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Won J, Kang HS, Kim NY, Dezhbord M, Marakkalage KG, Lee EH, Lee D, Park S, Kim DS, Kim KH. Tripartite motif-containing protein 21 is involved in IFN-γ-induced suppression of hepatitis B virus by regulating hepatocyte nuclear factors. J Virol 2024; 98:e0046824. [PMID: 38780244 PMCID: PMC11237615 DOI: 10.1128/jvi.00468-24] [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: 03/14/2024] [Accepted: 04/03/2024] [Indexed: 05/25/2024] Open
Abstract
The antiviral role of the tripartite motif-containing (TRIM) protein family , a member of the E3-ubiquitin ligase family, has recently been actively studied. Hepatitis B virus (HBV) infection is a major contributor to liver diseases; however, the host factors regulated by cytokine-inducible TRIM21 to suppress HBV remain unclear. In this study, we showed the antiviral efficacy of TRIM21 against HBV in hepatoma cell lines, primary human hepatocytes isolated from patient liver tissues, and mouse model. Using TRIM21 knock-out cells, we confirmed that the antiviral effects of interferon-gamma, which suppress HBV replication, are diminished when TRIM21 is deficient. Northern blot analysis confirmed a reduction of HBV RNA levels by TRIM21. Using Luciferase reporter assay, we also discovered that TRIM21 decreases the activity of HBV enhancers, which play a crucial role in covalently closed circular DNA transcription. The participation of the RING domain and PRY-SPRY domain in the anti-HBV effect of TRIM21 was demonstrated through experiments using deletion mutants. We identified a novel interaction between TRIM21 and hepatocyte nuclear factor 4α (HNF4α) through co-immunoprecipitation assay. More specifically, ubiquitination assay revealed that TRIM21 promotes ubiquitin-mediated proteasomal degradation of HNF4α. HNF1α transcription is down-regulated as a result of the degradation of HNF4α, an activator for the HNF1α promoter. Therefore, the reduction of key HBV enhancer activators, HNF4α and HNF1α, by TRIM21 resulted in a decline in HBV transcription, ultimately leading to the inhibition of HBV replication.IMPORTANCEDespite extensive research efforts, a definitive cure for chronic hepatitis B remains elusive, emphasizing the persistent importance of this viral infection as a substantial public health concern. Although the risks associated with hepatitis B virus (HBV) infection are well known, host factors capable of suppressing HBV are largely uncharacterized. This study elucidates that tripartite motif-containing protein 21 (TRIM21) suppresses HBV transcription and consequently inhibits HBV replication by downregulating the hepatocyte nuclear factors, which are host factors associated with the HBV enhancers. Our findings demonstrate a novel anti-HBV mechanism of TRIM21 in interferon-gamma-induced anti-HBV activity. These findings may contribute to new strategies to block HBV.
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Affiliation(s)
- Juhee Won
- Department of Precision Medicine, School of Medicine, Sungkyunkwan University, Seoul, Republic of Korea
- Department of Pharmacology, Center for Cancer Research and Diagnostic Medicine, IBST, School of Medicine, Konkuk University, Seoul, Republic of Korea
| | - Hong Seok Kang
- Department of Pharmacology, Center for Cancer Research and Diagnostic Medicine, IBST, School of Medicine, Konkuk University, Seoul, Republic of Korea
| | - Na Yeon Kim
- Department of Precision Medicine, School of Medicine, Sungkyunkwan University, Seoul, Republic of Korea
| | - Mehrangiz Dezhbord
- Department of Precision Medicine, School of Medicine, Sungkyunkwan University, Seoul, Republic of Korea
| | | | - Eun-Hwi Lee
- Department of Precision Medicine, School of Medicine, Sungkyunkwan University, Seoul, Republic of Korea
| | - Donghyo Lee
- Department of Precision Medicine, School of Medicine, Sungkyunkwan University, Seoul, Republic of Korea
| | - Soree Park
- Department of Precision Medicine, School of Medicine, Sungkyunkwan University, Seoul, Republic of Korea
| | - Dong-Sik Kim
- Department of Surgery, Division of HBP Surgery and Liver Transplantation, Korea University College of Medicine, Seoul, Republic of Korea
| | - Kyun-Hwan Kim
- Department of Precision Medicine, School of Medicine, Sungkyunkwan University, Seoul, Republic of Korea
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Atsuta Y, Lee C, Rodrigues AR, Colle C, Tomizawa RR, Lujan EG, Tschopp P, Galan L, Zhu M, Gorham JM, Vannier JP, Seidman CE, Seidman JG, Ros MA, Pourquié O, Tabin CJ. Direct reprogramming of non-limb fibroblasts to cells with properties of limb progenitors. Dev Cell 2024; 59:415-430.e8. [PMID: 38320485 PMCID: PMC10932627 DOI: 10.1016/j.devcel.2023.12.010] [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: 03/20/2022] [Revised: 09/25/2022] [Accepted: 12/20/2023] [Indexed: 02/08/2024]
Abstract
The early limb bud consists of mesenchymal limb progenitors derived from the lateral plate mesoderm (LPM). The LPM also gives rise to the mesodermal components of the flank and neck. However, the cells at these other levels cannot produce the variety of cell types found in the limb. Taking advantage of a direct reprogramming approach, we find a set of factors (Prdm16, Zbtb16, and Lin28a) normally expressed in the early limb bud and capable of imparting limb progenitor-like properties to mouse non-limb fibroblasts. The reprogrammed cells show similar gene expression profiles and can differentiate into similar cell types as endogenous limb progenitors. The further addition of Lin41 potentiates the proliferation of the reprogrammed cells. These results suggest that these same four factors may play pivotal roles in the specification of endogenous limb progenitors.
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Affiliation(s)
- Yuji Atsuta
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA; Department of Biology, Kyushu University, Fukuoka 819-0395, Japan
| | - ChangHee Lee
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
| | - Alan R Rodrigues
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA; The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Charlotte Colle
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Reiko R Tomizawa
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Ernesto G Lujan
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA; Department of Pathology, Brigham and Women's Hospital, 60 Fenwood Road, Boston, MA 02115, USA
| | - Patrick Tschopp
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA; Zoological Institute, University of Basel, 4051 Basel, Switzerland
| | - Laura Galan
- Instituto de Biomedicina y Biotecnologia de Cantabria, CSIC, SODERCAN- Universidad de Cantabria, 39011 Santander, Spain
| | - Meng Zhu
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Joshua M Gorham
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | | | - Christine E Seidman
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Jonathan G Seidman
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Marian A Ros
- Instituto de Biomedicina y Biotecnologia de Cantabria, CSIC, SODERCAN- Universidad de Cantabria, 39011 Santander, Spain
| | - Olivier Pourquié
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA; Department of Pathology, Brigham and Women's Hospital, 60 Fenwood Road, Boston, MA 02115, USA.
