1
|
Jindal U, Mamgain M, Nath UK, Sharma I, Pant B, Sharma A, Gupta A, Rahman K, Yadav S, Singh MP, Mishra S, Chaturvedi CP, Courty J, Singh N, Gupta S, Kumar S, Verma SP, Mallick S, Gogia A, Raghav S, Sarkar J, Srivastava KR, Datta D, Jain N. Targeting CERS6-AS1/FGFR1 axis as synthetic vulnerability to constrain stromal cells supported proliferation in Mantle cell lymphoma. Leukemia 2024:10.1038/s41375-024-02344-1. [PMID: 39003397 DOI: 10.1038/s41375-024-02344-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 07/04/2024] [Accepted: 07/08/2024] [Indexed: 07/15/2024]
Abstract
The interaction between stromal and tumor cells in tumor microenvironment is a crucial factor in Mantle cell lymphoma (MCL) progression and therapy resistance. We have identified a long non-coding RNA, CERS6-AS1, upregulated in MCL and associated with poor overall survival. CERS6-AS1 expression was elevated in primary MCL within stromal microenvironment and in a subset of MCL cells adhered to stromal layer. These stromal-adhered MCL-subsets exhibited cancer stem cell signatures than suspension counterparts. Mechanistically, we found that downregulating CERS6-AS1 in MCL reduced Fibroblast Growth Factor Receptor-1 (FGFR1), expression attributed to loss of its interaction with RNA-binding protein nucleolin. In addition, using in-silico approach, we have discovered a direct interaction between nucleolin and 5'UTR of FGFR1, thereby regulating FGFR1 transcript stability. We discovered a positive association of CERS6-AS1 with cancer stem cell signatures, and Wnt signaling. Building on these, we explored potential therapeutic strategies where combining nucleolin-targeting agent with FGFR1 inhibition significantly contributed to reversing cancer stem cell signatures and abrogated primary MCL cell growth on stromal layer. These findings provide mechanistic insights into regulatory network involving CERS6-AS1, nucleolin, and FGFR1 axis-associated crosstalk between tumor cells and stromal cell interaction and highlights therapeutic potential of targeting a non-coding RNA in MCL.
Collapse
Affiliation(s)
- Udita Jindal
- Division of Cancer Biology, CSIR-Central Drug Research Institute, Lucknow, Uttar Pradesh, 226031, India
- Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, 201002, India
| | - Mukesh Mamgain
- Department of Medical Oncology & Hematology, All India Institute of Medical Sciences, Rishikesh, 249203, India
| | - Uttam Kumar Nath
- Department of Medical Oncology & Hematology, All India Institute of Medical Sciences, Rishikesh, 249203, India
| | - Isha Sharma
- Division of Cancer Biology, CSIR-Central Drug Research Institute, Lucknow, Uttar Pradesh, 226031, India
| | - Bhaskar Pant
- Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, 201002, India
- Division of Medicinal and Process Chemistry, CSIR-Central Drug Research Institute, Lucknow, Uttar Pradesh, 226031, India
| | - Ankita Sharma
- Division of Cancer Biology, CSIR-Central Drug Research Institute, Lucknow, Uttar Pradesh, 226031, India
| | - Archita Gupta
- Division of Cancer Biology, CSIR-Central Drug Research Institute, Lucknow, Uttar Pradesh, 226031, India
| | - Khaliqur Rahman
- Department of Hematology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, 226014, India
| | - Sunil Yadav
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Manish Pratap Singh
- Department of Zoology, Deen Dayal Upadhyay Gorakhpur University, Gorakhpur, Uttar Pradesh, 273009, India
| | | | - Chandra Praksah Chaturvedi
- Department of Hematology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, 226014, India
| | - Jose Courty
- INSERM, Institut Mondor de Recherche Biomédicale (IMRB), Université Paris-Est Créteil, F-94010, Créteil, France
| | - Navin Singh
- Department of Radiotherapy, King George's Medical University, Lucknow, Uttar Pradesh, 226003, India
| | - Seema Gupta
- Department of Radiotherapy, King George's Medical University, Lucknow, Uttar Pradesh, 226003, India
| | - Sanjeev Kumar
- Department of General Surgery, King George's Medical University, Lucknow, Uttar Pradesh, 226003, India
| | - Shailendra Prasad Verma
- Department of Clinical Hematology, King George's Medical University, Lucknow, Uttar Pradesh, 226003, India
| | - Saumyaranjan Mallick
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Ajay Gogia
- Department of Medical Oncology, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Sunil Raghav
- Institute of Life Sciences, Bhubaneswar, 751023, Odisha, India
| | - Jayanta Sarkar
- Division of Cancer Biology, CSIR-Central Drug Research Institute, Lucknow, Uttar Pradesh, 226031, India
- Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, 201002, India
| | - Kinshuk Raj Srivastava
- Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, 201002, India
- Division of Medicinal and Process Chemistry, CSIR-Central Drug Research Institute, Lucknow, Uttar Pradesh, 226031, India
| | - Dipak Datta
- Division of Cancer Biology, CSIR-Central Drug Research Institute, Lucknow, Uttar Pradesh, 226031, India
- Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, 201002, India
| | - Neeraj Jain
- Division of Cancer Biology, CSIR-Central Drug Research Institute, Lucknow, Uttar Pradesh, 226031, India.
- Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, 201002, India.
| |
Collapse
|
2
|
Miyoshi M, Shimosato T, Takaya T. Myogenic Anti-Nucleolin Aptamer iSN04 Inhibits Proliferation and Promotes Differentiation of Vascular Smooth Muscle Cells. Biomolecules 2024; 14:709. [PMID: 38927112 PMCID: PMC11201766 DOI: 10.3390/biom14060709] [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: 04/25/2024] [Revised: 06/09/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024] Open
Abstract
De-differentiation and subsequent increased proliferation and inflammation of vascular smooth muscle cells (VSMCs) is one of the mechanisms of atherogenesis. Maintaining VSMCs in a contractile differentiated state is therefore a promising therapeutic strategy for atherosclerosis. We have reported the 18-base myogenetic oligodeoxynucleotide, iSN04, which serves as an anti-nucleolin aptamer and promotes skeletal and myocardial differentiation. The present study investigated the effect of iSN04 on VSMCs because nucleolin has been reported to contribute to VSMC de-differentiation under pathophysiological conditions. Nucleolin is localized in the nucleoplasm and nucleoli of both rat and human VSMCs. iSN04 without a carrier was spontaneously incorporated into VSMCs, indicating that iSN04 would serve as an anti-nucleolin aptamer. iSN04 treatment decreased the ratio of 5-ethynyl-2'-deoxyuridine (EdU)-positive proliferating VSMCs and increased the expression of α-smooth muscle actin, a contractile marker of VSMCs. iSN04 also suppressed angiogenesis of mouse aortic rings ex vivo, which is a model of pathological angiogenesis involved in plaque formation, growth, and rupture. These results demonstrate that antagonizing nucleolin with iSN04 preserves VSMC differentiation, providing a nucleic acid drug candidate for the treatment of vascular disease.
Collapse
MESH Headings
- Nucleolin
- Animals
- RNA-Binding Proteins/metabolism
- Muscle, Smooth, Vascular/cytology
- Muscle, Smooth, Vascular/drug effects
- Muscle, Smooth, Vascular/metabolism
- Aptamers, Nucleotide/pharmacology
- Cell Proliferation/drug effects
- Phosphoproteins/metabolism
- Cell Differentiation/drug effects
- Humans
- Rats
- Myocytes, Smooth Muscle/drug effects
- Myocytes, Smooth Muscle/metabolism
- Myocytes, Smooth Muscle/cytology
- Mice
- Cells, Cultured
- Oligodeoxyribonucleotides/pharmacology
- Male
- Rats, Sprague-Dawley
- Mice, Inbred C57BL
Collapse
Affiliation(s)
- Mana Miyoshi
- Department of Agriculture, Graduate School of Science and Technology, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan
| | - Takeshi Shimosato
- Department of Agriculture, Graduate School of Science and Technology, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan
- Department of Agricultural and Life Sciences, Faculty of Agriculture, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan
| | - Tomohide Takaya
- Department of Agriculture, Graduate School of Science and Technology, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan
- Department of Agricultural and Life Sciences, Faculty of Agriculture, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan
| |
Collapse
|
3
|
Zhu Y, Li X, Zhang Q, Yang X, Sun X, Pan Y, Yuan X, Ma Y, Xu B, Yang Z. Aptamer AS411 interacts with the KRAS promoter/hnRNP A1 complex and shows increased potency against drug-resistant lung cancer. RSC Med Chem 2024; 15:1515-1526. [PMID: 38784467 PMCID: PMC11110790 DOI: 10.1039/d3md00752a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 04/15/2024] [Accepted: 02/22/2024] [Indexed: 05/25/2024] Open
Abstract
G-quadruplex (G4) aptamers that can competitively binding protein with oncogene promoter G4 hold promise for cancer treatment. In this study, a neutral cytidinyl lipid, DNCA, was shown to transfect and deliver G4 aptamers (AS1411, TBA) into tumour cells, including multidrug-resistant tumour cells, and their nuclear localizations were clearly detected. Both AS1411/DNCA and TBA/DNCA showed excellent antitumour efficacies in the drug-resistant non-small cell lung cancer cell line A549/TXL at a low concentration (100 nM). Heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) was identified as a new target of AS1411 and TBA. The binding affinities were measured, and the Kd values of AS1411/hnRNP A1 and TBA/hnRNP A1 were 17.5 nM and 21.1 nM, respectively. Then the expression of KRAS mRNA in A549/TXL cells was found to be higher than that in A549 cells, and KRAS mRNA was reduced by approximately 40% after administration of AS1411 or TBA in A549/TXL cells. Further, it was confirmed for the first time that AS1411 targeted not only hnRNP A1 but also the KRAS promoter/hnRNP A1 complexes. And although TBA cannot target the KRAS promoter/hnRNP A1 complexes, the biolayer interferometry (BLI) experiment showed that TBA and AS1411 have similar effects on several key proteins in tumour cells, especially hnRNP A1. Molecular docking and molecular dynamics simulation showed that AS1411 and the KRAS promoter bound to the same domain of hnRNP A1 protein, while TBA bound to another domain.
Collapse
Affiliation(s)
- Yuejie Zhu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Beijing 100191 China +86 10 82802503 +86 10 82802503
| | - Xiang Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Beijing 100191 China +86 10 82802503 +86 10 82802503
| | - Qi Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Beijing 100191 China +86 10 82802503 +86 10 82802503
| | - Xiantao Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Beijing 100191 China +86 10 82802503 +86 10 82802503
- School of Pharmacy, Chengdu Medical College 783 Xindu Avenue, Xindu District Chengdu 610500 China
| | - Xudong Sun
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Beijing 100191 China +86 10 82802503 +86 10 82802503
| | - Yi Pan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Beijing 100191 China +86 10 82802503 +86 10 82802503
| | - Xia Yuan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Beijing 100191 China +86 10 82802503 +86 10 82802503
| | - Yuan Ma
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Beijing 100191 China +86 10 82802503 +86 10 82802503
| | - Bo Xu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Beijing 100191 China +86 10 82802503 +86 10 82802503
| | - Zhenjun Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Beijing 100191 China +86 10 82802503 +86 10 82802503
| |
Collapse
|
4
|
Umezawa K, Ikeda R, Sakamoto T, Enomoto Y, Nihashi Y, Shinji S, Shimosato T, Kagami H, Takaya T. Development of the 12-Base Short Dimeric Myogenetic Oligodeoxynucleotide That Induces Myogenic Differentiation. BIOTECH 2024; 13:11. [PMID: 38804293 PMCID: PMC11130974 DOI: 10.3390/biotech13020011] [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: 03/17/2024] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/29/2024] Open
Abstract
A myogenetic oligodeoxynucleotide (myoDN), iSN04 (5'-AGA TTA GGG TGA GGG TGA-3'), is a single-stranded 18-base telomeric DNA that serves as an anti-nucleolin aptamer and induces myogenic differentiation, which is expected to be a nucleic acid drug for the prevention of disease-associated muscle wasting. To improve the drug efficacy and synthesis cost of myoDN, shortening the sequence while maintaining its structure-based function is a major challenge. Here, we report the novel 12-base non-telomeric myoDN, iMyo01 (5'-TTG GGT GGG GAA-3'), which has comparable myogenic activity to iSN04. iMyo01 as well as iSN04 promoted myotube formation of primary-cultured human myoblasts with upregulation of myogenic gene expression. Both iMyo01 and iSN04 interacted with nucleolin, but iMyo01 did not bind to berberine, the isoquinoline alkaloid that stabilizes iSN04. Nuclear magnetic resonance revealed that iMyo01 forms a G-quadruplex structure despite its short sequence. Native polyacrylamide gel electrophoresis and a computational molecular dynamics simulation indicated that iMyo01 forms a homodimer to generate a G-quadruplex. These results provide new insights into the aptamer truncation technology that preserves aptamer conformation and bioactivity for the development of efficient nucleic acid drugs.
Collapse
Affiliation(s)
- Koji Umezawa
- Department of Agricultural and Life Sciences, Faculty of Agriculture, Shinshu University, 8304 Minami-minowa, Kami-ina 399-4598, Japan; (K.U.); (Y.E.); (T.S.); (H.K.)
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, 8304 Minami-minowa, Kami-ina 399-4598, Japan
| | - Rena Ikeda
- Department of Agriculture, Graduate School of Science and Technology, Shinshu University, 8304 Minami-minowa, Kami-ina 399-4598, Japan
| | - Taiichi Sakamoto
- Department of Life Science, Faculty of Advanced Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino-shi 275-0016, Japan;
| | - Yuya Enomoto
- Department of Agricultural and Life Sciences, Faculty of Agriculture, Shinshu University, 8304 Minami-minowa, Kami-ina 399-4598, Japan; (K.U.); (Y.E.); (T.S.); (H.K.)
| | - Yuma Nihashi
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Centoral 5-41, 1-1-1 Higashi, Tsukuba 305-8565, Japan;
| | - Sayaka Shinji
- Department of Agriculture, Graduate School of Science and Technology, Shinshu University, 8304 Minami-minowa, Kami-ina 399-4598, Japan
| | - Takeshi Shimosato
- Department of Agricultural and Life Sciences, Faculty of Agriculture, Shinshu University, 8304 Minami-minowa, Kami-ina 399-4598, Japan; (K.U.); (Y.E.); (T.S.); (H.K.)
