1
|
Malard F, Dias K, Baudy M, Thore S, Vialet B, Barthélémy P, Fribourg S, Karginov FV, Campagne S. Molecular Basis for the Calcium-Dependent Activation of the Ribonuclease EndoU. RESEARCH SQUARE 2024:rs.3.rs-4654759. [PMID: 39070628 PMCID: PMC11275989 DOI: 10.21203/rs.3.rs-4654759/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Ribonucleases (RNases) are ubiquitous enzymes that process or degrade RNA, essential for cellular functions and immune responses. The EndoU-like superfamily includes endoribonucleases conserved across bacteria, eukaryotes, and certain viruses, with an ancient evolutionary link to the ribonuclease A-like superfamily. Both bacterial EndoU and animal RNase A share a similar fold and function independently of cofactors. In contrast, the eukaryotic EndoU catalytic domain requires divalent metal ions for catalysis, possibly due to an N-terminal extension near the catalytic core. In this study, we used biophysical and computational techniques along with in vitro assays to investigate the calcium-dependent activation of human EndoU. We determined the crystal structure of EndoU bound to calcium and found that calcium binding remote from the catalytic triad triggers water-mediated intramolecular signaling and structural changes, activating the enzyme through allostery. Calcium-binding involves residues from both the catalytic core and the N-terminal extension, indicating that the N-terminal extension interacts with the catalytic core to modulate activity in response to calcium. Our findings suggest that similar mechanisms may be present across all eukaryotic EndoUs, highlighting a unique evolutionary adaptation that connects endoribonuclease activity to cellular signaling in eukaryotes.
Collapse
Affiliation(s)
- Florian Malard
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000 Bordeaux, France
- Univ. Bordeaux, CNRS, INSERM, IECB, US1, UAR 3033, F-33600 Pessac, France
| | - Kristen Dias
- Department of Molecular, Cell and Systems Biology, Institute for Integrative Genome Biology, University of California at Riverside, Riverside, CA, 92521, USA
| | - Margaux Baudy
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000 Bordeaux, France
- Univ. Bordeaux, CNRS, INSERM, IECB, US1, UAR 3033, F-33600 Pessac, France
| | - Stéphane Thore
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000 Bordeaux, France
| | - Brune Vialet
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000 Bordeaux, France
| | - Philippe Barthélémy
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000 Bordeaux, France
| | - Sébastien Fribourg
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000 Bordeaux, France
| | - Fedor V Karginov
- Department of Molecular, Cell and Systems Biology, Institute for Integrative Genome Biology, University of California at Riverside, Riverside, CA, 92521, USA
| | - Sébastien Campagne
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000 Bordeaux, France
- Univ. Bordeaux, CNRS, INSERM, IECB, US1, UAR 3033, F-33600 Pessac, France
| |
Collapse
|
2
|
Lee HC, Chao HT, Lee SYH, Lin CY, Tsai HJ. The Upstream 1350~1250 Nucleotide Sequences of the Human ENDOU-1 Gene Contain Critical Cis-Elements Responsible for Upregulating Its Transcription during ER Stress. Int J Mol Sci 2023; 24:17393. [PMID: 38139221 PMCID: PMC10744159 DOI: 10.3390/ijms242417393] [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: 10/25/2023] [Revised: 12/04/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
ENDOU-1 encodes an endoribonuclease that overcomes the inhibitory upstream open reading frame (uORF)-trap at 5'-untranslated region (UTR) of the CHOP transcript, allowing the downstream coding sequence of CHOP be translated during endoplasmic reticulum (ER) stress. However, transcriptional control of ENDOU-1 remains enigmatic. To address this, we cloned an upstream 2.1 kb (-2055~+77 bp) of human ENDOU-1 (pE2.1p) fused with reporter luciferase (luc) cDNA. The promoter strength driven by pE2.1p was significantly upregulated in both pE2.1p-transfected cells and pE2.1p-injected zebrafish embryos treated with stress inducers. Comparing the luc activities driven by pE2.1p and -1125~+77 (pE1.2p) segments, we revealed that cis-elements located at the -2055~-1125 segment might play a critical role in ENDOU-1 upregulation during ER stress. Since bioinformatics analysis predicted many cis-elements clustered at the -1850~-1250, we further deconstructed this segment to generate pE2.1p-based derivatives lacking -1850~-1750, -1749~-1650, -1649~-1486, -1485~-1350 or -1350~-1250 segments. Quantification of promoter activities driven by these five internal deletion plasmids suggested a repressor binding element within the -1649~-1486 and an activator binding element within the -1350~-1250. Since luc activities driven by the -1649~-1486 were not significantly different between normal and stress conditions, we herein propose that the stress-inducible activator bound at the -1350~-1250 segment makes a major contribution to the increased expression of human ENDOU-1 upon ER stresses.