| | - Clifford J Tabin
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
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Wu M, Jin MM, Cao XH, Zhao L, Li YH. Silencing TRIM29 Sensitizes Non-small Cell Lung Cancer Cells to Anlotinib by Promoting Apoptosis via Binding RAD50. Curr Cancer Drug Targets 2024; 24:445-454. [PMID: 37644752 DOI: 10.2174/1568009623666230829143148] [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: 03/08/2023] [Revised: 06/13/2023] [Accepted: 07/25/2023] [Indexed: 08/31/2023]
Abstract
BACKGROUND Previous studies have proposed that the transcriptional regulatory factor tripartite motif containing 29 (TRIM29) is involved in carcinogenesis via binding with nucleic acid. TRIM29 is confirmed to be highly expressed when the cancer cells acquire therapy-resistant properties. We noticed that TRIM29 levels were significantly increased in anlotinib-resistant NCIH1975 (NCI-H1975/AR) cells via mining data information from gene expression omnibus (GEO) gene microarray (GSE142031; log2 fold change > 1, p < 0.05). OBJECTIVE Our study aimed to investigate the function of TRIM29 on the resistance to anlotinib in non-small cell lung cancer (NSCLC) cells, including NCI-H1975 and A549 cells. METHODS Real-time RT-PCR and western blot were used to detect TRIM29 expression in anlotinib- resistant NSCLC (NSCLC/AR) cells. Apoptosis were determined through flow cytometry, acridine orange/ethidium bromide staining as well as western blot. ELISA was used to measure the content of C-X3-C motif chemokine ligand 1. Co-Immunoprecipitation assay was performed to verify the interaction between TRIM29 and RAD50 double-strand break repair protein (RAD50). RESULTS TRIM29 expression was shown to be elevated in the cytoplasm and nucleus of NSCLC/ AR cells compared to normal NSCLC cells. Next, we demonstrated that TRIM29 knockdown facilitated apoptosis and enhanced the sensitivity to anlotinib in NSCLC/AR cells. Based on the refined results citing from the database BioGRID, it was proved that TRIM29 interacted with RAD50. Herein, RAD50 overexpression diminished the pro-apoptotic effect induced by silencing TRIM29 in anlotinib-resistant A549 (A549/AR) cells. CONCLUSION Finally, we concluded that the increased sensitivity to anlotinib in NSCLC/AR cells was achieved by knocking down TRIM29, besides, the positive effects of TRIM29 knockdown were attributed to the promotion of apoptosis via binding to RAD50 in NSCLC/AR cell nucleus. Therefore, TRIM29 might become a potential target for overcoming anlotinib resistance in NSCLC treatment.
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Affiliation(s)
- Min Wu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Anhui Medical University, No. 100, Huaihai Avenue, Hefei, Anhui, People's Republic of China
- Department of Respiratory and Critical Care Medicine, Anhui Public Health Clinical Center, No. 100, Huaihai Avenue, Hefei, Anhui, People's Republic of China
| | - Meng-Meng Jin
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Anhui Medical University, No. 100, Huaihai Avenue, Hefei, Anhui, People's Republic of China
- Department of Respiratory and Critical Care Medicine, Anhui Public Health Clinical Center, No. 100, Huaihai Avenue, Hefei, Anhui, People's Republic of China
| | - Xiao-Hui Cao
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Anhui Medical University, No. 100, Huaihai Avenue, Hefei, Anhui, People's Republic of China
- Department of Respiratory and Critical Care Medicine, Anhui Public Health Clinical Center, No. 100, Huaihai Avenue, Hefei, Anhui, People's Republic of China
| | - Lei Zhao
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Anhui Medical University, No. 100, Huaihai Avenue, Hefei, Anhui, People's Republic of China
- Department of Respiratory and Critical Care Medicine, Anhui Public Health Clinical Center, No. 100, Huaihai Avenue, Hefei, Anhui, People's Republic of China
| | - Yong-Huai Li
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Anhui Medical University, No. 100, Huaihai Avenue, Hefei, Anhui, People's Republic of China
- Department of Respiratory and Critical Care Medicine, Anhui Public Health Clinical Center, No. 100, Huaihai Avenue, Hefei, Anhui, People's Republic of China
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Gu J, Chen J, Xiang S, Zhou X, Li J. Intricate confrontation: Research progress and application potential of TRIM family proteins in tumor immune escape. J Adv Res 2023; 54:147-179. [PMID: 36736694 DOI: 10.1016/j.jare.2023.01.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 01/06/2023] [Accepted: 01/12/2023] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Tripartite motif (TRIM) family proteins have more than 80 members and are widely found in various eukaryotic cells. Most TRIM family proteins participate in the ubiquitin-proteasome degradation system as E3-ubiquitin ligases; therefore, they play pivotal regulatory roles in the occurrence and development of tumors, including tumor immune escape. Due to the diversity of functional domains of TRIM family proteins, they can extensively participate in multiple signaling pathways of tumor immune escape through different substrates. In current research and clinical contexts, immune escape has become an urgent problem. The extensive participation of TRIM family proteins in curing tumors or preventing postoperative recurrence and metastasis makes them promising targets. AIM OF REVIEW The aim of the review is to make up for the gap in the current research on TRIM family proteins and tumor immune escape and propose future development directions according to the current progress and problems. KEY SCIENTIFIC CONCEPTS OF REVIEW This up-to-date review summarizes the characteristics and biological functions of TRIM family proteins, discusses the mechanisms of TRIM family proteins involved in tumor immune escape, and highlights the specific mechanism from the level of structure-function-molecule-pathway-phenotype, including mechanisms at the level of protein domains and functions, at the level of molecules and signaling pathways, and at the level of cells and microenvironments. We also discuss the application potential of TRIM family proteins in tumor immunotherapy, such as possible treatment strategies for combination targeting TRIM family protein drugs and checkpoint inhibitors for improving cancer treatment.
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Affiliation(s)
- Junjie Gu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, China
| | - Jingyi Chen
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, China
| | - Shuaixi Xiang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, China
| | - Xikun Zhou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China.
| | - Jing Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, China.
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Liu T, Chen J, Wu J, Du Q, Liu J, Tan S, Pan Y, Yao S. Role of the tripartite motif (TRIM) family in female genital neoplasms. Pathol Res Pract 2023; 250:154811. [PMID: 37713735 DOI: 10.1016/j.prp.2023.154811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/03/2023] [Accepted: 09/08/2023] [Indexed: 09/17/2023]
Abstract
The tripartite motif proteins (TRIMs) family represents a class of highly conservative proteins which play a large regulatory role in molecular processes. Recently, increasing evidence has demonstrated a role of TRIMs in female genital neoplasms. Our review thereby aimed to provide an overview of the biological involvement of TRIMs in female genital neoplasms, to provide a better understanding of its role in the development and progression of such diseases, and emphasize its potential as targeted cancer therapy. Overall, our review highlighted that the wide-ranging roles of TRIMs, in not only target protein ubiquitination, tumor migration and/or invasion, epithelial-mesenchymal transition, stemness, cell adhesion, proliferation, cell cycle regulation, and apoptosis, but also in influencing estrogenic, and chemotherapy response.
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Affiliation(s)
- Tianyu Liu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China; Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, Guangdong, China
| | - Jian Chen
- Department of Thyroid and Hernia Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Jinjie Wu
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Qiqiao Du
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China; Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, Guangdong, China
| | - Junxiu Liu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China; Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, Guangdong, China
| | - Silu Tan
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China; Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, Guangdong, China
| | - Yuwen Pan
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China; Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, Guangdong, China
| | - Shuzhong Yao
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China; Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, Guangdong, China.
