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Tong L, Ye K, Chen Q, Wang X, Hu C, Xu Q, Zhou L, Zhan R, Tong Y. Proteomics shows that brain metastases of lung adenocarcinoma overexpress ribosomal proteins in response to gamma knife radiosurgery. Sci Rep 2024; 14:15646. [PMID: 38977703 PMCID: PMC11231244 DOI: 10.1038/s41598-024-58967-y] [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: 01/18/2024] [Accepted: 04/05/2024] [Indexed: 07/10/2024] Open
Abstract
Gamma knife radiosurgery (GKRS) is recommended as the first-line treatment for brain metastases of lung adenocarcinoma (LUAD) in many guidelines, but its specific mechanism is unclear. We aimed to study the changes in the proteome of brain metastases of LUAD in response to the hyperacute phase of GKRS and further explore the mechanism of differentially expressed proteins (DEPs). Cancer tissues were collected from a clinical trial for neoadjuvant stereotactic radiosurgery before surgical resection of large brain metastases (ChiCTR2000038995). Five brain metastasis tissues of LUAD were collected within 24 h after GKRS. Five brain metastasis tissues without radiotherapy were collected as control samples. Proteomics analysis showed that 163 proteins were upregulated and 25 proteins were downregulated. GO and KEGG enrichment analyses showed that the DEPs were closely related to ribosomes. Fifty-three of 70 ribosomal proteins were significantly overexpressed, while none of them were underexpressed. The risk score constructed from 7 upregulated ribosomal proteins (RPL4, RPS19, RPS16, RPLP0, RPS2, RPS26 and RPS25) was an independent risk factor for the survival time of LUAD patients. Overexpression of ribosomal proteins may represent a desperate response to lethal radiotherapy. We propose that targeted inhibition of these ribosomal proteins may enhance the efficacy of GKRS.
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Affiliation(s)
- Luqing Tong
- Department of Neurosurgery, The First Affiliated Hospital, Zhejiang University School of Medicine, No.79 Qingchun Street, Shangcheng District, Hangzhou, 310003, Zhejiang, China
| | - Ke Ye
- Department of Neurosurgery, The First Affiliated Hospital, Zhejiang University School of Medicine, No.79 Qingchun Street, Shangcheng District, Hangzhou, 310003, Zhejiang, China
| | - Qun Chen
- Department of Neurosurgery, The First Affiliated Hospital, Zhejiang University School of Medicine, No.79 Qingchun Street, Shangcheng District, Hangzhou, 310003, Zhejiang, China
| | - Xiaoxi Wang
- Department of Pathology, The First Affiliated Hospital, Zhejiang University School of Medicine, No.79 Qingchun Street, Shangcheng District, Hangzhou, 310003, Zhejiang, China
| | - Chi Hu
- Department of Neurosurgery, The First Affiliated Hospital, Zhejiang University School of Medicine, No.79 Qingchun Street, Shangcheng District, Hangzhou, 310003, Zhejiang, China
| | - Qingsheng Xu
- Department of Neurosurgery, The First Affiliated Hospital, Zhejiang University School of Medicine, No.79 Qingchun Street, Shangcheng District, Hangzhou, 310003, Zhejiang, China
| | - Lihui Zhou
- Department of Neurosurgery, The First Affiliated Hospital, Zhejiang University School of Medicine, No.79 Qingchun Street, Shangcheng District, Hangzhou, 310003, Zhejiang, China
| | - Renya Zhan
- Department of Neurosurgery, The First Affiliated Hospital, Zhejiang University School of Medicine, No.79 Qingchun Street, Shangcheng District, Hangzhou, 310003, Zhejiang, China.
| | - Ying Tong
- Department of Neurosurgery, The First Affiliated Hospital, Zhejiang University School of Medicine, No.79 Qingchun Street, Shangcheng District, Hangzhou, 310003, Zhejiang, China.
- Gamma Knife Centre, The First Affiliated Hospital, Zhejiang University School of Medicine, No.79 Qingchun Street, Shangcheng District, Hangzhou, 310003, Zhejiang, China.
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Buck SA, Mabry SJ, Glausier JR, Banks-Tibbs T, Ward C, Kozel JG, Fu C, Fish KN, Lewis DA, Logan RW, Freyberg Z. Aging disrupts the coordination between mRNA and protein expression in mouse and human midbrain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.01.596950. [PMID: 38854057 PMCID: PMC11160743 DOI: 10.1101/2024.06.01.596950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Age-related dopamine (DA) neuron loss is a primary feature of Parkinson's disease. However, it remains unclear whether similar biological processes occur during healthy aging, albeit to a lesser degree. We therefore determined whether midbrain DA neurons degenerate during aging in mice and humans. In mice, we identified no changes in midbrain neuron numbers throughout aging. Despite this, we found age-related decreases in midbrain mRNA expression of tyrosine hydroxylase (Th), the rate limiting enzyme of DA synthesis. Among midbrain glutamatergic cells, we similarly identified age-related declines in vesicular glutamate transporter 2 (Vglut2) mRNA expression. In co-transmitting Th +/Vglut2 + neurons, Th and Vglut2 transcripts decreased with aging. Importantly, striatal Th and Vglut2 protein expression remained unchanged. In translating our findings to humans, we found no midbrain neurodegeneration during aging and identified age-related decreases in TH and VGLUT2 mRNA expression similar to mouse. Unlike mice, we discovered diminished density of striatal TH+ dopaminergic terminals in aged human subjects. However, TH and VGLUT2 protein expression were unchanged in the remaining striatal boutons. Finally, in contrast to Th and Vglut2 mRNA, expression of most ribosomal genes in Th + neurons was either maintained or even upregulated during aging. This suggests a homeostatic mechanism where age-related declines in transcriptional efficiency are overcome by ongoing ribosomal translation. Overall, we demonstrate species-conserved transcriptional effects of aging in midbrain dopaminergic and glutamatergic neurons that are not accompanied by marked cell death or lower striatal protein expression. This opens the door to novel therapeutic approaches to maintain neurotransmission and bolster neuronal resilience.
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Affiliation(s)
- Silas A. Buck
- Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Samuel J. Mabry
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jill R. Glausier
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Tabitha Banks-Tibbs
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
- College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Caroline Ward
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jenesis Gayden Kozel
- Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Chen Fu
- Department of Psychiatry, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Kenneth N. Fish
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - David A. Lewis
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ryan W. Logan
- Department of Psychiatry, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Zachary Freyberg
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, USA
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Tang Q, Tang J, Chen C, Zhu F, Yu Q, Chen H, Chen L, Ma S, Chen K, Li G. Bombyx mori RPL13 participates in UV-induced DNA damage repair of B. mori nucleopolyhedrovirus through interaction with Bm65. INSECT MOLECULAR BIOLOGY 2024. [PMID: 38801334 DOI: 10.1111/imb.12928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 05/01/2024] [Indexed: 05/29/2024]
Abstract
Ribosomal protein L13 (RPL13) is highly conserved in evolution. At present, the properties and functions of RPL13 have not been characterised in insects. In this study, Bombyx mori RPL13 (BmRPL13) was first found to be specifically recruited to the sites of ultraviolet (UV)-induced DNA damage and contributed to UV damage repair. Escherichia coli expressing BmRPL13 showed better resistance to UV radiation. After knocking down the expression of BmRPL13 in BmN cells, the repair speed of UV-damaged DNA slowed down. The further results showed that BmRPL13 interacted with B. mori nucleopolyhedrovirus (BmNPV) ORF65 (Bm65) protein to locate at the UV-induced DNA damage sites of BmNPV and helped repair UV-damaged viral DNA.
