1
|
Banerjee A, Ataman M, Smialek MJ, Mookherjee D, Rabl J, Mironov A, Mues L, Enkler L, Coto-Llerena M, Schmidt A, Boehringer D, Piscuoglio S, Spang A, Mittal N, Zavolan M. Ribosomal protein RPL39L is an efficiency factor in the cotranslational folding of a subset of proteins with alpha helical domains. Nucleic Acids Res 2024; 52:9028-9048. [PMID: 39041433 PMCID: PMC11347166 DOI: 10.1093/nar/gkae630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 07/05/2024] [Indexed: 07/24/2024] Open
Abstract
Increasingly many studies reveal how ribosome composition can be tuned to optimally translate the transcriptome of individual cell types. In this study, we investigated the expression pattern, structure within the ribosome and effect on protein synthesis of the ribosomal protein paralog 39L (RPL39L). With a novel mass spectrometric approach we revealed the expression of RPL39L protein beyond mouse germ cells, in human pluripotent cells, cancer cell lines and tissue samples. We generated RPL39L knock-out mouse embryonic stem cell (mESC) lines and demonstrated that RPL39L impacts the dynamics of translation, to support the pluripotency and differentiation, spontaneous and along the germ cell lineage. Most differences in protein abundance between WT and RPL39L KO lines were explained by widespread autophagy. By CryoEM analysis of purified RPL39 and RPL39L-containing ribosomes we found that, unlike RPL39, RPL39L has two distinct conformations in the exposed segment of the nascent peptide exit tunnel, creating a distinct hydrophobic patch that has been predicted to support the efficient co-translational folding of alpha helices. Our study shows that ribosomal protein paralogs provide switchable modular components that can tune translation to the protein production needs of individual cell types.
Collapse
Affiliation(s)
| | - Meric Ataman
- Biozentrum, University of Basel, Basel, Switzerland
| | - Maciej Jerzy Smialek
- Biozentrum, University of Basel, Basel, Switzerland
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | | | - Julius Rabl
- Cryo-EM Knowledge Hub (CEMK), ETH Zürich, Switzerland
| | | | - Lea Mues
- Biozentrum, University of Basel, Basel, Switzerland
| | - Ludovic Enkler
- Biozentrum, University of Basel, Basel, Switzerland
- University of Strasbourg, UMR7156 GMGM, Strasbourg, France
| | - Mairene Coto-Llerena
- Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Switzerland
| | | | | | - Salvatore Piscuoglio
- Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Switzerland
- IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | - Anne Spang
- Biozentrum, University of Basel, Basel, Switzerland
| | | | | |
Collapse
|
2
|
Miller SC, MacDonald CC, Kellogg MK, Karamysheva ZN, Karamyshev AL. Specialized Ribosomes in Health and Disease. Int J Mol Sci 2023; 24:ijms24076334. [PMID: 37047306 PMCID: PMC10093926 DOI: 10.3390/ijms24076334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/21/2023] [Accepted: 03/23/2023] [Indexed: 03/30/2023] Open
Abstract
Ribosomal heterogeneity exists within cells and between different cell types, at specific developmental stages, and occurs in response to environmental stimuli. Mounting evidence supports the existence of specialized ribosomes, or specific changes to the ribosome that regulate the translation of a specific group of transcripts. These alterations have been shown to affect the affinity of ribosomes for certain mRNAs or change the cotranslational folding of nascent polypeptides at the exit tunnel. The identification of specialized ribosomes requires evidence of the incorporation of different ribosomal proteins or of modifications to rRNA and/or protein that lead(s) to physiologically relevant changes in translation. In this review, we summarize ribosomal heterogeneity and specialization in mammals and discuss their relevance to several human diseases.
Collapse
Affiliation(s)
- Sarah C. Miller
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Clinton C. MacDonald
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Morgana K. Kellogg
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | | | - Andrey L. Karamyshev
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
- Correspondence: ; Tel.: +1-806-743-4102
| |
Collapse
|
3
|
Wei X, Hu W, Mao K. A methylomics-associated nomogram predicts the overall survival risk of stage III to IV ovarian cancer. Medicine (Baltimore) 2023; 102:e32766. [PMID: 36749233 PMCID: PMC9901957 DOI: 10.1097/md.0000000000032766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 01/05/2023] [Indexed: 02/08/2023] Open
Abstract
Accumulating studies demonstrated that DNA methylation may be potential prognostic hallmarks of various cancers. However, few studies have focused on the power of DNA methylation for prognostic prediction in patients with stage III to IV ovarian cancer (OC). Therefore, constructing a methylomics-related indicator to predict overall survival (OS) of stage III to IV OC was urgently required. A total of 520 OC patients with 485,577 DNA methylation sites from TCGA database were selected to develop a robust DNA methylation signature. The 520 patients were clustered into a training group (70%, n = 364 samples) and an internal validation group (30%, n = 156). The training group was used for digging a prognostic predictor based on univariate Cox proportional hazard analysis, least absolute shrinkage and selection operator (LASSO) as well as multivariate Cox regression analysis. The internal and external validation group (ICGC OV-AU project) were used for validating the predictive robustness of the predictor based on receiver operating characteristic (ROC) analysis and Kaplan-Meier survival analysis. We identified a 21-DNA methylation signature-based classifier for stage III-IV OC patients' OS. According to ROC analysis in the internal validation, external validation and entire TCGA set, we proved the high power of the 21-DNA methylation signature for predicting OS (area under the curve [AUC] at 1, 3, 5 years in internal validation set (0.782, 0.739, 0.777, respectively), external validation set (0.828, 0.760, 0.741, respectively), entire TCGA set (0.741, 0.748, 0.781, respectively). Besides, a nomogram was developed via methylation risk score as well as a few clinical variables, and the result showed a high ability of the predictive nomogram. In summary, we used integrated bioinformatics approaches to successfully identified a DNA methylation-associated nomogram, which can predict effectively the OS of patients with stage III to IV OC.