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Li X, Morgan C, Nadar‐Ponniah PT, Kolanus W, Doetzlhofer A. TRIM71 reactivation enhances the mitotic and hair cell-forming potential of cochlear supporting cells. EMBO Rep 2023; 24:e56562. [PMID: 37492931 PMCID: PMC10481673 DOI: 10.15252/embr.202256562] [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: 11/27/2022] [Revised: 06/27/2023] [Accepted: 07/04/2023] [Indexed: 07/27/2023] Open
Abstract
Cochlear hair cell loss is a leading cause of deafness in humans. Neighboring supporting cells have some capacity to regenerate hair cells. However, their regenerative potential sharply declines as supporting cells undergo maturation (postnatal day 5 in mice). We recently reported that reactivation of the RNA-binding protein LIN28B restores the hair cell-regenerative potential of P5 cochlear supporting cells. Here, we identify the LIN28B target Trim71 as a novel and equally potent enhancer of supporting cell plasticity. TRIM71 is a critical regulator of stem cell behavior and cell reprogramming; however, its role in cell regeneration is poorly understood. Employing an organoid-based assay, we show that TRIM71 re-expression increases the mitotic and hair cell-forming potential of P5 cochlear supporting cells by facilitating their de-differentiation into progenitor-like cells. Our mechanistic work indicates that TRIM71's RNA-binding activity is essential for such ability, and our transcriptomic analysis identifies gene modules that are linked to TRIM71 and LIN28B-mediated supporting cell reprogramming. Furthermore, our study uncovers that the TRIM71-LIN28B target Hmga2 is essential for supporting cell self-renewal and hair cell formation.
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Affiliation(s)
- Xiao‐Jun Li
- The Solomon H. Snyder Department of NeuroscienceJohns Hopkins University School of MedicineBaltimoreMDUSA
- Present address:
Frontier Institute of Science and TechnologyXi'an Jiaotong UniversityXi'an710054China
| | - Charles Morgan
- The Solomon H. Snyder Department of NeuroscienceJohns Hopkins University School of MedicineBaltimoreMDUSA
| | - Prathamesh T Nadar‐Ponniah
- The Solomon H. Snyder Department of NeuroscienceJohns Hopkins University School of MedicineBaltimoreMDUSA
| | - Waldemar Kolanus
- Molecular Immunology and Cell Biology, Life & Medical Sciences Institute (LIMES)University of BonnBonnGermany
| | - Angelika Doetzlhofer
- The Solomon H. Snyder Department of NeuroscienceJohns Hopkins University School of MedicineBaltimoreMDUSA
- Department of Otolaryngology and Center for Hearing and BalanceJohns Hopkins University School of MedicineBaltimoreMDUSA
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Starrett GJ, Yu K, Golubeva Y, Lenz P, Piaskowski ML, Petersen D, Dean M, Israni A, Hernandez BY, Tucker TC, Cheng I, Gonsalves L, Morris CR, Hussain SK, Lynch CF, Harris RS, Prokunina-Olsson L, Meltzer PS, Buck CB, Engels EA. Evidence for virus-mediated oncogenesis in bladder cancers arising in solid organ transplant recipients. eLife 2023; 12:e82690. [PMID: 36961501 PMCID: PMC10446826 DOI: 10.7554/elife.82690] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 03/22/2023] [Indexed: 03/25/2023] Open
Abstract
A small percentage of bladder cancers in the general population have been found to harbor DNA viruses. In contrast, up to 25% of tumors of solid organ transplant recipients, who are at an increased risk of developing bladder cancer and have an overall poorer outcomes, harbor BK polyomavirus (BKPyV). To better understand the biology of the tumors and the mechanisms of carcinogenesis from potential oncoviruses, we performed whole genome and transcriptome sequencing on bladder cancer specimens from 43 transplant patients. Nearly half of the tumors from this patient population contained viral sequences. The most common were from BKPyV (N=9, 21%), JC polyomavirus (N=7, 16%), carcinogenic human papillomaviruses (N=3, 7%), and torque teno viruses (N=5, 12%). Immunohistochemistry revealed variable Large T antigen expression in BKPyV-positive tumors ranging from 100% positive staining of tumor tissue to less than 1%. In most cases of BKPyV-positive tumors, the viral genome appeared to be clonally integrated into the host chromosome consistent with microhomology-mediated end joining and coincided with focal amplifications of the tumor genome similar to other virus-mediated cancers. Significant changes in host gene expression consistent with the functions of BKPyV Large T antigen were also observed in these tumors. Lastly, we identified four mutation signatures in our cases, with those attributable to APOBEC3 and SBS5 being the most abundant. Mutation signatures associated with an antiviral drug, ganciclovir, and aristolochic acid, a nephrotoxic compound found in some herbal medicines, were also observed. The results suggest multiple pathways to carcinogenesis in solid organ transplant recipients with a large fraction being virus-associated.
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Affiliation(s)
| | - Kelly Yu
- DCEG, NCI, NIHRockvilleUnited States
| | | | - Petra Lenz
- Leidos Biomedical Research IncFrederickUnited States
| | | | | | | | - Ajay Israni
- Department of Medicine, Nephrology Division, Hennepin Healthcare System, University of MinnesotaMinneapolisUnited States
| | | | - Thomas C Tucker
- The Kentucky Cancer Registry, University of KentuckyLexingtonUnited States
| | - Iona Cheng
- Department of Epidemiology and Biostatistics,and Helen Diller Family Comprehensive Cancer Center, University of California, San FranciscoFremontUnited States
| | - Lou Gonsalves
- Connecticut Tumor Registry, Connecticut Department of Public HealthHartfordUnited States
| | - Cyllene R Morris
- California Cancer Reporting and Epidemiologic Surveillance Program, University of California, DavisDavisUnited States
| | - Shehnaz K Hussain
- Cedars-Sinai Cancer and Department of Medicine, Cedars-Sinai Medical CenterLos AngelesUnited States
| | - Charles F Lynch
- The Iowa Cancer Registry, University of IowaIowa CityUnited States
| | - Reuben S Harris
- Howard Hughes Medical Institute, University of MinnesotaMinneapolisUnited States
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Cao L, Wang R, Liu G, Zhang Y, Thorne RF, Zhang XD, Li J, Xia Y, Guo L, Shao F, Gu H, Wu M. Glycolytic Pfkp acts as a Lin41 protein kinase to promote endodermal differentiation of embryonic stem cells. EMBO Rep 2023; 24:e55683. [PMID: 36660859 PMCID: PMC9986826 DOI: 10.15252/embr.202255683] [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: 06/30/2022] [Revised: 12/21/2022] [Accepted: 01/03/2023] [Indexed: 01/21/2023] Open
Abstract
Unveiling the principles governing embryonic stem cell (ESC) differentiation into specific lineages is critical for understanding embryonic development and for stem cell applications in regenerative medicine. Here, we establish an intersection between LIF-Stat3 signaling that is essential for maintaining murine (m) ESCs pluripotency, and the glycolytic enzyme, the platelet isoform of phosphofructokinase (Pfkp). In the pluripotent state, Stat3 transcriptionally suppresses Pfkp in mESCs while manipulating the cells to lift this repression results in differentiation towards the ectodermal lineage. Pfkp exhibits substrate specificity changes to act as a protein kinase, catalyzing serine phosphorylation of the developmental regulator Lin41. Such phosphorylation stabilizes Lin41 by impeding its autoubiquitination and proteasomal degradation, permitting Lin41-mediated binding and destabilization of mRNAs encoding ectodermal specification markers to favor the expression of endodermal specification genes. This provides new insights into the wiring of pluripotency-differentiation circuitry where Pfkp plays a role in germ layer specification during mESC differentiation.
