was conducted to identify the genes related to RPL21. The dual-luciferase reporter gene assay was performed to determine the transcriptional activity of transcription factor EB (TFEB). The GST/His pull-down assay was performed to investigate the specific binding sites of RPL21 and LAMP3. The cell adhesion assay was performed to determine the adhesion ability of CRC cells. Immunofluorescence staining was performed to observe focal adhesions (FAs). RESULTS RPL21 was highly expressed in CRC, contributing to tumor invasiveness and poor patient prognosis. Functionally, RPL21 promoted the migration and invasion of CRC cells in vitro and tumor metastasis in vivo. Moreover, LAMP3 was identified as being highly related to RPL21 and was essential in promoting the migration and invasion of CRC cells. Mechanistically, RPL21 activated the transcriptional function of TFEB to upregulate LAMP3 expression. RPL21 directly bound to the aa 341-416 domain of LAMP3 via its aa 1-40 and aa 111-160 segments. The combination of RPL21 and LAMP3 enhanced the stability of the RPL21 protein by suppressing the degradation of the ubiquitin-proteasome system. Furthermore, RPL21 and LAMP3 promoted the formation of immature FAs by activating the FAK/paxillin/ERK signaling pathway. CONCLUSIONS RPL21 promoted invasion and metastasis by regulating FA formation in a LAMP3-dependent manner during CRC progression. The interaction between RPL21 and LAMP3 may function as a potential therapeutic target against CRC.
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Affiliation(s)
- Jiaxian Zhu
- Department of Pathology, Shenzhen Hospital, Southern Medical University, 1333 Xinhu Road, Shenzhen, 518101, Guangdong, People's Republic of China
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, Guangdong, People's Republic of China
| | - Ting Long
- Department of Pathology, Shenzhen Hospital, Southern Medical University, 1333 Xinhu Road, Shenzhen, 518101, Guangdong, People's Republic of China
| | - Lingfang Gao
- Department of Pathology, Shenzhen Hospital, Southern Medical University, 1333 Xinhu Road, Shenzhen, 518101, Guangdong, People's Republic of China
| | - Yan Zhong
- Department of Pathology, Shenzhen Hospital, Southern Medical University, 1333 Xinhu Road, Shenzhen, 518101, Guangdong, People's Republic of China
| | - Ping Wang
- Department of Pathology, Shenzhen Hospital, Southern Medical University, 1333 Xinhu Road, Shenzhen, 518101, Guangdong, People's Republic of China
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, Guangdong, People's Republic of China
| | - Xiaoyan Wang
- Department of Pathology, Nanfang Hospital, Southern Medical University, 1838 Guangzhou Avenue North, Guangzhou, 510515, Guangdong, People's Republic of China
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, Guangdong, People's Republic of China
- Key Laboratory of Molecular Tumour Pathology of Guangdong Province, Guangzhou, 510515, Guangdong, People's Republic of China
| | - Zuguo Li
- Department of Pathology, Shenzhen Hospital, Southern Medical University, 1333 Xinhu Road, Shenzhen, 518101, Guangdong, People's Republic of China.
- Key Laboratory of Molecular Tumour Pathology of Guangdong Province, Guangzhou, 510515, Guangdong, People's Republic of China.
| | - Zhiyan Hu
- Department of Pathology, Nanfang Hospital, Southern Medical University, 1838 Guangzhou Avenue North, Guangzhou, 510515, Guangdong, People's Republic of China.
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, Guangdong, People's Republic of China.
- Key Laboratory of Molecular Tumour Pathology of Guangdong Province, Guangzhou, 510515, Guangdong, People's Republic of China.
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23
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Principi L, Ferrini E, Ciccimarra R, Pagani L, Chinello C, Previtali P, Smith A, Villetti G, Zoboli M, Ravanetti F, Stellari FF, Magni F, Piga I. Proteomic Fingerprint of Lung Fibrosis Progression and Response to Therapy in Bleomycin-Induced Mouse Model. Int J Mol Sci 2023; 24:ijms24054410. [PMID: 36901840 PMCID: PMC10002924 DOI: 10.3390/ijms24054410] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 02/14/2023] [Accepted: 02/16/2023] [Indexed: 02/25/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic lung disease characterized by the aberrant accumulation of extracellular matrix in the lungs. nintedanib is one of the two FDA-approved drugs for IPF treatment; however, the exact pathophysiological mechanisms of fibrosis progression and response to therapy are still poorly understood. In this work, the molecular fingerprint of fibrosis progression and response to nintedanib treatment have been investigated by mass spectrometry-based bottom-up proteomics in paraffin-embedded lung tissues from bleomycin-induced (BLM) pulmonary fibrosis mice. Our proteomics results unveiled that (i) samples clustered depending on the tissue fibrotic grade (mild, moderate, and severe) and not on the time course after BLM treatment; (ii) the dysregulation of different pathways involved in fibrosis progression such as the complement coagulation cascades, advanced glycation end products (AGEs) and their receptors (RAGEs) signaling, the extracellular matrix-receptor interaction, the regulation of actin cytoskeleton, and ribosomes; (iii) Coronin 1A (Coro1a) as the protein with the highest correlation when evaluating the progression of fibrosis, with an increased expression from mild to severe fibrosis; and (iv) a total of 10 differentially expressed proteins (padj-value ≤ 0.05 and Fold change ≤-1.5 or ≥1.5), whose abundance varied in the base of the severity of fibrosis (mild and moderate), were modulated by the antifibrotic treatment with nintedanib, reverting their trend. Notably, nintedanib significantly restored lactate dehydrogenase B (Ldhb) expression but not lactate dehydrogenase A (Ldha). Notwithstanding the need for further investigations to validate the roles of both Coro1a and Ldhb, our findings provide an extensive proteomic characterization with a strong relationship with histomorphometric measurements. These results unveil some biological processes in pulmonary fibrosis and drug-mediated fibrosis therapy.
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Affiliation(s)
- Lucrezia Principi
- Clinical Proteomics and Metabolomics Unit, Department of Medicine and Surgery, University of Milano-Bicocca, 20854 Monza, Italy
| | - Erica Ferrini
- Department of Veterinary Science, University of Parma, 43122 Parma, Italy
| | - Roberta Ciccimarra
- Department of Veterinary Science, University of Parma, 43122 Parma, Italy
| | - Lisa Pagani
- Clinical Proteomics and Metabolomics Unit, Department of Medicine and Surgery, University of Milano-Bicocca, 20854 Monza, Italy
| | - Clizia Chinello
- Clinical Proteomics and Metabolomics Unit, Department of Medicine and Surgery, University of Milano-Bicocca, 20854 Monza, Italy
| | - Paolo Previtali
- Clinical Proteomics and Metabolomics Unit, Department of Medicine and Surgery, University of Milano-Bicocca, 20854 Monza, Italy
| | - Andrew Smith
- Clinical Proteomics and Metabolomics Unit, Department of Medicine and Surgery, University of Milano-Bicocca, 20854 Monza, Italy
| | - Gino Villetti
- Experimental Pharmacology & Translational Science Department, Chiesi Farmaceutici S.p.A., 43122 Parma, Italy
| | - Matteo Zoboli
- Department of Veterinary Science, University of Parma, 43122 Parma, Italy
| | | | - Franco Fabio Stellari
- Experimental Pharmacology & Translational Science Department, Chiesi Farmaceutici S.p.A., 43122 Parma, Italy
- Correspondence: (F.F.S.); (I.P.)
| | - Fulvio Magni
- Clinical Proteomics and Metabolomics Unit, Department of Medicine and Surgery, University of Milano-Bicocca, 20854 Monza, Italy
| | - Isabella Piga
- Clinical Proteomics and Metabolomics Unit, Department of Medicine and Surgery, University of Milano-Bicocca, 20854 Monza, Italy
- Correspondence: (F.F.S.); (I.P.)
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24
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Protein-Coding Region Derived Small RNA in Exosomes from Influenza A Virus-Infected Cells. Int J Mol Sci 2023; 24:ijms24010867. [PMID: 36614310 PMCID: PMC9820831 DOI: 10.3390/ijms24010867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/28/2022] [Accepted: 12/30/2022] [Indexed: 01/05/2023] Open
Abstract
Exosomes may function as multifactorial mediators of cell-to-cell communication, playing crucial roles in both physiological and pathological processes. Exosomes released from virus-infected cells may contain RNA and proteins facilitating infection spread. The purpose of our study was to analyze how the small RNA content of exosomes is affected by infection with the influenza A virus (IAV). Exosomes were isolated by ultracentrifugation after hemadsorption of virions and their small RNA content was identified using high-throughput sequencing. As compared to mock-infected controls, 856 RNA transcripts were significantly differentially expressed in exosomes from IAV-infected cells, including fragments of 458 protein-coding (pcRNA), 336 small, 28 long intergenic non-coding RNA transcripts, and 33 pseudogene transcripts. Upregulated pcRNA species corresponded mainly to proteins associated with translation and antiviral response, and the most upregulated among them were RSAD2, CCDC141 and IFIT2. Downregulated pcRNA species corresponded to proteins associated with the cell cycle and DNA packaging. Analysis of differentially expressed pseudogenes showed that in most cases, an increase in the transcription level of pseudogenes was correlated with an increase in their parental genes. Although the role of exosome RNA in IAV infection remains undefined, the biological processes identified based on the corresponding proteins may indicate the roles of some of its parts in IAV replication.