Collapse
Affiliation(s)
- Xuan Wei
- Department of Gynaecology, Taikang Tongji (Wuhan) Hospital, Wuhan, China
| | - Wencheng Hu
- Department of Gynaecology, Taikang Tongji (Wuhan) Hospital, Wuhan, China
| | - Kexi Mao
- Department of Emergency, Taikang Tongji (Wuhan) Hospital, Wuhan, China
| |
Collapse
|
4
|
Zhu D, Chen J, Hou T. Development and Validation of a Prognostic Model of RNA-Binding Proteins in Colon Adenocarcinoma: A Study Based on TCGA and GEO Databases. Cancer Manag Res 2021; 13:7709-7722. [PMID: 34675667 PMCID: PMC8517423 DOI: 10.2147/cmar.s330434] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 09/20/2021] [Indexed: 12/24/2022] Open
Abstract
Background Previous studies reported that dysregulation of RNA-binding proteins (RBPs) is significantly associated with the development of cancer. However, there are few studies to date on the role of RBPs in colon adenocarcinoma (COAD). Methods RNA sequencing and clinical data for COAD patients were downloaded from The Cancer Genome Atlas (TCGA) database to identify differentially expressed (DE) RBPs between COAD tissue and normal colon tissue, and then the expression and prognostic significance of these RBPs were investigated in detail by systematic bioinformatics analysis. qRT-PCR was used to validate the expressions of prognosis-related RBP-encoding genes. Results Seven RBPs (RPL10L, ERI1, POP1, CAPRIN2, TDRD7, SNIP1 and PPARGC1A) were identified as hub genes associated with prognosis by a series of regression analyses, and were then used to construct a prognostic model. Further analysis based on this model indicated that the overall survival (OS) of the high-risk groups was lower than that of the low-risk groups. In this prognostic model, the area under the ROC curve (AUC) was 0.694, 0.709 and 0.665 for the TCGA cohort at 1, 3 and 5 years, respectively, while the AUC was 0.671, 0.633 and 0.601 for the GEO combined cohort at 1, 3 and 5 years, respectively, indicating the good predictive ability of the model. We also built a nomogram based on the 7 RBPs in the TCGA cohort, and the model showed good discriminatory ability for COAD. Conclusion We screened seven prognosis-related genes in COAD patients based on RBP-related genes, validated the expressions of the seven prognosis-related RBP-encoding genes by qRT-PCR and constructed a prognosis-related nomogram for patients with COAD.
Collapse
Affiliation(s)
- Dandan Zhu
- School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510006, People's Republic of China.,Department of Laboratory Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, 510080, People's Republic of China
| | - Jierong Chen
- Department of Laboratory Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, 510080, People's Republic of China
| | - Tieying Hou
- School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510006, People's Republic of China.,Department of Laboratory Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, 510080, People's Republic of China
| |
Collapse
|
5
|
Paul N, Kumaresan A, Das Gupta M, Nag P, Guvvala PR, Kuntareddi C, Sharma A, Selvaraju S, Datta TK. Transcriptomic Profiling of Buffalo Spermatozoa Reveals Dysregulation of Functionally Relevant mRNAs in Low-Fertile Bulls. Front Vet Sci 2021; 7:609518. [PMID: 33506000 PMCID: PMC7829312 DOI: 10.3389/fvets.2020.609518] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 11/13/2020] [Indexed: 12/12/2022] Open
Abstract
Although, it is known that spermatozoa harbor a variety of RNAs that may influence embryonic development, little is understood about sperm transcriptomic differences in relation to fertility, especially in buffaloes. In the present study, we compared the differences in sperm functional attributes and transcriptomic profile between high- and low-fertile buffalo bulls. Sperm membrane and acrosomal integrity were lower (P < 0.05), while protamine deficiency and lipid peroxidation were higher (P < 0.05) in low- compared to high-fertile bulls. Transcriptomic analysis using mRNA microarray technology detected a total of 51,282 transcripts in buffalo spermatozoa, of which 4,050 transcripts were differentially expressed, and 709 transcripts were found to be significantly dysregulated (P < 0.05 and fold change >1) between high- and low-fertile bulls. Majority of the dysregulated transcripts were related to binding activity, transcription, translation, and metabolic processes with primary localization in the cell nucleus, nucleoplasm, and in cytosol. Pathways related to MAPK signaling, ribosome pathway, and oxidative phosphorylation were dysregulated in low-fertile bull spermatozoa. Using bioinformatics analysis, we observed that several genes related to sperm functional attributes were significantly downregulated in low-fertile bull spermatozoa. Validation of the results of microarray analysis was carried out using real-time qPCR expression analysis of selected genes (YBX1, ORAI3, and TFAP2C). The relative expression of these genes followed the same trend in both the techniques. Collectively, this is the first study to report the transcriptomic profile of buffalo spermatozoa and to demonstrate the dysregulation of functionally relevant transcripts in low-fertile bull spermatozoa. The results of the present study open up new avenues for understanding the etiology for poor fertility in buffalo bulls and to identify fertility biomarkers.