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Affiliation(s)
- Leixi Cao
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical ScienceZhengzhou UniversityZhengzhouChina
| | - Ruijie Wang
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical ScienceZhengzhou UniversityZhengzhouChina
| | - Guangzhi Liu
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical ScienceZhengzhou UniversityZhengzhouChina
| | - Yuwei Zhang
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical ScienceZhengzhou UniversityZhengzhouChina
| | - Rick Francis Thorne
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical ScienceZhengzhou UniversityZhengzhouChina
- School of Biomedical Sciences & PharmacyUniversity of NewcastleNewcastleNSWAustralia
| | - Xu Dong Zhang
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical ScienceZhengzhou UniversityZhengzhouChina
- School of Environmental & Life SciencesUniversity of NewcastleNewcastleNSWAustralia
| | - Jinming Li
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical ScienceZhengzhou UniversityZhengzhouChina
| | - Yang Xia
- Department of Immunology, School of Basic Medical SciencesAnhui Medical UniversityHefeiChina
| | - Lili Guo
- Department of Immunology, School of Basic Medical SciencesAnhui Medical UniversityHefeiChina
| | - Fengmin Shao
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical ScienceZhengzhou UniversityZhengzhouChina
| | - Hao Gu
- Department of Immunology, School of Basic Medical SciencesAnhui Medical UniversityHefeiChina
| | - Mian Wu
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical ScienceZhengzhou UniversityZhengzhouChina
- School of Clinical MedicineHenan UniversityZhengzhouChina
- CAS Centre for Excellence in Molecular Cell Sciencethe First Affiliated Hospital of University of Science and Technology of ChinaHefeiChina
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9
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Multiple Roles of TRIM21 in Virus Infection. Int J Mol Sci 2023; 24:ijms24021683. [PMID: 36675197 PMCID: PMC9867090 DOI: 10.3390/ijms24021683] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/12/2023] [Accepted: 01/12/2023] [Indexed: 01/19/2023] Open
Abstract
The tripartite motif protein 21 (TRIM21) belongs to the TRIM family, possessing an E3 ubiquitin ligase activity. Similar to other TRIMs, TRIM21 also contains three domains (named RBCC), including the Really Interesting New Gene (RING) domain, one or two B-Box domains (B-Box), and one PRY/SPRY domain. Notably, we found that the RING and B-Box domains are relatively more conservative than the PRY/SPRY domain, suggesting that TRIM21 of different species had similar functions. Recent results showed that TRIM21 participates in virus infection by directly interacting with viral proteins or modulating immune and inflammatory responses. TRIM21 also acts as a cytosol high-affinity antibody Fc receptor, binding to the antibody-virus complex and triggering an indirect antiviral antibody-dependent intracellular neutralization (ADIN). This paper focuses on the recent progress in the mechanism of TRIM21 during virus infection and the application prospects of TRIM21 on virus infection.
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Li XJ, Morgan C, Nadar-Ponniah PT, Kolanus W, Doetzlhofer A. Reactivation of the progenitor gene Trim71 enhances the mitotic and hair cell-forming potential of cochlear supporting cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.12.523802. [PMID: 36711735 PMCID: PMC9882147 DOI: 10.1101/2023.01.12.523802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Cochlear hair cell loss is a leading cause of deafness in humans. Neighboring supporting cells have some capacity to regenerate hair cells. However, their regenerative potential sharply declines as supporting cells undergo maturation (postnatal day 5 in mice). We recently reported that reactivation of the RNA-binding protein LIN28B restores the hair cell-regenerative potential of P5 cochlear supporting cells. Here, we identify the LIN28B target Trim71 as a novel and equally potent enhancer of supporting cell plasticity. TRIM71 is a critical regulator of stem cell behavior and cell reprogramming, however, its role in cell regeneration is poorly understood. Employing an organoid-based assay, we show that TRIM71 reactivation increases the mitotic and hair cell-forming potential of P5 cochlear supporting cells by facilitating their de-differentiation into progenitor-like cells. Our mechanistic work indicates that TRIM71’s RNA-binding activity is essential for such ability, and our transcriptomic analysis identifies gene modules that are linked to TRIM71 and LIN28B-mediated supporting cell reprogramming. Furthermore, our study uncovers that the TRIM71-LIN28B target Hmga2 is essential for supporting cell self-renewal and hair cell formation.
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11
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Huang N, Sun X, Li P, Liu X, Zhang X, Chen Q, Xin H. TRIM family contribute to tumorigenesis, cancer development, and drug resistance. Exp Hematol Oncol 2022; 11:75. [PMID: 36261847 PMCID: PMC9583506 DOI: 10.1186/s40164-022-00322-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/16/2022] [Indexed: 11/26/2022] Open
Abstract
The tripartite-motif (TRIM) family represents one of the largest classes of putative single protein RING-finger E3 ubiquitin ligases. TRIM family is involved in a variety of cellular signaling transductions and biological processes. TRIM family also contributes to cancer initiation, progress, and therapy resistance, exhibiting oncogenic and tumor-suppressive functions in different human cancer types. Moreover, TRIM family members have great potential to serve as biomarkers for cancer diagnosis and prognosis. In this review, we focus on the specific mechanisms of the participation of TRIM family members in tumorigenesis, and cancer development including interacting with dysregulated signaling pathways such as JAK/STAT, PI3K/AKT, TGF-β, NF-κB, Wnt/β-catenin, and p53 hub. In addition, many studies have demonstrated that the TRIM family are related to tumor resistance; modulate the epithelial–mesenchymal transition (EMT) process, and guarantee the acquisition of cancer stem cells (CSCs) phenotype. In the end, we havediscussed the potential of TRIM family members for cancer therapeutic targets.
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Affiliation(s)
- Ning Huang
- Department of Pharmacology, School of Pharmacy & General Surgery of Minhang Hospital, Fudan University, Shanghai, 201203, China.,PharmaLegacy Laboratories Co.,Ltd, Shengrong Road No.388, Zhangjiang High-tech Park, Pudong New Area, Shanghai, China
| | - Xiaolin Sun
- Department of Pharmacology, School of Pharmacy & General Surgery of Minhang Hospital, Fudan University, Shanghai, 201203, China
| | - Peng Li
- Department of Pharmacology, School of Pharmacy & General Surgery of Minhang Hospital, Fudan University, Shanghai, 201203, China
| | - Xin Liu
- Department of Pharmacology, School of Pharmacy & General Surgery of Minhang Hospital, Fudan University, Shanghai, 201203, China.,PharmaLegacy Laboratories Co.,Ltd, Shengrong Road No.388, Zhangjiang High-tech Park, Pudong New Area, Shanghai, China
| | - Xuemei Zhang
- Department of Pharmacology, School of Pharmacy & General Surgery of Minhang Hospital, Fudan University, Shanghai, 201203, China.
| | - Qian Chen
- Department of Pharmacology, School of Pharmacy & General Surgery of Minhang Hospital, Fudan University, Shanghai, 201203, China.
| | - Hong Xin
- Department of Pharmacology, School of Pharmacy & General Surgery of Minhang Hospital, Fudan University, Shanghai, 201203, China.