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25
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Perez ÉS, Cury SS, Zanella BTT, Carvalho RF, Duran BOS, Dal-Pai-Silva M. Identification of Novel Genes Associated with Fish Skeletal Muscle Adaptation during Fasting and Refeeding Based on a Meta-Analysis. Genes (Basel) 2022; 13:genes13122378. [PMID: 36553644 PMCID: PMC9778430 DOI: 10.3390/genes13122378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/09/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
The regulation of the fish phenotype and muscle growth is influenced by fasting and refeeding periods, which occur in nature and are commonly applied in fish farming. However, the regulators associated with the muscle responses to these manipulations of food availability have not been fully characterized. We aimed to identify novel genes associated with fish skeletal muscle adaptation during fasting and refeeding based on a meta-analysis. Genes related to translational and proliferative machinery were investigated in pacus (Piaractus mesopotamicus) subjected to fasting (four and fifteen days) and refeeding (six hours, three and fifteen days). Our results showed that different fasting and refeeding periods modulate the expression of the genes mtor, rps27a, eef1a2, and cdkn1a. These alterations can indicate the possible protection of the muscle phenotype, in addition to adaptive responses that prioritize energy and substrate savings over cell division, a process regulated by ccnd1. Our study reveals the potential of meta-analysis for the identification of muscle growth regulators and provides new information on muscle responses to fasting and refeeding in fish that are of economic importance to aquaculture.
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Affiliation(s)
- Érika Stefani Perez
- Department of Structural and Functional Biology, São Paulo State University (UNESP), Botucatu 18618-689, Brazil
| | - Sarah Santiloni Cury
- Department of Structural and Functional Biology, São Paulo State University (UNESP), Botucatu 18618-689, Brazil
| | | | - Robson Francisco Carvalho
- Department of Structural and Functional Biology, São Paulo State University (UNESP), Botucatu 18618-689, Brazil
| | - Bruno Oliveira Silva Duran
- Department of Histology, Embryology and Cell Biology, Federal University of Goias (UFG), Goiania 74690-900, Brazil
| | - Maeli Dal-Pai-Silva
- Department of Structural and Functional Biology, São Paulo State University (UNESP), Botucatu 18618-689, Brazil
- Correspondence: ; Tel.: +55-(14)-3880-0470
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26
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Scott MA, Woolums AR, Swiderski CE, Finley A, Perkins AD, Nanduri B, Karisch BB. Hematological and gene co-expression network analyses of high-risk beef cattle defines immunological mechanisms and biological complexes involved in bovine respiratory disease and weight gain. PLoS One 2022; 17:e0277033. [PMID: 36327246 PMCID: PMC9632787 DOI: 10.1371/journal.pone.0277033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
Abstract
Bovine respiratory disease (BRD), the leading disease complex in beef cattle production systems, remains highly elusive regarding diagnostics and disease prediction. Previous research has employed cellular and molecular techniques to describe hematological and gene expression variation that coincides with BRD development. Here, we utilized weighted gene co-expression network analysis (WGCNA) to leverage total gene expression patterns from cattle at arrival and generate hematological and clinical trait associations to describe mechanisms that may predict BRD development. Gene expression counts of previously published RNA-Seq data from 23 cattle (2017; n = 11 Healthy, n = 12 BRD) were used to construct gene co-expression modules and correlation patterns with complete blood count (CBC) and clinical datasets. Modules were further evaluated for cross-populational preservation of expression with RNA-Seq data from 24 cattle in an independent population (2019; n = 12 Healthy, n = 12 BRD). Genes within well-preserved modules were subject to functional enrichment analysis for significant Gene Ontology terms and pathways. Genes which possessed high module membership and association with BRD development, regardless of module preservation (“hub genes”), were utilized for protein-protein physical interaction network and clustering analyses. Five well-preserved modules of co-expressed genes were identified. One module (“steelblue”), involved in alpha-beta T-cell complexes and Th2-type immunity, possessed significant correlation with increased erythrocytes, platelets, and BRD development. One module (“purple”), involved in mitochondrial metabolism and rRNA maturation, possessed significant correlation with increased eosinophils, fecal egg count per gram, and weight gain over time. Fifty-two interacting hub genes, stratified into 11 clusters, may possess transient function involved in BRD development not previously described in literature. This study identifies co-expressed genes and coordinated mechanisms associated with BRD, which necessitates further investigation in BRD-prediction research.
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Affiliation(s)
- Matthew A. Scott
- Veterinary Education, Research, and Outreach Center, Texas A&M University and West Texas A&M University, Canyon, TX, United States of America
- * E-mail:
| | - Amelia R. Woolums
- Department of Pathobiology and Population Medicine, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, United States of America
| | - Cyprianna E. Swiderski
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, Arizona, United States of America
| | - Abigail Finley
- Veterinary Education, Research, and Outreach Center, Texas A&M University and West Texas A&M University, Canyon, TX, United States of America
| | - Andy D. Perkins
- Department of Computer Science and Engineering, Mississippi State University, Mississippi State, MS, United States of America
| | - Bindu Nanduri
- Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, United States of America
| | - Brandi B. Karisch
- Department of Animal and Dairy Sciences, Mississippi State University, Mississippi State, MS, United States of America
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Aslebagh R, Whitham D, Channaveerappa D, Mutsengi P, Pentecost BT, Arcaro KF, Darie CC. Mass Spectrometry-Based Proteomics of Human Milk to Identify Differentially Expressed Proteins in Women with Breast Cancer versus Controls. Proteomes 2022; 10:36. [PMID: 36412635 PMCID: PMC9680319 DOI: 10.3390/proteomes10040036] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/17/2022] [Accepted: 10/25/2022] [Indexed: 12/14/2022] Open
Abstract
It is thought that accurate risk assessment and early diagnosis of breast cancer (BC) can help reduce cancer-related mortality. Proteomics analysis of breast milk may provide biomarkers of risk and occult disease. Our group works on the analysis of human milk samples from women with BC and controls to investigate alterations in protein patterns of milk that could be related to BC. In the current study, we used mass spectrometry (MS)-based proteomics analysis of 12 milk samples from donors with BC and matched controls. Specifically, we used one-dimensional (1D)-polyacrylamide gel electrophoresis (PAGE) coupled with nanoliquid chromatography tandem MS (nanoLC-MS/MS), followed by bioinformatics analysis. We confirmed the dysregulation of several proteins identified previously in a different set of milk samples. We also identified additional dysregulations in milk proteins shown to play a role in cancer development, such as Lactadherin isoform A, O-linked N-acetylglucosamine (GlcNAc) transferase, galactosyltransferase, recoverin, perilipin-3 isoform 1, histone-lysine methyltransferase, or clathrin heavy chain. Our results expand our current understanding of using milk as a biological fluid for identification of BC-related dysregulated proteins. Overall, our results also indicate that milk has the potential to be used for BC biomarker discovery, early detection and risk assessment in young, reproductively active women.
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Affiliation(s)
- Roshanak Aslebagh
- Biochemistry and Proteomics Laboratories, Department of Chemistry & Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA
| | - Danielle Whitham
- Biochemistry and Proteomics Laboratories, Department of Chemistry & Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA
| | - Devika Channaveerappa
- Biochemistry and Proteomics Laboratories, Department of Chemistry & Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA
| | - Panashe Mutsengi
- Biochemistry and Proteomics Laboratories, Department of Chemistry & Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA
| | - Brian T. Pentecost
- Department of Veterinary & Animal Sciences, University of Massachusetts, Amherst, MA 01003-9298, USA
| | - Kathleen F. Arcaro
- Department of Veterinary & Animal Sciences, University of Massachusetts, Amherst, MA 01003-9298, USA
| | - Costel C. Darie
- Biochemistry and Proteomics Laboratories, Department of Chemistry & Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA
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Wang J, Yang B, Lv C, Chen T, Sun L, Sun L, Hao J, Ding F, Wang T, Jiang J, Qin Y. Amino porphyrin-peptide assemblies induce ribosome damage and cancer stem cell inhibition for an enhanced photodynamic therapy. Biomaterials 2022; 289:121812. [PMID: 36152516 DOI: 10.1016/j.biomaterials.2022.121812] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 09/12/2022] [Accepted: 09/14/2022] [Indexed: 11/17/2022]
Abstract
Cancer stem cells (CSCs) are the subpopulation of tumor cells with the properties of tumorigenesis, multilineage differentiation potential and self-renewal, which is the driving force of tumor recurrence and metastasis. However, targeting CSCs is still the main challenge in cancer therapy due to their rapid growth and fast mutation rate. Herein, we developed a simple strategy of photodynamic therapy (PDT) targeting CSCs, dependent on much more abundant ribosomes in CSCs. The interactions between positively charged nanoparticles with negatively charged nucleic acids architectures in cancer cells could lead ribosomes targeting as well as CSCs targeting. The co-assembly of simple amino porphyrin (m-TAPP) with short peptide (Fmoc-L3-OMe) formed nanoparticles (NPs) with good biocompatibility and photoactivity, became positively charged due to low pH value of tumour microenvironment, and efficiently accessed cancer cell ribosome, approached cancer cell nuclei, therefore enriched in the fast-amplifying CSCs. The inhibitive effect on CSCs by m-TAPP assemblies was verified by the significant reduction of CSCs markers CD44, CD133 and ribosome amount in cancer cells and tissues. Upon light irradiation, the NPs induced ROS generation to provoke destructive cancer cell ribosome damage and subsequent apoptosis to prevent tumor growth markedly. Based on the assemblies of small organic molecules, our study not only achieves ribosome degradation induced cancer cells apoptosis, but also indicates new possibility of performing CSCs targeting PDT.