Collapse
Affiliation(s)
- Nilendu Paul
- Theriogenology Laboratory, Veterinary Gynaecology and Obstetrics, Southern Regional Station of ICAR - National Dairy Research Institute, Bengaluru, India
| | - Arumugam Kumaresan
- Theriogenology Laboratory, Veterinary Gynaecology and Obstetrics, Southern Regional Station of ICAR - National Dairy Research Institute, Bengaluru, India
| | - Mohua Das Gupta
- Theriogenology Laboratory, Veterinary Gynaecology and Obstetrics, Southern Regional Station of ICAR - National Dairy Research Institute, Bengaluru, India
| | - Pradeep Nag
- Theriogenology Laboratory, Veterinary Gynaecology and Obstetrics, Southern Regional Station of ICAR - National Dairy Research Institute, Bengaluru, India
| | - Pushpa Rani Guvvala
- Reproductive Physiology Laboratory, ICAR - National Institute of Animal Nutrition and Physiology, Bengaluru, India
| | - Channareddi Kuntareddi
- Theriogenology Laboratory, Veterinary Gynaecology and Obstetrics, Southern Regional Station of ICAR - National Dairy Research Institute, Bengaluru, India
| | - Ankur Sharma
- Theriogenology Laboratory, Veterinary Gynaecology and Obstetrics, Southern Regional Station of ICAR - National Dairy Research Institute, Bengaluru, India
| | - Sellappan Selvaraju
- Reproductive Physiology Laboratory, ICAR - National Institute of Animal Nutrition and Physiology, Bengaluru, India
| | - Tirtha Kumar Datta
- Animal Genomics Laboratory, ICAR - National Dairy Research Institute, Karnal, India
| |
Collapse
|
6
|
Liu J, Li R, Liao X, Jiang W. Comprehensive Bioinformatic Analysis Genes Associated to the Prognosis of Liposarcoma. Med Sci Monit 2018; 24:7329-7339. [PMID: 30317246 PMCID: PMC6198710 DOI: 10.12659/msm.913043] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Liposarcoma is the most common type of soft tissue sarcoma, but its molecular mechanism is poorly defined. This study aimed to identify genes crucial to the pathogenesis of liposarcoma and to explore their functions, related pathways, and prognostic value. MATERIAL AND METHODS Differentially expressed genes (DEGs) in the GSE59568 dataset were screened. Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were conducted to investigate the DEGs at the functional level. Protein-protein interaction (PPI) networks and module analysis were applied to identify hub genes from among the DEGs. The GSE30929 dataset was used to validate the relationship between hub genes and the distant recurrence-free survival (DRFS) of liposarcoma patients using Cox model analysis. RESULTS A total of 1111 DEGs were identified. GO and KEGG pathway analysis indicated that the DEGs were mainly associated with lipopolysaccharides and pathways in cancer. The PPI network and module analysis identified 10 hub genes from the DEG network. The Cox model identified 3 genes (NIP7, RPL10L, and MCM2) significantly associated with DRFS. The risk score calculated by the Cox model of the NIP7-RPL10L-MCM2 signature could largely predict the 1-, 3-, and 5-year DRFS of liposarcoma patients, and the prognostic value was even higher for subtypes of liposarcoma. CONCLUSIONS This study identified genes that might play critical roles in liposarcoma pathogenesis as well as a 3-gene-based signature that could be used as a candidate prognostic biomarker for patients with liposarcoma.
Collapse
Affiliation(s)
- Jianwei Liu
- Department of Osteology, The Third Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China (mainland)
| | - Rong Li
- Department of Osteology, The Third Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China (mainland)
| | - Xiwen Liao
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China (mainland)
| | - Weiping Jiang
- Department of Osteology, The Third Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China (mainland)
| |
Collapse
|
7
|
Ma T, Lu C, Guo Y, Zhang C, Du X. Human U3 protein 14a plays an anti-apoptotic role in cancer cells. Biol Chem 2017; 398:1247-1257. [PMID: 28672776 DOI: 10.1515/hsz-2017-0121] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 06/21/2017] [Indexed: 01/21/2023]
Abstract
Human U three protein 14a (hUTP14a) binds p53 and promotes p53 degradation. Here, we report that hUTP14a plays an anti-apoptotic role in tumor cells through a p53-independent pathway. Knockdown of hUTP14a activated the intrinsic pathway of apoptosis and sensitized tumor cells to chemotherapeutic drug-induced apoptosis. In addition, the protein level of hUTP14a decreased upon chemotherapeutic drug- or irradiation-induced apoptosis. Importantly, the decrease of hUTP14a during induced apoptosis was not blocked by pan-caspase inhibitor z-VAD-FMK, indicating that the down-regulation of hUTP14a is an upstream event in apoptosis. Furthermore, ectopically expressed hUTP14a protected tumor cells from chemotherapeutic drug-induced apoptosis. In summary, our data showed that hUTP14a protected tumor cells from chemotherapeutic drug-induced apoptosis and thus might possess a potential as a target for anti-tumor therapy.