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12
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Emerging Roles of TRIM Family Proteins in Gliomas Pathogenesis. Cancers (Basel) 2022; 14:cancers14184536. [PMID: 36139694 PMCID: PMC9496762 DOI: 10.3390/cancers14184536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/12/2022] [Accepted: 09/13/2022] [Indexed: 11/19/2022] Open
Abstract
Simple Summary Gliomas remain challenging tumors due to their increased heterogeneity, complex molecular profile, and infiltrative phenotype that are often associated with a dismal prognosis. In a constant search for molecular changes and associated mechanisms, the TRIM protein family has emerged as an important area of investigation because of the regulation of vital cellular processes involved in brain pathophysiology that may possibly lead to brain tumor development. Herein, we discuss the diverse role of TRIM proteins in glioma progression, aiming to detect potential targets for future intervention. Abstract Gliomas encompass a vast category of CNS tumors affecting both adults and children. Treatment and diagnosis are often impeded due to intratumor heterogeneity and the aggressive nature of the more malignant forms. It is therefore essential to elucidate the molecular mechanisms and explore the intracellular signaling pathways underlying tumor pathology to provide more promising diagnostic, prognostic, and therapeutic tools for gliomas. The tripartite motif-containing (TRIM) superfamily of proteins plays a key role in many physiological cellular processes, including brain development and function. Emerging evidence supports the association of TRIMs with a wide variety of cancers, exhibiting both an oncogenic as well as a tumor suppressive role depending on cancer type. In this review, we provide evidence of the pivotal role of TRIM proteins in gliomagenesis and exploit their potential as prognostic biomarkers and therapeutic targets.
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13
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Duy PQ, Weise SC, Marini C, Li XJ, Liang D, Dahl PJ, Ma S, Spajic A, Dong W, Juusola J, Kiziltug E, Kundishora AJ, Koundal S, Pedram MZ, Torres-Fernández LA, Händler K, De Domenico E, Becker M, Ulas T, Juranek SA, Cuevas E, Hao LT, Jux B, Sousa AMM, Liu F, Kim SK, Li M, Yang Y, Takeo Y, Duque A, Nelson-Williams C, Ha Y, Selvaganesan K, Robert SM, Singh AK, Allington G, Furey CG, Timberlake AT, Reeves BC, Smith H, Dunbar A, DeSpenza T, Goto J, Marlier A, Moreno-De-Luca A, Yu X, Butler WE, Carter BS, Lake EMR, Constable RT, Rakic P, Lin H, Deniz E, Benveniste H, Malvankar NS, Estrada-Veras JI, Walsh CA, Alper SL, Schultze JL, Paeschke K, Doetzlhofer A, Wulczyn FG, Jin SC, Lifton RP, Sestan N, Kolanus W, Kahle KT. Impaired neurogenesis alters brain biomechanics in a neuroprogenitor-based genetic subtype of congenital hydrocephalus. Nat Neurosci 2022; 25:458-473. [PMID: 35379995 PMCID: PMC9664907 DOI: 10.1038/s41593-022-01043-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 02/28/2022] [Indexed: 01/16/2023]
Abstract
Hydrocephalus, characterized by cerebral ventricular dilatation, is routinely attributed to primary defects in cerebrospinal fluid (CSF) homeostasis. This fosters CSF shunting as the leading reason for brain surgery in children despite considerable disease heterogeneity. In this study, by integrating human brain transcriptomics with whole-exome sequencing of 483 patients with congenital hydrocephalus (CH), we found convergence of CH risk genes in embryonic neuroepithelial stem cells. Of all CH risk genes, TRIM71/lin-41 harbors the most de novo mutations and is most specifically expressed in neuroepithelial cells. Mice harboring neuroepithelial cell-specific Trim71 deletion or CH-specific Trim71 mutation exhibit prenatal hydrocephalus. CH mutations disrupt TRIM71 binding to its RNA targets, causing premature neuroepithelial cell differentiation and reduced neurogenesis. Cortical hypoplasia leads to a hypercompliant cortex and secondary ventricular enlargement without primary defects in CSF circulation. These data highlight the importance of precisely regulated neuroepithelial cell fate for normal brain-CSF biomechanics and support a clinically relevant neuroprogenitor-based paradigm of CH.
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Affiliation(s)
- Phan Q Duy
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT, USA.,Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA.,Medical Scientist Training Program, Yale University School of Medicine, New Haven, CT, USA
| | - Stefan C Weise
- Molecular Immunology and Cell Biology, Life & Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
| | - Claudia Marini
- Institute for Cell Biology and Neurobiology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Xiao-Jun Li
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Center for Hearing and Balance, Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Dan Liang
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT, USA
| | - Peter J Dahl
- Microbial Sciences Institute, Yale University, West Haven, CT, USA.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Shaojie Ma
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT, USA
| | - Ana Spajic
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT, USA
| | - Weilai Dong
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | | | - Emre Kiziltug
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Adam J Kundishora
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Sunil Koundal
- Department of Anesthesiology, Yale University School of Medicine, New Haven, CT, USA
| | - Maysam Z Pedram
- Department of Anesthesiology, Yale University School of Medicine, New Haven, CT, USA
| | - Lucia A Torres-Fernández
- Molecular Immunology and Cell Biology, Life & Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
| | - Kristian Händler
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.,Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany.,Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE). PRECISE Platform for Genomics and Epigenomics at DZNE and University of Bonn, Bonn, Germany
| | - Elena De Domenico
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.,Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany.,Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE). PRECISE Platform for Genomics and Epigenomics at DZNE and University of Bonn, Bonn, Germany
| | - Matthias Becker
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.,Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany.,Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE). PRECISE Platform for Genomics and Epigenomics at DZNE and University of Bonn, Bonn, Germany
| | - Thomas Ulas
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.,Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany.,Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE). PRECISE Platform for Genomics and Epigenomics at DZNE and University of Bonn, Bonn, Germany
| | - Stefan A Juranek
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, Bonn, Germany
| | - Elisa Cuevas
- Stem Cells and Regenerative Medicine Section, University College London Great Ormond Street Institute of Child Health, London, UK
| | - Le Thi Hao
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Bettina Jux
- Molecular Immunology and Cell Biology, Life & Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
| | - André M M Sousa
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT, USA
| | - Fuchen Liu
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT, USA
| | - Suel-Kee Kim
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT, USA
| | - Mingfeng Li
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT, USA
| | - Yiying Yang
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA
| | - Yutaka Takeo
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Alvaro Duque
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT, USA
| | | | - Yonghyun Ha
- Department of Radiology and Biomedical Imaging, Yale University School of Medicine, New Haven, CT, USA
| | - Kartiga Selvaganesan
- Department of Radiology and Biomedical Imaging, Yale University School of Medicine, New Haven, CT, USA
| | - Stephanie M Robert
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Amrita K Singh
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Garrett Allington
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Charuta G Furey
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Andrew T Timberlake
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Benjamin C Reeves
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Hannah Smith
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Ashley Dunbar
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Tyrone DeSpenza
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - June Goto
- Division of Pediatric Neurosurgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Arnaud Marlier
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Andres Moreno-De-Luca
- Department of Radiology, Autism & Developmental Medicine Institute, Genomic Medicine Institute, Geisinger, Danville, PA, USA
| | - Xin Yu
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - William E Butler
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Bob S Carter
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Evelyn M R Lake
- Department of Radiology and Biomedical Imaging, Yale University School of Medicine, New Haven, CT, USA
| | - R Todd Constable
- Department of Radiology and Biomedical Imaging, Yale University School of Medicine, New Haven, CT, USA
| | - Pasko Rakic
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT, USA
| | - Haifan Lin
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA
| | - Engin Deniz
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
| | - Helene Benveniste
- Department of Anesthesiology, Yale University School of Medicine, New Haven, CT, USA
| | - Nikhil S Malvankar
- Microbial Sciences Institute, Yale University, West Haven, CT, USA.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Juvianee I Estrada-Veras
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA.,Pediatric Subspecialty Genetics Walter Reed National Military Medical Center, Bethesda, MD, USA.,Murtha Cancer Center/Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA.,Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Seth L Alper
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Division of Nephrology and Vascular Biology Research Center, Beth Israel Deaconess Medical Center and Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Joachim L Schultze
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.,Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany.,Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE). PRECISE Platform for Genomics and Epigenomics at DZNE and University of Bonn, Bonn, Germany
| | - Katrin Paeschke
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, Bonn, Germany
| | - Angelika Doetzlhofer
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Center for Hearing and Balance, Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - F Gregory Wulczyn
- Institute for Cell Biology and Neurobiology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Sheng Chih Jin
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Richard P Lifton
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Nenad Sestan
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT, USA
| | - Waldemar Kolanus
- Molecular Immunology and Cell Biology, Life & Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
| | - Kristopher T Kahle
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA. .,Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Harvard Center for Hydrocephalus and Neurodevelopmental Disorders, Massachusetts General Hospital, Boston, MA, USA.