Collapse
Affiliation(s)
- Hung-Chieh Lee
- Department of Life Science, Fu-Jen Catholic University, New Taipei City 242062, Taiwan
| | - Hsuan-Te Chao
- Department of Life Science, Fu-Jen Catholic University, New Taipei City 242062, Taiwan
| | - Selina Yi-Hsuan Lee
- Faculty of Sciences and Engineering, Maastricht University, 6211 LK Maastricht, The Netherlands
| | - Cheng-Yung Lin
- Institute of Biomedical Sciences, Mackay Medical College, New Taipei City 25245, Taiwan
| | - Huai-Jen Tsai
- Department of Life Science, Fu-Jen Catholic University, New Taipei City 242062, Taiwan
| |
Collapse
|
3
|
Gu H, Li T, Beeraka NM, Zheng Y, Zhang X, Song R, Zhou R, Wang X, Sukocheva O, Fan R, Liu J. Molecular classification of human papilloma virus-negative head and neck squamous cell carcinomas: Cell cycle-based classifier and prognostic signature. PLoS One 2023; 18:e0286414. [PMID: 37903125 PMCID: PMC10615317 DOI: 10.1371/journal.pone.0286414] [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: 11/17/2022] [Accepted: 05/15/2023] [Indexed: 11/01/2023] Open
Abstract
The molecular classification of human papillomavirus (HPV)-negative head and neck squamous cell carcinomas (HNSCCs) remains questionable. Differentially expressed genes were detected between tumor and normal tissues and GSEA showed they are associated with cell cycle pathways. This study aimed to classify HPV-negative HNSCCs based on cell cycle-related genes. The established gene pattern was correlated with tumor progression, clinical prognosis, and drug treatment efficacy. Biological analysis was performed using HNSCC patient sample data obtained from the Cancer Genome Atlas (TCGA), Clinical Proteomic Tumor Analysis Consortium (CPTAC), and Gene Expression Omnibus (GEO) databases. All samples included in this study contained survival information. RNA sequencing data from 740 samples were used for the analysis. Previously characterized cell cycle-related genes were included for unsupervised consensus clustering. Two subtypes of HPV-negative HNSCCs (C1, C2) were identified. Subtype C1 displayed low cell cycle activity, 'hot' tumor microenvironment (TME), earlier N stage, lower pathological grade, better prognosis, and higher response rate to the immunotherapy and targeted therapy. Subtype C2 was associated with higher cell cycle activity, 'cold' TME, later N stage, higher pathological grade, worse prognosis, and lower response rate to the treatment. According to the nearest template prediction method, classification rules were established and verified. Our work explored the molecular mechanism of HPV-negative HNSCCs in the view of cell cycle and might provide new sights for personalized anti-cancer treatment.