Collapse
|
8
|
Rohozinski J, Diaz-Arrastia C, Edwards CL. Do some epithelial ovarian cancers originate from a fallopian tube ciliate cell lineage? Med Hypotheses 2017; 107:16-21. [DOI: 10.1016/j.mehy.2017.07.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 07/10/2017] [Accepted: 07/15/2017] [Indexed: 01/16/2023]
|
9
|
Burton LJ, Rivera M, Hawsawi O, Zou J, Hudson T, Wang G, Zhang Q, Cubano L, Boukli N, Odero-Marah V. Muscadine Grape Skin Extract Induces an Unfolded Protein Response-Mediated Autophagy in Prostate Cancer Cells: A TMT-Based Quantitative Proteomic Analysis. PLoS One 2016; 11:e0164115. [PMID: 27755556 PMCID: PMC5068743 DOI: 10.1371/journal.pone.0164115] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 09/19/2016] [Indexed: 01/06/2023] Open
Abstract
Muscadine grape skin extract (MSKE) is derived from muscadine grape (Vitis rotundifolia), a common red grape used to produce red wine. Endoplasmic reticulum (ER) stress activates the unfolded protein response (UPR) that serves as a survival mechanism to relieve ER stress and restore ER homeostasis. However, when persistent, ER stress can alter the cytoprotective functions of the UPR to promote autophagy and cell death. Although MSKE has been documented to induce apoptosis, it has not been linked to ER stress/UPR/autophagy. We hypothesized that MSKE may induce a severe ER stress response-mediated autophagy leading to apoptosis. As a model, we treated C4-2 prostate cancer cells with MSKE and performed a quantitative Tandem Mass Tag Isobaric Labeling proteomic analysis. ER stress response, autophagy and apoptosis were analyzed by western blot, acridine orange and TUNEL/Annexin V staining, respectively. Quantitative proteomics analysis indicated that ER stress response proteins, such as GRP78 were greatly elevated following treatment with MSKE. The up-regulation of pro-apoptotic markers PARP, caspase-12, cleaved caspase-3, -7, BAX and down-regulation of anti-apoptotic marker BCL2 was confirmed by Western blot analysis and apoptosis was visualized by increased TUNEL/Annexin V staining upon MSKE treatment. Moreover, increased acridine orange, and LC3B staining was detected in MSKE-treated cells, suggesting an ER stress/autophagy response. Finally, MSKE-mediated autophagy and apoptosis was antagonized by co-treatment with chloroquine, an autophagy inhibitor. Our results indicate that MSKE can elicit an UPR that can eventually lead to apoptosis in prostate cancer cells.
Collapse
Affiliation(s)
- Liza J. Burton
- Center for Cancer Research and Therapeutic Development, Department of Biological Sciences, Clark Atlanta University, Atlanta, GA, 30314, United States of America
| | - Mariela Rivera
- Department of Microbiology and Immunology, School of Medicine, Universidad Central del Caribe, Bayamon, PR, 00956, United States of America
| | - Ohuod Hawsawi
- Center for Cancer Research and Therapeutic Development, Department of Biological Sciences, Clark Atlanta University, Atlanta, GA, 30314, United States of America
| | - Jin Zou
- Center for Cancer Research and Therapeutic Development, Department of Biological Sciences, Clark Atlanta University, Atlanta, GA, 30314, United States of America
| | - Tamaro Hudson
- Department of Medicine, Howard University, Washington, DC, 20060, United States of America
| | - Guangdi Wang
- Department of Chemistry, Xavier University, New Orleans, LA, 70125, United States of America
| | - Qiang Zhang
- Department of Chemistry, Xavier University, New Orleans, LA, 70125, United States of America
| | - Luis Cubano
- Department of Microbiology and Immunology, School of Medicine, Universidad Central del Caribe, Bayamon, PR, 00956, United States of America
| | - Nawal Boukli
- Department of Microbiology and Immunology, School of Medicine, Universidad Central del Caribe, Bayamon, PR, 00956, United States of America
| | - Valerie Odero-Marah
- Center for Cancer Research and Therapeutic Development, Department of Biological Sciences, Clark Atlanta University, Atlanta, GA, 30314, United States of America
- * E-mail:
| |
Collapse
|
10
|
Ansari-Pour N, Razaghi-Moghadam Z, Barneh F, Jafari M. Testis-Specific Y-Centric Protein-Protein Interaction Network Provides Clues to the Etiology of Severe Spermatogenic Failure. J Proteome Res 2016; 15:1011-22. [PMID: 26794825 DOI: 10.1021/acs.jproteome.5b01080] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Pinpointing causal genes for spermatogenic failure (SpF) on the Y chromosome has been an ever daunting challenge with setbacks during the past decade. Since complex diseases result from the interaction of multiple genes and also display considerable missing heritability, network analysis is more likely to explicate an etiological molecular basis. We therefore took a network medicine approach by integrating interactome (protein-protein interaction (PPI)) and transcriptome data to reconstruct a Y-centric SpF network. Two sets of seed genes (Y genes and SpF-implicated genes (SIGs)) were used for network reconstruction. Since no PPI was observed among Y genes, we identified their common immediate interactors. Interestingly, 81% (N = 175) of these interactors not only interacted directly with SIGs, but also they were enriched for differentially expressed genes (89.6%; N = 43). The SpF network, formed mainly by the dys-regulated interactors and the two seed gene sets, comprised three modules enriched for ribosomal proteins and nuclear receptors for sex hormones. Ribosomal proteins generally showed significant dys-regulation with RPL39L, thought to be expressed at the onset of spermatogenesis, strongly down-regulated. This network is the first global PPI network pertaining to severe SpF and if experimentally validated on independent data sets can lead to more accurate diagnosis and potential fertility recovery of patients.