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, 8304 Minami-minowa, Kami-ina 399-4598, Japan
- Department of Agriculture, Graduate School of Science and Technology, Shinshu University, 8304 Minami-minowa, Kami-ina 399-4598, Japan
| | - Hiroshi Kagami
- Department of Agricultural and Life Sciences, Faculty of Agriculture, Shinshu University, 8304 Minami-minowa, Kami-ina 399-4598, Japan; (K.U.); (Y.E.); (T.S.); (H.K.)
| | - Tomohide Takaya
- Department of Agricultural and Life Sciences, Faculty of Agriculture, Shinshu University, 8304 Minami-minowa, Kami-ina 399-4598, Japan; (K.U.); (Y.E.); (T.S.); (H.K.)
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, 8304 Minami-minowa, Kami-ina 399-4598, Japan
- Department of Agriculture, Graduate School of Science and Technology, Shinshu University, 8304 Minami-minowa, Kami-ina 399-4598, Japan
| |
Collapse
|
5
|
Hu X, Chen G, Huang Y, Cheng Q, Zhuo J, Su R, He C, Wu Y, Liu Z, Yang B, Wang S, Meng L, Zheng S, Lu D, Wei Q, Yang J, Wei X, Chen R, Xu X. Integrated Multiomics Reveals Silencing of has_circ_0006646 Promotes TRIM21-Mediated NCL Ubiquitination to Inhibit Hepatocellular Carcinoma Metastasis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306915. [PMID: 38357830 PMCID: PMC11040345 DOI: 10.1002/advs.202306915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 01/10/2024] [Indexed: 02/16/2024]
Abstract
Recent studies suggest that circular RNA (circRNA)-mediated post-translational modification of RNA-binding proteins (RBP) plays a pivotal role in metastasis of hepatocellular carcinoma (HCC). However, the specific mechanism and potential clinical therapeutic significance remain vague. This study attempts to profile the regulatory networks of circRNA and RBP using a multi-omics approach. Has_circ_0006646 (circ0006646) is an unreported circRNA in HCC and is associated with a poor prognosis. Silencing of circ0006646 significantly hinders metastasis in vivo. Mechanistically, circ0006646 prevents the interaction between nucleolin (NCL) and the E3 ligase tripartite motif-containing 21 to reduce the proteasome-mediated degradation of NCL via K48-linked polyubiquitylation. Furthermore, the change of NCL expression is proven to affect the phosphorylation levels of multiple proteins and inhibit p53 translation. Moreover, patient-derived tumor xenograft and lentivirus injection, which is conducted to simulate clinical treatment confirmed the potential therapeutic value. Overall, this study describes the integrated multi-omics landscape of circRNA-mediated NCL ubiquitination degradation in HCC metastasis and provides a novel therapeutic target.
Collapse
Affiliation(s)
- Xin Hu
- Zhejiang University School of MedicineHangzhou310058China
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang ProvinceHangzhou310006China
- NHC Key Laboratory of Combined Multi‐organ TransplantationHangzhou310003China
| | - Guanrong Chen
- The Fourth School of Clinical MedicineZhejiang Chinese Medical UniversityHangzhou310053China
| | - Yingchen Huang
- The Fourth School of Clinical MedicineZhejiang Chinese Medical UniversityHangzhou310053China
| | - Qiyang Cheng
- Department of Hepatobiliary SurgeryBeijing Chaoyang Hospital affiliated to Capital Medical UniversityBeijing100020China
| | - Jianyong Zhuo
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang ProvinceHangzhou310006China
- Department of Hepatobiliary and Pancreatic SurgeryAffiliated Hangzhou First People's HospitalZhejiang University School of MedicineHangzhou310006China
| | - Renyi Su
- Zhejiang University School of MedicineHangzhou310058China
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang ProvinceHangzhou310006China
| | - Chiyu He
- Zhejiang University School of MedicineHangzhou310058China
- Department of Hepatobiliary and Pancreatic SurgeryShulan (Hangzhou) HospitalHangzhou310022China
| | - Yichao Wu
- Zhejiang University School of MedicineHangzhou310058China
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang ProvinceHangzhou310006China
| | - Zhikun Liu
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang ProvinceHangzhou310006China
- Department of Hepatobiliary and Pancreatic SurgeryAffiliated Hangzhou First People's HospitalZhejiang University School of MedicineHangzhou310006China
| | - Beng Yang
- Department of Hepatobiliary and Pancreatic SurgeryThe First Affiliated HospitalZhejiang University School of MedicineHangzhou310006China
| | - Shuai Wang
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang ProvinceHangzhou310006China
- Department of Hepatobiliary and Pancreatic SurgeryAffiliated Hangzhou First People's HospitalZhejiang University School of MedicineHangzhou310006China
| | - Lijun Meng
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang ProvinceHangzhou310006China
- Department of Hepatobiliary and Pancreatic SurgeryAffiliated Hangzhou First People's HospitalZhejiang University School of MedicineHangzhou310006China
| | - Shusen Zheng
- NHC Key Laboratory of Combined Multi‐organ TransplantationHangzhou310003China
- Department of Hepatobiliary and Pancreatic SurgeryShulan (Hangzhou) HospitalHangzhou310022China
- Department of Hepatobiliary and Pancreatic SurgeryThe First Affiliated HospitalZhejiang University School of MedicineHangzhou310006China
| | - Di Lu
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang ProvinceHangzhou310006China
- Department of Hepatobiliary and Pancreatic SurgeryAffiliated Hangzhou First People's HospitalZhejiang University School of MedicineHangzhou310006China
| | - Qiang Wei
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang ProvinceHangzhou310006China
- Department of Hepatobiliary and Pancreatic SurgeryAffiliated Hangzhou First People's HospitalZhejiang University School of MedicineHangzhou310006China
| | - Jiayin Yang
- Department of Liver SurgeryLiver Transplantation CenterWest China Hospital of Sichuan UniversityChengdu332001China
| | - Xuyong Wei
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang ProvinceHangzhou310006China
- Department of Hepatobiliary and Pancreatic SurgeryAffiliated Hangzhou First People's HospitalZhejiang University School of MedicineHangzhou310006China
| | - Ronggao Chen
- NHC Key Laboratory of Combined Multi‐organ TransplantationHangzhou310003China
- Department of Hepatobiliary and Pancreatic SurgeryThe First Affiliated HospitalZhejiang University School of MedicineHangzhou310006China
| | - Xiao Xu
- Zhejiang University School of MedicineHangzhou310058China
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang ProvinceHangzhou310006China
- NHC Key Laboratory of Combined Multi‐organ TransplantationHangzhou310003China
| |
Collapse
|
6
|
Jiang Y, MacNeil LT. Simple model systems reveal conserved mechanisms of Alzheimer's disease and related tauopathies. Mol Neurodegener 2023; 18:82. [PMID: 37950311 PMCID: PMC10638731 DOI: 10.1186/s13024-023-00664-x] [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: 04/02/2023] [Accepted: 10/04/2023] [Indexed: 11/12/2023] Open
Abstract
The lack of effective therapies that slow the progression of Alzheimer's disease (AD) and related tauopathies highlights the need for a more comprehensive understanding of the fundamental cellular mechanisms underlying these diseases. Model organisms, including yeast, worms, and flies, provide simple systems with which to investigate the mechanisms of disease. The evolutionary conservation of cellular pathways regulating proteostasis and stress response in these organisms facilitates the study of genetic factors that contribute to, or protect against, neurodegeneration. Here, we review genetic modifiers of neurodegeneration and related cellular pathways identified in the budding yeast Saccharomyces cerevisiae, the nematode Caenorhabditis elegans, and the fruit fly Drosophila melanogaster, focusing on models of AD and related tauopathies. We further address the potential of simple model systems to better understand the fundamental mechanisms that lead to AD and other neurodegenerative disorders.
Collapse
Affiliation(s)
- Yuwei Jiang
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Lesley T MacNeil
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada.
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Canada.
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main St W, Hamilton, ON, L8S 4K1, Canada.
| |
Collapse
|
7
|
Shi H, Xie J, Pei S, He D, Hou H, Xu S, Fu Z, Shi X. Digging out the biology properties of tRNA-derived small RNA from black hole. Front Genet 2023; 14:1232325. [PMID: 37953919 PMCID: PMC10637384 DOI: 10.3389/fgene.2023.1232325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 10/18/2023] [Indexed: 11/14/2023] Open
Abstract
An unique subclass of functional non-coding RNAs generated by transfer RNA (tRNA) under stress circumstances is known as tRNA-derived small RNA (tsRNA). tsRNAs can be divided into tRNA halves and tRNA-derived fragments (tRFs) based on the different cleavage sites. Like microRNAs, tsRNAs can attach to Argonaute (AGO) proteins to target downstream mRNA in a base pairing manner, which plays a role in rRNA processing, gene silencing, protein expression and viral infection. Notably, tsRNAs can also directly bind to protein and exhibit functions in transcription, protein modification, gene expression, protein stabilization, and signaling pathways. tsRNAs can control the expression of tumor suppressor genes and participate in the initiation of cancer. It can also mediate the progression of diseases by regulating cell viability, migration ability, inflammatory factor content and autophagy ability. Precision medicine targeting tsRNAs and drug therapy of plant-derived tsRNAs are expected to be used in clinical practice. In addition, liquid biopsy technology based on tsRNAs indicates a new direction for the non-invasive diagnosis of diseases.
Collapse
Affiliation(s)
- Hengmei Shi
- Department of Obstetrics and Gynecology, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu, China
| | - Jiaheng Xie
- Department of Burn and Plastic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Shengbin Pei
- Department of Breast Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Danni He
- Department of Obstetrics and Gynecology, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu, China
| | - Huyang Hou
- Department of Obstetrics and Gynecology, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu, China
| | - Shipeng Xu
- Department of Biomedical Engineering, University of California, Davis, Davis, CA, United States
| | - Ziyi Fu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xiaoyan Shi
- Department of Obstetrics and Gynecology, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu, China
| |
Collapse
|
8
|
Thongchot S, Aksonnam K, Thuwajit P, Yenchitsomanus PT, Thuwajit C. Nucleolin‑based targeting strategies in cancer treatment: Focus on cancer immunotherapy (Review). Int J Mol Med 2023; 52:81. [PMID: 37477132 PMCID: PMC10555485 DOI: 10.3892/ijmm.2023.5284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/15/2023] [Indexed: 07/22/2023] Open
Abstract
The benefits of treating several types of cancers using immunotherapy have recently been established. The overexpression of nucleolin (NCL) in a number of types of cancer provides an attractive antigen target for the development of novel anticancer immunotherapeutic treatments. NCL is a multifunctional protein abundantly distributed in the nucleus, cytoplasm and cell membrane. It influences carcinogenesis, and the proliferation, survival and metastasis of cancer cells, leading to cancer progression. Additionally, the meta‑analysis of total and cytoplasmic NCL overexpression indicates a poor prognosis of patients with breast cancer. The AS1411 aptamers currently appear to have therapeutic action in the phase II clinical trial. The authors' research group has recently explored the anticancer function of NCL through the activation of T cells by dendritic cell‑based immunotherapy. The present review describes and discusses the mechanisms through which the multiple functions of NCL can participate in the progression of cancer. In addition, the studies that define the utility of NCL‑dependent anticancer therapies are summarized, with specific focus being paid to cancer immunotherapeutic approaches.
Collapse
Affiliation(s)
- Suyanee Thongchot
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University
- Siriraj Center of Research Excellence for Cancer Immunotherapy (SiCORE-CIT), Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University
| | - Krittaya Aksonnam
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University
| | - Peti Thuwajit
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University
| | - Pa-Thai Yenchitsomanus
- Siriraj Center of Research Excellence for Cancer Immunotherapy (SiCORE-CIT), Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University
- Division of Molecular Medicine, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Chanitra Thuwajit
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University
| |
Collapse
|
9
|
Kumar S, Verma R, Saha S, Agrahari AK, Shukla S, Singh ON, Berry U, Anurag, Maiti TK, Asthana S, Ranjith-Kumar CT, Surjit M. RNA-Protein Interactome at the Hepatitis E Virus Internal Ribosome Entry Site. Microbiol Spectr 2023; 11:e0282722. [PMID: 37382527 PMCID: PMC10434006 DOI: 10.1128/spectrum.02827-22] [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: 07/22/2022] [Accepted: 02/11/2023] [Indexed: 06/30/2023] Open
Abstract
Multiple processes exist in a cell to ensure continuous production of essential proteins either through cap-dependent or cap-independent translation processes. Viruses depend on the host translation machinery for viral protein synthesis. Therefore, viruses have evolved clever strategies to use the host translation machinery. Earlier studies have shown that genotype 1 hepatitis E virus (g1-HEV) uses both cap-dependent and cap-independent translation machineries for its translation and proliferation. Cap-independent translation in g1-HEV is driven by an 87-nucleotide-long RNA element that acts as a noncanonical, internal ribosome entry site-like (IRESl) element. Here, we have identified the RNA-protein interactome of the HEV IRESl element and characterized the functional significance of some of its components. Our study identifies the association of HEV IRESl with several host ribosomal proteins, demonstrates indispensable roles of ribosomal protein RPL5 and DHX9 (RNA helicase A) in mediating HEV IRESl activity, and establishes the latter as a bona fide internal translation initiation site. IMPORTANCE Protein synthesis is a fundamental process for survival and proliferation of all living organisms. The majority of cellular proteins are produced through cap-dependent translation. Cells also use a variety of cap-independent translation processes to synthesize essential proteins during stress. Viruses depend on the host cell translation machinery to synthesize their own proteins. Hepatitis E virus (HEV) is a major cause of hepatitis worldwide and has a capped positive-strand RNA genome. Viral nonstructural and structural proteins are synthesized through a cap-dependent translation process. An earlier study from our laboratory reported the presence of a fourth open reading frame (ORF) in genotype 1 HEV, which produces the ORF4 protein using a cap-independent internal ribosome entry site-like (IRESl) element. In the current study, we identified the host proteins that associate with the HEV-IRESl RNA and generated the RNA-protein interactome. Through a variety of experimental approaches, our data prove that HEV-IRESl is a bona fide internal translation initiation site.