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Affiliation(s)
- Qi Tang
- Department of Biological Sciences, School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Jingjing Tang
- Department of Biological Sciences, School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Ceru Chen
- Department of Biological Sciences, School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Feifei Zhu
- Department of Biological Sciences, School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Qian Yu
- Department of Biological Sciences, School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Huiqing Chen
- Department of Biological Sciences, School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Liang Chen
- Department of Biological Sciences, School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Shangshang Ma
- Department of Biological Sciences, School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Keping Chen
- Department of Biological Sciences, School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Guohui Li
- Department of Biological Sciences, School of Life Sciences, Jiangsu University, Zhenjiang, China
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Feng L, Wang G, Song Q, Feng X, Su J, Ji G, Li M. Proteomics revealed an association between ribosome-associated proteins and amyloid beta deposition in Alzheimer's disease. Metab Brain Dis 2024; 39:263-282. [PMID: 38019374 DOI: 10.1007/s11011-023-01330-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 11/22/2023] [Indexed: 11/30/2023]
Abstract
Most scholars believe that amyloid-beta (Aβ) has the potential to induce apoptosis, stimulate an inflammatory cascade, promote oxidative stress and exacerbate the pathological progression of Alzheimer's disease (AD). Therefore, it is crucial to investigate the deposition of Aβ in AD. At approximately 6 months of age, APP/PS1 double transgenic mice gradually exhibit the development of plaques, as well as spatial and learning impairment. Notably, the hippocampus is specifically affected in the course of AD. Herein, 6-month-old APP/PS1 double transgenic mice were utilized, and the differentially expressed (DE) proteins in the hippocampus were identified and analyzed using 4D label-free quantitative proteomics technology and parallel reaction monitoring (PRM). Compared to wild-type mice, 29 proteins were upregulated and 25 proteins were downregulated in the AD group. Gene Ontology (GO) enrichment analysis of biological processes (BP) indicated that the DE proteins were mainly involved in 'ribosomal large subunit biogenesis'. Molecular function (MF) analysis results were primarily associated with '5.8S rRNA binding' and 'structural constituent of ribosome'. In terms of cellular components (CC), the DE proteins were mainly found in 'polysomal ribosome', 'cytosolic large ribosomal subunit', 'cytosolic ribosome', and 'large ribosomal subunit', among others. Furthermore, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis demonstrated that the results were mainly enriched in the 'Ribosome signaling pathway'. The key target proteins identified were ribosomal protein (Rp)l18, Rpl17, Rpl19, Rpl24, Rpl35, and Rpl6. The PRM verification results were consistent with the findings of the 4D label-free quantitative proteomics analysis. Overall, these findings suggest that Rpl18, Rpl17, Rpl19, Rpl24, Rpl35, and Rpl6 may have potential therapeutic value for the treatment of AD by targeting Aβ.
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Affiliation(s)
- Lina Feng
- Department of Neurology, the Second Affiliated Hospital of Shandong First Medical University, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, Shandong, China
| | - Guojun Wang
- Department of Neurosurgery, The Affiliated Taian City Central Hospital of Qingdao University, Taian, 271000, Shandong, China
| | - Qile Song
- Department of Neurology, the Second Affiliated Hospital of Shandong First Medical University, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, Shandong, China
| | - Xiaotong Feng
- Department of Neurology, the Second Affiliated Hospital of Shandong First Medical University, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, Shandong, China
| | - Jing Su
- Department of Geriatric Cardiovascular, The Affiliated Taian City Central Hospital of Qingdao University, Longtan Road, Taian, 271000, Shandong, China.
| | - Guangcheng Ji
- Department of Neurology, the Third Affiliated Clinical Hospital of the Changchun University of Chinese Medicine, Boshuo Road, Changchun, 130117, Jilin, China.
| | - Mingquan Li
- Department of Neurology, the Third Affiliated Clinical Hospital of the Changchun University of Chinese Medicine, Boshuo Road, Changchun, 130117, Jilin, China.
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Kołacz K, Robaszkiewicz A. PARP1 at the crossroad of cellular senescence and nucleolar processes. Ageing Res Rev 2024; 94:102206. [PMID: 38278370 DOI: 10.1016/j.arr.2024.102206] [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: 11/07/2023] [Revised: 01/09/2024] [Accepted: 01/22/2024] [Indexed: 01/28/2024]
Abstract
Senescent cells that occur in response to telomere shortening, oncogenes, extracellular and intracellular stress factors are characterized by permanent cell cycle arrest, the morphological and structural changes of the cell that include the senescence-associated secretory phenotype (SASP) and nucleoli rearrangement. The associated DNA lesions induce DNA damage response (DDR), which activates the DNA repair protein - poly-ADP-ribose polymerase 1 (PARP1). This protein consumes NAD+ to synthesize ADP-ribose polymer (PAR) on its own protein chain and on other interacting proteins. The involvement of PARP1 in nucleoli processes, such as rRNA transcription and ribosome biogenesis, the maintenance of heterochromatin and nucleoli structure, as well as controlling the crucial DDR protein release from the nucleoli to nucleus, links PARP1 with cellular senescence and nucleoli functioning. In this review we describe and discuss the impact of PARP1-mediated ADP-ribosylation on early cell commitment to senescence with the possible role of senescence-induced PARP1 transcriptional repression and protein degradation on nucleoli structure and function. The cause-effect interplay between PARP1 activation/decline and nucleoli functioning during senescence needs to be studied in detail.
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Affiliation(s)
- Kinga Kołacz
- Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland; Bio-Med-Chem Doctoral School of the University of Lodz and Lodz Institutes of the Polish Academy of Sciences, University of Lodz, Banacha 12 /16, 90-237 Lodz, Poland.
| | - Agnieszka Robaszkiewicz
- Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland; Johns Hopkins University School of Medicine, Institute for Fundamental Biomedical Research (IFBR), 600 5th Street South, St. Petersburgh, FL 33701, USA.
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6
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Wu D, Huang H, Chen T, Gai X, Li Q, Wang C, Yao J, Liu Y, Cai S, Yu X. The BRCA1/BARD1 complex recognizes pre-ribosomal RNA to facilitate homologous recombination. Cell Discov 2023; 9:99. [PMID: 37789001 PMCID: PMC10547766 DOI: 10.1038/s41421-023-00590-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 07/16/2023] [Indexed: 10/05/2023] Open
Abstract
The BRCA1/BARD1 complex plays a key role in the repair of DNA double-strand breaks (DSBs) in both somatic cells and germ cells. However, the underlying molecular mechanism by which this complex mediates DSB repair is not fully understood. Here, we examined the XY body of male germ cells, where DSBs are accumulated. We show that the recruitment of the BRCA1/BARD1 complex to the unsynapsed axis of the XY body is mediated by pre-ribosomal RNA (pre-rRNA). Similarly, the BRCA1/BARD1 complex associates with pre-rRNA in somatic cells, which not only forms nuclear foci in response to DSBs, but also targets the BRCA1/BARD1 complex to DSBs. The interactions between the BRCT domains of the BRCA1/BARD1 complex and pre-rRNA induce liquid-liquid phase separations, which may be the molecular basis of DSB-induced nuclear foci formation of the BRCA1/BARD1 complex. Moreover, cancer-associated mutations in the BRCT domains of BRCA1 and BARD1 abolish their interactions with pre-rRNA. Pre-rRNA also mediates BRCA1-dependent homologous recombination, and suppression of pre-rRNA biogenesis sensitizes cells to PARP inhibitor treatment. Collectively, this study reveals that pre-rRNA is a functional partner of the BRCA1/BARD1 complex in the DSB repair.
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Affiliation(s)
- Duo Wu
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Huang Huang
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Tenglong Chen
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Xiaochen Gai
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Qilin Li
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Chunhui Wang
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Disease Modeling Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Jia Yao
- The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yu Liu
- The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Shang Cai
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Disease Modeling Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Xiaochun Yu
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China.
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China.
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Wang G, Qin M, Zhang B, Yan Y, Yang F, Chen Q, Liu Y, Qiao F, Ni Y. Decreased expression of RPL15 and RPL18 exacerbated the calcification of valve interstitial cells during aortic valve calcification. Cell Biol Int 2023; 47:1749-1759. [PMID: 37431269 DOI: 10.1002/cbin.12070] [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: 09/27/2022] [Revised: 06/19/2023] [Accepted: 07/02/2023] [Indexed: 07/12/2023]
Abstract
Calcific aortic valve disease (CAVD) is the most common valvular heart disease, with an increasing prevalence due to an aging population. The pathobiology of CAVD is a multifaceted and actively regulated process, but the detailed mechanisms have not been elucidated. The present study aims to identify the differentially expressed genes (DEGs) in calcified aortic valve tissues, and to analyze the correlation between DEGs and clinical features in CAVD patients. The DEGs were screened by microarray in normal and CAVD groups (n = 2 for each group), and confirmed by quantitative real-time polymerase chain reaction in normal (n = 12) and calcified aortic valve tissues (n = 34). A total of 1048 DEGs were identified in calcified aortic valve tissues, including 227 upregulated mRNAs and 821 downregulated mRNAs. Based on multiple bioinformatic analyses, three 60S ribosomal subunit components (RPL15, RPL18, and RPL18A), and two 40S ribosomal subunit components (RPS15 and RPS21) were identified as the top 5 hub genes in the protein-protein interaction network of DEGs. The expression of RPL15 and RPL18 was also found significantly decreased in calcified aortic valve tissues (both p < .01), and negatively correlated with the osteogenic differentiation marker OPN in CAVD patients (both p < .01). Moreover, inhibition of RPL15 or RPL18 exacerbated the calcification of valve interstitial cells under osteogenic induction conditions. The present study proved that decreased expression of RPL15 and RPL18 was closely associated with aortic valve calcification, which provided valuable clues to find therapeutic targets for CAVD.