Collapse
Affiliation(s)
- Naser Ansari-Pour
- Faculty of New Sciences and Technology, University of Tehran , North Kargar Street, Tehran 143995-7131, Iran.,School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM) , Tehran 19395-5531, Iran
| | - Zahra Razaghi-Moghadam
- Faculty of New Sciences and Technology, University of Tehran , North Kargar Street, Tehran 143995-7131, Iran.,School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM) , Tehran 19395-5531, Iran
| | - Farnaz Barneh
- Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences , Tehran 198396-3113, Iran
| | - Mohieddin Jafari
- Drug Design and Bioinformatics Unit, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran , Tehran 131694-3551, Iran.,School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM) , Tehran 19395-5531, Iran
| |
Collapse
|
11
|
Kamien B, Digilio MC, Novelli A, O'Donnell S, Bain N, Meldrum C, Dudding-Byth T, Scott RJ, Goel H. Narrowing the critical region for overgrowth within 13q14.2-q14.3 microdeletions. Eur J Med Genet 2015; 58:629-33. [PMID: 26475974 DOI: 10.1016/j.ejmg.2015.10.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 08/30/2015] [Accepted: 10/07/2015] [Indexed: 10/22/2022]
Abstract
Large chromosomal deletions from 13q13.3 to 13q21.3 have previously been associated with overgrowth. We present two patients with deletions at 13q14.2q14.3 who have macrocephaly, tall stature relative to their parents, cardiac phenotypes, and intellectual disability. This report narrows the critical region for tall stature, macrocephaly, and possibly cardiac disease.
Collapse
Affiliation(s)
- Benjamin Kamien
- Hunter Genetics, Newcastle, New South Wales, Australia; The University of Newcastle, School of Medicine and Public Health, Newcastle, New South Wales, Australia; The University of Newcastle, School of Biomedical Sciences and Pharmacy, Newcastle, New South Wales, Australia.
| | - M Cristina Digilio
- Department of Medical Genetics, Bambino Gesù Pediatric Hospital, IRCCS, Rome, Italy
| | - Antonio Novelli
- Laboratory of Medical Genetics, Bambino Gesù Pediatric Hospital, IRCCS, Rome, Italy
| | | | - Nicole Bain
- Molecular Medicine, Pathology North, Newcastle, New South Wales, Australia
| | - Cliff Meldrum
- Molecular Medicine, Pathology North, Newcastle, New South Wales, Australia
| | - Tracy Dudding-Byth
- Hunter Genetics, Newcastle, New South Wales, Australia; The University of Newcastle, School of Medicine and Public Health, Newcastle, New South Wales, Australia
| | - Rodney J Scott
- The University of Newcastle, School of Biomedical Sciences and Pharmacy, Newcastle, New South Wales, Australia; Molecular Medicine, Pathology North, Newcastle, New South Wales, Australia
| | - Himanshu Goel
- Hunter Genetics, Newcastle, New South Wales, Australia; The University of Newcastle, School of Medicine and Public Health, Newcastle, New South Wales, Australia
| |
Collapse
|
12
|
Habibi L, Pedram M, AmirPhirozy A, Bonyadi K. Mobile DNA Elements: The Seeds of Organic Complexity on Earth. DNA Cell Biol 2015. [DOI: 10.1089/dna.2015.2938] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Laleh Habibi
- Department of Pharmaceutics, School of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
- Cellular and Molecular Nutrition Department, School of Nutritional Science and Dietetics, Tehran University of Medical Sciences, Tehran, Iran
| | - Mehrdad Pedram
- Department of Genetics and Molecular Medicine, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Akbar AmirPhirozy
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Khadijeh Bonyadi
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| |
Collapse
|
13
|
Sondalle SB, Baserga SJ. Human diseases of the SSU processome. BIOCHIMICA ET BIOPHYSICA ACTA 2014; 1842:758-64. [PMID: 24240090 PMCID: PMC4058823 DOI: 10.1016/j.bbadis.2013.11.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 10/31/2013] [Accepted: 11/05/2013] [Indexed: 12/18/2022]
Abstract
Ribosomes are the cellular machines responsible for protein synthesis. Ribosome biogenesis, the production of ribosomes, is a complex process involving pre-ribosomal RNA (rRNA) cleavages and modifications as well as ribosomal protein assembly around the rRNAs to create the functional ribosome. The small subunit (SSU) processome is a large ribonucleoprotein (RNP) in eukaryotes required for the assembly of the SSU of the ribosome as well as for the maturation of the 18S rRNA. Despite the fundamental nature of the SSU processome to the survival of any eukaryotic cell, mutations in SSU processome components have been implicated in human diseases. Three SSU processome components and their related human diseases will be explored in this review: hUTP4/Cirhin, implicated in North American Indian childhood cirrhosis (NAIC); UTP14, implicated in infertility, ovarian cancer, and scleroderma; and EMG1, implicated in Bowen-Conradi syndrome (BCS). Diseases with suggestive, though inconclusive, evidence for the involvement of the SSU processome in their pathogenesis are also discussed, including a novel putative ribosomopathy. This article is part of a Special Issue entitled: Role of the Nucleolus in Human Disease.
Collapse
Affiliation(s)
- Samuel B Sondalle
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA.
| | - Susan J Baserga
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA.