Collapse
Affiliation(s)
- Shiv Kumar
- Virology Laboratory, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Rohit Verma
- Virology Laboratory, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Sandhini Saha
- Laboratory of Functional Proteomics, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Ashish Kumar Agrahari
- Noncommunicable Disease Group, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Shivangi Shukla
- Virology Laboratory, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Oinam Ningthemmani Singh
- Virology Laboratory, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Umang Berry
- Virology Laboratory, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Anurag
- Virology Laboratory, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Tushar Kanti Maiti
- Laboratory of Functional Proteomics, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Shailendra Asthana
- Noncommunicable Disease Group, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - C. T. Ranjith-Kumar
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, India
| | - Milan Surjit
- Virology Laboratory, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| |
Collapse
|
10
|
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.
Collapse
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
| |
Collapse
|
11
|
Kiliszek A, Rypniewski W, Błaszczyk L. Exploring structural determinants and the role of nucleolin in formation of the long-range interactions between untranslated regions of p53 mRNA. RNA (NEW YORK, N.Y.) 2023; 29:630-643. [PMID: 36653114 PMCID: PMC10158990 DOI: 10.1261/rna.079378.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 01/02/2023] [Indexed: 05/06/2023]
Abstract
p53 protein is a key regulator of cellular homeostasis by coordinating the framework of antiproliferative pathways as a response to various stress factors. Although the main mechanism of stress-dependent induction of p53 protein relies on post-translational modifications influencing its stability and activity, a growing amount of evidence suggests that complex regulation of p53 expression occurs also at the mRNA level. This study explores structural determinants of long-range RNA-RNA interactions in p53 mRNA, crucial for stress-dependent regulation of p53 protein translation. We demonstrate that the 8-nt bulge motif plays a key structural role in base-pairing of complementary sequences from the 5' and 3' untranslated regions of p53 mRNA. We also show that one of the p53 translation regulators, nucleolin, displays an RNA chaperone activity and facilitates the association of sequences involved in the formation of long-range interactions in p53 mRNA. Nucleolin promotes base-pairing of complementary sequences through the bulge motif, because mutations of this region reduce or inhibit pairing while compensatory mutations restore this interaction. Mutational analysis of nucleolin reveals that all four RNA recognition motifs are indispensable for optimal RNA chaperone activity of nucleolin. These observations help to decipher the unique mechanism of p53 protein translation regulation pointing to bulge motif and nucleolin as the critical factors during intramolecular RNA-RNA recognition in p53 mRNA.
Collapse
Affiliation(s)
- Agnieszka Kiliszek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznań, Poland
| | - Wojciech Rypniewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznań, Poland
| | - Leszek Błaszczyk
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznań, Poland
| |
Collapse
|
12
|
McCann JJ, Fleenor DE, Chen J, Lai CH, Bass TE, Kastan MB. Participation of ATM, SMG1, and DDX5 in a DNA Damage-Induced Alternative Splicing Pathway. Radiat Res 2023; 199:406-421. [PMID: 36921295 PMCID: PMC10162594 DOI: 10.1667/rade-22-00219.1] [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: 12/09/2022] [Accepted: 02/03/2023] [Indexed: 03/17/2023]
Abstract
Altered cellular responses to DNA damage can contribute to cancer development, progression, and therapeutic resistance. Mutations in key DNA damage response factors occur across many cancer types, and the DNA damage-responsive gene, TP53, is frequently mutated in a high percentage of cancers. We recently reported that an alternative splicing pathway induced by DNA damage regulates alternative splicing of TP53 RNA and further modulates cellular stress responses. Through damage-induced inhibition of the SMG1 kinase, TP53 pre-mRNA is alternatively spliced to generate TP53b mRNA and p53b protein is required for optimal induction of cellular senescence after ionizing radiation-induced DNA damage. Herein, we confirmed and extended these observations by demonstrating that the ATM protein kinase is required for repression of SMG1 kinase activity after ionizing radiation. We found that the RNA helicase and splicing factor, DDX5, interacts with SMG1, is required for alternative splicing of TP53 pre-mRNA to TP53b and TP53c mRNAs after DNA damage, and contributes to radiation-induced cellular senescence. Interestingly, the role of SMG1 in alternative splicing of p53 appears to be distinguishable from its role in regulating nonsense-mediated RNA decay. Thus, ATM, SMG1, and DDX5 participate in a DNA damage-induced alternative splicing pathway that regulates TP53 splicing and modulates radiation-induced cellular senescence.
Collapse
Affiliation(s)
- Jennifer J. McCann
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina 27710
| | - Donald E. Fleenor
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina 27710
| | - Jing Chen
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina 27710
| | - Chun-Hsiang Lai
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina 27710
| | - Thomas E. Bass
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina 27710
| | - Michael B. Kastan
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina 27710
| |
Collapse
|
13
|
Guo J, Peng Y. A tRF oligomerizes Nucleolin to stabilize metastasis-favoring transcripts. SCIENCE CHINA. LIFE SCIENCES 2023; 66:646-648. [PMID: 36422759 DOI: 10.1007/s11427-022-2234-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 10/21/2022] [Indexed: 11/25/2022]
Affiliation(s)
- Jiawei Guo
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yong Peng
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China.
| |
Collapse
|
14
|
Paris EA, Bahr JM, Basu S, Barua A. Changes in Nucleolin Expression during Malignant Transformation Leading to Ovarian High-Grade Serous Carcinoma. Cancers (Basel) 2023; 15:cancers15030661. [PMID: 36765618 PMCID: PMC9913361 DOI: 10.3390/cancers15030661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/19/2023] [Accepted: 01/20/2023] [Indexed: 01/24/2023] Open
Abstract
OBJECTIVE Ovarian high-grade serous carcinoma (HGSC) is a fatal malignancy of women. Alterations in the expression of nuclear proteins are early steps in malignant transformation; nucleolin is one such protein. Changes in nucleolin expression and circulatory levels during ovarian HGSC development are unknown. The study goal was to determine if tissue and circulatory levels of nucleolin change in response to malignant transformation leading to ovarian HGSC. METHODS Sera, ovaries, and BRCA+ fimbria from healthy subjects, and sera and tumor tissues from patients (n = 10 each), and healthy hens and hens with HGSC were examined in exploratory and prospective studies for nucleolin expression by immunohistochemistry, immunoblotting, gene expression, and immunoassay, and analyzed by analysis of variance (ANOVA). RESULTS Compared with normal, nucleolin expression was higher in patients and hens with ovarian HGSC and in women with a risk of HGSC (P < 0.05). Compared with normal (1400 + 105 pg/mL, n = 8), serum nucleolin levels were 1.5 and 1.7-fold higher in patients with early- (n = 5) and late-stage (n = 5) HGSC, respectively. Additionally, serum nucleolin levels increased significantly (P < 0.05) prior to the formation of detectable masses. CONCLUSION This pilot study concluded that tissue and serum levels of nucleolin increase in association with malignant changes in ovaries and fimbriae leading to ovarian HGSC.
Collapse
Affiliation(s)
- Elizabeth A. Paris
- Department of Anatomy & Cell Biology, Rush University Medical Center, Chicago, IL 60612, USA
| | - Janice M. Bahr
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Sanjib Basu
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL 60612, USA
| | - Animesh Barua
- Department of Anatomy & Cell Biology, Rush University Medical Center, Chicago, IL 60612, USA
- Department of Pathology, Rush University Medical Center, Chicago, IL 60612, USA
- Department of Obstetrics and Gynecology, Rush University Medical Center, Chicago, IL 60612, USA
- Correspondence:
| |
Collapse
|
15
|
Bhoopalan SV, Yen JS, Mayuranathan T, Mayberry KD, Yao Y, Lillo Osuna MA, Jang Y, Liyanage JS, Blanc L, Ellis SR, Wlodarski MW, Weiss MJ. An RPS19-edited model for Diamond-Blackfan anemia reveals TP53-dependent impairment of hematopoietic stem cell activity. JCI Insight 2023; 8:e161810. [PMID: 36413407 PMCID: PMC9870085 DOI: 10.1172/jci.insight.161810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 11/16/2022] [Indexed: 11/24/2022] Open
Abstract
Diamond-Blackfan anemia (DBA) is a genetic blood disease caused by heterozygous loss-of-function mutations in ribosomal protein (RP) genes, most commonly RPS19. The signature feature of DBA is hypoplastic anemia occurring in infants, although some older patients develop multilineage cytopenias with bone marrow hypocellularity. The mechanism of anemia in DBA is not fully understood and even less is known about the pancytopenia that occurs later in life, in part because patient hematopoietic stem and progenitor cells (HSPCs) are difficult to obtain, and the current experimental models are suboptimal. We modeled DBA by editing healthy human donor CD34+ HSPCs with CRISPR/Cas9 to create RPS19 haploinsufficiency. In vitro differentiation revealed normal myelopoiesis and impaired erythropoiesis, as observed in DBA. After transplantation into immunodeficient mice, bone marrow repopulation by RPS19+/- HSPCs was profoundly reduced, indicating hematopoietic stem cell (HSC) impairment. The erythroid and HSC defects resulting from RPS19 haploinsufficiency were partially corrected by transduction with an RPS19-expressing lentiviral vector or by Cas9 disruption of TP53. Our results define a tractable, biologically relevant experimental model of DBA based on genome editing of primary human HSPCs and they identify an associated HSC defect that emulates the pan-hematopoietic defect of DBA.
Collapse
Affiliation(s)
| | | | | | | | - Yu Yao
- Department of Hematology, and
| | | | | | - Janaka S.S. Liyanage
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Lionel Blanc
- Institute of Molecular Medicine, Feinstein Institutes for Medical Research, Manhasset, New York, USA
| | - Steven R. Ellis
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, Kentucky, USA
| | | | | |
Collapse
|
16
|
Nucleolin; A tumor associated antigen as a potential lung cancer biomarker. Pathol Res Pract 2022; 240:154160. [DOI: 10.1016/j.prp.2022.154160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 08/11/2022] [Accepted: 10/05/2022] [Indexed: 11/06/2022]
|
17
|
San A, Palmieri D, Saxena A, Singh S. In silico study predicts a key role of RNA-binding domains 3 and 4 in nucleolin-miRNA interactions. Proteins 2022; 90:1837-1850. [PMID: 35514080 DOI: 10.1002/prot.26355] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 04/07/2022] [Accepted: 04/26/2022] [Indexed: 12/17/2023]
Abstract
RNA binding proteins (RBPs) regulate many important cellular processes through their interactions with RNA molecules. RBPs are critical for posttranscriptional mechanisms keeping gene regulation in a fine equilibrium. Conversely, dysregulation of RBPs and RNA metabolism pathways is an established hallmark of tumorigenesis. Human nucleolin (NCL) is a multifunctional RBP that interacts with different types of RNA molecules, in part through its four RNA binding domains (RBDs). Particularly, NCL interacts directly with microRNAs (miRNAs) and is involved in their aberrant processing linked with many cancers, including breast cancer. Nonetheless, molecular details of the NCL-miRNA interaction remain obscure. In this study, we used an in silico approach to characterize how NCL targets miRNAs and whether this specificity is imposed by a definite RBD-interface. Here, we present structural models of NCL-RBDs and miRNAs, as well as predict scenarios of NCL-miRNA interactions generated using docking algorithms. Our study suggests a predominant role of NCL RBDs 3 and 4 (RBD3-4) in miRNA binding. We provide detailed analyses of specific motifs/residues at the NCL-substrate interface in both these RBDs and miRNAs. Finally, we propose that the evolutionary emergence of more than two RBDs in NCL in higher organisms coincides with its additional role/s in miRNA processing. Our study shows that RBD3-4 display sequence/structural determinants to specifically recognize miRNA precursor molecules. Moreover, the insights from this study can ultimately support the design of novel antineoplastic drugs aimed at regulating NCL-dependent biological pathways with a causal role in tumorigenesis.
Collapse
Affiliation(s)
- Avdar San
- Department of Biology, Brooklyn College, The City University of New York, Brooklyn, New York, USA
- The Biochemistry PhD Program, The Graduate Center of the City University of New York, New York, New York, USA
| | - Dario Palmieri
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Anjana Saxena
- Department of Biology, Brooklyn College, The City University of New York, Brooklyn, New York, USA
- The Biochemistry PhD Program, The Graduate Center of the City University of New York, New York, New York, USA
| | - Shaneen Singh
- Department of Biology, Brooklyn College, The City University of New York, Brooklyn, New York, USA
- The Biochemistry PhD Program, The Graduate Center of the City University of New York, New York, New York, USA
| |
Collapse
|
18
|
Xu Y, Ruggero D. A tRF nucleator for Nucleolin in cancer metastasis. Mol Cell 2022; 82:2536-2538. [PMID: 35868253 DOI: 10.1016/j.molcel.2022.06.025] [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] [Indexed: 11/19/2022]
Abstract
In this issue of Molecular Cell, Liu et al. (2022) report that 5'-tRFCys, a stress-induced transfer RNA-derived RNA fragment (tRF) derived from the 5' halves of cysteine tRNAs, regulates post-transcriptional gene expression, enabling the survival and lung metastasis formation of breast cancers.
Collapse
Affiliation(s)
- Yichen Xu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China; Department of Pharmacy, Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, China
| | - Davide Ruggero
- Department of Urology, University of California San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA.
| |
Collapse
|
19
|
Liu X, Mei W, Padmanaban V, Alwaseem H, Molina H, Passarelli MC, Tavora B, Tavazoie SF. A pro-metastatic tRNA fragment drives Nucleolin oligomerization and stabilization of its bound metabolic mRNAs. Mol Cell 2022; 82:2604-2617.e8. [PMID: 35654044 PMCID: PMC9444141 DOI: 10.1016/j.molcel.2022.05.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 04/04/2022] [Accepted: 05/05/2022] [Indexed: 01/09/2023]
Abstract
Stress-induced cleavage of transfer RNAs (tRNAs) into tRNA-derived fragments (tRFs) occurs across organisms from yeast to humans; yet, its mechanistic underpinnings and pathological consequences remain poorly defined. Small RNA profiling revealed increased abundance of a cysteine tRNA fragment (5'-tRFCys) during breast cancer metastatic progression. 5'-tRFCys was required for efficient breast cancer metastatic lung colonization and cancer cell survival. We identified Nucleolin as the direct binding partner of 5'-tRFCys. 5'-tRFCys promoted the oligomerization of Nucleolin and its bound metabolic transcripts Mthfd1l and Pafah1b1 into a higher-order transcript stabilizing ribonucleoprotein complex, which protected these transcripts from exonucleolytic degradation. Consistent with this, Mthfd1l and Pafah1b1 mediated pro-metastatic and metabolic effects downstream of 5'-tRFCys-impacting folate, one-carbon, and phosphatidylcholine metabolism. Our findings reveal that a tRF can promote oligomerization of an RNA-binding protein into a transcript stabilizing ribonucleoprotein complex, thereby driving specific metabolic pathways underlying cancer progression.