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14
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The Involvement of Ubiquitination Machinery in Cell Cycle Regulation and Cancer Progression. Int J Mol Sci 2021; 22:ijms22115754. [PMID: 34072267 PMCID: PMC8198665 DOI: 10.3390/ijms22115754] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/12/2021] [Accepted: 05/26/2021] [Indexed: 02/07/2023] Open
Abstract
The cell cycle is a collection of events by which cellular components such as genetic materials and cytoplasmic components are accurately divided into two daughter cells. The cell cycle transition is primarily driven by the activation of cyclin-dependent kinases (CDKs), which activities are regulated by the ubiquitin-mediated proteolysis of key regulators such as cyclins, CDK inhibitors (CKIs), other kinases and phosphatases. Thus, the ubiquitin-proteasome system (UPS) plays a pivotal role in the regulation of the cell cycle progression via recognition, interaction, and ubiquitination or deubiquitination of key proteins. The illegitimate degradation of tumor suppressor or abnormally high accumulation of oncoproteins often results in deregulation of cell proliferation, genomic instability, and cancer occurrence. In this review, we demonstrate the diversity and complexity of the regulation of UPS machinery of the cell cycle. A profound understanding of the ubiquitination machinery will provide new insights into the regulation of the cell cycle transition, cancer treatment, and the development of anti-cancer drugs.
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15
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let-7 microRNAs: Their Role in Cerebral and Cardiovascular Diseases, Inflammation, Cancer, and Their Regulation. Biomedicines 2021; 9:biomedicines9060606. [PMID: 34073513 PMCID: PMC8227213 DOI: 10.3390/biomedicines9060606] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 05/21/2021] [Accepted: 05/24/2021] [Indexed: 12/14/2022] Open
Abstract
The let-7 family is among the first microRNAs found. Recent investigations have indicated that it is highly expressed in many systems, including cerebral and cardiovascular systems. Numerous studies have implicated the aberrant expression of let-7 members in cardiovascular diseases, such as stroke, myocardial infarction (MI), cardiac fibrosis, and atherosclerosis as well as in the inflammation related to these diseases. Furthermore, the let-7 microRNAs are involved in development and differentiation of embryonic stem cells in the cardiovascular system. Numerous genes have been identified as target genes of let-7, as well as a number of the let-7’ regulators. Further studies are necessary to identify the gene targets and signaling pathways of let-7 in cardiovascular diseases and inflammatory processes. The bulk of the let-7’ regulatory proteins are well studied in development, proliferation, differentiation, and cancer, but their roles in inflammation, cardiovascular diseases, and/or stroke are not well understood. Further knowledge on the regulation of let-7 is crucial for therapeutic advances. This review focuses on research progress regarding the roles of let-7 and their regulation in cerebral and cardiovascular diseases and associated inflammation.
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16
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Torres-Fernández LA, Emich J, Port Y, Mitschka S, Wöste M, Schneider S, Fietz D, Oud MS, Di Persio S, Neuhaus N, Kliesch S, Hölzel M, Schorle H, Friedrich C, Tüttelmann F, Kolanus W. TRIM71 Deficiency Causes Germ Cell Loss During Mouse Embryogenesis and Is Associated With Human Male Infertility. Front Cell Dev Biol 2021; 9:658966. [PMID: 34055789 PMCID: PMC8155544 DOI: 10.3389/fcell.2021.658966] [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: 01/26/2021] [Accepted: 03/30/2021] [Indexed: 12/21/2022] Open
Abstract
Mutations affecting the germline can result in infertility or the generation of germ cell tumors (GCT), highlighting the need to identify and characterize the genes controlling germ cell development. The RNA-binding protein and E3 ubiquitin ligase TRIM71 is essential for embryogenesis, and its expression has been reported in GCT and adult mouse testes. To investigate the role of TRIM71 in mammalian germ cell embryonic development, we generated a germline-specific conditional Trim71 knockout mouse (cKO) using the early primordial germ cell (PGC) marker Nanos3 as a Cre-recombinase driver. cKO mice are infertile, with male mice displaying a Sertoli cell-only (SCO) phenotype which in humans is defined as a specific subtype of non-obstructive azoospermia characterized by the absence of germ cells in the seminiferous tubules. Infertility in male Trim71 cKO mice originates during embryogenesis, as the SCO phenotype was already apparent in neonatal mice. The in vitro differentiation of mouse embryonic stem cells (ESCs) into PGC-like cells (PGCLCs) revealed reduced numbers of PGCLCs in Trim71-deficient cells. Furthermore, TCam-2 cells, a human GCT-derived seminoma cell line which was used as an in vitro model for PGCs, showed proliferation defects upon TRIM71 knockdown. Additionally, in vitro growth competition assays, as well as proliferation assays with wild type and CRISPR/Cas9-generated TRIM71 mutant NCCIT cells showed that TRIM71 also promotes proliferation in this malignant GCT-derived non-seminoma cell line. Importantly, the PGC-specific markers BLIMP1 and NANOS3 were consistently downregulated in Trim71 KO PGCLCs, TRIM71 knockdown TCam-2 cells and TRIM71 mutant NCCIT cells. These data collectively support a role for TRIM71 in PGC development. Last, via exome sequencing analysis, we identified several TRIM71 variants in a cohort of infertile men, including a loss-of-function variant in a patient with an SCO phenotype. Altogether, our work reveals for the first time an association of TRIM71 deficiency with human male infertility, and uncovers further developmental roles for TRIM71 in the germline during mouse embryogenesis.