| |
Collapse
|
14
|
Kim JJ, Rajagopalan K, Hussain B, Williams BH, Kulkarni P, Mooney SM. CETN1 is a cancer testis antigen with expression in prostate and pancreatic cancers. Biomark Res 2013; 1:22. [PMID: 24252580 PMCID: PMC4177615 DOI: 10.1186/2050-7771-1-22] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2013] [Accepted: 06/03/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Cancer Testis Antigens (CTAs) are a group of genes that are highly expressed in the normal testis and several types of cancer. Due to their restricted expression in normal adult tissues, CTAs have been attractive targets for immunotherapy and biomarker development. In this work, we discovered that Centrin 1 (CETN1) which is found in the centrosome of all eukaryotes, may be a member of this group and is highly expressed in prostate and pancreatic cancer. Three members of the centrin family of calcium binding proteins (CETN) are localized to the centrosome in all eukaryotes with CDC31 being the sole yeast homolog. CETN1 is a retrogene that probably arose from a retrotransposition of CETN2, an X-linked gene. A previous mouse study shows that CETN1 is expressed solely in the testis, while CETN2 is expressed in all organs. RESULTS In this work, we show that CETN1 is a new member of the growing group of CTAs. Through the mining of publicly available microarray data, we discovered that human CETN1 expression but not CETN2 or CETN3 is restricted to the testis. In fact, CETN1 is actually down-regulated in testicular malignancies compared to normal testis. Using q-PCR, CETN1 expression is shown to be highly up-regulated in cancer of the prostate and in pancreatic xenografts. Unexpectedly however, CETN1 expression was virtually absent in various cell lines until they were treated with the DNA demethylation agent 5'AZA-2'Deoxycytidine (AZA) but showed no increased expression upon incubation with Histone deacetylase inhibitor Trichostatin-A (TSA) alone. Additionally, like most CTAs, CETN1 appears to be an intrinsically disordered protein which implies that it may occupy a hub position in key protein interaction networks in cancer. Neither CETN1 nor CETN2 could compensate for loss of CDC31 expression in yeast which is analogous to published data for CETN3. CONCLUSIONS This work suggests that CETN1 is a novel CTA with expression in cancer of the prostate and pancreas. In cell lines, the expression is probably regulated by promoter methylation, while the method of regulation in normal adult tissues remains unknown.
Collapse
Affiliation(s)
- John J Kim
- Department of Urology, James Buchanan Brady Urological Institute, The Johns Hopkins University, School of Medicine, Baltimore, MD, 21287, USA.
| | | | | | | | | | | |
Collapse
|
15
|
Vijayaraghavalu S, Dermawan JK, Cheriyath V, Labhasetwar V. Highly synergistic effect of sequential treatment with epigenetic and anticancer drugs to overcome drug resistance in breast cancer cells is mediated via activation of p21 gene expression leading to G2/M cycle arrest. Mol Pharm 2012; 10:337-52. [PMID: 23215027 DOI: 10.1021/mp3004622] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Epigenetic alterations such as aberrant DNA methylation and histone modifications contribute substantially to both the cause and maintenance of drug resistance. These epigenetic changes lead to silencing of tumor suppressor genes involved in key DNA damage-response pathways, making drug-resistant cancer cells nonresponsive to conventional anticancer drug therapies. Our hypothesis is that treating drug-resistant cells with epigenetic drugs could restore the sensitivity to anticancer drugs by reactivating previously silenced genes. To test our hypothesis, we used drug-resistant breast cancer cells (MCF-7/ADR) and two epigenetic drugs that act via different mechanisms--5-aza-2'-deoxycytidine (decitabine, DAC), a demethylating agent, and suberoylanilide hydroxamic acid (SAHA), a histone deacetylase inhibitor--in combination with doxorubicin. We show that the sequential treatment of resistant cells, first with an epigenetic drug (DAC), and then with doxorubicin, induces a highly synergistic effect, thus reducing the IC(50) of doxorubicin by several thousand fold. The sequential treatment caused over 90% resistant cells to undergo G2/M cell cycle arrest, determined to be due to upregulation of p21(WAF1/CIP1) expression, which is responsible for cell-cycle regulation. The induction of p21(WAF1/CIP1) correlated well with the depletion of DNA methyltransferase1 (DNMT1), an enzyme that promotes methylation of DNA, suggesting that the p21(WAF1/CIP1) gene may have been methylated and hence is inactive in MCF-7/ADR cells. Microarray analysis shows expression of several tumor suppressor genes and downregulation of tumor promoter genes, particularly in sequentially treated resistant cells. Sequential treatment was found to be significantly more effective than simultaneous treatment, and DAC was more effective than SAHA in overcoming doxorubicin resistance. Synergistic effect with sequential treatment was also seen in drug-sensitive breast cancer cells, but the effect was significantly more pronounced in resistant cells. In conclusion, the sequential treatment of an epigenetic drug in combination with doxorubicin induces a highly synergistic effect that overcomes doxorubicin resistance in breast cancer cells.
Collapse
Affiliation(s)
- Sivakumar Vijayaraghavalu
- Department of Biomedical Engineering, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, United States
| | | | | | | |
Collapse
|
16
|
Rohozinski J, Edwards CL, Anderson ML. Does expression of the retrogene UTP14c in the ovary pre-dispose women to ovarian cancer? Med Hypotheses 2012; 78:446-9. [PMID: 22285623 DOI: 10.1016/j.mehy.2011.12.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Revised: 12/15/2011] [Accepted: 12/23/2011] [Indexed: 12/16/2022]
Abstract
It has been previously shown that the spermatogenesis associated retrogene, UTP14c, is expressed in over 50% of normal human ovaries and 80% of ovarian cancers. UTP14c is located on chromosome 13 as an intronless copy of the X-linked housekeeping gene, UTP14a. Like all spermatogenesis associated retrogenes, UTP14c is expressed in the testis and is essential for sperm production. It has no known role in the female and is not normally expressed in any cells or organs outside of the gonads. By comparison the protein encoded by UTP14a is found in all cell types and has a dual function. It is primarily involved in the biosynthesis of 18S ribosomal RNA in the nucleolus where it is a component of the U3 small nucleolar RNA associated protein complex. In addition, it down regulates TP53 in both the nucleus and cytoplasm by targeting it for proteolytic degradation. By analogy, we propose that the UTP14c peptide also targets TP53 for degradation. This in turn may prevent cells expressing UTP14c from entering apoptosis. The loss of TP53 in ovarian cells can also result in the down regulation of microRNA-145 (miR-145) expression. The loss of miR-145 can result in the activation of factors that promote oncogenesis and cellular pluripotency which in turn could lead to the development of ovarian cancer. We hypothesize that women, whose ovaries express UTP14c, are predisposed to ovarian cancer due to the disruption of protective signals that normally trigger TP53-mediated apoptosis and the dysregulation of genes that promote oncogenesis, such as c-Myc, that occurs when miR-145 synthesis is disrupted.