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Affiliation(s)
- Guokun Wang
- Department of Cardiovascular Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Department of Cardiovascular Surgery, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Ming Qin
- Department of Cardiovascular Surgery, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Boyao Zhang
- Department of Cardiovascular Surgery, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Yan Yan
- Department of Cardiovascular Surgery, Changhai Hospital, Naval Medical University, Shanghai, China
- Department of Cardiothoracic Surgery, No.903 Hospital of PLA, Hangzhou, Zhejiang, China
| | - Fan Yang
- Department of Cardiovascular Surgery, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Qian Chen
- Department of Cardiovascular Surgery, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Yang Liu
- Department of Cardiovascular Surgery, Changhai Hospital, Naval Medical University, Shanghai, China
- Department of Critical Care Medicine, Naval Medical Center of PLA, Shanghai, China
| | - Fan Qiao
- Department of Cardiovascular Surgery, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Yiming Ni
- Department of Cardiovascular Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
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Lee SO, Kelliher JL, Song W, Tengler K, Sarkar A, Dray E, Leung JWC. UBA80 and UBA52 fine-tune RNF168-dependent histone ubiquitination and DNA repair. J Biol Chem 2023; 299:105043. [PMID: 37451480 PMCID: PMC10413357 DOI: 10.1016/j.jbc.2023.105043] [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: 12/24/2022] [Revised: 06/29/2023] [Accepted: 07/02/2023] [Indexed: 07/18/2023] Open
Abstract
The ubiquitin signaling pathway is crucial for the DNA damage response pathway. More specifically, RNF168 is integral in regulating DNA repair proteins at damaged chromatin. However, the detailed mechanism by which RNF168 is regulated in cells is not fully understood. Here, we identify the ubiquitin-ribosomal fusion proteins UBA80 (also known as RPS27A) and UBA52 (also known as RPL40) as interacting proteins for H2A/H2AX histones and RNF168. Both UBA80 and UBA52 are recruited to laser-induced micro-irradiation DNA damage sites and are required for DNA repair. Ectopic expression of UBA80 and UBA52 inhibits RNF168-mediated H2A/H2AX ubiquitination at K13/15 and impairs 53BP1 recruitment to DNA lesions. Mechanistically, the C-terminal ribosomal fragments of UBA80 and UBA52, S27A and L40, respectively, limit RNF168-nucleosome engagement by masking the regulatory acidic residues at E143/E144 and the nucleosome acidic patch. Together, our results reveal that UBA80 and UBA52 antagonize the ubiquitination signaling pathway and fine-tune the spatiotemporal regulation of DNA repair proteins at DNA damage sites.
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Affiliation(s)
- Seong-Ok Lee
- Department of Pharmacology and Toxicology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA; Department of Radiation Oncology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Jessica L Kelliher
- Department of Radiation Oncology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA; Department of Biochemistry and Molecular Biology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Wan Song
- Department of Radiation Oncology, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Kyle Tengler
- Department of Radiation Oncology, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Aradhan Sarkar
- Department of Radiation Oncology, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Eloise Dray
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Justin W C Leung
- Department of Radiation Oncology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA; Department of Radiation Oncology, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA.
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Arzumanian V, Pyatnitskiy M, Poverennaya E. Comparative Transcriptomic Analysis of Three Common Liver Cell Lines. Int J Mol Sci 2023; 24:ijms24108791. [PMID: 37240140 DOI: 10.3390/ijms24108791] [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: 04/18/2023] [Revised: 05/07/2023] [Accepted: 05/12/2023] [Indexed: 05/28/2023] Open
Abstract
BACKGROUND Comparative transcriptomic analysis is a powerful approach for investigating the molecular mechanisms underlying various physiological and pathological processes, including liver disease. The liver is a vital organ with diverse functions, including metabolism and detoxification. In vitro models of liver cells, such as HepG2, Huh7, and Hep3B, have been widely used to study liver biology and pathology. However, there is limited information on the heterogeneity of these cell lines at the transcriptomic level. OBJECTIVE This study aimed to conduct a comparative transcriptomic analysis of three common liver cell lines (HepG2, Huh7, and Hep3B) using publicly available RNA-sequencing data. In addition, we compared these cell lines to primary hepatocytes, cells isolated directly from liver tissue and considered the gold standard for studying liver function and disease. METHODS Our study included sequencing data with the following criteria: total number of reads over 20,000,000, average read length of over 60 base pairs, Illumina sequencing, and non-treated cells. The data for the three cell lines were compiled: HepG2 (97 samples), Huh7 (39 samples), and Hep3B (16 samples). We performed differential gene expression analysis using the DESeq2 package, principal component analysis, hierarchical clustering on principal components, and correlation analysis to explore the heterogeneity within each cell line. RESULTS We identified numerous genes and pathways differentially expressed between HepG2, Huh7, and Hep3B, such as oxidative phosphorylation, cholesterol metabolism, and DNA damage. We report that the expression levels of important genes differ significantly between primary hepatocytes and liver cell lines. CONCLUSION Our study provides new insights into the transcriptional heterogeneity of commonly used liver cell lines and highlights the importance of considering specific cell line. Consequently, transferring results without considering the heterogeneity of cell lines is impractical and may lead to inaccurate or distorted conclusions.
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Chang X, Xiao Y, Cheng L, Gu X, Yang L, Chamba Y, Zhang J, Geng F. Quantitative Proteomic Analysis of Yorkshire Pig Liver Reveals Its Response to High Altitude. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:7618-7629. [PMID: 37140090 DOI: 10.1021/acs.jafc.3c01724] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
In this study, the protein profiles in the livers of Shannan Yorkshire pigs (SNY), Linzhi Yorkshire pigs (LZY), and Jiuzhaigou Yorkshire pigs (JZY) were comparatively analyzed using quantitative proteomics. A total of 6804 proteins were identified, of which 6471 were quantified and 774 differentially expressed proteins (DEPs) were screened. The higher level of energy metabolism in LZY livers was in response to the critical altitude environment compared to that in JZY, while the high-altitude environment suppressed energy output in SNY livers. Several key antioxidant enzymes were locally regulated in Yorkshire pig liver to balance antioxidant levels in a high-altitude, low-oxygen environment. In addition, ribosomal proteins were differentially expressed in Yorkshire pig livers in response to different altitudinal environments. These findings provide clues to the adaptation of the Yorkshire pig liver to the three altitudinal environments and the molecular links that exist between them.
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Affiliation(s)
- Xinping Chang
- Meat Processing Key Laboratory of Sichuan Province, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China
| | - Yu Xiao
- Meat Processing Key Laboratory of Sichuan Province, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China
| | - Lei Cheng
- School of Food and Health, Beijing Technology & Business University (BTBU), Beijing 100048, China
| | - Xuedong Gu
- College of Food Science, Tibet Agriculture and Animal Husbandry University, Linzhi 860000, China
- Provincial and Ministerial Co-Founded Collaborative Innovation Center for R & D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Tibet Agricultural and Animal Husbandry University, Linzhi 860000, China
| | - Lin Yang
- Provincial and Ministerial Co-Founded Collaborative Innovation Center for R & D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Tibet Agricultural and Animal Husbandry University, Linzhi 860000, China
| | - Yangzom Chamba
- College of Food Science, Tibet Agriculture and Animal Husbandry University, Linzhi 860000, China
- Provincial and Ministerial Co-Founded Collaborative Innovation Center for R & D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Tibet Agricultural and Animal Husbandry University, Linzhi 860000, China
| | - Jiamin Zhang
- Meat Processing Key Laboratory of Sichuan Province, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China
| | - Fang Geng
- Meat Processing Key Laboratory of Sichuan Province, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China
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11
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Tan Y, Lu S, Wang B, Duan X, Zhang Y, Peng X, Li H, Lin A, Zhan Z, Liu X. Single-cell transcriptome atlas reveals protective characteristics of COVID-19 mRNA vaccine. J Med Virol 2022; 95:e28161. [PMID: 36124363 PMCID: PMC9538852 DOI: 10.1002/jmv.28161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 09/09/2022] [Accepted: 09/15/2022] [Indexed: 01/11/2023]
Abstract
Messenger RNA (mRNA) vaccines are promising alternatives to conventional vaccines in many aspects. We previously developed a lipopolyplex (LPP)-based mRNA vaccine (SW0123) that demonstrated robust immunogenicity and strong protective capacity against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection in mice and rhesus macaques. However, the immune profiles and mechanisms of pulmonary protection induced by SW0123 remain unclear. Through high-resolution single-cell analysis, we found that SW0123 vaccination effectively suppressed SARS-CoV-2-induced inflammatory responses by inhibiting the recruitment of proinflammatory macrophages and increasing the frequency of polymorphonuclear myeloid-derived suppressor cells. In addition, the apoptotic process in both lung epithelial and endothelial cells was significantly inhibited, which was proposed to be one major mechanism contributing to vaccine-induced lung protection. Cell-cell interaction in the lung compartment was also altered by vaccination. These data collectively unravel the mechanisms by which the SW0123 protects against lung damage caused by SARS-CoV-2 infection.