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Affiliation(s)
| | - Jana Emich
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Yasmine Port
- Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Sibylle Mitschka
- Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Marius Wöste
- Institute of Medical Informatics, University of Münster, Münster, Germany
| | - Simon Schneider
- Institute of Pathology, University Hospital Bonn, Bonn, Germany
| | - Daniela Fietz
- Institute for Veterinary Anatomy, Histology and Embryology, Justus Liebig University Gießen, Gießen, Germany
- Hessian Centre of Reproductive Medicine (HZRM), Justus Liebig University Gießen, Gießen, Germany
| | - Manon S. Oud
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Sara Di Persio
- Centre of Reproductive Medicine and Andrology, Institute of Reproductive and Regenerative Biology, University Hospital Münster, Münster, Germany
| | - Nina Neuhaus
- Centre of Reproductive Medicine and Andrology, Institute of Reproductive and Regenerative Biology, University Hospital Münster, Münster, Germany
| | - Sabine Kliesch
- Centre of Reproductive Medicine and Andrology, Department of Clinical and Surgical Andrology, University Hospital Münster, Münster, Germany
| | - Michael Hölzel
- Institute of Experimental Oncology, University Hospital Bonn, Bonn, Germany
| | - Hubert Schorle
- Institute of Pathology, University Hospital Bonn, Bonn, Germany
| | - Corinna Friedrich
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Frank Tüttelmann
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Waldemar Kolanus
- Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
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17
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Torres Fernández LA, Mitschka S, Ulas T, Weise S, Dahm K, Becker M, Händler K, Beyer M, Windhausen J, Schultze JL, Kolanus W. The stem cell-specific protein TRIM71 inhibits maturation and activity of the pro-differentiation miRNA let-7 via two independent molecular mechanisms. RNA (NEW YORK, N.Y.) 2021; 27:rna.078696.121. [PMID: 33975917 PMCID: PMC8208056 DOI: 10.1261/rna.078696.121] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 04/29/2021] [Indexed: 05/05/2023]
Abstract
The stem cell-specific RNA-binding protein TRIM71/LIN-41 was the first identified target of the pro-differentiation and tumor suppressor miRNA let-7. TRIM71 has essential functions in embryonic development and a proposed oncogenic role in several cancer types, such as hepatocellular carcinoma. Here, we show that TRIM71 regulates let-7 expression and activity via two independent mechanisms. On the one hand, TRIM71 enhances pre-let-7 degradation through its direct interaction with LIN28 and TUT4, thereby inhibiting let-7 maturation and indirectly promoting the stabilization of let-7 targets. On the other hand, TRIM71 represses the activity of mature let-7 via its RNA-dependent interaction with the RNA-Induced Silencing Complex (RISC) effector protein AGO2. We found that TRIM71 directly binds and stabilizes let-7 targets, suggesting that let-7 activity inhibition occurs on active RISCs. MiRNA enrichment analysis of several transcriptomic datasets from mouse embryonic stem cells and human hepatocellular carcinoma cells suggests that these let-7 regulatory mechanisms shape transcriptomic changes during developmental and oncogenic processes. Altogether, our work reveals a novel role for TRIM71 as a miRNA repressor and sheds light on a dual mechanism of let-7 regulation.
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Affiliation(s)
| | | | - Thomas Ulas
- German Center for Neurodegenerative Diseases (DZNE) & Life and Medical Sciences Institute (LIMES), University of Bonn
| | - Stefan Weise
- Life and Medical Sciences Institute (LIMES), University of Bonn
| | - Kilian Dahm
- Life and Medical Sciences Institute (LIMES), University of Bonn
| | - Matthias Becker
- German Center for Neurodegenerative Diseases (DZNE), University of Bonn
| | - Kristian Händler
- German Center for Neurodegenerative Diseases (DZNE), University of Bonn
| | - Marc Beyer
- Life and Medical Sciences Institute (LIMES)
| | | | - Joachim L Schultze
- German Center for Neurodegenerative Diseases (DZNE) & Life and Medical Sciences Institute (LIMES), University of Bonn
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Shariati L, Esmaeili Y, Javanmard SH, Bidram E, Amini A. Organoid Technology: Current Standing and Future Perspectives. STEM CELLS (DAYTON, OHIO) 2021; 39:1625-1649. [PMID: 33786925 DOI: 10.1002/stem.3379] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 03/01/2021] [Indexed: 11/12/2022]
Abstract
Organoids are powerful systems to facilitate the study of individuals' disorders and personalized treatments. Likewise, emerging this technology has improved the chance of translatability of drugs for pre-clinical therapies and mimicking the complexity of organs, while it proposes numerous approaches for human disease modeling, tissue engineering, drug development, diagnosis, and regenerative medicine. In this review, we outline the past/present organoid technology and summarize its faithful applications, then, we discuss the challenges and limitations encountered by 3D organoids. In the end, we offer the human organoids as basic mechanistic infrastructure for "human modelling" systems to prescribe personalized medicines. © AlphaMed Press 2021 SIGNIFICANCE STATEMENT: This concise review concerns about organoids, available methods for in vitro organoid formation and different types of human organoid models. We, then, summarize biological approaches to improve 3D organoids complexity and therapeutic potentials of organoids. Despite the existing incomprehensive review articles in literature that examine partial aspects of the organoid technology, the present review article comprehensively and critically presents this technology from different aspects. It effectively provides a systematic overview on the past and current applications of organoids and discusses the future perspectives and suggestions to improve this technology and its applications.
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Affiliation(s)
- Laleh Shariati
- Applied Physiology Research Center, Isfahan Cardiovascular Research Institute, Isfahan University of Medical Sciences, Isfahan, Iran.,Department of Biomaterials, Nanotechnology and Tissue Engineering, School of Advanced Technologies in Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Yasaman Esmaeili
- Biosensor Research Center, School of Advanced Technologies in Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Shaghayegh Haghjooy Javanmard
- Applied Physiology Research Center, Isfahan Cardiovascular Research Institute, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Elham Bidram
- Department of Biomaterials, Nanotechnology and Tissue Engineering, School of Advanced Technologies in Medicine, Isfahan University of Medical Sciences, Isfahan, Iran.,Biosensor Research Center, School of Advanced Technologies in Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Abbas Amini
- Department of Mechanical Engineering, Australian College of Kuwait, Mishref, Safat, Kuwait.,Centre for Infrastructure Engineering, Western Sydney University, Penrith, NSW, Australia
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19
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Hao Q, Chen J, Liao J, Huang Y, Gan Y, Larisch S, Zeng SX, Lu H, Zhou X. p53 induces ARTS to promote mitochondrial apoptosis. Cell Death Dis 2021; 12:204. [PMID: 33627621 PMCID: PMC7904775 DOI: 10.1038/s41419-021-03463-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 01/13/2021] [Accepted: 01/19/2021] [Indexed: 11/09/2022]
Abstract
Apoptosis related protein in TGF-β signaling pathway (ARTS) was originally discovered in cells undergoing apoptosis in response to TGF-β, but ARTS also acts downstream of many other apoptotic stimuli. ARTS induces apoptosis by antagonizing the anti-apoptotic proteins XIAP and Bcl-2. Here we identified the pro-apoptotic Sept4/ARTS gene as a p53-responsive target gene. Ectopic p53 and a variety of p53-inducing agents increased both mRNA and protein levels of ARTS, whereas ablation of p53 reduced ARTS expression in response to multiple stress conditions. Also, γ-irradiation induced p53-dependent ARTS expression in mice. Consistently, p53 binds to the responsive DNA element on the ARTS promoter and transcriptionally activated the promoter-driven expression of a luciferase reporter gene. Interestingly, ARTS binds to and sequesters p53 at mitochondria, enhancing the interaction of the latter with Bcl-XL. Ectopic ARTS markedly augments DNA damage stress- or Nutlin-3-triggered apoptosis, while ablation of ARTS preferentially impairs p53-induced apoptosis. Altogether, these findings demonstrate that ARTS collaborates with p53 in mitochondria-engaged apoptosis.