Collapse
Affiliation(s)
- Jan Rohozinski
- Institute for Regenerative Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA.
| | | | | |
Collapse
|
17
|
Wang Y, Wang D, Ren F, Zhang Y, Lin F, Hou N, Cheng X, Zhang P, Wang Y, Jia B, Yang X, Chang Z. Generation of mice with conditional null allele for GdX/Ubl4A. Genesis 2012; 50:534-42. [PMID: 22139977 DOI: 10.1002/dvg.20832] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Revised: 10/26/2011] [Accepted: 11/23/2011] [Indexed: 11/12/2022]
Abstract
GdX (also named Ubl4A) is a house-keeping gene located on the X chromosome and encodes a protein harboring an ubiquitin-like domain in human and mouse. Although identified in 1988, the function of GdX remains unknown. To elucidate the role of GdX in vivo, we generated a conditional GdX knockout mouse in which Exon 2 was flanked by two loxP sites. We obtained viable and fertile mice with homozygous GdX(flox/flox) or GdX(flox/Y) allele. Germ-line transmission was confirmed by crossing the mouse bearing conditionally targeted allele with an EIIα-Cre transgenic mouse. GdX was successfully depleted in tissues of EIIα-Cre-GdX-null mice. GdX(-/-) and GdX(-/Y) mice are viable and exhibit normal development compared with wild-type littermates within 6 months during our observation. We also observed that GdX knockout male mice were functionally normal in the reproductive system where Ubl4B was specifically expressed. GdX(flox/flox) and GdX(flox/Y) conditional mice provide a tool for further tissue-specific function analysis of the GdX protein under different conditions.
Collapse
Affiliation(s)
- Yangmeng Wang
- State Key Laboratory of Biomembrane and Membrane Biotechnology, School of Medicine, Tsinghua University, Beijing, China
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Serão NVL, Delfino KR, Southey BR, Beever JE, Rodriguez-Zas SL. Cell cycle and aging, morphogenesis, and response to stimuli genes are individualized biomarkers of glioblastoma progression and survival. BMC Med Genomics 2011; 4:49. [PMID: 21649900 PMCID: PMC3127972 DOI: 10.1186/1755-8794-4-49] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Accepted: 06/07/2011] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Glioblastoma is a complex multifactorial disorder that has swift and devastating consequences. Few genes have been consistently identified as prognostic biomarkers of glioblastoma survival. The goal of this study was to identify general and clinical-dependent biomarker genes and biological processes of three complementary events: lifetime, overall and progression-free glioblastoma survival. METHODS A novel analytical strategy was developed to identify general associations between the biomarkers and glioblastoma, and associations that depend on cohort groups, such as race, gender, and therapy. Gene network inference, cross-validation and functional analyses further supported the identified biomarkers. RESULTS A total of 61, 47 and 60 gene expression profiles were significantly associated with lifetime, overall, and progression-free survival, respectively. The vast majority of these genes have been previously reported to be associated with glioblastoma (35, 24, and 35 genes, respectively) or with other cancers (10, 19, and 15 genes, respectively) and the rest (16, 4, and 10 genes, respectively) are novel associations. Pik3r1, E2f3, Akr1c3, Csf1, Jag2, Plcg1, Rpl37a, Sod2, Topors, Hras, Mdm2, Camk2g, Fstl1, Il13ra1, Mtap and Tp53 were associated with multiple survival events.Most genes (from 90 to 96%) were associated with survival in a general or cohort-independent manner and thus the same trend is observed across all clinical levels studied. The most extreme associations between profiles and survival were observed for Syne1, Pdcd4, Ighg1, Tgfa, Pla2g7, and Paics. Several genes were found to have a cohort-dependent association with survival and these associations are the basis for individualized prognostic and gene-based therapies. C2, Egfr, Prkcb, Igf2bp3, and Gdf10 had gender-dependent associations; Sox10, Rps20, Rab31, and Vav3 had race-dependent associations; Chi3l1, Prkcb, Polr2d, and Apool had therapy-dependent associations. Biological processes associated glioblastoma survival included morphogenesis, cell cycle, aging, response to stimuli, and programmed cell death. CONCLUSIONS Known biomarkers of glioblastoma survival were confirmed, and new general and clinical-dependent gene profiles were uncovered. The comparison of biomarkers across glioblastoma phases and functional analyses offered insights into the role of genes. These findings support the development of more accurate and personalized prognostic tools and gene-based therapies that improve the survival and quality of life of individuals afflicted by glioblastoma multiforme.