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Affiliation(s)
- Yong Tan
- Research Center for Translational Medicine, Shanghai East HospitalTongji University School of MedicineShanghaiChina,Department of Liver Surgery, Shanghai Institute of TransplantationRenji Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Shuaiyao Lu
- National Kunming High‐level Biosafety Primate Research Center, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical CollegeYunnanChina
| | - Bo Wang
- Research Center for Translational Medicine, Shanghai East HospitalTongji University School of MedicineShanghaiChina
| | - Xuewen Duan
- Research Center for Translational Medicine, Shanghai East HospitalTongji University School of MedicineShanghaiChina
| | - Yunkai Zhang
- Department of Pathogen BiologyNaval Medical UniversityShanghaiChina,National Key Laboratory of Medical ImmunologyNaval Medical UniversityShanghaiChina
| | - Xiaozhong Peng
- National Kunming High‐level Biosafety Primate Research Center, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical CollegeYunnanChina
| | | | - Ang Lin
- Vaccine Center, School of Basic Medicine and Clinical PharmacyChina Pharmaceutical UniversityNanjingChina
| | - Zhenzhen Zhan
- Research Center for Translational Medicine, Shanghai East HospitalTongji University School of MedicineShanghaiChina,Department of Liver Surgery, Shanghai Institute of TransplantationRenji Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Xingguang Liu
- Department of Pathogen BiologyNaval Medical UniversityShanghaiChina,National Key Laboratory of Medical ImmunologyNaval Medical UniversityShanghaiChina
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12
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Jin Q, Zuo C, Cui H, Li L, Yang Y, Dai H, Chen L. Single-cell entropy network detects the activity of immune cells based on ribosomal protein genes. Comput Struct Biotechnol J 2022; 20:3556-3566. [PMID: 35860411 PMCID: PMC9287362 DOI: 10.1016/j.csbj.2022.06.056] [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: 03/05/2022] [Revised: 06/25/2022] [Accepted: 06/26/2022] [Indexed: 11/16/2022] Open
Abstract
We developed a new computational method, Single-Cell Entropy Network (SCEN) to analyze single-cell RNA-seq data, which used the information of gene-gene associations to discover new heterogeneity of immune cells as well as identify existing cell types. Based on SCEN, we defined association-entropy (AE) for each cell and each gene through single-cell gene co-expression networks to measure the strength of association between each gene and all other genes at a single-cell resolution. Analyses of public datasets indicated that the AE of ribosomal protein genes (RP genes) varied greatly even in the same cell type of immune cells and the average AE of RP genes of immune cells in each person was significantly associated with the healthy/disease state of this person. Based on existing research and theory, we inferred that the AE of RP genes represented the heterogeneity of ribosomes and reflected the activity of immune cells. We believe SCEN can provide more biological insights into the heterogeneity and diversity of immune cells, especially the change of immune cells in the diseases.
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Affiliation(s)
- Qiqi Jin
- Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chunman Zuo
- Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Haoyue Cui
- Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lin Li
- Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yiwen Yang
- Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hao Dai
- Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Luonan Chen
- Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.,Guangdong Institute of Intelligence Science and Technology, Hengqin, Zhuhai, Guangdong 519031, China.,Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou 310024, China
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13
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RNA-Seq Transcriptome Analysis of Differentiated Human Oligodendrocytic MO3.13 Cells Shows Upregulation of Genes Involved in Myogenesis. Int J Mol Sci 2022; 23:ijms23115969. [PMID: 35682649 PMCID: PMC9181232 DOI: 10.3390/ijms23115969] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 01/27/2023] Open
Abstract
In this work, we examined the differentiation of oligodendrocytic MO3.13 cells and changes in their gene expression after treatment with phorbol 12-myristate 13-acetate, PMA, or with RNA polymerase I (Pol I) inhibitor, CX-5461. We found that MO3.13 cells changed their morphology when treated with both agents. Interestingly, CX-5461, but not PMA, induced noticeable changes in the integrity of the nucleoli. Then, we analyzed the p53 transcriptional activity in MO3.13 cells and found that it was increased in both cell populations, but particularly in cells treated with PMA. Interestingly, this high p53 transcriptional activity in PMA-treated cells coincided with a lower level of an unmodified (non-phosphorylated) form of this protein. Since morphological changes in MO3.13 cells after PMA and CX-5461 treatment were evident, suggesting that cells were induced to differentiate, we performed RNA-seq analysis of PMA-treated cells, to reveal the direction of alterations in gene expression. The analysis showed that the largest group of upregulated genes consisted of those involved in myogenesis and K-RAS signaling, rather than those associated with oligodendrocyte lineage progression.
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14
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Pagano A, Zannino L, Pagano P, Doria E, Dondi D, Macovei A, Biggiogera M, Araújo SDS, Balestrazzi A. Changes in genotoxic stress response, ribogenesis and PAP (3'-phosphoadenosine 5'-phosphate) levels are associated with loss of desiccation tolerance in overprimed Medicago truncatula seeds. PLANT, CELL & ENVIRONMENT 2022; 45:1457-1473. [PMID: 35188276 PMCID: PMC9311706 DOI: 10.1111/pce.14295] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 02/04/2022] [Accepted: 02/05/2022] [Indexed: 05/06/2023]
Abstract
Re-establishment of desiccation tolerance is essential for the survival of germinated seeds facing water deficit in the soil. The molecular and ultrastructural features of desiccation tolerance maintenance and loss within the nuclear compartment are not fully resolved. In the present study, the impact of desiccation-induced genotoxic stress on nucleolar ultrastructure and ribogenesis was explored along the rehydration-dehydration cycle applied in standard seed vigorization protocols. Primed and overprimed Medicago truncatula seeds, obtained through hydropriming followed by desiccation (dry-back), were analysed. In contrast to desiccation-tolerant primed seeds, overprimed seeds enter irreversible germination and do not survive dry-back. Reactive oxygen species, DNA damage and expression profiles of antioxidant/DNA Damage Response genes were measured, as main hallmarks of the seed response to desiccation stress. Nuclear ultrastructural features were also investigated. Overprimed seeds subjected to dry-back revealed altered rRNA accumulation profiles and up-regulation of genes involved in ribogenesis control. The signal molecule PAP (3'-phosphoadenosine 5'-phosphate) accumulated during dry-back only in primed seeds, as a distinctive feature of desiccation tolerance. The presented results show the molecular and ultrastructural landscapes of the seed desiccation response, including substantial changes in nuclear organization.
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Affiliation(s)
- Andrea Pagano
- Department of Biology and Biotechnology ‘L. Spallanzani'University of PaviaPaviaItaly
| | - Lorena Zannino
- Department of Biology and Biotechnology ‘L. Spallanzani'University of PaviaPaviaItaly
| | - Paola Pagano
- Department of Biology and Biotechnology ‘L. Spallanzani'University of PaviaPaviaItaly
| | - Enrico Doria
- Department of Biology and Biotechnology ‘L. Spallanzani'University of PaviaPaviaItaly
| | - Daniele Dondi
- Department of ChemistryUniversity of PaviaPaviaItaly
| | - Anca Macovei
- Department of Biology and Biotechnology ‘L. Spallanzani'University of PaviaPaviaItaly
| | - Marco Biggiogera
- Department of Biology and Biotechnology ‘L. Spallanzani'University of PaviaPaviaItaly
| | - Susana de Sousa Araújo
- Association BLC3‐Technology and Innovation CampusCentre Bio R&D UnitMacedo de CavaleirosPortugal
| | - Alma Balestrazzi
- Department of Biology and Biotechnology ‘L. Spallanzani'University of PaviaPaviaItaly
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15
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Appels R, Wang P, Islam S. Integrating Wheat Nucleolus Structure and Function: Variation in the Wheat Ribosomal RNA and Protein Genes. FRONTIERS IN PLANT SCIENCE 2021; 12:686586. [PMID: 35003148 PMCID: PMC8739226 DOI: 10.3389/fpls.2021.686586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 11/08/2021] [Indexed: 06/13/2023]
Abstract
We review the coordinated production and integration of the RNA (ribosomal RNA, rRNA) and protein (ribosomal protein, RP) components of wheat cytoplasmic ribosomes in response to changes in genetic constitution, biotic and abiotic stresses. The components examined are highly conserved and identified with reference to model systems such as human, Arabidopsis, and rice, but have sufficient levels of differences in their DNA and amino acid sequences to form fingerprints or gene haplotypes that provide new markers to associate with phenotype variation. Specifically, it is argued that populations of ribosomes within a cell can comprise distinct complements of rRNA and RPs to form units with unique functionalities. The unique functionalities of ribosome populations within a cell can become central in situations of stress where they may preferentially translate mRNAs coding for proteins better suited to contributing to survival of the cell. In model systems where this concept has been developed, the engagement of initiation factors and elongation factors to account for variation in the translation machinery of the cell in response to stresses provided the precedents. The polyploid nature of wheat adds extra variation at each step of the synthesis and assembly of the rRNAs and RPs which can, as a result, potentially enhance its response to changing environments and disease threats.