Collapse
Affiliation(s)
- Xuhang Liu
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY 10065, USA
| | - Wenbin Mei
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY 10065, USA
| | - Veena Padmanaban
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY 10065, USA
| | - Hanan Alwaseem
- Proteomics Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Henrik Molina
- Proteomics Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Maria C Passarelli
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY 10065, USA
| | - Bernardo Tavora
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY 10065, USA
| | - Sohail F Tavazoie
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY 10065, USA.
| |
Collapse
|
20
|
Yangngam S, Prasopsiri J, Hatthakarnkul P, Thongchot S, Thuwajit P, Yenchitsomanus PT, Edwards J, Thuwajit C. Cellular localization of nucleolin determines the prognosis in cancers: a meta-analysis. J Mol Med (Berl) 2022; 100:1145-1157. [PMID: 35861882 PMCID: PMC9329415 DOI: 10.1007/s00109-022-02228-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 06/09/2022] [Accepted: 06/22/2022] [Indexed: 12/01/2022]
Abstract
Nucleolin (NCL) is a multifunctional protein expressed in the nucleus, cytoplasm, and cell membrane. Overexpression of NCL has a controversial role as a poor prognostic marker in cancers. In this study, a meta-analysis was performed to evaluate the prognostic value of NCL in different subcellular localizations (cytoplasmic (CyNCL) and nuclear (NuNCL)) across a range of cancers. PubMed was searched for relevant publications. Data were extracted and analyzed from 12 studies involving 1221 patients with eight cancer types. The results revealed high total NCL was significantly associated with poor overall survival (OS) (HR = 2.85 (1.94, 4.91), p < 0.00001, I2 = 59%) and short disease-free survival (DFS) (HR = 3.57 (2.76, 4.62), p < 0.00001, I2 = 2%). High CyNCL was significantly associated with poor OS (HR = 4.32 (3.01, 6.19), p < 0.00001, I2 = 0%) and short DFS (HR = 3.00 (2.17, 4.15), p < 0.00001, I2 = 0%). In contrast, high NuNCL correlated with increased patient OS (HR = 0.42 (0.20, 0.86), p = 0.02, I2 = 66%), with no significant correlation to DFS observed (HR = 0.46 (0.19, 1.14), p = 0.09, I2 = 57%). This study supports the role of subcellular NCL as a poor prognostic cancer biomarker.
Collapse
Affiliation(s)
- Supaporn Yangngam
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Jaturawitt Prasopsiri
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Phimmada Hatthakarnkul
- Biomedical Sciences Graduate Program, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand.,Institute of Cancer Sciences, University of Glasgow, Wolfson Wohl Cancer Research Centre, Garscube Estate, Glasgow, G61 1QH, UK
| | - Suyanee Thongchot
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand.,Siriraj Center of Research Excellence for Cancer Immunotherapy (SiCORE-CIT), Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Peti Thuwajit
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Pa-Thai Yenchitsomanus
- Siriraj Center of Research Excellence for Cancer Immunotherapy (SiCORE-CIT), Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Joanne Edwards
- Institute of Cancer Sciences, University of Glasgow, Wolfson Wohl Cancer Research Centre, Garscube Estate, Glasgow, G61 1QH, UK
| | - Chanitra Thuwajit
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand.
| |
Collapse
|
21
|
Wang D, Hou L, Zhu N, Yang X, Zhou J, Cui Y, Guo J, Feng X, Liu J. Interaction of Nucleolin with the Fusion Protein of Avian Metapneumovirus Subgroup C Contributes to Viral Replication. Viruses 2022; 14:v14071402. [PMID: 35891383 PMCID: PMC9317408 DOI: 10.3390/v14071402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 06/23/2022] [Accepted: 06/24/2022] [Indexed: 12/02/2022] Open
Abstract
Avian metapneumovirus subgroup C (aMPV/C) is highly pathogenic to various avian species with acute respiratory tract clinicopathology and/or drops in egg production. Nucleolin (NCL), an important nucleolar protein, has been shown to regulate multiple viral replication and serve as a functional receptor for viral entry and internalization. Whether NCL is involved in aMPV/C pathogenesis is not known. In this study, we found that aMPV/C infection altered the subcellular localization of NCL in cultured cells. siRNA-targeted NCL resulted in a remarkable decline in aMPV/C replication in Vero cells. DF-1 cells showed a similar response after CRISPR/Cas9-mediated knock out of NCL during aMPV/C infection. Conversely, NCL overexpression significantly increased aMPV/C replication. Pretreatment with AS1411-a aptamer, a guanine (G)-rich oligonucleotide that forms four-stranded structures and competitively binding to NCL, decreased aMPV/C replication and viral titers in cultured cells. Additionally, we found that the aMPV/C fusion (F) protein specifically interacts with NCL through its central domain and that AS1411 disrupts this interaction, thus inhibiting viral replication. Taken together, these results reveal that the aMPV/C F protein interacts with NCL, which is employed by aMPV/C for efficient replication, thereby highlighting the strategic potential for control and therapy of aMPV/C infection.
Collapse
Affiliation(s)
- Dedong Wang
- College of Veterimary Medicine, Yangzhou University, Yangzhou 225009, China; (D.W.); (L.H.); (N.Z.); (X.Y.); (J.Z.); (Y.C.); (J.G.); (X.F.)
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Lei Hou
- College of Veterimary Medicine, Yangzhou University, Yangzhou 225009, China; (D.W.); (L.H.); (N.Z.); (X.Y.); (J.Z.); (Y.C.); (J.G.); (X.F.)
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Ning Zhu
- College of Veterimary Medicine, Yangzhou University, Yangzhou 225009, China; (D.W.); (L.H.); (N.Z.); (X.Y.); (J.Z.); (Y.C.); (J.G.); (X.F.)
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Xiaoyu Yang
- College of Veterimary Medicine, Yangzhou University, Yangzhou 225009, China; (D.W.); (L.H.); (N.Z.); (X.Y.); (J.Z.); (Y.C.); (J.G.); (X.F.)
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Jianwei Zhou
- College of Veterimary Medicine, Yangzhou University, Yangzhou 225009, China; (D.W.); (L.H.); (N.Z.); (X.Y.); (J.Z.); (Y.C.); (J.G.); (X.F.)
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Yongqiu Cui
- College of Veterimary Medicine, Yangzhou University, Yangzhou 225009, China; (D.W.); (L.H.); (N.Z.); (X.Y.); (J.Z.); (Y.C.); (J.G.); (X.F.)
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Jinshuo Guo
- College of Veterimary Medicine, Yangzhou University, Yangzhou 225009, China; (D.W.); (L.H.); (N.Z.); (X.Y.); (J.Z.); (Y.C.); (J.G.); (X.F.)
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Xufei Feng
- College of Veterimary Medicine, Yangzhou University, Yangzhou 225009, China; (D.W.); (L.H.); (N.Z.); (X.Y.); (J.Z.); (Y.C.); (J.G.); (X.F.)
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Jue Liu
- College of Veterimary Medicine, Yangzhou University, Yangzhou 225009, China; (D.W.); (L.H.); (N.Z.); (X.Y.); (J.Z.); (Y.C.); (J.G.); (X.F.)
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
- Correspondence:
| |
Collapse
|
22
|
Dash S, Trainor PA. Nucleolin loss of function leads to aberrant Fibroblast Growth Factor signaling and craniofacial anomalies. Development 2022; 149:dev200349. [PMID: 35762670 PMCID: PMC9270975 DOI: 10.1242/dev.200349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 04/25/2022] [Indexed: 11/23/2022]
Abstract
Ribosomal RNA (rRNA) transcription and ribosome biogenesis are global processes required for growth and proliferation of all cells, yet perturbation of these processes in vertebrates leads to tissue-specific defects termed ribosomopathies. Mutations in rRNA transcription and processing proteins often lead to craniofacial anomalies; however, the cellular and molecular reasons for these defects are poorly understood. Therefore, we examined the function of the most abundant nucleolar phosphoprotein, Nucleolin (Ncl), in vertebrate development. ncl mutant (ncl-/-) zebrafish present with craniofacial anomalies such as mandibulofacial hypoplasia. We observed that ncl-/- mutants exhibited decreased rRNA synthesis and p53-dependent apoptosis, consistent with a role in ribosome biogenesis. However, we found that Nucleolin also performs functions not associated with ribosome biogenesis. We discovered that the half-life of fgf8a mRNA was reduced in ncl-/- mutants, which perturbed Fgf signaling, resulting in misregulated Sox9a-mediated chondrogenesis and Runx2-mediated osteogenesis. Consistent with this model, exogenous FGF8 treatment significantly rescued the cranioskeletal phenotype in ncl-/- zebrafish, suggesting that Nucleolin regulates osteochondroprogenitor differentiation. Our work has therefore uncovered tissue-specific functions for Nucleolin in rRNA transcription and post-transcriptional regulation of growth factor signaling during embryonic craniofacial development.
Collapse
Affiliation(s)
- Soma Dash
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Paul A. Trainor
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| |
Collapse
|
23
|
Yin A, Feng M, Zhang L, Cheng Z, Li Y, Qian L. Identification of a novel native peptide derived from 60S ribosomal protein L23a that translationally regulates p53 to reduce myocardial ischemia-reperfusion. Pharmacol Res 2022; 175:105988. [PMID: 34808368 DOI: 10.1016/j.phrs.2021.105988] [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: 08/24/2021] [Revised: 10/22/2021] [Accepted: 11/11/2021] [Indexed: 11/22/2022]
Abstract
Myocardial ischemia-reperfusion (I/R) is a severe disease,but its underlying mechanism is not fully elucidated and no effective clinical treatment is available. Utilizing intracellular peptidomics, we identified a novel native peptide PDRL23A (Peptide Derived from RPL23A), that is intimately related to hypoxic stress. We further show that PDRL23A effectively alleviates hypoxia-induced cardiomyocyte injury in vitro, along with improvements in mitochondrial function and redox homeostasis, including ROS accumulation, oxidative phosphorylation, and mitochondrial membrane potential. Strikingly, the in vivo results indicate that, short-term pretreatment with PDRL23A could effectively inhibit I/R-induced cardiomyocyte death, myocardial fibrosis and decreased cardiac function. Interestingly, PDRL23A was found to interact with 60 S ribosomal protein L26 (RPL26), hampering RPL26-governed p53 translation, and resulting in a reduction in the level of p53 protein, which in turn reduced p53-mediated apoptosis under hypoxic conditions. Collectively, a native peptide, PDRL23A, which translationally regulates p53 to protect against myocardial I/R injury, has been identified for the first time. Our findings provide insight into the adaptive mechanisms of hypoxia and present a potential new treatment for myocardial I/R.
Collapse
Affiliation(s)
- Anwen Yin
- Hongqiao International Institute of Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200336, China
| | - Mengwen Feng
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Li Zhang
- Hongqiao International Institute of Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200336, China
| | - Zijie Cheng
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Yun Li
- Hongqiao International Institute of Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200336, China.
| | - Lingmei Qian
- Hongqiao International Institute of Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200336, China; Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China.
| |
Collapse
|
24
|
Godet AC, Roussel E, David F, Hantelys F, Morfoisse F, Alves J, Pujol F, Ader I, Bertrand E, Burlet-Schiltz O, Froment C, Henras AK, Vitali P, Lacazette E, Tatin F, Garmy-Susini B, Prats AC. Long non-coding RNA Neat1 and paraspeckle components are translational regulators in hypoxia. eLife 2022; 11:69162. [PMID: 36546462 PMCID: PMC9799981 DOI: 10.7554/elife.69162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 12/18/2022] [Indexed: 12/24/2022] Open
Abstract
Internal ribosome entry sites (IRESs) drive translation initiation during stress. In response to hypoxia, (lymph)angiogenic factors responsible for tissue revascularization in ischemic diseases are induced by the IRES-dependent mechanism. Here, we searched for IRES trans-acting factors (ITAFs) active in early hypoxia in mouse cardiomyocytes. Using knock-down and proteomics approaches, we show a link between a stressed-induced nuclear body, the paraspeckle, and IRES-dependent translation. Furthermore, smiFISH experiments demonstrate the recruitment of IRES-containing mRNA into paraspeckle during hypoxia. Our data reveal that the long non-coding RNA Neat1, an essential paraspeckle component, is a key translational regulator, active on IRESs of (lymph)angiogenic and cardioprotective factor mRNAs. In addition, paraspeckle proteins p54nrb and PSPC1 as well as nucleolin and RPS2, two p54nrb-interacting proteins identified by mass spectrometry, are ITAFs for IRES subgroups. Paraspeckle thus appears as a platform to recruit IRES-containing mRNAs and possibly host IRESome assembly. Polysome PCR array shows that Neat1 isoforms regulate IRES-dependent translation and, more widely, translation of mRNAs involved in stress response.