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Affiliation(s)
- Jian Wang
- Beijing Advanced Innovation Center for Materials Genome Engineering, Beijing Key Laboratory for Science and Application of Functional Molecular and Crystalline Materials, Department of Chemistry and Chemical Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China; Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China
| | - Baochan Yang
- Beijing Advanced Innovation Center for Materials Genome Engineering, Beijing Key Laboratory for Science and Application of Functional Molecular and Crystalline Materials, Department of Chemistry and Chemical Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China; Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China
| | - Chaofan Lv
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China
| | - Tiancheng Chen
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China
| | - Lixin Sun
- Beijing Advanced Innovation Center for Materials Genome Engineering, Beijing Key Laboratory for Science and Application of Functional Molecular and Crystalline Materials, Department of Chemistry and Chemical Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China; Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China
| | - Lei Sun
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China
| | - Junfeng Hao
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China
| | - Fang Ding
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China.
| | - Tianyu Wang
- Beijing Advanced Innovation Center for Materials Genome Engineering, Beijing Key Laboratory for Science and Application of Functional Molecular and Crystalline Materials, Department of Chemistry and Chemical Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China.
| | - Jianzhuang Jiang
- Beijing Advanced Innovation Center for Materials Genome Engineering, Beijing Key Laboratory for Science and Application of Functional Molecular and Crystalline Materials, Department of Chemistry and Chemical Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China.
| | - Yan Qin
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China.
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Ribosome-Directed Therapies in Cancer. Biomedicines 2022; 10:biomedicines10092088. [PMID: 36140189 PMCID: PMC9495564 DOI: 10.3390/biomedicines10092088] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/22/2022] [Accepted: 08/22/2022] [Indexed: 12/29/2022] Open
Abstract
The human ribosomes are the cellular machines that participate in protein synthesis, which is deeply affected during cancer transformation by different oncoproteins and is shown to provide cancer cell proliferation and therefore biomass. Cancer diseases are associated with an increase in ribosome biogenesis and mutation of ribosomal proteins. The ribosome represents an attractive anti-cancer therapy target and several strategies are used to identify specific drugs. Here we review the role of different drugs that may decrease ribosome biogenesis and cancer cell proliferation.
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Paredes GF, Viehboeck T, Markert S, Mausz MA, Sato Y, Liebeke M, König L, Bulgheresi S. Differential regulation of degradation and immune pathways underlies adaptation of the ectosymbiotic nematode Laxus oneistus to oxic-anoxic interfaces. Sci Rep 2022; 12:9725. [PMID: 35697683 PMCID: PMC9192688 DOI: 10.1038/s41598-022-13235-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 05/13/2022] [Indexed: 11/09/2022] Open
Abstract
Eukaryotes may experience oxygen deprivation under both physiological and pathological conditions. Because oxygen shortage leads to a reduction in cellular energy production, all eukaryotes studied so far conserve energy by suppressing their metabolism. However, the molecular physiology of animals that naturally and repeatedly experience anoxia is underexplored. One such animal is the marine nematode Laxus oneistus. It thrives, invariably coated by its sulfur-oxidizing symbiont Candidatus Thiosymbion oneisti, in anoxic sulfidic or hypoxic sand. Here, transcriptomics and proteomics showed that, whether in anoxia or not, L. oneistus mostly expressed genes involved in ubiquitination, energy generation, oxidative stress response, immune response, development, and translation. Importantly, ubiquitination genes were also highly expressed when the nematode was subjected to anoxic sulfidic conditions, together with genes involved in autophagy, detoxification and ribosome biogenesis. We hypothesize that these degradation pathways were induced to recycle damaged cellular components (mitochondria) and misfolded proteins into nutrients. Remarkably, when L. oneistus was subjected to anoxic sulfidic conditions, lectin and mucin genes were also upregulated, potentially to promote the attachment of its thiotrophic symbiont. Furthermore, the nematode appeared to survive oxygen deprivation by using an alternative electron carrier (rhodoquinone) and acceptor (fumarate), to rewire the electron transfer chain. On the other hand, under hypoxia, genes involved in costly processes (e.g., amino acid biosynthesis, development, feeding, mating) were upregulated, together with the worm's Toll-like innate immunity pathway and several immune effectors (e.g., bactericidal/permeability-increasing proteins, fungicides). In conclusion, we hypothesize that, in anoxic sulfidic sand, L. oneistus upregulates degradation processes, rewires the oxidative phosphorylation and reinforces its coat of bacterial sulfur-oxidizers. In upper sand layers, instead, it appears to produce broad-range antimicrobials and to exploit oxygen for biosynthesis and development.
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Affiliation(s)
- Gabriela F Paredes
- Department of Functional and Evolutionary Ecology, Environmental Cell Biology Group, University of Vienna, Vienna, Austria
| | - Tobias Viehboeck
- Department of Functional and Evolutionary Ecology, Environmental Cell Biology Group, University of Vienna, Vienna, Austria
- Vienna Doctoral School of Ecology and Evolution, Vienna, Austria
- Division of Microbial Ecology, Center for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Stephanie Markert
- Department of Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | | | - Yui Sato
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Manuel Liebeke
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Lena König
- Department of Functional and Evolutionary Ecology, Environmental Cell Biology Group, University of Vienna, Vienna, Austria
| | - Silvia Bulgheresi
- Department of Functional and Evolutionary Ecology, Environmental Cell Biology Group, University of Vienna, Vienna, Austria.
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Suppramote O, Prasopporn S, Aroonpruksakul S, Ponvilawan B, Makjaroen J, Suntiparpluacha M, Korphaisarn K, Charngkaew K, Chanwat R, Pisitkun T, Okada S, Sampattavanich S, Jirawatnotai S. The Acquired Vulnerability Caused by CDK4/6 Inhibition Promotes Drug Synergism Between Oxaliplatin and Palbociclib in Cholangiocarcinoma. Front Oncol 2022; 12:877194. [PMID: 35664774 PMCID: PMC9157389 DOI: 10.3389/fonc.2022.877194] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 04/12/2022] [Indexed: 11/16/2022] Open
Abstract
Cholangiocarcinoma (CCA) is one of the most difficult to treat cancers, and its nature of being largely refractory to most, if not all, current treatments results in generally poor prognosis and high mortality. Efficacious alternative therapies that can be used ubiquitously are urgently needed. Using acquired vulnerability screening, we observed that CCA cells that reprofile and proliferate under CDK4/6 inhibition became vulnerable to ribosomal biogenesis stress and hypersensitive to the anti-ribosome chemotherapy oxaliplatin. CCA cells overexpress the oncogenic ribosomal protein RPL29 under CDK4/6 inhibition in a manner that correlated with CDK4/6 inhibitor resistance. Depletion of RPL29 by small interfering RNAs (siRNAs) restored the sensitivity of CCA cells to CDK4/6 inhibition. Oxaliplatin treatment suppressed the RPL29 expression in the CDK4/6 inhibitor treated CCA cells and triggered RPL5/11-MDM2-dependent p53 activation and cancer apoptosis. In addition, we found that combination treatment with oxaliplatin and the CDK4/6 inhibitor palbociclib synergistically inhibited both parental and CDK4/6 inhibitor-resistant CCA, and prevented the emergence of CDK4/6 and oxaliplatin-resistant CCA. This drug combination also exerted suppressive and apoptosis effects on CCA in the in vitro 3-dimensional culture, patient-derived organoid, and in vivo xenograft CCA models. These results suggest the combination of the CDK4/6 inhibitor palbociclib and the anti-ribosome drug oxaliplatin as a potentially promising treatment for cholangiocarcinoma.
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Affiliation(s)
- Orawan Suppramote
- Siriraj Center of Research Excellence (SiCORE) for Systems Pharmacology, Department of Pharmacology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Princess Srisavangavadhana College of Medicine, Chulabhorn Royal Academy, Bangkok, Thailand
| | - Sunisa Prasopporn
- Siriraj Center of Research Excellence (SiCORE) for Systems Pharmacology, Department of Pharmacology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Satinee Aroonpruksakul
- Siriraj Center of Research Excellence (SiCORE) for Systems Pharmacology, Department of Pharmacology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Ben Ponvilawan
- Siriraj Center of Research Excellence (SiCORE) for Systems Pharmacology, Department of Pharmacology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Jiradej Makjaroen
- Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Monthira Suntiparpluacha
- Siriraj Center of Research Excellence (SiCORE) for Systems Pharmacology, Department of Pharmacology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Krittiya Korphaisarn
- Division of Medical Oncology, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Komgrid Charngkaew
- Department of Pathology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Rawisak Chanwat
- Hepato-Pancreato-Biliary Surgery Unit, Department of Surgical Oncology, National Cancer Institute, Bangkok, Thailand
| | - Trairak Pisitkun
- Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Seiji Okada
- Division of Hematopoiesis, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Somponnat Sampattavanich
- Siriraj Center of Research Excellence (SiCORE) for Systems Pharmacology, Department of Pharmacology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Siwanon Jirawatnotai
- Siriraj Center of Research Excellence (SiCORE) for Systems Pharmacology, Department of Pharmacology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
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Zhang L, Lin J, Weng M, Wen Y, Zhang Y, Deng W. RPLP1, an NS4B-interacting protein, enhances production of CSFV through promoting translation of viral genome. Virulence 2022; 13:370-386. [PMID: 35129423 PMCID: PMC8824197 DOI: 10.1080/21505594.2022.2033500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Classical swine fever virus (CSFV), the etiological agent of classical swine fever (CSF), causes serious financial losses to the pig industry. Using yeast two-hybrid screening, we have previously identified ribosomal protein RPLP1 as a potential binding partner of CSFV NS4B. In this study, the interaction between host RPLP1 and CSFV NS4B was further characterized by co-immunoprecipitation (co-IP), glutathione S-transferase (GST) pulldown, and confocal microscopy. In addition, lentivirus-mediated shRNA knockdown of RPLP1 drastically attenuated CSFV growth, while stable overexpression of RPLP1 markedly enhanced CSFV production. Moreover, cellular RPLP1 expression was found to be significantly up-regulated along with CSFV infection. Dual-luciferase reporter assay showed that depletion of RPLP1 had no effects on the activity of CSFV internal ribosome entry site (IRES). In the first life cycle of CSFV, further studies revealed that RPLP1 depletion did not influence the intracellular viral RNA abundance but diminished the intracellular and extracellular progeny virus titers as well as the viral E2 protein expression, which indicates that RPLP1 is crucial for CSFV genome translation. In summary, this study demonstrated that RPLP1 interacts with CSFV NS4B and enhances virus production via promoting translation of viral genome.