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Affiliation(s)
- Rudi Appels
- AgriBio, Centre for AgriBioscience, La Trobe University, Bundoora, VIC, Australia
- Faculty of Veterinary and Agricultural Science, Melbourne, VIC, Australia
| | - Penghao Wang
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, Australia
| | - Shahidul Islam
- Centre for Crop Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
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16
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Kachaev ZM, Ivashchenko SD, Kozlov EN, Lebedeva LA, Shidlovskii YV. Localization and Functional Roles of Components of the Translation Apparatus in the Eukaryotic Cell Nucleus. Cells 2021; 10:3239. [PMID: 34831461 PMCID: PMC8623629 DOI: 10.3390/cells10113239] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/11/2021] [Accepted: 11/16/2021] [Indexed: 12/15/2022] Open
Abstract
Components of the translation apparatus, including ribosomal proteins, have been found in cell nuclei in various organisms. Components of the translation apparatus are involved in various nuclear processes, particularly those associated with genome integrity control and the nuclear stages of gene expression, such as transcription, mRNA processing, and mRNA export. Components of the translation apparatus control intranuclear trafficking; the nuclear import and export of RNA and proteins; and regulate the activity, stability, and functional recruitment of nuclear proteins. The nuclear translocation of these components is often involved in the cell response to stimulation and stress, in addition to playing critical roles in oncogenesis and viral infection. Many components of the translation apparatus are moonlighting proteins, involved in integral cell stress response and coupling of gene expression subprocesses. Thus, this phenomenon represents a significant interest for both basic and applied molecular biology. Here, we provide an overview of the current data regarding the molecular functions of translation factors and ribosomal proteins in the cell nucleus.
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Affiliation(s)
- Zaur M. Kachaev
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; (Z.M.K.); (S.D.I.); (E.N.K.); (L.A.L.)
- Center for Genetics and Life Science, Sirius University of Science and Technology, 354340 Sochi, Russia
| | - Sergey D. Ivashchenko
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; (Z.M.K.); (S.D.I.); (E.N.K.); (L.A.L.)
| | - Eugene N. Kozlov
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; (Z.M.K.); (S.D.I.); (E.N.K.); (L.A.L.)
| | - Lyubov A. Lebedeva
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; (Z.M.K.); (S.D.I.); (E.N.K.); (L.A.L.)
| | - Yulii V. Shidlovskii
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; (Z.M.K.); (S.D.I.); (E.N.K.); (L.A.L.)
- Center for Genetics and Life Science, Sirius University of Science and Technology, 354340 Sochi, Russia
- Department of Biology and General Genetics, Sechenov First Moscow State Medical University (Sechenov University), 119992 Moscow, Russia
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17
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Gueiderikh A, Maczkowiak-Chartois F, Rosselli F. A new frontier in Fanconi anemia: From DNA repair to ribosome biogenesis. Blood Rev 2021; 52:100904. [PMID: 34750031 DOI: 10.1016/j.blre.2021.100904] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 10/14/2021] [Accepted: 10/26/2021] [Indexed: 12/27/2022]
Abstract
Described by Guido Fanconi almost 100 years ago, Fanconi anemia (FA) is a rare genetic disease characterized by developmental abnormalities, bone marrow failure (BMF) and cancer predisposition. The proteins encoded by FA-mutated genes (FANC proteins) and assembled in the so-called FANC/BRCA pathway have key functions in DNA repair and replication safeguarding, which loss leads to chromosome structural aberrancies. Therefore, since the 1980s, FA has been considered a genomic instability and chromosome fragility syndrome. However, recent findings have demonstrated new and unexpected roles of FANC proteins in nucleolar homeostasis and ribosome biogenesis, the alteration of which impacts cellular proteostasis. Here, we review the different cellular, biochemical and molecular anomalies associated with the loss of function of FANC proteins and discuss how these anomalies contribute to BMF by comparing FA to other major inherited BMF syndromes. Our aim is to determine the extent to which alterations in the DNA damage response in FA contribute to BMF compared to the consequences of the loss of function of the FANC/BRCA pathway on the other roles of the pathway.
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Affiliation(s)
- Anna Gueiderikh
- CNRS - UMR9019, Équipe labellisée "La Ligue contre le Cancer", 94805 Villejuif, France; Gustave Roussy Cancer Center, 94805 Villejuif, France; Université Paris-Saclay - Paris Sud, Orsay, France.
| | - Frédérique Maczkowiak-Chartois
- CNRS - UMR9019, Équipe labellisée "La Ligue contre le Cancer", 94805 Villejuif, France; Gustave Roussy Cancer Center, 94805 Villejuif, France; Université Paris-Saclay - Paris Sud, Orsay, France.
| | - Filippo Rosselli
- CNRS - UMR9019, Équipe labellisée "La Ligue contre le Cancer", 94805 Villejuif, France; Gustave Roussy Cancer Center, 94805 Villejuif, France; Université Paris-Saclay - Paris Sud, Orsay, France.
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18
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Jia C, Wang Q, Yao X, Yang J. The Role of DNA Damage Induced by Low/High Dose Ionizing Radiation in Cell Carcinogenesis. EXPLORATORY RESEARCH AND HYPOTHESIS IN MEDICINE 2021; 000:000-000. [DOI: 10.14218/erhm.2021.00020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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19
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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: 5] [Impact Index Per Article: 1.7] [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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20
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Ribosome Biogenesis and Cancer: Overview on Ribosomal Proteins. Int J Mol Sci 2021; 22:ijms22115496. [PMID: 34071057 PMCID: PMC8197113 DOI: 10.3390/ijms22115496] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/16/2021] [Accepted: 05/19/2021] [Indexed: 12/11/2022] Open
Abstract
Cytosolic ribosomes (cytoribosomes) are macromolecular ribonucleoprotein complexes that are assembled from ribosomal RNA and ribosomal proteins, which are essential for protein biosynthesis. Mitochondrial ribosomes (mitoribosomes) perform translation of the proteins essential for the oxidative phosphorylation system. The biogenesis of cytoribosomes and mitoribosomes includes ribosomal RNA processing, modification and binding to ribosomal proteins and is assisted by numerous biogenesis factors. This is a major energy-consuming process in the cell and, therefore, is highly coordinated and sensitive to several cellular stressors. In mitochondria, the regulation of mitoribosome biogenesis is essential for cellular respiration, a process linked to cell growth and proliferation. This review briefly overviews the key stages of cytosolic and mitochondrial ribosome biogenesis; summarizes the main steps of ribosome biogenesis alterations occurring during tumorigenesis, highlighting the changes in the expression level of cytosolic ribosomal proteins (CRPs) and mitochondrial ribosomal proteins (MRPs) in different types of tumors; focuses on the currently available information regarding the extra-ribosomal functions of CRPs and MRPs correlated to cancer; and discusses the role of CRPs and MRPs as biomarkers and/or molecular targets in cancer treatment.
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21
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Xiong W, Zhang J, Lan T, Kong W, Wang X, Liu L, Chen X, Mo B. High resolution RNA-seq profiling of genes encoding ribosomal proteins across different organs and developmental stages in Arabidopsis thaliana. PLANT DIRECT 2021; 5:e00320. [PMID: 34095740 PMCID: PMC8156134 DOI: 10.1002/pld3.320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 03/16/2021] [Accepted: 03/18/2021] [Indexed: 05/12/2023]
Abstract
In Arabidopsis thaliana, each ribosomal protein (RP) is encoded by a small gene family consisting of two or more highly homologous paralogues, which results in ribosome heterogeneity. It is largely unknown that how genes from multiple member containing RP families are regulated at transcriptional level to accommodate the needs of different plant organs and developmental stages. In this study, we investigated the transcript accumulation profiles of RP genes and found that the expression levels of RP genes are varied dramatically in different organs and developmental stages. Although most RP genes are found to be ubiquitously transcribed, some are obviously transcribed with spatiotemporal specificity. The hierarchical clustering trees of transcript accumulation intensity of RP genes revealed that different organs and developmental stages have different population of RP gene transcripts. By interrogating of the expression fluctuation trend of RP genes, we found that in spite of the fact that most groups of paralogous RP genes are transcribed in concerted manners, some RPs gene have contrasting expression patterns. When transcripts of paralogous RP genes from the same family are considered together, the expression level of most RP genes are well-matched but some are obviously higher or lower, therefore we speculate that some superfluous RPs may act outside the ribosome and a portion of ribosomes may lack one or even more RP(s). Altogether, our analysis results suggested that functional divergence may exist among heterogeneous ribosomes that resulted from different combination of RP paralogues, and substoichiometry of several RP gene families may lead to another layer of heterogeneous ribosomes which also have divergent functions in plants.