Collapse
Affiliation(s)
| | - Emilie Roussel
- UMR 1297-I2MC, Inserm, Université de ToulouseToulouseFrance
| | - Florian David
- UMR 1297-I2MC, Inserm, Université de ToulouseToulouseFrance
| | | | | | - Joffrey Alves
- UMR 1297-I2MC, Inserm, Université de ToulouseToulouseFrance
| | | | - Isabelle Ader
- UMR 1301-RESTORE, Inserm, CNRS 5070, Etablissement Français du Sang-Occitanie (EFS), National Veterinary School of Toulouse (ENVT), Université de ToulouseToulouseFrance
| | | | - Odile Burlet-Schiltz
- Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, CNRSToulouseFrance
| | - Carine Froment
- Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, CNRSToulouseFrance
| | - Anthony K Henras
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), Université de ToulouseToulouseFrance
| | - Patrice Vitali
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), Université de ToulouseToulouseFrance
| | - Eric Lacazette
- UMR 1297-I2MC, Inserm, Université de ToulouseToulouseFrance
| | - Florence Tatin
- UMR 1297-I2MC, Inserm, Université de ToulouseToulouseFrance
| | | | | |
Collapse
|
25
|
Janecki DM, Swiatkowska A, Szpotkowska J, Urbanowicz A, Kabacińska M, Szpotkowski K, Ciesiołka J. Poly(C)-binding Protein 2 Regulates the p53 Expression via Interactions with the 5'-Terminal Region of p53 mRNA. Int J Mol Sci 2021; 22:ijms222413306. [PMID: 34948101 PMCID: PMC8708005 DOI: 10.3390/ijms222413306] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/03/2021] [Accepted: 12/07/2021] [Indexed: 11/16/2022] Open
Abstract
The p53 protein is one of the major transcriptional factors which guards cell homeostasis. Here, we showed that poly(C)-binding protein 2 (PCBP2) can bind directly to the 5′ terminus of p53 mRNA by means of electrophoretic mobility shift assay. Binding sites of PCBP2 within this region of p53 mRNA were mapped using Pb2+-induced cleavage and SAXS methods. Strikingly, the downregulation of PCBP2 in HCT116 cells resulted in a lower level of p53 protein under normal and stress conditions. Quantitative analysis of p53 mRNA in PCBP2-downregulated cells revealed a lower level of p53 mRNA under normal conditions suggesting the involvement of PCBP2 in p53 mRNA stabilisation. However, no significant change in p53 mRNA level was observed upon PCBP2 depletion under genotoxic stress. Moreover, a higher level of p53 protein in the presence of rapamycin or doxorubicin and the combination of both antibiotics was noticed in PCBP2-overexpressed cells compared to control cells. These observations indicate the potential involvement of PCBP2 in cap-independent translation of p53 mRNA especially occurring under stress conditions. It has been postulated that the PCBP2 protein is engaged in the enhancement of p53 mRNA stability, probably via interacting with its 3′ end. Our data show that under stress conditions PCBP2 also modulates p53 translation through binding to the 5′ terminus of p53 mRNA. Thus PCBP2 emerges as a double-function factor in the p53 expression.
Collapse
|
26
|
Salomón R, Furones MD, Reyes-López FE, Tort L, Firmino JP, Esteban MA, Espinosa Ruíz C, Quintela JC, Pinilla-Rosas JM, Vallejos-Vidal E, Gisbert E. A Bioactive Extract Rich in Triterpenic Acid and Polyphenols from Olea europaea Promotes Systemic Immunity and Protects Atlantic Salmon Smolts Against Furunculosis. Front Immunol 2021; 12:737601. [PMID: 34867959 PMCID: PMC8633542 DOI: 10.3389/fimmu.2021.737601] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 10/18/2021] [Indexed: 12/14/2022] Open
Abstract
In the present study, the modulation of the transcriptional immune response (microarray analysis) in the head kidney (HK) of the anadromous fish Atlantic salmon (Salmo salar) fed a diet supplemented with an olive fruit extract (AQUOLIVE®) was evaluated. At the end of the trial (133 days), in order to investigate the immunomodulatory properties of the phytogenic tested against a bacterial infection, an in vivo challenge with Aeromonas salmonicida was performed. A total number of 1,027 differentially expressed genes (DEGs) (805 up- and 222 downregulated) were found when comparing the transcriptomic profiling of the HK from fish fed the control and AQUOLIVE® diets. The HK transcripteractome revealed an expression profile that mainly favored biological processes related to immunity. Particularly, the signaling of i-kappa B kinase/NF-kappa and the activation of leukocytes, such as granulocytes and neutrophils degranulation, were suggested to be the primary actors of the innate immune response promoted by the tested functional feed additive in the HK. Moreover, the bacterial challenge with A. salmonicida that lasted 12 days showed that the cumulative survival was higher in fish fed the AQUOLIVE® diet (96.9 ± 6.4%) than the control group (60.7 ± 13.5%). These results indicate that the dietary supplementation of AQUOLIVE® at the level of 0.15% enhanced the systemic immune response and reduced the A. salmonicida cumulative mortality in Atlantic salmon smolts.
Collapse
Affiliation(s)
- Ricardo Salomón
- Aquaculture Program, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Centre de Sant Carles de la Ràpita (IRTA-SCR), Sant Carles de la Ràpita, Spain.,PhD Program in Aquaculture, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - M Dolors Furones
- Aquaculture Program, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Centre de Sant Carles de la Ràpita (IRTA-SCR), Sant Carles de la Ràpita, Spain
| | - Felipe E Reyes-López
- Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, Bellaterra, Spain.,Facultad de Medicina Veterinaria y Agronomía, Universidad de Las Américas, Santiago, Chile.,Centro de Biotecnología Acuícola, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Lluis Tort
- Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Joana P Firmino
- Aquaculture Program, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Centre de Sant Carles de la Ràpita (IRTA-SCR), Sant Carles de la Ràpita, Spain
| | - M Angeles Esteban
- Department of Cell Biology and Histology, Faculty of Biology, University of Murcia, Murcia, Spain
| | - Cristóbal Espinosa Ruíz
- Department of Cell Biology and Histology, Faculty of Biology, University of Murcia, Murcia, Spain
| | - José C Quintela
- Scientific Department, Natac Biotech, Alcorcón, Madrid, Spain
| | | | - Eva Vallejos-Vidal
- Centro de Biotecnología Acuícola, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Enric Gisbert
- Aquaculture Program, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Centre de Sant Carles de la Ràpita (IRTA-SCR), Sant Carles de la Ràpita, Spain
| |
Collapse
|
27
|
Vadivel Gnanasundram S, Bonczek O, Wang L, Chen S, Fahraeus R. p53 mRNA Metabolism Links with the DNA Damage Response. Genes (Basel) 2021; 12:genes12091446. [PMID: 34573428 PMCID: PMC8465283 DOI: 10.3390/genes12091446] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/10/2021] [Accepted: 09/13/2021] [Indexed: 12/14/2022] Open
Abstract
Human cells are subjected to continuous challenges by different genotoxic stress attacks. DNA damage leads to erroneous mutations, which can alter the function of oncogenes or tumor suppressors, resulting in cancer development. To circumvent this, cells activate the DNA damage response (DDR), which mainly involves cell cycle regulation and DNA repair processes. The tumor suppressor p53 plays a pivotal role in the DDR by halting the cell cycle and facilitating the DNA repair processes. Various pathways and factors participating in the detection and repair of DNA have been described, including scores of RNA-binding proteins (RBPs) and RNAs. It has become increasingly clear that p53’s role is multitasking, and p53 mRNA regulation plays a prominent part in the DDR. This review is aimed at covering the p53 RNA metabolism linked to the DDR and highlights the recent findings.
Collapse
Affiliation(s)
- Sivakumar Vadivel Gnanasundram
- Department of Medical Biosciences, Umeå University, 901-87 Umeå, Sweden; (O.B.); (L.W.); (S.C.)
- Correspondence: (S.V.G.); (R.F.)
| | - Ondrej Bonczek
- Department of Medical Biosciences, Umeå University, 901-87 Umeå, Sweden; (O.B.); (L.W.); (S.C.)
- RECAMO, Masaryk Memorial Cancer Institute, Zluty Kopec 7, 656-53 Brno, Czech Republic
| | - Lixiao Wang
- Department of Medical Biosciences, Umeå University, 901-87 Umeå, Sweden; (O.B.); (L.W.); (S.C.)
| | - Sa Chen
- Department of Medical Biosciences, Umeå University, 901-87 Umeå, Sweden; (O.B.); (L.W.); (S.C.)
| | - Robin Fahraeus
- Department of Medical Biosciences, Umeå University, 901-87 Umeå, Sweden; (O.B.); (L.W.); (S.C.)
- RECAMO, Masaryk Memorial Cancer Institute, Zluty Kopec 7, 656-53 Brno, Czech Republic
- Inserm UMRS1131, Institut de Genetique Moleculaire, Universite Paris 7, Hopital St Louis, F-75010 Paris, France
- International Centre for Cancer Vaccine Science, University of Gdansk, 80-822 Gdansk, Poland
- Correspondence: (S.V.G.); (R.F.)
| |
Collapse
|
28
|
Hagerty JR, Kim HC, Jolly ER. Multiomic analysis of Schistosoma mansoni reveals unique expression profiles in cercarial heads and tails. Commun Biol 2021; 4:860. [PMID: 34253841 PMCID: PMC8275615 DOI: 10.1038/s42003-021-02366-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 06/15/2021] [Indexed: 02/06/2023] Open
Abstract
Schistosomes require both molluscan and mammalian hosts for development. The larval cercaria exits the snail host and swims to identify and invade the mammalian host. The cercaria has two macrostructures, the head and the tail. The head invades the host, where it matures into an adult worm. The tail is lost after host invasion. Translation in the cercaria differs in each macrostructure, with higher levels of translation in the cercarial tail and little to no translational activity in the cercarial head. We compared the transcriptome and proteome of the cercarial head and tail and observed stark differences between the two macrostructures. We identified unique and differentially expressed transcripts and proteins, including ribosomal components expressed in higher levels in tails than in heads, which may explain the differences in translation levels between heads and tails. We also characterized the weak correlation between transcription and translation in infectious cercarial heads and tails.
Collapse
Affiliation(s)
- James R Hagerty
- Case Western Reserve University, Department of Biology, Cleveland, OH, USA
| | - Hyung Chul Kim
- Case Western Reserve University, Department of Biology, Cleveland, OH, USA
| | - Emmitt R Jolly
- Case Western Reserve University, Department of Biology, Cleveland, OH, USA.
- Case Western Reserve University, Center for Global Health and Disease, Cleveland, OH, USA.
| |
Collapse
|
29
|
Han S, Wang X, Guan J, Wu J, Zhang Y, Li P, Liu Z, Abdullah SW, Zhang Z, Jin Y, Sun S, Guo H. Nucleolin Promotes IRES-Driven Translation of Foot-and-Mouth Disease Virus by Supporting the Assembly of Translation Initiation Complexes. J Virol 2021; 95:e0023821. [PMID: 33853964 PMCID: PMC8315980 DOI: 10.1128/jvi.00238-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 04/06/2021] [Indexed: 12/12/2022] Open
Abstract
Nucleolin (NCL), a stress-responsive RNA-binding protein, has been implicated in the translation of internal ribosome entry site (IRES)-containing mRNAs, which encode proteins involved in cell proliferation, carcinogenesis, and viral infection (type I IRESs). However, the details of the mechanisms by which NCL participates in IRES-driven translation have not hitherto been described. Here, we identified NCL as a protein that interacts with the IRES of foot-and-mouth disease virus (FMDV), which is a type II IRES. We also mapped the interactive regions within FMDV IRES and NCL in vitro. We found that NCL serves as a substantial regulator of FMDV IRES-driven translation but not of bulk cellular or vesicular stomatitis virus cap-dependent translation. NCL also modulates the translation of and infection by Seneca Valley virus (type III-like IRES) and classical swine fever virus (type III IRES), which suggests that its function is conserved in unrelated IRES-containing viruses. We also show that NCL affects viral replication by directly regulating the production of viral proteins and indirectly regulating FMDV RNA synthesis. Importantly, we observed that the cytoplasmic relocalization of NCL during FMDV infection is a substantial step for viral IRES-driven translation and that NCL specifically promotes the initiation phase of the translation process by recruiting translation initiation complexes to viral IRES. Finally, the functional importance of NCL in FMDV pathogenicity was confirmed in vivo. Taken together, our findings demonstrate a specific function for NCL in selective mRNA translation and identify a target for the development of a broad-spectrum class of antiviral interventions. IMPORTANCE FMDV usurps the cellular translation machinery to initiate viral protein synthesis via a mechanism driven by IRES elements. It allows the virus to shut down bulk cellular translation, while providing an advantage for its own gene expression. With limited coding capacity in its own genome, FMDV has evolved a mechanism to hijack host proteins to promote the recruitment of the host translation machinery, a process that is still not well understood. Here, we identified nucleolin (NCL) as a positive regulator of the IRES-driven translation of FMDV. Our study supports a model in which NCL relocalizes from the nucleus to the cytoplasm during the course of FMDV infection, where the cytoplasmic NCL promotes FMDV IRES-driven translation by bridging the translation initiation complexes with viral IRES. Our study demonstrates a previously uncharacterized role of NCL in the translation initiation of IRES-containing viruses, with important implications for the development of broad antiviral interventions.
Collapse
Affiliation(s)
- Shichong Han
- State Key Laboratory of Veterinary Etiological Biology, OIE/China National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, People’s Republic of China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, China Agricultural University, Beijing, People’s Republic of China
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, People’s Republic of China
| | - Xiaojia Wang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, China Agricultural University, Beijing, People’s Republic of China
| | - Junyong Guan
- State Key Laboratory of Veterinary Etiological Biology, OIE/China National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, People’s Republic of China
| | - Jinen Wu
- State Key Laboratory of Veterinary Etiological Biology, OIE/China National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, People’s Republic of China
| | - Yun Zhang
- State Key Laboratory of Veterinary Etiological Biology, OIE/China National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, People’s Republic of China
| | - Pinghua Li
- State Key Laboratory of Veterinary Etiological Biology, OIE/China National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, People’s Republic of China
| | - Zaixin Liu
- State Key Laboratory of Veterinary Etiological Biology, OIE/China National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, People’s Republic of China
| | - Sahibzada Waheed Abdullah
- State Key Laboratory of Veterinary Etiological Biology, OIE/China National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, People’s Republic of China
| | - Zhihui Zhang
- State Key Laboratory of Veterinary Etiological Biology, OIE/China National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, People’s Republic of China
| | - Ye Jin
- State Key Laboratory of Veterinary Etiological Biology, OIE/China National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, People’s Republic of China
| | - Shiqi Sun
- State Key Laboratory of Veterinary Etiological Biology, OIE/China National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, People’s Republic of China
| | - Huichen Guo
- State Key Laboratory of Veterinary Etiological Biology, OIE/China National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, People’s Republic of China
- College of Animal Science, Yangtze University, Jingzhou, Hubei, People’s Republic of China
| |
Collapse
|
30
|
p53/p73 Protein Network in Colorectal Cancer and Other Human Malignancies. Cancers (Basel) 2021; 13:cancers13122885. [PMID: 34207603 PMCID: PMC8227208 DOI: 10.3390/cancers13122885] [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: 05/13/2021] [Revised: 06/02/2021] [Accepted: 06/03/2021] [Indexed: 12/16/2022] Open
Abstract
Simple Summary The p53 family of proteins comprises p53, p63, and p73, which share high structural and functional similarity. The two distinct promoters of each locus, the alternative splicing, and the alternative translation initiation sites enable the generation of numerous isoforms with different protein-interacting domains and distinct activities. The co-expressed p53/p73 isoforms have significant but distinct roles in carcinogenesis. Their activity is frequently impaired in human tumors including colorectal carcinoma due to dysregulated expression and a dominant-negative effect accomplished by some isoforms and p53 mutants. The interactions between isoforms are particularly important to understand the onset of tumor formation, progression, and therapeutic response. The understanding of the p53/p73 network can contribute to the development of new targeted therapies. Abstract The p53 tumor suppressor protein is crucial for cell growth control and the maintenance of genomic stability. Later discovered, p63 and p73 share structural and functional similarity with p53. To understand the p53 pathways more profoundly, all family members should be considered. Each family member possesses two promoters and alternative translation initiation sites, and they undergo alternative splicing, generating multiple isoforms. The resulting isoforms have important roles in carcinogenesis, while their expression is dysregulated in several human tumors including colorectal carcinoma, which makes them potential targets in cancer treatment. Their activities arise, at least in part, from the ability to form tetramers that bind to specific DNA sequences and activate the transcription of target genes. In this review, we summarize the current understanding of the biological activities and regulation of the p53/p73 isoforms, highlighting their role in colorectal tumorigenesis. The analysis of the expression patterns of the p53/p73 isoforms in human cancers provides an important step in the improvement of cancer therapy. Furthermore, the interactions among the p53 family members which could modulate normal functions of the canonical p53 in tumor tissue are described. Lastly, we emphasize the importance of clinical studies to assess the significance of combining the deregulation of different members of the p53 family to define the outcome of the disease.