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Affiliation(s)
- Longxiang Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Jihui Lin
- School of Nursing, Southwest Medical University, Luzhou, Sichuan, China
| | - Maoyang Weng
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Ying Wen
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Yanming Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Wen Deng
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
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The oncogenic role of treacle ribosome biogenesis factor 1 ( TCOF1) in human tumors: a pan-cancer analysis. Aging (Albany NY) 2022; 14:943-960. [PMID: 35093935 PMCID: PMC8833134 DOI: 10.18632/aging.203852] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 01/11/2022] [Indexed: 11/25/2022]
Abstract
Treacle ribosome biogenesis factor 1 (TCOF1) plays a crucial role in multiple processes, including ribosome biogenesis, DNA damage response (DDR), mitotic regulation, and telomere integrity. However, its role in cancers remains unclear. We aimed to visualize the expression, prognostic, and mutational landscapes of TCOF1 across cancers and to explore its association with immune infiltration. In this work, we integrated information from TCGA and GEO to explore the differential expression and prognostic value of TCOF1. Then, the mutational profiles of TCOF1 in cancers were investigated. We further determined the correlation between TCOF1 and immune cell infiltration levels. Additionally, we determined correlations among certain immune checkpoints, microsatellite instability, tumor mutational burden (TMB), and TCOF1. Potential pathways of TCOF1 in tumorigenesis were analyzed as well. In general, tumor tissue had a higher expression level of TCOF1 than normal tissue. The prognostic value of TCOF1 was multifaceted, depending on type of cancer. TCOF1 was correlated with tumor purity, CD8+ T cells, CD4+ T cells, B cells, neutrophils, macrophages, and dendritic cells (DCs) in 6, 14, 16, 12, 20, 13, and 17 cancer types, respectively. TCOF1 might act on ATPase activity, microtubule binding, tubulin binding, and catalytic activity (on DNA), and participate in tumorigenesis through “cell cycle” and “cellular-senescence” pathways. TCOF1 could affect pan-cancer prognosis and was correlated with immune cell infiltration. “Cell cycle” and “cellular-senescence” pathways were involved in the functional mechanisms of TCOF1, a finding that awaits further experimental validation.
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Neto JLS, de Carli RF, Lehmann M, de Souza CT, Niekraszewicz LAB, Dias JF, da Silva FR, da Silva J, Dihl RR. In vivo and in silico approaches to assess surface water genotoxicity from Tocantins River, in the cities of Porto Nacional and Palmas, Brazil. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART C, TOXICOLOGY AND CARCINOGENESIS 2022; 40:27-45. [PMID: 35895928 DOI: 10.1080/26896583.2021.2014278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The main environmental problem in urban areas, especially in Brazil, is the discharge of untreated sewage. The in vivo Drosophila melanogaster Somatic Mutation and Recombination Test (SMART) was used to assess the genotoxicity of surface waters from three different sites in the Tocantins River, Brazil. The in silico approach was used to search for known and predicted interactions between environmental chemicals found in our samples and Drosophila and human proteins. The genotoxicity tests were performed in standard (ST) and high bioactivation (HB) crosses with samples collected at two periods, the rainy and dry seasons. Mutant spot frequencies found in treatments with unprocessed water from the test sites were compared with the frequencies observed in negative controls. The collection points were represented as sites A, B and C along Tocantins River. Sites A and B are located in Porto Nacional City, whereas site C is located in Palmas City. Considering the rainy season collection, positive responses in the ST cross were observed for sites A and C (89.47% and 85% of recombination, respectively) and in the HB cross for sites A, B and C (88.24%, 84.21% and 82.35% of recombination, respectively). The positive results in the dry season were restricted to sites A and B (88.89% and 85.71% of recombination, respectively) in the HB cross. In accordance with in vivo and in silico results, we hypothesize that ribosomal proteins (RPs) in fruit fly and humans are depleted in cells exposed to heavy metal causing DNA damage and chromosome instability, increasing homologous recombination.
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Affiliation(s)
- José Lopes Soares Neto
- Laboratory of Genetic Toxicity (TOXIGEN), Graduate Program in Molecular and Cellular Biology Applied to Health, Lutheran University of Brazil (ULBRA), Canoas, Brazil
| | - Raíne Fogliati de Carli
- Laboratory of Genetic Toxicity (TOXIGEN), Graduate Program in Molecular and Cellular Biology Applied to Health, Lutheran University of Brazil (ULBRA), Canoas, Brazil
| | - Mauricio Lehmann
- Laboratory of Genetic Toxicity (TOXIGEN), Graduate Program in Molecular and Cellular Biology Applied to Health, Lutheran University of Brazil (ULBRA), Canoas, Brazil
| | - Cláudia Telles de Souza
- Ion Implantation Laboratory, Institute of Physics, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | | | - Johnny Ferraz Dias
- Ion Implantation Laboratory, Institute of Physics, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Fernanda Rabaioli da Silva
- Laboratory of Genetic Toxicity (TOXIGEN), Graduate Program in Molecular and Cellular Biology Applied to Health, Lutheran University of Brazil (ULBRA), Canoas, Brazil
- Ion Implantation Laboratory, Institute of Physics, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
- UniLaSalle, Canoas, Brazil
| | - Juliana da Silva
- Laboratory of Genetic Toxicity (TOXIGEN), Graduate Program in Molecular and Cellular Biology Applied to Health, Lutheran University of Brazil (ULBRA), Canoas, Brazil
- UniLaSalle, Canoas, Brazil
| | - Rafael Rodrigues Dihl
- Laboratory of Genetic Toxicity (TOXIGEN), Graduate Program in Molecular and Cellular Biology Applied to Health, Lutheran University of Brazil (ULBRA), Canoas, Brazil
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HAMIN NETO YAA, GARZON NGDR, COITINHO LB, SOBRAL LM, LEOPOLDINO AM, CATALDI TR, LABATE CA, CABRAL H. Fungal metalloprotease generate whey-derived peptides that may be involved in apoptosis in B16F10 melanoma cells. FOOD SCIENCE AND TECHNOLOGY 2022. [DOI: 10.1590/fst.43022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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36
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Yi YW, You KS, Park JS, Lee SG, Seong YS. Ribosomal Protein S6: A Potential Therapeutic Target against Cancer? Int J Mol Sci 2021; 23:ijms23010048. [PMID: 35008473 PMCID: PMC8744729 DOI: 10.3390/ijms23010048] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 12/19/2021] [Accepted: 12/20/2021] [Indexed: 12/12/2022] Open
Abstract
Ribosomal protein S6 (RPS6) is a component of the 40S small ribosomal subunit and participates in the control of mRNA translation. Additionally, phospho (p)-RPS6 has been recognized as a surrogate marker for the activated PI3K/AKT/mTORC1 pathway, which occurs in many cancer types. However, downstream mechanisms regulated by RPS6 or p-RPS remains elusive, and the therapeutic implication of RPS6 is underappreciated despite an approximately half a century history of research on this protein. In addition, substantial evidence from RPS6 knockdown experiments suggests the potential role of RPS6 in maintaining cancer cell proliferation. This motivates us to investigate the current knowledge of RPS6 functions in cancer. In this review article, we reviewed the current information about the transcriptional regulation, upstream regulators, and extra-ribosomal roles of RPS6, with a focus on its involvement in cancer. We also discussed the therapeutic potential of RPS6 in cancer.
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Affiliation(s)
- Yong Weon Yi
- Department of Biochemistry, College of Medicine, Dankook University, Cheonan 31116, Chungcheongnam-do, Korea; (Y.W.Y.); (K.S.Y.); (J.-S.P.)
- Department of Nanobiomedical Science, Dankook University, Cheonan 31116, Chungcheongnam-do, Korea
| | - Kyu Sic You
- Department of Biochemistry, College of Medicine, Dankook University, Cheonan 31116, Chungcheongnam-do, Korea; (Y.W.Y.); (K.S.Y.); (J.-S.P.)
- Graduate School of Convergence Medical Science, Dankook University, Cheonan 31116, Chungcheongnam-do, Korea
| | - Jeong-Soo Park
- Department of Biochemistry, College of Medicine, Dankook University, Cheonan 31116, Chungcheongnam-do, Korea; (Y.W.Y.); (K.S.Y.); (J.-S.P.)
| | - Seok-Geun Lee
- Graduate School, Kyung Hee University, Seoul 02447, Korea
- Correspondence: (S.-G.L.); (Y.-S.S.); Tel.: +82-2-961-2355 (S.-G.L.); +82-41-550-3875 (Y.-S.S.); Fax: +82-2-961-9623 (S.-G.L.)
| | - Yeon-Sun Seong
- Department of Biochemistry, College of Medicine, Dankook University, Cheonan 31116, Chungcheongnam-do, Korea; (Y.W.Y.); (K.S.Y.); (J.-S.P.)
- Graduate School of Convergence Medical Science, Dankook University, Cheonan 31116, Chungcheongnam-do, Korea
- Correspondence: (S.-G.L.); (Y.-S.S.); Tel.: +82-2-961-2355 (S.-G.L.); +82-41-550-3875 (Y.-S.S.); Fax: +82-2-961-9623 (S.-G.L.)