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Affiliation(s)
- Wei Xiong
- Guangdong Provincial Key Laboratory for Plant EpigeneticsLonghua Bioindustry and Innovation Research InstituteCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenChina
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong ProvinceCollege of Optoelectronic EngineeringShenzhen UniversityShenzhenChina
| | - Jiancong Zhang
- Guangdong Provincial Key Laboratory for Plant EpigeneticsLonghua Bioindustry and Innovation Research InstituteCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenChina
| | - Ting Lan
- Guangdong Provincial Key Laboratory for Plant EpigeneticsLonghua Bioindustry and Innovation Research InstituteCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenChina
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong ProvinceCollege of Optoelectronic EngineeringShenzhen UniversityShenzhenChina
| | - Wenwen Kong
- Guangdong Provincial Key Laboratory for Plant EpigeneticsLonghua Bioindustry and Innovation Research InstituteCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenChina
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong ProvinceCollege of Optoelectronic EngineeringShenzhen UniversityShenzhenChina
| | - Xiaoyan Wang
- Guangdong Provincial Key Laboratory for Plant EpigeneticsLonghua Bioindustry and Innovation Research InstituteCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenChina
| | - Lin Liu
- Guangdong Provincial Key Laboratory for Plant EpigeneticsLonghua Bioindustry and Innovation Research InstituteCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenChina
| | - Xuemei Chen
- Department of Botany and Plant SciencesInstitute of Integrative Genome BiologyUniversity of CaliforniaRiversideCAUSA
| | - Beixin Mo
- Guangdong Provincial Key Laboratory for Plant EpigeneticsLonghua Bioindustry and Innovation Research InstituteCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenChina
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22
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Moin M, Saha A, Bakshi A, Madhav MS, Kirti PB. Constitutive expression of Ribosomal Protein L6 modulates salt tolerance in rice transgenic plants. Gene 2021; 789:145670. [PMID: 33892070 DOI: 10.1016/j.gene.2021.145670] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 03/14/2021] [Accepted: 04/15/2021] [Indexed: 12/17/2022]
Abstract
We have functionally characterized the RPL6, a Ribosomal Protein Large subunit gene for salt stress tolerance in rice. The overexpression of RPL6 resulted in tolerance to moderate (150 mM) to high (200 mM) levels of salt (NaCl). The transgenic rice plants expressing RPL6 constitutively showed better phenotypic and physiological responses with high quantum efficiency, accumulation of higher chlorophyll and proline contents, and an overall increase in seed yield compared with the wild type in salt stress treatments. An iTRAQ-based comparative proteomic analysis revealed the high expression of about 333 proteins among the 4378 DAPs in a selected overexpression line of RPL6 treated with 200 mM of NaCl. The functional analysis showed that these highly accumulated proteins (HAPs) are involved in photosynthesis, ribosome and chloroplast biogenesis, ion transportation, transcription and translation regulation, phytohormone and secondary metabolite signal transduction. An in silico network analysis of HAPs predicted that RPL6 binds with translation-related proteins and helicases, which coordinately affect the activities of a comprehensive signaling network, thereby inducing tolerance and promoting growth and productivity in response to salt stress. Our overall findings identified a novel candidate, RPL6, whose characterization contributed to the existing knowledge on the complexity of salt tolerance mechanism in plants.
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Affiliation(s)
- Mazahar Moin
- Biotechnology Division, ICAR-Indian Institute of Rice Research (IIRR), Hyderabad 500030, India.
| | - Anusree Saha
- Department of Plant Sciences, University of Hyderabad, Hyderabad 500046, India
| | - Achala Bakshi
- Biotechnology Division, ICAR-Indian Institute of Rice Research (IIRR), Hyderabad 500030, India
| | - M S Madhav
- Biotechnology Division, ICAR-Indian Institute of Rice Research (IIRR), Hyderabad 500030, India
| | - P B Kirti
- Department of Plant Sciences, University of Hyderabad, Hyderabad 500046, India; Agri-Biotech Foundation, PJTS Agricultural University, Hyderabad 500030, India
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Moin M, Saha A, Bakshi A, D. D, M.S. M, P.B. K. Study on Transcriptional Responses and Identification of Ribosomal Protein Genes for Potential Resistance against Brown Planthopper and Gall Midge Pests in Rice. Curr Genomics 2021; 22:98-110. [PMID: 34220297 PMCID: PMC8188583 DOI: 10.2174/1389202922666210219113220] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 10/04/2020] [Accepted: 01/02/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Our previous studies have revealed the roles of ribosomal protein (RP) genes in the abiotic stress responses of rice. METHODS In the current investigation, we examine the possible involvement of these genes in insect stress responses. We have characterized the RP genes that included both Ribosomal Protein Large (RPL) and Ribosomal Protein Small (RPS) subunit genes in response to infestation by two economically important insect pests, the brown planthopper (BPH) and the Asian rice gall midge (GM) in rice. Differential transcript patterns of seventy selected RP genes were studied in a susceptible and a resistant genotype of indica rice: BPT5204 and RPNF05, respectively. An in silico analyses of the upstream regions of these genes also revealed the presence of cis-elements that are associated with wound signaling. RESULTS We identified the genes that were up or downregulated in either one of the genotypes, or both of them after pest infestation. The transcript patterns of a majority of the genes were found to be temporally-regulated by both the pests. In the resistant RPNF05, BPH infestation activated RPL15, L51 and RPS5a genes while GM infestation induced RPL15, L18a, L22, L36.2, L38, RPS5, S9.2 and S25a at a certain point of time. These genes that were particularly upregulated in the resistant genotype, RPNF05, but not in BPT5204 suggest their potential involvement in plant resistance against either of the two pests studied. CONCLUSION Taken together, RPL15, L51, L18a, RPS5, S5a, S9.2, and S25a appear to be the genes with possible roles in insect resistance in rice.
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Affiliation(s)
- Mazahar Moin
- Biotechnology Division, ICAR-Indian Institute of Rice Research (IIRR), Hyderabad-500030, India
| | - Anusree Saha
- Department of Plant Sciences, University of Hyderabad, Hyderabad-500046, India
| | - Achala Bakshi
- Biotechnology Division, ICAR-Indian Institute of Rice Research (IIRR), Hyderabad-500030, India
| | - Divya D.
- Agri-Biotech Foundation, PJTS Agricultural University, Hyderabad-500030, India
| | - Madhav M.S.
- Biotechnology Division, ICAR-Indian Institute of Rice Research (IIRR), Hyderabad-500030, India
| | - Kirti P.B.
- Department of Plant Sciences, University of Hyderabad, Hyderabad-500046, India
- Agri-Biotech Foundation, PJTS Agricultural University, Hyderabad-500030, India
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24
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Wang J, Ma Z, Li C, Ren P, Yao L, Li B, Meng Y, Ma X, Si E, Yang K, Shang X, Wang H. Dynamic Responses of Barley Root Succinyl-Proteome to Short-Term Phosphate Starvation and Recovery. FRONTIERS IN PLANT SCIENCE 2021; 12:649147. [PMID: 33868348 PMCID: PMC8045032 DOI: 10.3389/fpls.2021.649147] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 03/03/2021] [Indexed: 05/05/2023]
Abstract
Barley (Hordeum vulgare L.)-a major cereal crop-has low Pi demand, which is a distinct advantage for studying the tolerance mechanisms of phosphorus deficiency. We surveyed dynamic protein succinylation events in barley roots in response to and recovery from Pi starvation by firstly evaluating the impact of Pi starvation in a Pi-tolerant (GN121) and Pi-sensitive (GN42) barley genotype exposed to long-term low Pi (40 d) followed by a high-Pi recovery for 10 d. An integrated proteomics approach involving label-free, immune-affinity enrichment, and high-resolution LC-MS/MS spectrometric analysis was then used to quantify succinylome and proteome in GN121 roots under short-term Pi starvation (6, 48 h) and Pi recovery (6, 48 h). We identified 2,840 succinylation sites (Ksuc) across 884 proteins; of which, 11 representative Ksuc motifs had the preferred amino acid residue (lysine). Furthermore, there were 81 differentially abundant succinylated proteins (DFASPs) from 119 succinylated sites, 83 DFASPs from 110 succinylated sites, 93 DFASPs from 139 succinylated sites, and 91 DFASPs from 123 succinylated sites during Pi starvation for 6 and 48 h and during Pi recovery for 6 and 48 h, respectively. Pi starvation enriched ribosome pathways, glycolysis, and RNA degradation. Pi recovery enriched the TCA cycle, glycolysis, and oxidative phosphorylation. Importantly, many of the DFASPs identified during Pi starvation were significantly overexpressed during Pi recovery. These results suggest that barley roots can regulate specific Ksuc site changes in response to Pi stress as well as specific metabolic processes. Resolving the metabolic pathways of succinylated protein regulation characteristics will improve phosphate acquisition and utilization efficiency in crops.