Collapse
|
31
|
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.
Collapse
Affiliation(s)
- Gayatri Mohanan
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Amiyaranjan Das
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | | |
Collapse
|
32
|
Nakamura S, Yonekura S, Shimosato T, Takaya T. Myogenetic Oligodeoxynucleotide (myoDN) Recovers the Differentiation of Skeletal Muscle Myoblasts Deteriorated by Diabetes Mellitus. Front Physiol 2021; 12:679152. [PMID: 34108889 PMCID: PMC8181739 DOI: 10.3389/fphys.2021.679152] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/03/2021] [Indexed: 12/15/2022] Open
Abstract
Skeletal muscle wasting in patients with diabetes mellitus (DM) is a complication of decreased muscle mass and strength, and is a serious risk factor that may result in mortality. Deteriorated differentiation of muscle precursor cells, called myoblasts, in DM patients is considered to be one of the causes of muscle wasting. We recently developed myogenetic oligodeoxynucleotides (myoDNs), which are 18-base single-strand DNAs that promote myoblast differentiation by targeting nucleolin. Herein, we report the applicability of a myoDN, iSN04, to myoblasts isolated from patients with type 1 and type 2 DM. Myogenesis of DM myoblasts was exacerbated concordantly with a delayed shift of myogenic transcription and induction of interleukins. Analogous phenotypes were reproduced in healthy myoblasts cultured with excessive glucose or palmitic acid, mimicking hyperglycemia or hyperlipidemia. iSN04 treatment recovered the deteriorated differentiation of plural DM myoblasts by downregulating myostatin and interleukin-8 (IL-8). iSN04 also ameliorated the impaired myogenic differentiation induced by glucose or palmitic acid. These results demonstrate that myoDNs can directly facilitate myoblast differentiation in DM patients, making them novel candidates for nucleic acid drugs to treat muscle wasting in patients with DM.
Collapse
Affiliation(s)
- Shunichi Nakamura
- Department of Agriculture, Graduate School of Science and Technology, Shinshu University, Nagano, Japan
| | - Shinichi Yonekura
- Department of Agricultural and Life Sciences, Faculty of Agriculture, Shinshu University, Nagano, Japan
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, Nagano, Japan
| | - Takeshi Shimosato
- Department of Agriculture, Graduate School of Science and Technology, Shinshu University, Nagano, Japan
- Department of Agricultural and Life Sciences, Faculty of Agriculture, Shinshu University, Nagano, Japan
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, Nagano, Japan
| | - Tomohide Takaya
- Department of Agriculture, Graduate School of Science and Technology, Shinshu University, Nagano, Japan
- Department of Agricultural and Life Sciences, Faculty of Agriculture, Shinshu University, Nagano, Japan
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, Nagano, Japan
| |
Collapse
|
33
|
Cruz C, Pedro AQ, Carvalho J, Santos T, Talhada D, Paiva A, Queiroz JA, Andrade M, Pinto M, Montenegro L, Delgado L, Pereira P. Nucleolin as a potential biomarker for canine malignant neoplasia. Res Vet Sci 2021; 135:297-303. [PMID: 33077166 DOI: 10.1016/j.rvsc.2020.10.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 10/02/2020] [Accepted: 10/07/2020] [Indexed: 01/03/2023]
Abstract
Human nucleolin (NCL) is a multifunctional protein that is involved in diverse pathological processes. Recent evidences have shown that NCL is markedly overexpressed on the surface of most human cancer cells when compared to normal cells, being overexpressed in several malignant cells. Based on the exposed, the purpose of this pilot study is to investigate the expression pattern of NCL in canine malignant neoplasia and control groups. NCL expression at both messenger RNA and protein levels in the subcellular fractions were respectively detected by RT-PCR and western blotting, allowing to infer the NCL positivity rate in canine neoplasia. The identity of NCL amplicons obtained by RT-PCR was confirmed by Sanger sequencing and found to correspond to Canis lupus familiaris. Using flow cytometry, the blood cells expressing NCL from canine neoplasms were also identified using several cell surface markers and their levels quantified. These results showed that NCL expressed in lymphocytes, monocytes and neutrophils in dogs with malignant neoplasia is higher (> 50%) when compared with the control group. We found an increased expression of surface and cytoplasmic NCL in canine malignant neoplasia group, while nuclear NCL is predominantly found in the control group. Overall, this study discloses and identifies for the first time the presence of NCL in canine blood.
Collapse
Affiliation(s)
- Carla Cruz
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal.
| | - Augusto Q Pedro
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal
| | - Josué Carvalho
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal
| | - Tiago Santos
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal
| | - Daniela Talhada
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal
| | - Artur Paiva
- Unidade de Gestão Operacional em Citometria, Centro Hospitalar e Universitário de Coimbra (CHUC), Portugal; Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, Coimbra, Portugal; Instituto Politécnico de Coimbra, ESTESC-Coimbra Health School, Ciências Biomédicas Laboratoriais, Portugal
| | - João A Queiroz
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal
| | | | | | | | - Leonor Delgado
- Pathology Department, INNO Serviços Especializados em Veterinária, Braga, Portugal; Cancer Research Group, Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde (IINFACTS), Instituto Universitário de Ciências da Saúde (IUCS), CESPU, Gandra, Portugal
| | - Patrícia Pereira
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal.
| |
Collapse
|
34
|
Lin Q, Ma X, Hu S, Li R, Wei X, Han B, Ma Y, Liu P, Pang Y. Overexpression of Nucleolin is a Potential Prognostic Marker in Endometrial Carcinoma. Cancer Manag Res 2021; 13:1955-1965. [PMID: 33658856 PMCID: PMC7920503 DOI: 10.2147/cmar.s294035] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/05/2021] [Indexed: 12/18/2022] Open
Abstract
Purpose Nucleolin (NCL) is a multifunctional protein with oncogenic properties. NCL expression levels have been linked to the outcomes of various malignancies, but the clinical value of NCL in patients with endometrial carcinoma (EC) remains unclear. Here, the expression of NCL in EC tissues and its associations with patient outcomes were assessed. Patients and Methods Data on NCL mRNA expression in EC and adjacent nonneoplastic tissues from The Cancer Genome Atlas (TCGA) were analyzed. In addition, NCL protein expression in 82 endometroid endometrial adenocarcinoma tissues and 15 non-malignant tissues was detected by immunohistochemistry. Results Elevated NCL expression was markedly correlated with serous endometrial carcinoma (P<0.001), advanced stage (P=0.029), and grade 3 (P<0.001). High NCL levels were associated with poorer overall survival (OS) and disease-free survival (DFS) compared with intermediate or low NCL levels (OS: P=0.001, DFS: P=0.006). The multivariate Cox proportional hazards model showed that NCL expression was an independent poor prognostic factor for DFS (HR=1.282, CI=1.027–1.601, P=0.028). A similar correlation between high expression levels of NCL and unfavorable DFS was found in endometrioid endometrial adenocarcinoma (HR=1.411, CI=1.083–1.840, P=0.011). Positive extra-nuclear NCL expression (HR=3.377, 95% CI=1.029–11.186, P=0.046) and low nuclear NCL expression (HR=0.233, 95% CI=0.068–0.796, P=0.020) were independent prognostic factors for DFS in endometrioid endometrial adenocarcinoma. Conclusion Heterotopic NCL is a potential prognostic biomarker for EC. Inhibiting the distribution of NCL from the nucleus to the cytoplasm and membrane may be a promising therapeutic strategy to improve outcomes in patients with EC with high NCL expression.
Collapse
Affiliation(s)
- Qianhan Lin
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan, 250012, Shandong, People's Republic of China.,Key Laboratory of Gynecologic Oncology of Shandong Province, Jinan, 250012, Shandong, People's Republic of China
| | - Xiaoxue Ma
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan, 250012, Shandong, People's Republic of China.,Key Laboratory of Gynecologic Oncology of Shandong Province, Jinan, 250012, Shandong, People's Republic of China
| | - Shunxue Hu
- Department of Pathology, Qilu Hospital of Shandong University, Jinan, 250012, Shandong, People's Republic of China
| | - Rui Li
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan, 250012, Shandong, People's Republic of China.,Key Laboratory of Gynecologic Oncology of Shandong Province, Jinan, 250012, Shandong, People's Republic of China
| | - Xuan Wei
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan, 250012, Shandong, People's Republic of China.,Key Laboratory of Gynecologic Oncology of Shandong Province, Jinan, 250012, Shandong, People's Republic of China
| | - Bing Han
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan, 250012, Shandong, People's Republic of China
| | - Yanhui Ma
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan, 250012, Shandong, People's Republic of China
| | - Peishu Liu
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan, 250012, Shandong, People's Republic of China.,Key Laboratory of Gynecologic Oncology of Shandong Province, Jinan, 250012, Shandong, People's Republic of China.,Shandong Engineering Laboratory for Urogynecology, Jinan, 250012, Shandong, People's Republic of China
| | - Yingxin Pang
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan, 250012, Shandong, People's Republic of China.,Key Laboratory of Gynecologic Oncology of Shandong Province, Jinan, 250012, Shandong, People's Republic of China.,Shandong Engineering Laboratory for Urogynecology, Jinan, 250012, Shandong, People's Republic of China
| |
Collapse
|
35
|
Qazi IH, Cao Y, Yang H, Angel C, Pan B, Zhou G, Han H. Impact of Dietary Selenium on Modulation of Expression of Several Non-Selenoprotein Genes Related to Key Ovarian Functions, Female Fertility, and Proteostasis: a Transcriptome-Based Analysis of the Aging Mice Ovaries. Biol Trace Elem Res 2021; 199:633-648. [PMID: 32430805 DOI: 10.1007/s12011-020-02192-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 05/10/2020] [Indexed: 02/07/2023]
Abstract
Female reproductive (ovarian) aging is characterized by a marked decline in quantity and quality of follicles and oocytes, as well as alterations in the surrounding ovarian stroma. In our previous report, we have shown that dietary selenium (Se) insufficiency and supplementation differentially impacted the reproductive efficiency in aging mice; however, the precise understanding of such modulation is still incomplete. In the present study, we sought to determine the impact of low (mildly low level) and moderately high (medium level) Se diets on expression profile of non-selenoprotein genes in the ovaries of aging mice. For this purpose, the aged mice were divided in two groups and fed either a low Se (Se-L; 0.08 mg Se/kg) diet or a moderately high Se (Se-M; 0.33 mg Se/kg) diet. RNA-seq analysis revealed that a total of 168 genes were differentially expressed between the two groups. From these, 72 and 96 differentially expressed genes (DEGs) were found to be upregulated and downregulated, respectively. Gene Ontology (GO) and pathways enrichment (KEGG) analyses revealed that these DEGs were enriched in several key GO terms and biological pathways including PI3K-Akt signaling pathway, steroid hormone biosynthesis, signaling pathways regulating pluripotency of stem cells, Hippo signaling pathway, ovarian steroidogenesis, and Wnt signaling pathway. Further filtering of RNA-seq data revealed that several DEGs such as Star, Hsd3b6, Scd1, Bmp7, Aqp8, Gas1, Fzd1, and Wwc1 were implicated in key ovarian- and fertility-related functions. In addition, some of the DEGs were related to ER homeostasis and/or proteostasis. These results highlight that dietary low and moderately high (medium level) Se diets, in addition to modulation of selenoproteins, can also have an impact on expression of several non-selenoprotein genes in the ovaries of aging mice. To sum up, these findings add more value to our understanding of Se modulation of ovarian functions and female fertility and will pave a way for the focused mechanistic and functional studies in this domain.
Collapse
Affiliation(s)
- Izhar Hyder Qazi
- Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
- Department of Veterinary Anatomy & Histology, Shaheed Benazir Bhutto University of Veterinary and Animal Sciences, Sakrand, 67210, Sindh, Pakistan
| | - Yutao Cao
- Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Haoxuan Yang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Christiana Angel
- Department of Veterinary Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China
- Department of Veterinary Parasitology, Faculty of Veterinary Sciences, Shaheed Benazir Bhutto University of Veterinary and Animal Sciences, Sakrand, 67210, Sindh, Pakistan
| | - Bo Pan
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guangbin Zhou
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Hongbing Han
- Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
| |
Collapse
|
36
|
Chen J, Zhang D, Qin X, Owzar K, McCann JJ, Kastan MB. DNA-Damage-Induced Alternative Splicing of p53. Cancers (Basel) 2021; 13:E251. [PMID: 33445417 PMCID: PMC7827558 DOI: 10.3390/cancers13020251] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/25/2020] [Accepted: 01/04/2021] [Indexed: 11/18/2022] Open
Abstract
Cellular responses to DNA damage and other stresses are important determinants of mutagenesis and impact the development of a wide range of human diseases. TP53 is highly mutated in human cancers and plays an essential role in stress responses and cell fate determination. A central dogma of p53 induction after DNA damage has been that the induction results from a transient increase in the half-life of the p53 protein. Our laboratory recently demonstrated that this long-standing paradigm is an incomplete picture of p53 regulation by uncovering a critical role for protein translational regulation in p53 induction after DNA damage. These investigations led to the discovery of a DNA-damage-induced alternative splicing (AS) pathway that affects p53 and other gene products. The damage-induced AS of p53 pre-mRNA generates the beta isoform of p53 (p53β) RNA and protein, which is specifically required for the induction of cellular senescence markers after ionizing irradiation (IR). In an attempt to elucidate the mechanisms behind the differential regulation and apparent functional divergence between full-length (FL) p53 and the p53β isoform (apoptosis versus senescence, respectively), we identified the differential transcriptome and protein interactome between these two proteins that may result from the unique 10-amino-acid tail in p53β protein.