Collapse
Affiliation(s)
- Nicola VL Serão
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Kristin R Delfino
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Bruce R Southey
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Jonathan E Beever
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Sandra L Rodriguez-Zas
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Statistics, University of Illinois at Urbana-Champaign, Champaign, Illinois, USA
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| |
Collapse
|
19
|
Winter N, Nimzyk R, Bösche C, Meyer A, Bullerdiek J. Chromatin immunoprecipitation to analyze DNA binding sites of HMGA2. PLoS One 2011; 6:e18837. [PMID: 21533145 PMCID: PMC3077414 DOI: 10.1371/journal.pone.0018837] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2010] [Accepted: 03/21/2011] [Indexed: 12/17/2022] Open
Abstract
Background HMGA2 is an architectonic transcription factor abundantly expressed during embryonic and fetal development and it is associated with the progression of malignant tumors. The protein harbours three basically charged DNA binding domains and an acidic protein binding C-terminal domain. DNA binding induces changes of DNA conformation and hence results in global overall change of gene expression patterns. Recently, using a PCR-based SELEX (Systematic Evolution of Ligands by Exponential Enrichment) procedure two consensus sequences for HMGA2 binding have been identified. Methodology/Principal Findings In this investigation chromatin immunoprecipitation (ChIP) experiments and bioinformatic methods were used to analyze if these binding sequences can be verified on chromatin of living cells as well. Conclusion After quantification of HMGA2 protein in different cell lines the colon cancer derived cell line HCT116 was chosen for further ChIP experiments because of its 3.4-fold higher HMGA2 protein level. 49 DNA fragments were obtained by ChIP. These fragments containing HMGA2 binding sites have been analyzed for their AT-content, location in the human genome and similarities to sequences generated by a SELEX study. The sequences show a significantly higher AT-content than the average of the human genome. The artificially generated SELEX sequences and short BLAST alignments (11 and 12 bp) of the ChIP fragments from living cells show similarities in their organization. The flanking regions are AT-rich, whereas a lower conservation is present in the center of the sequences.
Collapse
Affiliation(s)
- Nina Winter
- Centre for Human Genetics, University of Bremen, Bremen, Germany
| | - Rolf Nimzyk
- Centre for Human Genetics, University of Bremen, Bremen, Germany
| | - Carolin Bösche
- Centre for Human Genetics, University of Bremen, Bremen, Germany
| | - Anke Meyer
- Centre for Human Genetics, University of Bremen, Bremen, Germany
| | - Jörn Bullerdiek
- Centre for Human Genetics, University of Bremen, Bremen, Germany
- Clinic for Small Animals and Research Cluster REBIRTH, University of Veterinary Medicine, Hannover, Germany
- * E-mail:
| |
Collapse
|
20
|
Hu L, Wang J, Liu Y, Zhang Y, Zhang L, Kong R, Zheng Z, Du X, Ke Y. A small ribosomal subunit (SSU) processome component, the human U3 protein 14A (hUTP14A) binds p53 and promotes p53 degradation. J Biol Chem 2010; 286:3119-28. [PMID: 21078665 PMCID: PMC3024804 DOI: 10.1074/jbc.m110.157842] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Ribosome biogenesis is required for normal cell function, and aberrant ribosome biogenesis can lead to p53 activation. However, how p53 is activated by defects of ribosome biogenesis remains to be determined. Here, we identified human UTP14a as an SSU processome component by showing that hUTP14a is nucleolar, associated with U3 snoRNA and involved in 18 S rRNA processing. Interestingly, ectopic expression of hUTP14a resulted in a decrease and knockdown of hUTP14a led to an increase of p53 protein levels. We showed that hUTP14a physically interacts with p53 and functionally promotes p53 turn-over, and that hUTP14a promotion of p53 destabilization is sensitive to a proteasome inhibitor but independent of ubiquitination. Significantly, knockdown of hUTP14a led to cell cycle arrest and apoptosis. Our data identified a novel pathway for p53 activation through a defect in rRNA processing and suggest that a ribosome biogenesis factor itself could act as a sensor for nucleolar stress to regulate p53.
Collapse
Affiliation(s)
- Lelin Hu
- Department of Cell Biology, Peking University Health Science Center, Beijing 100191, China
| | | | | | | | | | | | | | | | | |
Collapse
|
21
|
Choo KB, Chuang TJ, Lin WY, Chang CM, Tsai YH, Huang CJ. Evolutionary expansion of SPOP and associated TD/POZ gene family: impact of evolutionary route on gene expression pattern. Gene 2010; 460:39-47. [PMID: 20399258 DOI: 10.1016/j.gene.2010.04.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2010] [Revised: 04/02/2010] [Accepted: 04/08/2010] [Indexed: 12/19/2022]
Abstract
Evolutionary expansion of a gene family may occur at both the DNA and RNA levels. The rat testis-specific Rtdpoz-T2 and -T1 (rT2 and rT1) retrogenes are members of the TD/POZ gene family which also includes the well-characterized SPOP gene. In this study, rT2/rT1 transcriptional activation in cancer cells is demonstrated; the cancer rT2/rT1 transcripts are structurally similar to the embryonic transcripts reported previously in frequent exonization of transposed elements. On database interrogation, we have identified an uncharacterized rT2/rT1-like SPOP paralog, designated as SPOP-like (SPOPL), in the human and rodent genomes. Ka/Ks analysis indicates that the SPOPL genes are under functional constraints implicating biological functions. Phylogenetic analyses further suggest that segmental duplication and retrotransposition events had occurred giving rise to new gene members or retrogenes in the human-rodent ancestors during the evolution of the TD/POZ gene family. Based on this and previous works, a model is proposed to map the routes of evolutionary expansion of the TD/POZ gene family. More importantly, different gene expression patterns of members of the family are depicted: intron-harboring members are ubiquitously expressed whereas retrogenes are expressed in tissue-specific and developmentally regulated manner, and are fortuitously re-activated in cancer cells involving exonization of transposed elements.
Collapse
Affiliation(s)
- Kong-Bung Choo
- Department of Medical Research and Education, Taipei Veterans General Hospital, Shipai, Taipei, Taiwan
| | | | | | | | | | | |
Collapse
|