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Affiliation(s)
- Juncheng Wang
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Zengke Ma
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Chengdao Li
- Western Barley Genetics Alliance, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Panrong Ren
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Lirong Yao
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Baochun Li
- Department of Botany, College of Life Sciences and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yaxiong Meng
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Xiaole Ma
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Erjing Si
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Ke Yang
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Xunwu Shang
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Huajun Wang
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
- *Correspondence: Huajun Wang
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25
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Sun S, He H, Ma Y, Xu J, Chen G, Sun Y, Xiong X. Inactivation of ribosomal protein S27-like impairs DNA interstrand cross-link repair by destabilization of FANCD2 and FANCI. Cell Death Dis 2020; 11:852. [PMID: 33051438 PMCID: PMC7555897 DOI: 10.1038/s41419-020-03082-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 10/01/2020] [Accepted: 10/02/2020] [Indexed: 12/16/2022]
Abstract
Ribosomal protein S27-like (RPS27L), an evolutionarily conserved ribosomal protein and a direct p53 target, plays an important role in maintenance of genome integrity. We have previously reported that RPS27L regulates radiation sensitivity via the MDM2-p53 and MDM2-MRN-ATM axes. Whether and how RPS27L modulates DNA interstrand cross-link (ICL) repair is unknown. Here we identified that RPS27L binds to FANCD2 and FANCI, two Fanconi anemia (FA) proteins functioning in ICL repair pathway. Upon RPS27L knockdown, the levels of FANCD2 and FANCI are reduced due to accelerated degradation via p62-mediated autophagy-lysosome pathway, which is abrogated by chloroquine (CQ) treatment or Beclin 1 knockdown. Biologically, RPS27L knockdown suppresses FANCD2 foci formation and impairs ICL repair upon exposure to ICL-inducing agent mitomycin C (MMC) in lung cancer cells. This effect of MMC sensitization can be partially reversed by CQ treatment. Together, our study shows that RPS27L positively regulates ICL repair by binding with FANCD2 and FANCI to prevent their degradation via autophagy-lysosome system.
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Affiliation(s)
- Siyuan Sun
- Cancer Institute of the Second Affiliated Hospital, and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, P. R. China
| | - Hengqian He
- Cancer Institute of the Second Affiliated Hospital, and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, P. R. China
| | - Yuanyuan Ma
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jie Xu
- Department of Urology, the Second Affiliated Hospital, Third Military Medical University (Army Medical University), Chongqing, P. R. China
| | - Guoan Chen
- School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong, P. R. China
| | - Yi Sun
- Cancer Institute of the Second Affiliated Hospital, and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, P. R. China
| | - Xiufang Xiong
- Cancer Institute of the Second Affiliated Hospital, and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, P. R. China.
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26
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Zhou P, Wang J, Mishail D, Wang CY. Recent advancements in PARP inhibitors-based targeted cancer therapy. PRECISION CLINICAL MEDICINE 2020; 3:187-201. [PMID: 32983586 PMCID: PMC7501589 DOI: 10.1093/pcmedi/pbaa030] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 08/27/2020] [Accepted: 08/27/2020] [Indexed: 12/11/2022] Open
Abstract
Poly(ADP-ribose) polymerase inhibitors (PARPi) are a new class of agents with unparalleled clinical achievement for driving synthetic lethality in BRCA-deficient cancers. Recent FDA approval of PARPi has motivated clinical trials centered around the optimization of PARPi-associated therapies in a variety of BRCA-deficient cancers. This review highlights recent advancements in understanding the molecular mechanisms of PARP ‘trapping’ and synthetic lethality. Particular attention is placed on the potential extension of PARPi therapies from BRCA-deficient patients to populations with other homologous recombination-deficient backgrounds, and common characteristics of PARPi and non-homologous end-joining have been elucidated. The synergistic antitumor effect of combining PARPi with various immune checkpoint blockades has been explored to evaluate the potential of combination therapy in attaining greater therapeutic outcome. This has shed light onto the differing classifications of PARPi as well as the factors that result in altered PARPi activity. Lastly, acquired chemoresistance is a crucial issue for clinical application of PARPi. The molecular mechanisms underlying PARPi resistance and potential overcoming strategies are discussed.
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Affiliation(s)
- Ping Zhou
- Laboratory of Molecular Signaling, Division of Oral Biology and Medicine, School of Dentistry, UCLA, Los Angeles, CA 90095, USA
| | - Justin Wang
- Laboratory of Molecular Signaling, Division of Oral Biology and Medicine, School of Dentistry, UCLA, Los Angeles, CA 90095, USA
| | - Daniel Mishail
- Laboratory of Molecular Signaling, Division of Oral Biology and Medicine, School of Dentistry, UCLA, Los Angeles, CA 90095, USA
| | - Cun-Yu Wang
- Laboratory of Molecular Signaling, Division of Oral Biology and Medicine, School of Dentistry, UCLA, Los Angeles, CA 90095, USA
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27
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Jakopovic B, Horvatić A, Klobučar M, Gelemanović A, Grbčić P, Oršolić N, Jakopovich I, Kraljević Pavelić S. Treatment With Medicinal Mushroom Extract Mixture Inhibits Translation and Reprograms Metabolism in Advanced Colorectal Cancer Animal Model as Evidenced by Tandem Mass Tags Proteomics Analysis. Front Pharmacol 2020; 11:1202. [PMID: 32973493 PMCID: PMC7472604 DOI: 10.3389/fphar.2020.01202] [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: 05/14/2020] [Accepted: 07/23/2020] [Indexed: 01/01/2023] Open
Abstract
Colorectal cancer (CRC) is the third most frequent cancer type in both males and females, with about 35% of patients being diagnosed in stage IV metastatic disease. Despite advancements in treatment, life expectancy in patients with metastatic disease is still not satisfying. Due to frequent drug resistance during conventional and targeted cancer treatments, the development and testing of multi-target therapies is an important research field. Medicinal mushrooms specific isolated compounds as well as complex extract mixtures have been studied in depth, and many mushroom species have been proven to be non-toxic multi-target inhibitors of specific oncogenic pathways, as well as potent immunomodulators. In this study, we have performed a tandem mass tags qualitative and quantitative proteomic analyses of CT26.WT colon cancer tumor tissues from Balb/c mice treated with the studied medicinal mushroom extract mixture, with or without 5-fluorouracil. Besides significantly improved survival, obtained results reveal that Agarikon.1 alone, and in combination with 5-fluorouracil exert their anticancer effects by affecting several fundamental processes important in CRC progression. Bioinformatic analysis of up- and downregulated proteins revealed that ribosomal biogenesis and translation is downregulated in treatment groups, while the unfolded protein response (UPR), lipid metabolism and tricarboxylic acid cycle (TCA) are upregulated. Moreover, we found that many known clinical biomarkers and protein clusters important in CRC progression and prognosis are affected, which are a good basis for an expanded translational study of the herein presented treatment.
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Affiliation(s)
| | - Anita Horvatić
- Proteomics Laboratory, Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | - Marko Klobučar
- Department of Biotechnology, University of Rijeka, Rijeka, Croatia
| | | | - Petra Grbčić
- Department of Biotechnology, University of Rijeka, Rijeka, Croatia
| | - Nada Oršolić
- Division of Animal Physiology, Faculty of Science, University of Zagreb, Zagreb, Croatia
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28
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Liang S, Zhu S, Zhao Q, Yu Y, Dong H, Wang Q, Wang H, Yu S, Huang B, Han H. Molecular characterization of 60S ribosomal protein L12 of E. tenella. Exp Parasitol 2020; 217:107963. [PMID: 32781092 DOI: 10.1016/j.exppara.2020.107963] [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: 01/15/2020] [Revised: 07/22/2020] [Accepted: 07/27/2020] [Indexed: 11/17/2022]
Abstract
This study analyzed the large-subunit (60S) ribosomal protein L12 of Eimeria tenella (Et60s-RPL12). A full-length cDNA was cloned, and the recombinant protein was expressed in E. coli BL21 and inoculated in rabbits to produce the polyclonal antibody. Quantitative real-time polymerase chain reaction and western blotting were used to analyze the transcription levels of Et60s-RPL12 and translation levels in different developmental stages of E. tenella. The results showed that the mRNA transcription level of Et60s-RPL12 was highest in second-generation merozoites, whereas the translation level was highest in unsporulated oocysts. Indirect immunofluorescence showed that Et60s-RPL12 was localized to the anterior region and surface of sporozoites, except for the two refractile bodies. As the invasion of DF-1 cells progressed, fluorescence intensity was increased, and Et60s-RPL12 was localized to the parasitophorous vacuole membrane (PVM). The secretion assay results using staurosporine indicated that this protein was secreted, but not from micronemes. The role of Et60s-RPL12 in invasion was evaluated in vitro. The results of the invasion assay showed that polyclonal antibody inhibited host cell invasion by the parasite, which reached about 12%. However, the rate of invasion was not correlated with the concentration of IgG.