Collapse
Affiliation(s)
- Jing Chen
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, USA; (J.C.); (J.J.M.)
- Current Address-Crown Bioscience, Inc., San Diego, CA 92127, USA
| | - Dadong Zhang
- Duke Cancer Institute, Durham, NC 27710, USA; (D.Z.); (X.Q.); (K.O.)
| | - Xiaodi Qin
- Duke Cancer Institute, Durham, NC 27710, USA; (D.Z.); (X.Q.); (K.O.)
| | - Kouros Owzar
- Duke Cancer Institute, Durham, NC 27710, USA; (D.Z.); (X.Q.); (K.O.)
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC 27710, USA
| | - Jennifer J. McCann
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, USA; (J.C.); (J.J.M.)
| | - Michael B. Kastan
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, USA; (J.C.); (J.J.M.)
- Duke Cancer Institute, Durham, NC 27710, USA; (D.Z.); (X.Q.); (K.O.)
| |
Collapse
|
37
|
Shinji S, Umezawa K, Nihashi Y, Nakamura S, Shimosato T, Takaya T. Identification of the Myogenetic Oligodeoxynucleotides (myoDNs) That Promote Differentiation of Skeletal Muscle Myoblasts by Targeting Nucleolin. Front Cell Dev Biol 2021; 8:616706. [PMID: 33585451 PMCID: PMC7874222 DOI: 10.3389/fcell.2020.616706] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 12/07/2020] [Indexed: 12/18/2022] Open
Abstract
Herein we report that the 18-base telomeric oligodeoxynucleotides (ODNs) designed from the Lactobacillus rhamnosus GG genome promote differentiation of skeletal muscle myoblasts which are myogenic precursor cells. We termed these myogenetic ODNs (myoDNs). The activity of one of the myoDNs, iSN04, was independent of Toll-like receptors, but dependent on its conformational state. Molecular simulation and iSN04 mutants revealed stacking of the 13-15th guanines as a core structure for iSN04. The alkaloid berberine bound to the guanine stack and enhanced iSN04 activity, probably by stabilizing and optimizing iSN04 conformation. We further identified nucleolin as an iSN04-binding protein. Results showed that iSN04 antagonizes nucleolin, increases the levels of p53 protein translationally suppressed by nucleolin, and eventually induces myotube formation by modulating the expression of genes involved in myogenic differentiation and cell cycle arrest. This study shows that bacterial-derived myoDNs serve as aptamers and are potential nucleic acid drugs directly targeting myoblasts.
Collapse
Affiliation(s)
- Sayaka Shinji
- Department of Agriculture, Graduate School of Science and Technology, Shinshu University, Nagano, Japan
| | - Koji Umezawa
- Department of Agricultural and Life Science, Faculty of Agriculture, Shinshu University, Nagano, Japan
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, Nagano, Japan
| | - Yuma Nihashi
- Department of Science and Technology, Graduate School of Medicine, Science and Technology, Shinshu University, Nagano, Japan
| | - Shunichi Nakamura
- Department of Agriculture, Graduate School of Science and Technology, Shinshu University, Nagano, Japan
| | - Takeshi Shimosato
- Department of Agriculture, Graduate School of Science and Technology, Shinshu University, Nagano, Japan
- Department of Agricultural and Life Science, Faculty of Agriculture, Shinshu University, Nagano, Japan
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, Nagano, Japan
- Department of Science and Technology, Graduate School of Medicine, Science and Technology, Shinshu University, Nagano, Japan
| | - Tomohide Takaya
- Department of Agriculture, Graduate School of Science and Technology, Shinshu University, Nagano, Japan
- Department of Agricultural and Life Science, Faculty of Agriculture, Shinshu University, Nagano, Japan
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, Nagano, Japan
- Department of Science and Technology, Graduate School of Medicine, Science and Technology, Shinshu University, Nagano, Japan
| |
Collapse
|
38
|
Sawyer JK, Kabiri Z, Montague RA, Allen SR, Stewart R, Paramore SV, Cohen E, Zaribafzadeh H, Counter CM, Fox DT. Exploiting codon usage identifies intensity-specific modifiers of Ras/MAPK signaling in vivo. PLoS Genet 2020; 16:e1009228. [PMID: 33296356 PMCID: PMC7752094 DOI: 10.1371/journal.pgen.1009228] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 12/21/2020] [Accepted: 10/27/2020] [Indexed: 01/05/2023] Open
Abstract
Signal transduction pathways are intricately fine-tuned to accomplish diverse biological processes. An example is the conserved Ras/mitogen-activated-protein-kinase (MAPK) pathway, which exhibits context-dependent signaling output dynamics and regulation. Here, by altering codon usage as a novel platform to control signaling output, we screened the Drosophila genome for modifiers specific to either weak or strong Ras-driven eye phenotypes. Our screen enriched for regions of the genome not previously connected with Ras phenotypic modification. We mapped the underlying gene from one modifier to the ribosomal gene RpS21. In multiple contexts, we show that RpS21 preferentially influences weak Ras/MAPK signaling outputs. These data show that codon usage manipulation can identify new, output-specific signaling regulators, and identify RpS21 as an in vivo Ras/MAPK phenotypic regulator. Cellular communication is critical in controlling the growth of organs and must be carefully regulated to prevent disease. The Ras signaling pathway is frequently used for cellular communication of tissue growth regulation but can operate at different signaling strengths. Here, we used a novel strategy to identify genes that specifically tune weak or strong Ras signaling states. We find that the gene RpS21 preferentially tunes weak Ras signaling states.
Collapse
Affiliation(s)
- Jessica K. Sawyer
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Zahra Kabiri
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Ruth A. Montague
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Scott R. Allen
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Rebeccah Stewart
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Sarah V. Paramore
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Erez Cohen
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Hamed Zaribafzadeh
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Christopher M. Counter
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
- Duke Cancer Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
- * E-mail: (CMC); (DTF)
| | - Donald T. Fox
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
- Duke Cancer Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
- * E-mail: (CMC); (DTF)
| |
Collapse
|
39
|
Swiatkowska A, Dutkiewicz M, Machtel P, Janecki DM, Kabacinska M, Żydowicz-Machtel P, Ciesiołka J. Regulation of the p53 expression profile by hnRNP K under stress conditions. RNA Biol 2020; 17:1402-1415. [PMID: 32449427 DOI: 10.1080/15476286.2020.1771944] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The p53 protein is one of the transcription factors responsible for cell cycle regulation and prevention of cancer development. Its expression is regulated at the transcriptional, translational and post-translational levels. Recent years of research have shown that the 5' terminus of p53 mRNA plays an important role in this regulation. This region seems to be a docking platform for proteins involved in p53 expression, particularly under stress conditions. Here, we applied RNA-centric affinity chromatography to search for proteins that bind to the 5' terminus of p53 mRNA and thus may be able to regulate the p53 expression profile. We found heterogeneous nuclear ribonucleoprotein K, hnRNP K, to be one of the top candidates. Binding of hnRNP K to the 5'-terminal region of p53 mRNA was confirmed in vitro. We demonstrated that changes in the hnRNP K level in the cell strongly affected the p53 expression profile under various stress conditions. Downregulation or overexpression of hnRNP K caused a decrease or an increase in the p53 mRNA amount, respectively, pointing to the transcriptional mode of expression regulation. However, when hnRNP K was overexpressed under endoplasmic reticulum stress and the p53 amount has elevated no changes in the p53 mRNA level were detected suggesting translational regulation of p53 expression. Our findings have shown that hnRNP K is not only a mutual partner of p53 in the transcriptional activation of target genes under stress conditions but it also acts as a regulator of p53 expression at the transcriptional and potentially translational levels.
Collapse
Affiliation(s)
- Agata Swiatkowska
- Polish Academy of Sciences, Institute of Bioorganic Chemistry , Poznan, Poland
| | - Mariola Dutkiewicz
- Polish Academy of Sciences, Institute of Bioorganic Chemistry , Poznan, Poland
| | - Piotr Machtel
- Polish Academy of Sciences, Institute of Bioorganic Chemistry , Poznan, Poland
| | - Damian M Janecki
- Polish Academy of Sciences, Institute of Bioorganic Chemistry , Poznan, Poland
| | - Martyna Kabacinska
- Polish Academy of Sciences, Institute of Bioorganic Chemistry , Poznan, Poland
| | | | - Jerzy Ciesiołka
- Polish Academy of Sciences, Institute of Bioorganic Chemistry , Poznan, Poland
| |
Collapse
|
40
|
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.
Collapse
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.
| |
Collapse
|
41
|
Falconi M, Giangrossi M, Zabaleta ME, Wang J, Gambini V, Tilio M, Bencardino D, Occhipinti S, Belletti B, Laudadio E, Galeazzi R, Marchini C, Amici A. A novel 3'-tRNA Glu-derived fragment acts as a tumor suppressor in breast cancer by targeting nucleolin. FASEB J 2019; 33:13228-13240. [PMID: 31560576 DOI: 10.1096/fj.201900382rr] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 08/19/2019] [Indexed: 12/17/2022]
Abstract
tRNA-derived fragments (tRFs) have been defined as a novel class of small noncoding RNAs. tRFs have been reported to be deregulated in cancer, but their biologic function remains to be fully understood. We have identified a new tRF (named tRF3E), derived from mature tRNAGlu, that is specifically expressed in healthy mammary glands but not in breast cancer (BC). Consistently, tRF3E levels significantly decrease in the blood of patients with epidermal growth factor receptor 2 (HER2)-positive BC reflecting tumor status (control > early cancer > metastatic cancer). tRF3E down-regulation was recapitulated in Δ16HER2 transgenic mice, representing a BC preclinical model. Pulldown assays, used to search for proteins capable to selectively bind tRF3E, have shown that this tRF specifically interacts with nucleolin (NCL), an RNA-binding protein overexpressed in BC and able to repress the translation of p53 mRNA. The binding properties of NCL-tRF3E complex, predicted in silico and analyzed by EMSA assays, are congruent with a competitive displacement of p53 mRNA by tRF3E, leading to an increased p53 expression and consequently to a modulation of cancer cell growth. Here, we provide evidence that tRF3E plays an important role in the pathogenesis of BC displaying tumor-suppressor functions through a NCL-mediated mechanism.-Falconi, M., Giangrossi, M., Elexpuru Zabaleta, M., Wang, J., Gambini, V., Tilio, M., Bencardino, D., Occhipinti, S., Belletti, B., Laudadio, E., Galeazzi, R., Marchini, C., Amici, A. A novel 3'-tRNAGlu-derived fragment acts as a tumor suppressor in breast cancer by targeting nucleolin.
Collapse
Affiliation(s)
- Maurizio Falconi
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Mara Giangrossi
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | | | - Junbiao Wang
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Valentina Gambini
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Martina Tilio
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Daniela Bencardino
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Sergio Occhipinti
- Department of Molecular Biotechnology and Health Sciences, Center for Experimental Research and Medical Studies, University of Torino, Torino, Italy
| | - Barbara Belletti
- Division of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO) Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), National Cancer Institute, Aviano, Italy
| | - Emiliano Laudadio
- Dipartimento Scienze e Ingegneria della Materia, dell'Ambiente ed Urbanistica, Università Politecnica delle Marche, Ancona, Italy
| | - Roberta Galeazzi
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Cristina Marchini
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Augusto Amici
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| |
Collapse
|
42
|
Gomez GN, Abrar F, Dodhia MP, Gonzalez FG, Nag A. SARS coronavirus protein nsp1 disrupts localization of Nup93 from the nuclear pore complex. Biochem Cell Biol 2019; 97:758-766. [PMID: 30943371 DOI: 10.1139/bcb-2018-0394] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus nonstructural protein 1 (nsp1) is a key factor in virus-induced down-regulation of host gene expression. In infected cells, nsp1 engages in a multipronged mechanism to inhibit host gene expression by binding to the 40S ribosome to block the assembly of translationally competent ribosome, and then inducing endonucleolytic cleavage and the degradation of host mRNAs. Here, we report a previously undetected mechanism by which nsp1 exploits the nuclear pore complex and disrupts the nuclear-cytoplasmic transport of biomolecules. We identified members of the nuclear pore complex from the nsp1-associated protein assembly and found that the expression of nsp1 in HEK cells disrupts Nup93 localization around the nuclear envelope without triggering proteolytic degradation, while the nuclear lamina remains unperturbed. Consistent with its role in host shutoff, nsp1 alters the nuclear-cytoplasmic distribution of an RNA binding protein, nucleolin. Our results suggest that nsp1, alone, can regulate multiple steps of gene expression including nuclear-cytoplasmic transport.