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37
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Pungpapong V. Incorporating biological networks into high-dimensional Bayesian survival analysis using an ICM/M algorithm. J Bioinform Comput Biol 2021; 19:2150027. [PMID: 34693885 DOI: 10.1142/s021972002150027x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The Cox proportional hazards model has been widely used in cancer genomic research that aims to identify genes from high-dimensional gene expression space associated with the survival time of patients. With the increase in expertly curated biological pathways, it is challenging to incorporate such complex networks in fitting a high-dimensional Cox model. This paper considers a Bayesian framework that employs the Ising prior to capturing relations among genes represented by graphs. A spike-and-slab prior is also assigned to each of the coefficients for the purpose of variable selection. The iterated conditional modes/medians (ICM/M) algorithm is proposed for the implementation for Cox models. The ICM/M estimates hyperparameters using conditional modes and obtains coefficients through conditional medians. This procedure produces some coefficients that are exactly zero, making the model more interpretable. Comparisons of the ICM/M and other regularized Cox models were carried out with both simulated and real data. Compared to lasso, adaptive lasso, elastic net, and DegreeCox, the ICM/M yielded more parsimonious models with consistent variable selection. The ICM/M model also provided a smaller number of false positives than the other methods and showed promising results in terms of predictive accuracy. In terms of computing times among the network-aware methods, the ICM/M algorithm is substantially faster than DegreeCox even when incorporating a large complex network. The implementation of the ICM/M algorithm for Cox regression model is provided in R package icmm, available on the Comprehensive R Archive Network (CRAN).
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Affiliation(s)
- Vitara Pungpapong
- Department of Statistics, Greater Data Science Lab, Chulalongkorn Business School, Chulalongkorn University, Phyathai Road, Pathumwan, Bangkok, Thailand
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38
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Cho SM, Lee HJ, Karuso P, Kwon HJ. Daptomycin suppresses tumor migration and angiogenesis via binding to ribosomal protein S19 in humans. J Antibiot (Tokyo) 2021; 74:726-733. [PMID: 34253886 DOI: 10.1038/s41429-021-00446-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 06/03/2021] [Accepted: 06/03/2021] [Indexed: 02/06/2023]
Abstract
We have previously reported that daptomycin (DAP), a last resort antibiotic, binds to ribosomal protein S19 (RPS19) in humans and exhibits selective anti-cancer activity against MCF7 breast cancer cells. Here, we investigated the role of RPS19 in the anti-cancer effects of DAP and have found that DAP does not induce autophagy, apoptosis or cell viability but does reduce cell proliferation. Our results suggest that an extraribosomal function of RPS19 involves the regulation of vascular endothelial growth factor (VEGF) but not EGF, PDGF or FGF. Engagement of RPS19 by DAP was shown by CETSA and ITDRFCETSA assays, and knocking down of RPS19 with siRNA increased the potency of DAP in MCF7 cells. In addition, DAP suppressed the secretion of VEGF in cancer cells and thereby inhibited cell migration. Collectively, these data provide an outline of the underlying mechanism of how DAP exhibits anti-cancer activity and suggests that RPS19 could be a promising target for the development of new anticancer drugs.
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Affiliation(s)
- Sung Min Cho
- Chemical Genomics Global Research Laboratory, Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Hwa Jung Lee
- Chemical Genomics Global Research Laboratory, Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Peter Karuso
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Ho Jeong Kwon
- Chemical Genomics Global Research Laboratory, Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea.
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Li S, Huang J, Guo Y, Wang J, Lu S, Wang B, Gong Y, Qin S, Zhao S, Wang S, Liu Y, Fang Y, Guo Y, Xu Z, Ulloa L. PAC1 Receptor Mediates Electroacupuncture-Induced Neuro and Immune Protection During Cisplatin Chemotherapy. Front Immunol 2021; 12:714244. [PMID: 34552585 PMCID: PMC8450570 DOI: 10.3389/fimmu.2021.714244] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 08/12/2021] [Indexed: 01/02/2023] Open
Abstract
Platinum-based chemotherapy is an effective treatment used in multiple tumor treatments, but produces severe side effects including neurotoxicity, anemia, and immunosuppression, which limits its anti-tumor efficacy and increases the risk of infections. Electroacupuncture (EA) is often used to ameliorate these side effects, but its mechanism is unknown. Here, we report that EA on ST36 and SP6 prevents cisplatin-induced neurotoxicity and immunosuppression. EA induces neuroprotection, prevents pain-related neurotoxicity, preserves bone marrow (BM) hematopoiesis, and peripheral levels of leukocytes. EA activates sympathetic BM terminals to release pituitary adenylate cyclase activating polypeptide (PACAP). PACAP-receptor PAC1-antagonists abrogate the effects of EA, whereas PAC1-agonists mimic EA, prevent neurotoxicity, immunosuppression, and preserve BM hematopoiesis during cisplatin chemotherapy. Our results indicate that PAC1-agonists may provide therapeutic advantages during chemotherapy to treat patients with advanced neurotoxicity or neuropathies limiting EA efficacy.
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Affiliation(s)
- Shanshan Li
- Research Center of Experimental Acupuncture Science, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Jin Huang
- Research Center of Experimental Acupuncture Science, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Yi Guo
- Research Center of Experimental Acupuncture Science, Tianjin University of Traditional Chinese Medicine, Tianjin, China.,School of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China.,National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, China
| | - Jiaqi Wang
- Research Center of Experimental Acupuncture Science, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Shanshan Lu
- Research Center of Experimental Acupuncture Science, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Bin Wang
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Yinan Gong
- Research Center of Experimental Acupuncture Science, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Siru Qin
- Research Center of Experimental Acupuncture Science, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Suhong Zhao
- Research Center of Experimental Acupuncture Science, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Shenjun Wang
- Research Center of Experimental Acupuncture Science, Tianjin University of Traditional Chinese Medicine, Tianjin, China.,National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, China.,School of Acupuncture & Moxibustion and Tuina, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Yangyang Liu
- Research Center of Experimental Acupuncture Science, Tianjin University of Traditional Chinese Medicine, Tianjin, China.,National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, China.,School of Acupuncture & Moxibustion and Tuina, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Yuxin Fang
- Research Center of Experimental Acupuncture Science, Tianjin University of Traditional Chinese Medicine, Tianjin, China.,National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, China.,School of Acupuncture & Moxibustion and Tuina, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Yongming Guo
- Research Center of Experimental Acupuncture Science, Tianjin University of Traditional Chinese Medicine, Tianjin, China.,National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, China.,School of Acupuncture & Moxibustion and Tuina, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Zhifang Xu
- Research Center of Experimental Acupuncture Science, Tianjin University of Traditional Chinese Medicine, Tianjin, China.,National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, China.,School of Acupuncture & Moxibustion and Tuina, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Luis Ulloa
- Center for Perioperative Organ Protection, Department of Anesthesiology, Duke University, Durham, NC, United States
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40
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Charton C, Youm DJ, Ko BJ, Seol D, Kim B, Chai HH, Lim D, Kim H. The transcriptomic blueprint of molt in rooster using various tissues from Ginkkoridak (Korean long-tailed chicken). BMC Genomics 2021; 22:594. [PMID: 34348642 PMCID: PMC8340483 DOI: 10.1186/s12864-021-07903-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 07/13/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Annual molt is a critical stage in the life cycle of birds. Although the most extensively documented aspects of molt are the renewing of plumage and the remodeling of the reproductive tract in laying hens, in chicken, molt deeply affects various tissues and physiological functions. However, with exception of the reproductive tract, the effect of molt on gene expression across the tissues known to be affected by molt has to date never been investigated. The present study aimed to decipher the transcriptomic effects of molt in Ginkkoridak, a Korean long-tailed chicken. Messenger RNA data available across 24 types of tissue samples (9 males) and a combination of mRNA and miRNA data on 10 males and 10 females blood were used. RESULTS The impact of molt on gene expression and gene transcript usage appeared to vary substantially across tissues types in terms of histological entities or physiological functions particularly related to nervous system. Blood was the tissue most affected by molt in terms of differentially expressed genes in both sexes, closely followed by meninges, bone marrow and heart. The effect of molt in blood appeared to differ between males and females, with a more than fivefold difference in the number of down-regulated genes between both sexes. The blueprint of molt in roosters appeared to be specific to tissues or group of tissues, with relatively few genes replicating extensively across tissues, excepted for the spliceosome genes (U1, U4) and the ribosomal proteins (RPL21, RPL23). By integrating miRNA and mRNA data, when chickens molt, potential roles of miRNA were discovered such as regulation of neurogenesis, regulation of immunity and development of various organs. Furthermore, reliable candidate biomarkers of molt were found, which are related to cell dynamics, nervous system or immunity, processes or functions that have been shown to be extensively modulated in response to molt. CONCLUSIONS Our results provide a comprehensive description at the scale of the whole organism deciphering the effects of molt on the transcriptome in chicken. Also, the conclusion of this study can be used as a valuable resource in transcriptome analyses of chicken in the future and provide new insights related to molt.
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Affiliation(s)
- Clémentine Charton
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Dong-Jae Youm
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Byung June Ko
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Donghyeok Seol
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- eGnome, Inc, Seoul, Republic of Korea
| | - Bongsang Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- eGnome, Inc, Seoul, Republic of Korea
| | - Han-Ha Chai
- Animal Genomics & Bioinformatics Division, National Institute of Animal Science, RDA, 1500, Wanju, Republic of Korea
| | - Dajeong Lim
- Animal Genomics & Bioinformatics Division, National Institute of Animal Science, RDA, 1500, Wanju, Republic of Korea
| | - Heebal Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.
- eGnome, Inc, Seoul, Republic of Korea.