Collapse
Affiliation(s)
- Hao Gu
- Department of Radiation Oncology & Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Tingxuan Li
- Department of Radiation Oncology & Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Narasimha M. Beeraka
- Raghavendra Institute of Pharmaceutical Education and Research (RIPER), Anantapuramu, Andhra Pradesh, India
- Department of Human Anatomy, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russian Federation
- Herman B. Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, United States of America
| | - Yufei Zheng
- Department of Radiation Oncology & Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xintan Zhang
- Department of Radiation Oncology & Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ruixia Song
- Department of Radiation Oncology & Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Runze Zhou
- Department of Radiation Oncology & Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiaoyan Wang
- Endocrinology Department, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Olga Sukocheva
- Discipline of Health Sciences, College of Nursing and Health Sciences, Flinders University, Bedford Park, South Australia, Australia
- Department of Hepatology, Royal Adelaide Hospital, SA Health, Adelaide, SA, Australia
| | - Ruitai Fan
- Department of Radiation Oncology & Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Junqi Liu
- Department of Radiation Oncology & Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| |
Collapse
|
4
|
Sun X, Shen J, Perrimon N, Kong X, Wang D. The endoribonuclease Arlr is required to maintain lipid homeostasis by downregulating lipolytic genes during aging. Nat Commun 2023; 14:6254. [PMID: 37803019 PMCID: PMC10558556 DOI: 10.1038/s41467-023-42042-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 09/28/2023] [Indexed: 10/08/2023] Open
Abstract
While disorders in lipid metabolism have been associated with aging and age-related diseases, how lipid metabolism is regulated during aging is poorly understood. Here, we characterize the Drosophila endoribonuclease CG2145, an ortholog of mammalian EndoU that we named Age-related lipid regulator (Arlr), as a regulator of lipid homeostasis during aging. In adult adipose tissues, Arlr is necessary for maintenance of lipid storage in lipid droplets (LDs) as flies age, a phenotype that can be rescued by either high-fat or high-glucose diet. Interestingly, RNA-seq of arlr mutant adipose tissues and RIP-seq suggest that Arlr affects lipid metabolism through the degradation of the mRNAs of lipolysis genes - a model further supported by the observation that knockdown of Lsd-1, regucalcin, yip2 or CG5162, which encode genes involved in lipolysis, rescue the LD defects of arlr mutants. In addition, we characterize DendoU as a functional paralog of Arlr and show that human ENDOU can rescue arlr mutants. Altogether, our study reveals a role of ENDOU-like endonucleases as negative regulator of lipolysis.
Collapse
Affiliation(s)
- Xiaowei Sun
- Department of Plant Biosecurity and MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing, China
| | - Jie Shen
- Department of Plant Biosecurity and MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing, China
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Xue Kong
- Department of Plant Biosecurity and MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing, China
| | - Dan Wang
- Department of Plant Biosecurity and MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing, China.
| |
Collapse
|
5
|
Xu F, Li R, von Gromoff ED, Drepper F, Knapp B, Warscheid B, Baumeister R, Qi W. Reprogramming of the transcriptome after heat stress mediates heat hormesis in Caenorhabditis elegans. Nat Commun 2023; 14:4176. [PMID: 37443152 PMCID: PMC10345090 DOI: 10.1038/s41467-023-39882-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 07/03/2023] [Indexed: 07/15/2023] Open
Abstract
Transient stress experiences not only trigger acute stress responses, but can also have long-lasting effects on cellular functions. In Caenorhabditis elegans, a brief exposure to heat shock during early adulthood extends lifespan and improves stress resistance, a phenomenon known as heat hormesis. Here, we investigated the prolonged effect of hormetic heat stress on the transcriptome of worms and found that the canonical heat shock response is followed by a profound transcriptional reprogramming in the post-stress period. This reprogramming relies on the endoribonuclease ENDU-2 but not the heat shock factor 1. ENDU-2 co-localizes with chromatin and interacts with RNA polymerase II, enabling specific regulation of transcription after the stress period. Failure to activate the post-stress response does not affect the resistance of animals to heat shock but eliminates the beneficial effects of hormetic heat stress. In summary, our work discovers that the RNA-binding protein ENDU-2 mediates the long-term impacts of transient heat stress via reprogramming transcriptome after stress exposure.