Collapse
Affiliation(s)
- Garret N Gomez
- Furman University, 3300 Poinsett Highway, Greenville, SC 29613, USA
- Furman University, 3300 Poinsett Highway, Greenville, SC 29613, USA
| | - Fareeha Abrar
- Furman University, 3300 Poinsett Highway, Greenville, SC 29613, USA
- Furman University, 3300 Poinsett Highway, Greenville, SC 29613, USA
| | - Maya P Dodhia
- Furman University, 3300 Poinsett Highway, Greenville, SC 29613, USA
- Furman University, 3300 Poinsett Highway, Greenville, SC 29613, USA
| | - Fabiola G Gonzalez
- Furman University, 3300 Poinsett Highway, Greenville, SC 29613, USA
- Furman University, 3300 Poinsett Highway, Greenville, SC 29613, USA
| | - Anita Nag
- Furman University, 3300 Poinsett Highway, Greenville, SC 29613, USA
| |
Collapse
|
43
|
Swiatkowska A, Dutkiewicz M, Zydowicz-Machtel P, Szpotkowska J, Janecki DM, Ciesiołka J. Translational Control in p53 Expression: The Role of 5'-Terminal Region of p53 mRNA. Int J Mol Sci 2019; 20:E5382. [PMID: 31671760 PMCID: PMC6862623 DOI: 10.3390/ijms20215382] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 10/14/2019] [Accepted: 10/27/2019] [Indexed: 01/05/2023] Open
Abstract
In this review, the latest research concerning the structure and function of the 5'-terminal region of p53 mRNA was discussed. Special attention was focused on defined structural motifs which are present in this region, as well as their conservation and plausible functional role in translation. It is known that the length of the 5'-terminal region and the structural environment of initiation codons can strongly modulate translation initiation. The ability of this region of p53 mRNA to bind protein factors was also described with special emphasis on general principles that govern, such RNA-protein interactions. The structural alterations within the 5'-terminal region of p53 mRNA and proteins that bind to this region have a strong impact on the rate of mRNA scanning and on translation efficiency in in vitro assays, in selected cell lines, and under stress conditions. Thus, the structural features of the 5'-terminal region of p53 mRNA seem to be very important for translation and for translation regulation mechanisms. Finally, we suggested topics that, in our opinion, should be further explored for better understanding of the mechanisms of the p53 gene expression regulation at the translational level.
Collapse
Affiliation(s)
- Agata Swiatkowska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
| | - Mariola Dutkiewicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
| | - Paulina Zydowicz-Machtel
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
| | - Joanna Szpotkowska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
| | - Damian M Janecki
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
| | - Jerzy Ciesiołka
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
| |
Collapse
|
44
|
Haronikova L, Olivares-Illana V, Wang L, Karakostis K, Chen S, Fåhraeus R. The p53 mRNA: an integral part of the cellular stress response. Nucleic Acids Res 2019; 47:3257-3271. [PMID: 30828720 PMCID: PMC6468297 DOI: 10.1093/nar/gkz124] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 02/12/2019] [Accepted: 02/21/2019] [Indexed: 12/16/2022] Open
Abstract
A large number of signalling pathways converge on p53 to induce different cellular stress responses that aim to promote cell cycle arrest and repair or, if the damage is too severe, to induce irreversible senescence or apoptosis. The differentiation of p53 activity towards specific cellular outcomes is tightly regulated via a hierarchical order of post-translational modifications and regulated protein-protein interactions. The mechanisms governing these processes provide a model for how cells optimize the genetic information for maximal diversity. The p53 mRNA also plays a role in this process and this review aims to illustrate how protein and RNA interactions throughout the p53 mRNA in response to different signalling pathways control RNA stability, translation efficiency or alternative initiation of translation. We also describe how a p53 mRNA platform shows riboswitch-like features and controls the rate of p53 synthesis, protein stability and modifications of the nascent p53 protein. A single cancer-derived synonymous mutation disrupts the folding of this platform and prevents p53 activation following DNA damage. The role of the p53 mRNA as a target for signalling pathways illustrates how mRNA sequences have co-evolved with the function of the encoded protein and sheds new light on the information hidden within mRNAs.
Collapse
Affiliation(s)
- Lucia Haronikova
- RECAMO, Masaryk Memorial Cancer Institute, Zluty kopec 7, 656 53 Brno, Czech Republic
| | - Vanesa Olivares-Illana
- Laboratorio de Interacciones Biomoleculares y cáncer. Instituto de Física Universidad Autónoma de San Luis Potosí, Manuel Nava 6, Zona universitaria, 78290 SLP, México
| | - Lixiao Wang
- Department of Medical Biosciences, Umeå University, 90185 Umeå, Sweden
| | | | - Sa Chen
- Department of Medical Biosciences, Umeå University, 90185 Umeå, Sweden
| | - Robin Fåhraeus
- RECAMO, Masaryk Memorial Cancer Institute, Zluty kopec 7, 656 53 Brno, Czech Republic.,Department of Medical Biosciences, Umeå University, 90185 Umeå, Sweden.,Inserm U1162, 27 rue Juliette Dodu, 75010 Paris, France.,ICCVS, University of Gdańsk, Science, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland
| |
Collapse
|
45
|
Fang Z, Pan Z. Essential Role of Ubiquitin-Fold Modifier 1 Conjugation in DNA Damage Response. DNA Cell Biol 2019; 38:1030-1039. [PMID: 31368785 DOI: 10.1089/dna.2019.4861] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Both endogenous and exogenous factors can cause DNA damage that compromises genomic integrity and cell viability. A proper DNA damage response (DDR) plays a role in maintaining genome stability and preventing tumorigenesis. DNA double-strand breaks (DSBs) are the most toxic DNA lesion, whose response is dominated by the ataxia-telangiectasia mutated (ATM) protein kinase. After being activated by the sensor Mre11-Rad50-Nbs1 (MRN) complex or acetyltransferase Tip60, ATM rapidly phosphorylates downstream targets to launch DDR signaling when DNA is damaged. However, the exact mechanism of DDR is complex and ambiguous. Ufmylation, one type of ubiquitin-like modification, proceeds mainly through a three-step enzymatic reaction to help ubiquitin-fold modifier 1 (Ufm1), attach to substrates with ubiquitin-like modifier-activating enzyme 5 (Uba5), Ufm1-conjugating enzyme 1 (Ufc1) and Ufm1-specific ligase 1 (Ufl1). Although ubiquitination is essential to the DSBs response, the potential function of ufmylation in DDR is largely unknown. Herein, we review the relationship between ufmylation and DDR to elucidate the function and mechanism of ufmylation in DDR, which would reveal the pathogenesis of some diseases and provide new guidance to create a therapeutic method.
Collapse
Affiliation(s)
- Zhi Fang
- Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Zezheng Pan
- Faculty of Basic Medical Science, Jiangxi Medical College, Nanchang University, Nanchang, China
| |
Collapse
|
46
|
Abstract
Nucleolin is an RNA binding protein that is involved in many post-transcriptional regulation steps of messenger RNAs in addition to its nucleolar role in ribosomal RNA transcription and assembly in pre-ribosomes. Acetylated nucleolin was found to be associated with nuclear speckles and to co-localize with the splicing factor SC35. Previous nuclear pull down of nucleolin identified several splicing components and factors involved in RNA polymerase II transcription associated with nucleolin. In this report, we show that these splicing components are specifics of the pre-catalytic A and B spliceosomes, while proteins recruited in the Bact, C and P complexes are absent from the nucleolin interacting proteins. Furthermore, we show that acetylated nucleolin co-localized with P-SF3B1, a marker of co-transcriptional active spliceosomes. P-SF3B1 complexes can be pulled down with nucleolin specific antibodies. Interestingly, the alternative splicing of Fibronectin at the IIICS and EDB sites was affected by nucleolin depletion. These data are consistent with a model where nucleolin could be a factor bridging RNA polymerase II transcription and assembly of pre-catalytic spliceosome similarly to its function in the co-transcriptional maturation of pre-rRNA.
Collapse
|
47
|
Godet AC, David F, Hantelys F, Tatin F, Lacazette E, Garmy-Susini B, Prats AC. IRES Trans-Acting Factors, Key Actors of the Stress Response. Int J Mol Sci 2019; 20:ijms20040924. [PMID: 30791615 PMCID: PMC6412753 DOI: 10.3390/ijms20040924] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 02/12/2019] [Accepted: 02/14/2019] [Indexed: 12/16/2022] Open
Abstract
The cellular stress response corresponds to the molecular changes that a cell undergoes in response to various environmental stimuli. It induces drastic changes in the regulation of gene expression at transcriptional and posttranscriptional levels. Actually, translation is strongly affected with a blockade of the classical cap-dependent mechanism, whereas alternative mechanisms are activated to support the translation of specific mRNAs. A major mechanism involved in stress-activated translation is the internal ribosome entry site (IRES)-driven initiation. IRESs, first discovered in viral mRNAs, are present in cellular mRNAs coding for master regulators of cell responses, whose expression must be tightly controlled. IRESs allow the translation of these mRNAs in response to different stresses, including DNA damage, amino-acid starvation, hypoxia or endoplasmic reticulum stress, as well as to physiological stimuli such as cell differentiation or synapse network formation. Most IRESs are regulated by IRES trans-acting factor (ITAFs), exerting their action by at least nine different mechanisms. This review presents the history of viral and cellular IRES discovery as well as an update of the reported ITAFs regulating cellular mRNA translation and of their different mechanisms of action. The impact of ITAFs on the coordinated expression of mRNA families and consequences in cell physiology and diseases are also highlighted.
Collapse
Affiliation(s)
- Anne-Claire Godet
- UMR 1048-I2MC, Inserm, Université de Toulouse, UT3, 31432 Toulouse cedex 4, France.
| | - Florian David
- UMR 1048-I2MC, Inserm, Université de Toulouse, UT3, 31432 Toulouse cedex 4, France.
| | - Fransky Hantelys
- UMR 1048-I2MC, Inserm, Université de Toulouse, UT3, 31432 Toulouse cedex 4, France.
| | - Florence Tatin
- UMR 1048-I2MC, Inserm, Université de Toulouse, UT3, 31432 Toulouse cedex 4, France.
| | - Eric Lacazette
- UMR 1048-I2MC, Inserm, Université de Toulouse, UT3, 31432 Toulouse cedex 4, France.
| | - Barbara Garmy-Susini
- UMR 1048-I2MC, Inserm, Université de Toulouse, UT3, 31432 Toulouse cedex 4, France.
| | - Anne-Catherine Prats
- UMR 1048-I2MC, Inserm, Université de Toulouse, UT3, 31432 Toulouse cedex 4, France.
| |
Collapse
|
48
|
Molavi G, Samadi N, Hosseingholi EZ. The roles of moonlight ribosomal proteins in the development of human cancers. J Cell Physiol 2018; 234:8327-8341. [PMID: 30417503 DOI: 10.1002/jcp.27722] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 09/23/2018] [Indexed: 12/13/2022]
Abstract
"Moonlighting protein" is a term used to define a single protein with multiple functions and different activities that are not derived from gene fusions, multiple RNA splicing, or the proteolytic activity of promiscuous enzymes. Different proteinous constituents of ribosomes have been shown to have important moonlighting extra-ribosomal functions. In this review, we introduce the impact of key moonlight ribosomal proteins and dependent signal transduction in the initiation and progression of various cancers. As a future perspective, the potential role of these moonlight ribosomal proteins in the diagnosis, prognosis, and development of novel strategies to improve the efficacy of therapies for human cancers has been suggested.
Collapse
Affiliation(s)
- Ghader Molavi
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Molecular Medicine, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Nasser Samadi
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Molecular Medicine, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Biochemistry, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | | |
Collapse
|
49
|
Abstract
The rates of ribosome production by a nucleolus and of protein biosynthesis by ribosomes are tightly correlated with the rate of cell growth and proliferation. All these processes must be matched and appropriately regulated to provide optimal cell functioning. Deregulation of certain factors, including oncogenes, controlling these processes, especially ribosome biosynthesis, can lead to cell transformation. Cancer cells are characterized by intense ribosome biosynthesis which is advantageous for their growth and proliferation. On the other hand, this feature can be engaged as an anticancer strategy. Numerous nucleolar factors such as nucleolar and ribosomal proteins as well as different RNAs, in addition to their role in ribosome biosynthesis, have other functions, including those associated with cancer biology. Some of them can contribute to cell transformation and cancer development. Others, under stress evoked by different factors which often hamper function of nucleoli and thus induce nucleolar/ribosomal stress, can participate in combating cancer cells. In this sense, intentional application of therapeutic agents affecting ribosome biosynthesis can cause either release of these molecules from nucleoli or their de novo biosynthesis to mediate the activation of pathways leading to elimination of harmful cells. This review underlines the role of a nucleolus not only as a ribosome constituting apparatus but also as a hub of both positive and negative control of cancer development. The article is mainly based on original papers concerning mechanisms in which the nucleolus is implicated directly or indirectly in processes associated with neoplasia.
Collapse
Affiliation(s)
- Dariusz Stępiński
- Department of Cytophysiology, Faculty of Biology and Environmental Protection, University of Łódź, Pomorska 141/143, 90-236, Łódź, Poland.
| |
Collapse
|
50
|
Holoubek A, Herman P, Sýkora J, Brodská B, Humpolíčková J, Kráčmarová M, Gášková D, Hof M, Kuželová K. Monitoring of nucleophosmin oligomerization in live cells. Methods Appl Fluoresc 2018; 6:035016. [PMID: 29901450 DOI: 10.1088/2050-6120/aaccb9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Oligomerization plays a crucial role in the function of nucleophosmin (NPM), an abundant nucleolar phosphoprotein. Two dual-color methods based on modern fluorescence confocal microscopy are applied for tracking NPM aggregates in live cells: cross-correlation Number and Brightness analysis (ccN&B) combined with pulsed interleaved excitation (PIE) and fluorescence-lifetime imaging microscopy (FLIM) utilizing resonance energy transfer (FRET). HEK-293T cells were transfected with mixture of plasmids designed for tagging with fluorescent proteins so that the cells express mixed population of NPM labeled either with eGFP or mRFP1. We observe joint oligomers formed from the fluorescently labeled NPM. Having validated the in vivo methods, we study an effect of substitutions in cysteine 21 (Cys21) of the NPM N-terminus on the oligomerization to demonstrate applicability of the methods. Inhibitory effect of mutations of the Cys21 to nonpolar Ala or to aromatic Phe on the oligomerization was reported in literature using in vitro semi-native electrophoresis. However, we do not detect any break-up of the joint NPM oligomers due to the Cys21 mutations in live cells. In vivo microscopy observations are supported by an in vitro method, the GFP-Trap immunoprecipitation assay. Our results therefore show importance of utilizing several methods for detection of biologically relevant protein aggregates. In vivo monitoring of the NPM oligomerization, a potential cancer therapy target, by the presented methods offers a new way to monitor effects of drugs that are tested as NPM oligomerization inhibitors directly in live cells.
Collapse
Affiliation(s)
- Aleš Holoubek
- Department of Proteomics, Institute of Hematology and Blood Transfusion, U Nemocnice 2094/1, 128 20 Praha 2, Czechia
| | | | | | | | | | | | | | | | | |
Collapse
|