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Xia Y, Zhang X, Sun D, Gao Y, Zhang X, Wang L, Cai Q, Wang Q, Sun J. Effects of water-soluble components of atmospheric particulates from rare earth mining areas in China on lung cancer cell cycle. Part Fibre Toxicol 2021; 18:27. [PMID: 34340691 PMCID: PMC8330054 DOI: 10.1186/s12989-021-00416-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 06/02/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND This study aims to investigate the effects of water soluble particulate matter (WSPM) on the viability and protein expression profile of human lung adenocarcinoma cell A549 in the Bayou Obo rare earth mining area, and explore the influence of WSPM on the A549 cell cycle. RESULTS It was found that WSPM can inhibit the viability of A549 cells and induce cell arrest in the G2/M phase. Compared with controls, exposure to WSPM10 and WSPM2.5 induced 134 and 116 proteins to be differentially expressed in A549 cells, respectively. In addition, 33 and 31 differentially expressed proteins were further confirmed, and was consistent with the proteomic analysis. The most prominent enrichment in ribosome-associated proteins were presented. When RPL6, RPL13, or RPL18A gene expression was inhibited, A549 cells were arrested in the G1 phase, affecting the expression of Cyclin D1, p21, RB1, Cyclin A2, Cyclin B1, CDC25A, CDK2, CHEK2 and E2F1. Furthermore, the La3+, Ce3+, Nd3+ and F- in WSPM also inhibited the viability of A549 cells. After 24 h of exposure to 2 mM of NaF, A549 cells were also arrested in the G2/M phase, while the other three compounds did not have this effect. These four compounds affected the cell cycle regulatory factors in A549 cells, mainly focusing on effecting the expression of CDK2, CDK4, RB1, ATM, TP53 and MDM2 genes. These results are consistent with the those from WSPM exposure. CONCLUSIONS These results revealed that WSPM from rare earth mines decreased the viability of A549 cells, and induced cell cycle G2/M phase arrest, and even apoptosis, which may be independent of the NF-κB/MYD88 pathway, and be perceived by the TLR4 receptor. The dysfunction of the cell cycle is correlated to the down-expression of ribosomal proteins (RPs). However, it is not the direct reason for the A549 cell arrest in the G2/M phase. La3+, Ce3+, and F- are probably the main toxic substances in WSPM, and may be regulate the A549 cell cycle by affecting the expression of genes, such as MDM2, RB1, ATM, TP53, E2F1, CDK2 and CDK4. These results indicate the importance for further research into the relationship between APM and lung cancer.
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Affiliation(s)
- Yuan Xia
- School of Public Health, Inner Mongolia Autonomous Region, Jinshan Economic and Technological Development Zone, Inner Mongolia Medical University, Inner Mongolia Autonomous Region, 010010, Hohhot, China
| | - Xulong Zhang
- Department of Immunology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Dejun Sun
- Inner Mongolia People's Hospital, Inner Mongolia Autonomous Region, Hohhot, China
| | - Yumin Gao
- School of Public Health, Inner Mongolia Autonomous Region, Jinshan Economic and Technological Development Zone, Inner Mongolia Medical University, Inner Mongolia Autonomous Region, 010010, Hohhot, China
| | - Xiaoe Zhang
- School of Public Health, Inner Mongolia Autonomous Region, Jinshan Economic and Technological Development Zone, Inner Mongolia Medical University, Inner Mongolia Autonomous Region, 010010, Hohhot, China
| | - Li Wang
- School of Public Health, Inner Mongolia Autonomous Region, Jinshan Economic and Technological Development Zone, Inner Mongolia Medical University, Inner Mongolia Autonomous Region, 010010, Hohhot, China
| | - Qingjun Cai
- School of Public Health, Inner Mongolia Autonomous Region, Jinshan Economic and Technological Development Zone, Inner Mongolia Medical University, Inner Mongolia Autonomous Region, 010010, Hohhot, China
| | - Qihao Wang
- School of Public Health, Inner Mongolia Autonomous Region, Jinshan Economic and Technological Development Zone, Inner Mongolia Medical University, Inner Mongolia Autonomous Region, 010010, Hohhot, China
| | - Juan Sun
- School of Public Health, Inner Mongolia Autonomous Region, Jinshan Economic and Technological Development Zone, Inner Mongolia Medical University, Inner Mongolia Autonomous Region, 010010, Hohhot, China.
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Liu Y, Ma J, Zhang L, Lin J, Liu X. Overexpressed MPS-1 contributes to endometrioma development through the NF-κB signaling pathway. Reprod Biol Endocrinol 2021; 19:111. [PMID: 34266426 PMCID: PMC8281640 DOI: 10.1186/s12958-021-00796-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 07/04/2021] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Endometriosis is a benign gynecological disease that shares some characteristics with malignant tumors and affects approximately 10% of women of reproductive age. Endometrioma refers to endometriosis that appears in the ovary. Metallopanstimulin-1 (MPS-1) is a component of the 40S subunit of ribosomes that has extra-ribosomal functions that contribute to the development of diseases. This study aimed to explore the expression pattern and role of MPS-1 in endometrioma development. METHODS Quantitative real time polymerase chain reaction, western blotting, immunohistochemistry, and enzyme-linked immunosorbent assay were used to determine the expression of MPS-1 in patients with endometrioma. Following the successful knockdown of MPS-1 by siRNA, CCK-8 assays, flow cytometry, and transwell assays were performed to detect ectopic endometrial stromal cells (EcESCs) proliferation, the rate of apoptosis, and cell cycle, migration, and invasion, respectively. Western blotting was used to explore the effect of MPS-1 knockdown on protein levels in the NF-κB signaling pathway. RESULTS The expression of MPS-1 was significantly higher in endometrioma and the serum of endometrioma patients than in the patients without endometriosis. In addition, the downregulation of MPS-1 expression inhibited EcESCs proliferation, migration, and invasion. This downregulation led to the arrest of the EcESCs cycle in the G0/G1 phase and apoptosis and depressed the NF-κB signaling pathway. CONCLUSION MPS-1 can regulate EcESCs proliferation, motility, invasion, apoptosis, and cell cycle via the NF-κB signaling pathway in endometrioma. This may contribute to the formation or development of endometriotic foci. This study suggests the potential role of MPS-1 in the pathogenesis of endometriosis and enabled further research into the use of MPS-1 in the clinical diagnosis of endometrioma.
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Affiliation(s)
- Yang Liu
- Department of Obstetrics and Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, People's Republic of China
| | - Junyan Ma
- Department of Key Laboratory, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310006, People's Republic of China
| | - Liqi Zhang
- Department of Obstetrics and Gynecology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310006, People's Republic of China
| | - Jun Lin
- Department of Obstetrics and Gynecology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310006, People's Republic of China.
| | - Xiaohua Liu
- Department of Obstetrics and Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, People's Republic of China.
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Sim EUH, Lee CW, Narayanan K. The roles of ribosomal proteins in nasopharyngeal cancer: culprits, sentinels or both. Biomark Res 2021; 9:51. [PMID: 34193301 PMCID: PMC8247250 DOI: 10.1186/s40364-021-00311-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 06/20/2021] [Indexed: 12/15/2022] Open
Abstract
Ribosomal protein genes encode products that are essential for cellular protein biosynthesis and are major components of ribosomes. Canonically, they are involved in the complex system of ribosome biogenesis pivotal to the catalysis of protein translation. Amid this tightly organised process, some ribosomal proteins have unique spatial and temporal physiological activity giving rise to their extra-ribosomal functions. Many of these extra-ribosomal roles pertain to cellular growth and differentiation, thus implicating the involvement of some ribosomal proteins in organogenesis. Consequently, dysregulated functions of these ribosomal proteins could be linked to oncogenesis or neoplastic transformation of human cells. Their suspected roles in carcinogenesis have been reported but not specifically explained for malignancy of the nasopharynx. This is despite the fact that literature since one and half decade ago have documented the association of ribosomal proteins to nasopharyngeal cancer. In this review, we explain the association and contribution of dysregulated expression among a subset of ribosomal proteins to nasopharyngeal oncogenesis. The relationship of these ribosomal proteins with the cancer are explained. We provide information to indicate that the dysfunctional extra-ribosomal activities of specific ribosomal proteins are tightly involved with the molecular pathogenesis of nasopharyngeal cancer albeit mechanisms yet to be precisely defined. The complete knowledge of this will impact future applications in the effective management of nasopharyngeal cancer.
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Affiliation(s)
- Edmund Ui-Hang Sim
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia.
| | - Choon-Weng Lee
- Institute of Biological Sciences, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Kumaran Narayanan
- School of Science, Monash University, 46150, Bandar Sunway, Selangor, Malaysia.,Department of Genetics and Genomics Sciences, Mount Sinai School of Medicine, New York, NY, 10029, USA
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44
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Hiu JJ, Yap MKK. The effects of Naja sumatrana venom cytotoxin, sumaCTX on alteration of the secretome in MCF-7 breast cancer cells following membrane permeabilization. Int J Biol Macromol 2021; 184:776-786. [PMID: 34174307 DOI: 10.1016/j.ijbiomac.2021.06.145] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 06/21/2021] [Accepted: 06/21/2021] [Indexed: 12/24/2022]
Abstract
Naja sumatrana venom cytotoxin (sumaCTX) is a basic protein which belongs to three-finger toxin family. It has been shown to induce caspase-dependent, mitochondrial-mediated apoptosis in MCF-7 cells at lower concentrations. This study aimed to investigate the alteration of secretome in MCF-7 cells following membrane permeabilization by high concentrations of sumaCTX, using label-free quantitative (LFQ) approach. The degree of membrane permeabilization of sumaCTX was determined by lactate dehydrogenase (LDH) assay and calcein-propidium iodide (PI) assays. LDH and calcein-PI assays revealed time-dependent membrane permeabilization within a narrow concentration range. However, as toxin concentrations increased, prolonged exposure of MCF-7 cells to sumaCTX did not promote the progression of membrane permeabilization. The secretome analyses showed that membrane permeabilization was an event preceding the release of intracellular proteins. Bioinformatics analyses of the LFQ secretome revealed the presence of 105 significantly distinguished proteins involved in metabolism, structural supports, inflammatory responses, and necroptosis in MCF-7 cells treated with 29.8 μg/mL of sumaCTX. Necroptosis was presumably an initial stress response in MCF-7 cells when exposed to high sumaCTX concentration. Collectively, sumaCTX-induced the loss of membrane integrity in a concentration-dependent manner, whereby the cell death pattern of MCF-7 cells transformed from apoptosis to necroptosis with increasing toxin concentrations.