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Affiliation(s)
- Shanshan Liang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology of Ministry of Agriculture, Minhang, Shanghai, 200241, PR China; College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Shunhai Zhu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology of Ministry of Agriculture, Minhang, Shanghai, 200241, PR China
| | - Qiping Zhao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology of Ministry of Agriculture, Minhang, Shanghai, 200241, PR China
| | - Yu Yu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology of Ministry of Agriculture, Minhang, Shanghai, 200241, PR China; College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Hui Dong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology of Ministry of Agriculture, Minhang, Shanghai, 200241, PR China
| | - Qingjie Wang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology of Ministry of Agriculture, Minhang, Shanghai, 200241, PR China
| | - Haixia Wang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology of Ministry of Agriculture, Minhang, Shanghai, 200241, PR China
| | - Shuilan Yu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology of Ministry of Agriculture, Minhang, Shanghai, 200241, PR China
| | - Bing Huang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology of Ministry of Agriculture, Minhang, Shanghai, 200241, PR China
| | - Hongyu Han
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology of Ministry of Agriculture, Minhang, Shanghai, 200241, PR China.
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29
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Engbrecht M, Mangerich A. The Nucleolus and PARP1 in Cancer Biology. Cancers (Basel) 2020; 12:cancers12071813. [PMID: 32640701 PMCID: PMC7408768 DOI: 10.3390/cancers12071813] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 06/26/2020] [Accepted: 07/01/2020] [Indexed: 12/13/2022] Open
Abstract
The nucleolus has been known for a long time to fulfill crucial functions in ribosome biogenesis, of which cancer cells can become addicted to in order to produce sufficient amounts of proteins for cell proliferation. Recently, the nucleolus has emerged as a central regulatory hub in many other cancer-relevant processes, including stress sensing, DNA damage response, cell cycle control, and proteostasis. This fostered the idea that nucleolar processes can be exploited in cancer therapy. Interestingly, a significant proportion of poly(ADP-ribose) polymerase 1 (PARP1) molecules are localized in the nucleolus and PARP1 also plays crucial roles in many processes that are important in cancer biology, including genome maintenance, replication, transcription, and chromatin remodeling. Furthermore, during the last years, PARP1 came into focus in oncology since it represents a promising target of pharmacological PARP inhibitors in various types of cancers. Here, we provide an overview of our current understanding on the role of PARP1 in nucleolar functions and discuss potential implications in cancer biology and therapy.
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30
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Sluzalska KD, Slawski J, Sochacka M, Lampart A, Otlewski J, Zakrzewska M. Intracellular partners of fibroblast growth factors 1 and 2 - implications for functions. Cytokine Growth Factor Rev 2020; 57:93-111. [PMID: 32475760 DOI: 10.1016/j.cytogfr.2020.05.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 05/04/2020] [Accepted: 05/07/2020] [Indexed: 01/01/2023]
Abstract
Fibroblast growth factors 1 and 2 (FGF1 and FGF2) are mainly considered as ligands of surface receptors through which they regulate a broad spectrum of biological processes. They are secreted in non-canonical way and, unlike other growth factors, they are able to translocate from the endosome to the cell interior. These unique features, as well as the role of the intracellular pool of FGF1 and FGF2, are far from being fully understood. An increasing number of reports address this problem, focusing on the intracellular interactions of FGF1 and 2. Here, we summarize the current state of knowledge of the FGF1 and FGF2 binding partners inside the cell and the possible role of these interactions. The partner proteins are grouped according to their function, including proteins involved in secretion, cell signaling, nucleocytoplasmic transport, binding and processing of nucleic acids, ATP binding, and cytoskeleton assembly. An in-depth analysis of the network of these binding partners could indicate novel, non-classical functions of FGF1 and FGF2 and uncover an additional level of a fine control of the well-known FGF-regulated cellular processes.
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Affiliation(s)
- Katarzyna Dominika Sluzalska
- Department of Protein Engineering, Faculty of Biotechnology, University of Wroclaw, ul. F. Joliot-Curie 14a, 50-383 Wroclaw, Poland
| | - Jakub Slawski
- Department of Biophysics, Faculty of Biotechnology, University of Wroclaw, ul. F. Joliot-Curie 14a, 50-383 Wroclaw, Poland
| | - Martyna Sochacka
- Department of Protein Engineering, Faculty of Biotechnology, University of Wroclaw, ul. F. Joliot-Curie 14a, 50-383 Wroclaw, Poland
| | - Agata Lampart
- Department of Protein Engineering, Faculty of Biotechnology, University of Wroclaw, ul. F. Joliot-Curie 14a, 50-383 Wroclaw, Poland
| | - Jacek Otlewski
- Department of Protein Engineering, Faculty of Biotechnology, University of Wroclaw, ul. F. Joliot-Curie 14a, 50-383 Wroclaw, Poland
| | - Malgorzata Zakrzewska
- Department of Protein Engineering, Faculty of Biotechnology, University of Wroclaw, ul. F. Joliot-Curie 14a, 50-383 Wroclaw, Poland.
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31
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Gao Y, Wang Z, Zhu Y, Zhu Q, Yang Y, Jin Y, Zhang F, Jiang L, Ye Y, Li H, Zhang Y, Liang H, Xiang S, Miao H, Liu Y, Hao Y. NOP2/Sun RNA methyltransferase 2 promotes tumor progression via its interacting partner RPL6 in gallbladder carcinoma. Cancer Sci 2019; 110:3510-3519. [PMID: 31487418 PMCID: PMC6825013 DOI: 10.1111/cas.14190] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 08/27/2019] [Accepted: 08/29/2019] [Indexed: 12/31/2022] Open
Abstract
NOP2/Sun domain family, member 2 (NSUN2) is a nuclear RNA methyl-transferase catalyzing 5-methylcytosine formation. Evidence shows that NSUN2 is correlated with cell unlimited proliferation. However, its functional role in gallbladder carcinoma (GBC), which is the most common biliary tract malignancy and has a poor prognosis, remains to be determined. Here we found that NSUN2 was highly expressed in GBC tissues as well as cell lines. NSUN2 silencing repressed GBC cell proliferation and tumorigenesis both in vitro and in vivo. Conversely, upregulation of NSUN2 enhanced GBC cell growth and colony formation. We further discovered that RPL6 was a closely interacting partner with NSUN2. Silencing RPL6 resulted in insufficient NSUN2 translational level and accumulative NSUN2 transcriptional level. Exogenous expression of NSUN2 partially rescued the effect of RPL6 in gallbladder cancer progression. Taken together, our data provided novel mechanic insights into the function of NSUN2 in GBC, thus pointing to NSUN2 as a potential and effective therapeutic approach to GBC treatment.
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Affiliation(s)
- Yuan Gao
- Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, China.,Shanghai Research Center of Biliary Tract Disease, Shanghai, China
| | - Zheng Wang
- Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, China.,Shanghai Research Center of Biliary Tract Disease, Shanghai, China
| | - Yidi Zhu
- Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, China.,Shanghai Research Center of Biliary Tract Disease, Shanghai, China
| | - Qin Zhu
- Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, China.,Shanghai Research Center of Biliary Tract Disease, Shanghai, China
| | - Yang Yang
- Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, China.,Shanghai Research Center of Biliary Tract Disease, Shanghai, China
| | - Yunpeng Jin
- Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, China.,Shanghai Research Center of Biliary Tract Disease, Shanghai, China
| | - Fei Zhang
- Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, China.,Shanghai Research Center of Biliary Tract Disease, Shanghai, China
| | - Lin Jiang
- Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, China.,Shanghai Research Center of Biliary Tract Disease, Shanghai, China
| | - Yuanyuan Ye
- Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, China.,Shanghai Research Center of Biliary Tract Disease, Shanghai, China
| | - Huaifeng Li
- Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, China.,Shanghai Research Center of Biliary Tract Disease, Shanghai, China
| | - Yichi Zhang
- Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, China.,Shanghai Research Center of Biliary Tract Disease, Shanghai, China
| | - Haibin Liang
- Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, China.,Shanghai Research Center of Biliary Tract Disease, Shanghai, China
| | - Shanshan Xiang
- Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, China.,Shanghai Research Center of Biliary Tract Disease, Shanghai, China
| | - Huijie Miao
- Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, China.,Shanghai Research Center of Biliary Tract Disease, Shanghai, China
| | - Yingbin Liu
- Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, China.,Shanghai Research Center of Biliary Tract Disease, Shanghai, China
| | - Yajuan Hao
- Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, China.,Shanghai Research Center of Biliary Tract Disease, Shanghai, China
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