Collapse
Affiliation(s)
- Fan Xu
- Bioinformatics and Molecular Genetics (Faculty of Biology), Albert-Ludwigs-University Freiburg, Freiburg, 79104, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), Albert-Ludwigs-University Freiburg, Freiburg, 79104, Germany
| | - Ruoyao Li
- Bioinformatics and Molecular Genetics (Faculty of Biology), Albert-Ludwigs-University Freiburg, Freiburg, 79104, Germany
| | - Erika D von Gromoff
- Bioinformatics and Molecular Genetics (Faculty of Biology), Albert-Ludwigs-University Freiburg, Freiburg, 79104, Germany
| | - Friedel Drepper
- Biochemistry-Functional Proteomics, Institute of Biology II, Faculty of Biology, Albert-Ludwigs-University Freiburg, Freiburg, 79104, Germany
| | - Bettina Knapp
- Biochemistry-Functional Proteomics, Institute of Biology II, Faculty of Biology, Albert-Ludwigs-University Freiburg, Freiburg, 79104, Germany
| | - Bettina Warscheid
- Biochemistry-Functional Proteomics, Institute of Biology II, Faculty of Biology, Albert-Ludwigs-University Freiburg, Freiburg, 79104, Germany
- Signalling Research Centers BIOSS and CIBSS, Albert-Ludwigs-University Freiburg, Freiburg, 79104, Germany
- Biochemistry II, Theodor Boveri-Institute, Biocenter, University of Würzburg, 97074, Würzburg, Germany
| | - Ralf Baumeister
- Bioinformatics and Molecular Genetics (Faculty of Biology), Albert-Ludwigs-University Freiburg, Freiburg, 79104, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), Albert-Ludwigs-University Freiburg, Freiburg, 79104, Germany
- Signalling Research Centers BIOSS and CIBSS, Albert-Ludwigs-University Freiburg, Freiburg, 79104, Germany
- Center for Biochemistry and Molecular Cell Research (Faculty of Medicine), Albert-Ludwigs-University Freiburg, Freiburg, 79104, Germany
| | - Wenjing Qi
- Bioinformatics and Molecular Genetics (Faculty of Biology), Albert-Ludwigs-University Freiburg, Freiburg, 79104, Germany.
| |
Collapse
|
6
|
Interactive bioinformatics analysis for the screening of hub genes and molecular docking of phytochemicals present in kitchen spices to inhibit CDK1 in cervical cancer. Comput Biol Med 2022; 149:105994. [DOI: 10.1016/j.compbiomed.2022.105994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 07/07/2022] [Accepted: 08/14/2022] [Indexed: 11/17/2022]
|
7
|
Basic V, Zhang B, Domert J, Pellas U, Tot T. Integrative meta-analysis of gene expression profiles identifies FEN1 and ENDOU as potential diagnostic biomarkers for cervical squamous cell carcinoma. Oncol Lett 2021; 22:840. [PMID: 34712364 PMCID: PMC8548783 DOI: 10.3892/ol.2021.13101] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 09/16/2021] [Indexed: 12/23/2022] Open
Abstract
Cervical carcinoma is a global public health burden. Given that it is usually asymptomatic at potentially curative stages, the development of clinically accurate tests is critical for early detection and individual risk stratification. The present study performed an integrative meta-analysis of the transcriptomes from 10 cervical carcinoma cohorts, with the aim of identifying biomarkers that are associated with malignant transformation of cervical epithelium, and establish their clinical applicability. From among the top ranked differentially expressed genes, flap structure-specific endonuclease 1 (FEN1) and poly (U)-specific endoribonuclease (ENDOU) were selected for further validation, and their clinical applicability was assessed using immunohistochemically stained microarrays comprising 110 tissue cores, using p16 and Ki67 staining as the comparator tests. The results demonstrated that FEN1 expression was significantly upregulated in 65% of tumor specimens (P=0.0001), with no detectable expression in the non-tumor tissues. Furthermore, its expression was significantly associated with Ki67 staining in tumor samples (P<0.0001), but no association was observed with p16 expression or the presence of human papilloma virus types 16/18, patient age, tumor grade or stage. FEN1 staining demonstrated lower sensitivity than p16 (69.3 vs. 96.8%) and Ki67 (69.3 vs. 76.3%); however, the specificity was identical to p16 and higher than that of Ki67 (100 vs. 71.4%).ENDOU staining was consistent with the microarray results, demonstrating 1% positivity in tumors and 40% positivity in non-tumor tissues. Gene set enrichment analysis of cervical tumors overexpressing FEN1 revealed its association with enhanced growth factor signaling, immune response inhibition and extracellular matrix remodeling, whereas tumors with low ENDOU expression exhibited inhibition of epithelial development and differentiation processes. Taken together, the results of the present study demonstrate the feasibility of the integrative meta-analysis approach to identify relevant biomarkers associated with cervical carcinogenesis. Thus, FEN1 and ENDOU may be useful diagnostic biomarkers for squamous cervical carcinoma. However, further studies are required to determine their diagnostic performance in larger patient cohorts and validate the results presented here.