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Affiliation(s)
- Jia Jin Hiu
- School of Science, Monash University Malaysia, Bandar Sunway, Malaysia.
| | - Michelle Khai Khun Yap
- School of Science, Monash University Malaysia, Bandar Sunway, Malaysia; Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia, Bandar Sunway, Malaysia.
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45
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Khan MIK, Charles RCM, Ramachandran R, Gupta S, Govindaraju G, Mishra R, Rajavelu A, Coumar MS, Chavali S, Dhayalan A. The ribosomal protein eL21 interacts with the protein lysine methyltransferase SMYD2 and regulates its steady state levels. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021; 1868:119079. [PMID: 34147559 DOI: 10.1016/j.bbamcr.2021.119079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 05/24/2021] [Accepted: 06/13/2021] [Indexed: 01/23/2023]
Abstract
The protein lysine methyltransferase, SMYD2 is involved in diverse cellular events by regulating protein functions through lysine methylation. Though several substrate proteins of SMYD2 are well-studied, only a limited number of its interaction partners have been identified and characterized. Here, we performed a yeast two-hybrid screening of SMYD2 and found that the ribosomal protein, eL21 could interact with SMYD2. SMYD2-eL21 interaction in the human cells was confirmed by immunoprecipitation methods. In vitro pull-down assays revealed that SMYD2 interacts with eL21 directly through its SET and MYND domain. Computational mapping, followed by experimental studies identified that Lys81 and Lys83 residues of eL21 are important for the SMYD2-eL21 interaction. Evolutionary analysis showed that these residues might have co-evolved with the emergence of SMYD2. We found that eL21 regulates the steady state levels of SMYD2 by promoting its transcription and inhibiting its proteasomal degradation. Importantly, SMYD2-eL21 interaction plays an important role in regulating cell proliferation and its dysregulation might lead to tumorigenesis. Our findings highlight a novel extra-ribosomal function of eL21 on regulating SMYD2 levels and imply that ribosomal proteins might regulate wide range of cellular functions through protein-protein interactions in addition to their core function in translation.
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Affiliation(s)
- Mohd Imran K Khan
- Department of Biotechnology, Pondicherry University, Puducherry 605 014, India
| | | | - Reshma Ramachandran
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati 517 507, India
| | - Somlee Gupta
- Department of Biotechnology, Pondicherry University, Puducherry 605 014, India
| | - Gayathri Govindaraju
- Interdisciplinary Biology, Rajiv Gandhi Centre for Biotechnology, Trivandrum 695 014, India
| | - Rashmi Mishra
- Department of Biotechnology, Pondicherry University, Puducherry 605 014, India
| | - Arumugam Rajavelu
- Interdisciplinary Biology, Rajiv Gandhi Centre for Biotechnology, Trivandrum 695 014, India
| | | | - Sreenivas Chavali
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati 517 507, India.
| | - Arunkumar Dhayalan
- Department of Biotechnology, Pondicherry University, Puducherry 605 014, India.
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Mohanan G, Das A, Rajyaguru PI. Genotoxic stress response: What is the role of cytoplasmic mRNA fate? Bioessays 2021; 43:e2000311. [PMID: 34096096 DOI: 10.1002/bies.202000311] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 05/15/2021] [Accepted: 05/18/2021] [Indexed: 12/18/2022]
Abstract
Genotoxic stress leads to DNA damage which can be detrimental to the cell. A well-orchestrated cellular response is mounted to manage and repair the genotoxic stress-induced DNA damage. Our understanding of genotoxic stress response is derived mainly from studies focused on transcription, mRNA splicing, and protein turnover. Surprisingly not as much is understood about the role of mRNA translation and decay in genotoxic stress response. This is despite the fact that regulation of gene expression at the level of mRNA translation and decay plays a critical role in a myriad of cellular processes. This review aims to summarize some of the known findings of the role of mRNA translation and decay by focusing on two categories of examples. We discuss examples of mRNA whose fates are regulated in the cytoplasm and RNA-binding proteins that regulate mRNA fates in response to genotoxic stress.
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Affiliation(s)
- Gayatri Mohanan
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Amiyaranjan Das
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
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Sun Z, Qiu Z, Wang Z, Chi H, Shan P. Silencing Ribosomal Protein L22 Promotes Proliferation and Migration, and Inhibits Apoptosis of Gastric Cancer Cells by Regulating the Murine Double Minute 2-Protein 53 (MDM2-p53) Signaling Pathway. Med Sci Monit 2021; 27:e928375. [PMID: 34050122 PMCID: PMC8168286 DOI: 10.12659/msm.928375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Background The aim of this study was to investigate the effect of ribosomal protein L22 (RPL22) on gastric cancer (GC) cell proliferation, migration, and apoptosis, and its correlation with the murine double minute 2-protein 53 (MDM2-p53) signaling pathway. Material/Methods The RPL22 expression in GC tissues and cells was detected by quantitative reverse transcription-polymerase chain reaction and western blotting. RPL22 was overexpressed in the MKN-45 cells by the transfection of a vector, pcDNA3.1 (pcDNA)-RPL22, whereas it was silenced in the MGC-803 cells by the transfection of short interfering (si) RNA (si-RPL22). Flow cytometric analysis, cell viability assays, wound healing assays, and transwell assays were utilized to explore the influences of RPL22 on the apoptosis, proliferation, migration, and invasion. Nutlin-3 (an MDM2-p53 inhibitor) was used to inhibit MDM2-p53 signaling. Results The RPL22 expression was downregulated in GC tissues and cells. It was significantly lower in the advanced GC tissues than in the early GC tissues, and was significantly lower in the lymphatic metastatic tissues than in the non-lymphatic metastatic tissues. The transfection of si-RPL22 accelerated the ability of GC cells to proliferate and metastasize, whereas apoptosis was dampened. The transfection of pcDNA-RPL22 exerted the opposite effect on the GC cells; MDM2 expression was upregulated in RPL22-silenced GC cells, while the expression of p53 was downregulated. In vitro, treatment with nutlin-3 reversed the promoting effects of si-RPL22 on GC progression. Conclusions In vitro, the silencing of RPL22 aggravates GC by regulating the MDM2-p53 signaling pathway.
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Affiliation(s)
- Zhenqing Sun
- Department of Gastrointestinal Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China (mainland)
| | - Zhigang Qiu
- Department of Gastrointestinal Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China (mainland)
| | - Zhengkun Wang
- Department of Gastrointestinal Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China (mainland)
| | - Honghui Chi
- Department of Cardiovascular Surgery II, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China (mainland)
| | - Peipei Shan
- Institute for Translational Medicine, College of Medicine of Qingdao University, Qingdao, Shandong, China (mainland)
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Kang J, Li Y, Zhao Z, Zhang H. Differentiation between thyroid-associated orbitopathy and Graves' disease by iTRAQ-based quantitative proteomic analysis. FEBS Open Bio 2021; 11:1930-1940. [PMID: 33934566 PMCID: PMC8255837 DOI: 10.1002/2211-5463.13172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/17/2021] [Indexed: 11/12/2022] Open
Abstract
Graves' ophthalmopathy, also known as thyroid-associated orbitopathy (TAO), is the most common inflammatory eye disease in adults. The most common etiology for TAO is Graves' disease (GD); however, proteomic research focusing on differences between GD and TAO is limited. This study aimed to identify differentially expressed proteins between thyroid-associated orbitopathy (TAO) and GD. Furthermore, we sought to explore the pathogenesis of TAO and elucidate the differentiation process via specific markers. Serum samples of three patients with TAO, GD, and healthy controls, respectively, were collected. These samples were measured using the iTRAQ technique coupled with mass spectrometry. Differentially expressed proteins in TAO and GD were identified by proteomics; 3172 quantified proteins were identified. Compared with TAO, we identified 110 differential proteins (27 proteins were upregulated and 83 were downregulated). In addition, these differentially expressed proteins were closely associated with cellular processes, metabolic processes, macromolecular complexes, signal transduction, and the immune system. The corresponding functions were protein, calcium ion, and nucleic acid binding. Among the differential proteins, MYH11, P4HB, and C4A were markedly upregulated in TAO patients and have been reported to participate in apoptosis, autophagy, the inflammatory response, and the immune system. A protein-protein interaction network analysis was performed. Proteomics demonstrated valuable large-scale protein-related information for expounding the pathogenic mechanism underlying TAO. This research provides new insights and potential targets for studying GD with TAO.