Collapse
Affiliation(s)
- Vladimir Basic
- Pathology and Cytology Dalarna, County Hospital Falun, Falun 791 82, Sweden
- Clinical Research Center Dalarna, Uppsala University, Falun 791 82, Sweden
| | - Boxi Zhang
- Department of Physiology and Pharmacology, Karolinska Institute, Stockholm 171 65, Sweden
| | - Jakob Domert
- Pathology and Cytology Dalarna, County Hospital Falun, Falun 791 82, Sweden
| | - Ulrika Pellas
- Clinical Research Center Dalarna, Uppsala University, Falun 791 82, Sweden
| | - Tibor Tot
- Pathology and Cytology Dalarna, County Hospital Falun, Falun 791 82, Sweden
| |
Collapse
|
8
|
Chi LH, Wu ATH, Hsiao M, Li YC(J. A Transcriptomic Analysis of Head and Neck Squamous Cell Carcinomas for Prognostic Indications. J Pers Med 2021; 11:782. [PMID: 34442426 PMCID: PMC8399099 DOI: 10.3390/jpm11080782] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/03/2021] [Accepted: 08/04/2021] [Indexed: 01/27/2023] Open
Abstract
Survival analysis of the Cancer Genome Atlas (TCGA) dataset is a well-known method for discovering gene expression-based prognostic biomarkers of head and neck squamous cell carcinoma (HNSCC). A cutoff point is usually used in survival analysis for patient dichotomization when using continuous gene expression values. There is some optimization software for cutoff determination. However, the software's predetermined cutoffs are usually set at the medians or quantiles of gene expression values. There are also few clinicopathological features available in pre-processed datasets. We applied an in-house workflow, including data retrieving and pre-processing, feature selection, sliding-window cutoff selection, Kaplan-Meier survival analysis, and Cox proportional hazard modeling for biomarker discovery. In our approach for the TCGA HNSCC cohort, we scanned human protein-coding genes to find optimal cutoff values. After adjustments with confounders, clinical tumor stage and surgical margin involvement were found to be independent risk factors for prognosis. According to the results tables that show hazard ratios with Bonferroni-adjusted p values under the optimal cutoff, three biomarker candidates, CAMK2N1, CALML5, and FCGBP, are significantly associated with overall survival. We validated this discovery by using the another independent HNSCC dataset (GSE65858). Thus, we suggest that transcriptomic analysis could help with biomarker discovery. Moreover, the robustness of the biomarkers we identified should be ensured through several additional tests with independent datasets.
Collapse
Affiliation(s)
- Li-Hsing Chi
- The Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan; (L.-H.C.); (A.T.H.W.)
- Division of Oral and Maxillofacial Surgery, Department of Dentistry, Wan Fang Hospital, Taipei Medical University, Taipei 11600, Taiwan
- Division of Oral and Maxillofacial Surgery, Department of Dentistry, Taipei Medical University Hospital, Taipei Medical University, Taipei 11031, Taiwan
| | - Alexander T. H. Wu
- The Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan; (L.-H.C.); (A.T.H.W.)
| | - Michael Hsiao
- Genomics Research Center, Academia Sinica, Taipei 115024, Taiwan
- Department of Biochemistry, College of Medicine, Kaohsiung Medical University, Kaohsiung 807378, Taiwan
| | - Yu-Chuan (Jack) Li
- The Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan; (L.-H.C.); (A.T.H.W.)
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, No.172-1, Sec. 2, Keelung Rd., Taipei 106339, Taiwan
| |
Collapse
|