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Affiliation(s)
- Jianshu Kang
- Department of Ophthalmology, The Second People's Hospital of Yunnan Province, The Fourth Affiliated Hospital of Kunming Medical University, China.,Yunnan Eye Institute, Kunming, China.,Key Laboratory of Yunnan Province for the Prevention and Treatment of Ophthalmologya, Kunming, China.,Yunnan Eye Disease Clinical Medical Center, Kunming, China.,Yunnan Eye Disease Clinical Medical Research Center, Kunming, China
| | - Yunqin Li
- Department of Ophthalmology, The Second People's Hospital of Yunnan Province, The Fourth Affiliated Hospital of Kunming Medical University, China.,Yunnan Eye Institute, Kunming, China.,Key Laboratory of Yunnan Province for the Prevention and Treatment of Ophthalmologya, Kunming, China.,Yunnan Eye Disease Clinical Medical Center, Kunming, China.,Yunnan Eye Disease Clinical Medical Research Center, Kunming, China
| | - Zhijian Zhao
- Department of Ophthalmology, The Second People's Hospital of Yunnan Province, The Fourth Affiliated Hospital of Kunming Medical University, China.,Yunnan Eye Institute, Kunming, China.,Key Laboratory of Yunnan Province for the Prevention and Treatment of Ophthalmologya, Kunming, China.,Yunnan Eye Disease Clinical Medical Center, Kunming, China.,Yunnan Eye Disease Clinical Medical Research Center, Kunming, China
| | - Hong Zhang
- Department of Ophthalmology, The Second People's Hospital of Yunnan Province, The Fourth Affiliated Hospital of Kunming Medical University, China.,Yunnan Eye Institute, Kunming, China.,Key Laboratory of Yunnan Province for the Prevention and Treatment of Ophthalmologya, Kunming, China.,Yunnan Eye Disease Clinical Medical Center, Kunming, China.,Yunnan Eye Disease Clinical Medical Research Center, Kunming, China
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Eichelmann AK, Mayne GC, Chiam K, Due SL, Bastian I, Butz F, Wang T, Sykes PJ, Clemons NJ, Liu DS, Michael MZ, Karapetis CS, Hummel R, Watson DI, Hussey DJ. Mutant p53 Mediates Sensitivity to Cancer Treatment Agents in Oesophageal Adenocarcinoma Associated with MicroRNA and SLC7A11 Expression. Int J Mol Sci 2021; 22:5547. [PMID: 34074015 PMCID: PMC8197322 DOI: 10.3390/ijms22115547] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/12/2021] [Accepted: 05/19/2021] [Indexed: 12/18/2022] Open
Abstract
TP53 gene mutations occur in 70% of oesophageal adenocarcinomas (OACs). Given the central role of p53 in controlling cellular response to therapy we investigated the role of mutant (mut-) p53 and SLC7A11 in a CRISPR-mediated JH-EsoAd1 TP53 knockout model. Response to 2 Gy irradiation, cisplatin, 5-FU, 4-hydroxytamoxifen, and endoxifen was assessed, followed by a TaqMan OpenArray qPCR screening for differences in miRNA expression. Knockout of mut-p53 resulted in increased chemo- and radioresistance (2 Gy survival fraction: 38% vs. 56%, p < 0.0001) and in altered miRNA expression levels. Target mRNA pathways analyses indicated several potential mechanisms of treatment resistance. SLC7A11 knockdown restored radiosensitivity (2 Gy SF: 46% vs. 73%; p = 0.0239), possibly via enhanced sensitivity to oxidative stress. Pathway analysis of the mRNA targets of differentially expressed miRNAs indicated potential involvement in several pathways associated with apoptosis, ribosomes, and p53 signaling pathways. The data suggest that mut-p53 in JH-EsoAd1, despite being classified as non-functional, has some function related to radio- and chemoresistance. The results also highlight the important role of SLC7A11 in cancer metabolism and redox balance and the influence of p53 on these processes. Inhibition of the SLC7A11-glutathione axis may represent a promising approach to overcome resistance associated with mut-p53.
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Affiliation(s)
- Ann-Kathrin Eichelmann
- Flinders Health and Medical Research Institute—Cancer Program, Flinders University, Bedford Park, Adelaide, SA 5042, Australia; (G.C.M.); (K.C.); (S.L.D.); (I.B.); (F.B.); (T.W.); (P.J.S.); (M.Z.M.); (C.S.K.); (D.I.W.)
- Department of General, Visceral and Transplant Surgery, University Hospital of Münster, Waldeyerstrasse 1, 48149 Münster, Germany
| | - George C. Mayne
- Flinders Health and Medical Research Institute—Cancer Program, Flinders University, Bedford Park, Adelaide, SA 5042, Australia; (G.C.M.); (K.C.); (S.L.D.); (I.B.); (F.B.); (T.W.); (P.J.S.); (M.Z.M.); (C.S.K.); (D.I.W.)
- Department of Surgery, Flinders Medical Centre, Bedford Park, Adelaide, SA 5042, Australia
| | - Karen Chiam
- Flinders Health and Medical Research Institute—Cancer Program, Flinders University, Bedford Park, Adelaide, SA 5042, Australia; (G.C.M.); (K.C.); (S.L.D.); (I.B.); (F.B.); (T.W.); (P.J.S.); (M.Z.M.); (C.S.K.); (D.I.W.)
| | - Steven L. Due
- Flinders Health and Medical Research Institute—Cancer Program, Flinders University, Bedford Park, Adelaide, SA 5042, Australia; (G.C.M.); (K.C.); (S.L.D.); (I.B.); (F.B.); (T.W.); (P.J.S.); (M.Z.M.); (C.S.K.); (D.I.W.)
| | - Isabell Bastian
- Flinders Health and Medical Research Institute—Cancer Program, Flinders University, Bedford Park, Adelaide, SA 5042, Australia; (G.C.M.); (K.C.); (S.L.D.); (I.B.); (F.B.); (T.W.); (P.J.S.); (M.Z.M.); (C.S.K.); (D.I.W.)
| | - Frederike Butz
- Flinders Health and Medical Research Institute—Cancer Program, Flinders University, Bedford Park, Adelaide, SA 5042, Australia; (G.C.M.); (K.C.); (S.L.D.); (I.B.); (F.B.); (T.W.); (P.J.S.); (M.Z.M.); (C.S.K.); (D.I.W.)
| | - Tingting Wang
- Flinders Health and Medical Research Institute—Cancer Program, Flinders University, Bedford Park, Adelaide, SA 5042, Australia; (G.C.M.); (K.C.); (S.L.D.); (I.B.); (F.B.); (T.W.); (P.J.S.); (M.Z.M.); (C.S.K.); (D.I.W.)
| | - Pamela J. Sykes
- Flinders Health and Medical Research Institute—Cancer Program, Flinders University, Bedford Park, Adelaide, SA 5042, Australia; (G.C.M.); (K.C.); (S.L.D.); (I.B.); (F.B.); (T.W.); (P.J.S.); (M.Z.M.); (C.S.K.); (D.I.W.)
| | - Nicholas J. Clemons
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000, Australia; (N.J.C.); (D.S.L.)
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - David S. Liu
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000, Australia; (N.J.C.); (D.S.L.)
- Department of Surgery, Austin Health, Heidelberg, VIC 3084, Australia
| | - Michael Z. Michael
- Flinders Health and Medical Research Institute—Cancer Program, Flinders University, Bedford Park, Adelaide, SA 5042, Australia; (G.C.M.); (K.C.); (S.L.D.); (I.B.); (F.B.); (T.W.); (P.J.S.); (M.Z.M.); (C.S.K.); (D.I.W.)
- Department of Gastroenterology, Flinders Medical Centre, Bedford Park, Adelaide, SA 5042, Australia
| | - Christos S. Karapetis
- Flinders Health and Medical Research Institute—Cancer Program, Flinders University, Bedford Park, Adelaide, SA 5042, Australia; (G.C.M.); (K.C.); (S.L.D.); (I.B.); (F.B.); (T.W.); (P.J.S.); (M.Z.M.); (C.S.K.); (D.I.W.)
- Department of Medical Oncology, Flinders Medical Centre, Bedford Park, Adelaide, SA 5042, Australia
| | - Richard Hummel
- Department of Surgery, University Hospital of Schleswig-Holstein, Ratzeburger Allee 160, 23538 Lübeck, Germany;
| | - David I. Watson
- Flinders Health and Medical Research Institute—Cancer Program, Flinders University, Bedford Park, Adelaide, SA 5042, Australia; (G.C.M.); (K.C.); (S.L.D.); (I.B.); (F.B.); (T.W.); (P.J.S.); (M.Z.M.); (C.S.K.); (D.I.W.)
- Department of Surgery, Flinders Medical Centre, Bedford Park, Adelaide, SA 5042, Australia
| | - Damian J. Hussey
- Flinders Health and Medical Research Institute—Cancer Program, Flinders University, Bedford Park, Adelaide, SA 5042, Australia; (G.C.M.); (K.C.); (S.L.D.); (I.B.); (F.B.); (T.W.); (P.J.S.); (M.Z.M.); (C.S.K.); (D.I.W.)
- Department of Surgery, Flinders Medical Centre, Bedford Park, Adelaide, SA 5042, Australia
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50
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Bozinovic G, Shea D, Feng Z, Hinton D, Sit T, Oleksiak MF. PAH-pollution effects on sensitive and resistant embryos: Integrating structure and function with gene expression. PLoS One 2021; 16:e0249432. [PMID: 33822796 PMCID: PMC8023486 DOI: 10.1371/journal.pone.0249432] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 03/17/2021] [Indexed: 11/18/2022] Open
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are among the most widespread natural and anthropogenic pollutants, and some PAHs are proven developmental toxicants. We chemically characterized clean and heavily polluted sites and exposed fish embryos to PAH polluted sediment extracts during four critical developmental stages. Embryos were collected from Fundulus heteroclitus populations inhabiting the clean and heavily polluted Superfund estuary. Embryos of parents from the clean sites are sensitive to PAH pollutants while those of parents from the heavily polluted site are resistant. Chemical analysis of embryos suggests PAH accumulation and pollution-induced toxicity among sensitive embryos during development that ultimately kills all sensitive embryos before hatching, while remarkably, the resistant embryos develop normally. The adverse effects on sensitive embryos are manifested as developmental delays, reduced heart rates, and severe heart, liver, and kidney morphological abnormalities. Gene expression analysis of early somitogenesis, heartbeat initiation, late organogenesis, and pre-hatching developmental stages reveals genes whose expression significantly differs between sensitive and resistant embryo populations and helps to explain mechanisms of sensitivity and resistance to polluted environments during vertebrate animal development.
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Affiliation(s)
- Goran Bozinovic
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
- Boz Life Science Research and Teaching Institute, San Diego, California, United States of America
| | - Damian Shea
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Zuying Feng
- Boz Life Science Research and Teaching Institute, San Diego, California, United States of America
| | - David Hinton
- Nicholas School of the Environment, Duke University, Durham, North Carolina, United States of America
| | - Tim Sit
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Marjorie F. Oleksiak
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
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