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Affiliation(s)
- Qian Hao
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Jiaxiang Chen
- Department of Biochemistry & Molecular Biology and Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, 70112, USA
- Department of Physiology, Medical College of Nanchang University, Nanchang, 330006, China
| | - Junming Liao
- Department of Biochemistry & Molecular Biology and Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Yingdan Huang
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Yu Gan
- Department of Physiology, Medical College of Nanchang University, Nanchang, 330006, China
| | - Sarit Larisch
- Cell Death and Cancer Research Laboratory, Department of Biology, University of Haifa, Haifa, 31905, Israel
| | - Shelya X Zeng
- Department of Biochemistry & Molecular Biology and Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Hua Lu
- Department of Biochemistry & Molecular Biology and Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, 70112, USA.
| | - Xiang Zhou
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
- Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, China.
- Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China.
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20
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Pan M, Blattner C. Regulation of p53 by E3s. Cancers (Basel) 2021; 13:745. [PMID: 33670160 PMCID: PMC7916862 DOI: 10.3390/cancers13040745] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 01/15/2021] [Accepted: 02/05/2021] [Indexed: 12/18/2022] Open
Abstract
More than 40 years of research on p53 have given us tremendous knowledge about this protein. Today we know that p53 plays a role in different biological processes such as proliferation, invasion, pluripotency, metabolism, cell cycle control, ROS (reactive oxygen species) production, apoptosis, inflammation and autophagy. In the nucleus, p53 functions as a bona-fide transcription factor which activates and represses transcription of a number of target genes. In the cytoplasm, p53 can interact with proteins of the apoptotic machinery and by this also induces cell death. Despite being so important for the fate of the cell, expression levels of p53 are kept low in unstressed cells and the protein is largely inactive. The reason for the low expression level is that p53 is efficiently degraded by the ubiquitin-proteasome system and the vast inactivity of the tumor suppressor protein under normal growth conditions is due to the absence of activating and the presence of inactivating posttranslational modifications. E3s are important enzymes for these processes as they decorate p53 with ubiquitin and small ubiquitin-like proteins and by this control p53 degradation, stability and its subcellular localization. In this review, we provide an overview about E3s that target p53 and discuss the connection between p53, E3s and tumorigenesis.
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Affiliation(s)
| | - Christine Blattner
- Institute of Biological and Chemical Systems—Biological Information Processing, Karlsruhe Institute of Technology, PO-box 3640, 76021 Karlsruhe, Germany;
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21
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Xu Z, Wu W, Yan H, Hu Y, He Q, Luo P. Regulation of p53 stability as a therapeutic strategy for cancer. Biochem Pharmacol 2021; 185:114407. [PMID: 33421376 DOI: 10.1016/j.bcp.2021.114407] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/21/2020] [Accepted: 01/04/2021] [Indexed: 12/17/2022]
Abstract
The tumor suppressor protein p53 participates in the control of key biological functions such as cell death, metabolic homeostasis and immune function, which are closely related to various diseases such as tumors, metabolic disorders, infection and neurodegeneration. The p53 gene is also mutated in approximately 50% of human cancer cells. Mutant p53 proteins escape from the ubiquitination-dependent degradation, gain oncogenic function and promote the carcinogenesis, malignant progression, metastasis and chemoresistance. Therefore, the stability of both wild type and mutant p53 needs to be precisely regulated to maintain normal functions and targeting the p53 stability is one of the therapeutic strategies against cancer. Here, we focus on compound-induced degradation of p53 by both the ubiquitination-dependent proteasome and autophagy-lysosome degradation pathways. We also review other posttranslational modifications which control the stability of p53 and the biological functions involved in these processes. This review provides the current theoretical basis for the regulation of p53 abundance and its possible applications in different diseases.
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Affiliation(s)
- Zhifei Xu
- Center for Drug Safety Evaluation and Research of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Wentong Wu
- Center for Drug Safety Evaluation and Research of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Hao Yan
- Center for Drug Safety Evaluation and Research of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yuhuai Hu
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Hangzhou 310018, China
| | - Qiaojun He
- Center for Drug Safety Evaluation and Research of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Hangzhou 310018, China
| | - Peihua Luo
- Center for Drug Safety Evaluation and Research of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.
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22
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Zhan W, Zhang S. TRIM proteins in lung cancer: Mechanisms, biomarkers and therapeutic targets. Life Sci 2021; 268:118985. [PMID: 33412211 DOI: 10.1016/j.lfs.2020.118985] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 12/13/2020] [Accepted: 12/22/2020] [Indexed: 12/24/2022]
Abstract
The tripartite motif (TRIM) family is defined by the presence of a Really Interesting New Gene (RING) domain, one or two B-box motifs and a coiled-coil region. TRIM proteins play key roles in many biological processes, including innate immunity, tumorigenesis, cell differentiation and ontogenetic development. Alterations in TRIM gene and protein levels frequently emerge in a wide range of tumors and affect tumor progression. As canonical E3 ubiquitin ligases, TRIM proteins participate in ubiquitin-dependent proteolysis of prominent components of the p53, NF-κB and PI3K/AKT signaling pathways. The occurrence of ubiquitylation events induced by TRIM proteins sustains internal balance between tumor suppressive and tumor promoting genes. In this review, we summarized the diverse mechanism of TRIM proteins responsible for the most common malignancy, lung cancer. Furthermore, we also discussed recent progress in both the diagnosis and therapeutics of tumors contributed by TRIM proteins.
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Affiliation(s)
- Weihua Zhan
- Ecology and Health Institute, Hangzhou Vocational & Technical College, Hangzhou 310018, China.
| | - Song Zhang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.
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23
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Yan P, Ren J, Zhang W, Qu J, Liu GH. Protein quality control of cell stemness. CELL REGENERATION (LONDON, ENGLAND) 2020; 9:22. [PMID: 33179756 PMCID: PMC7658286 DOI: 10.1186/s13619-020-00064-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 09/14/2020] [Indexed: 02/07/2023]
Abstract
Protein quality control (PQC) systems play essential roles in the recognition, refolding and clearance of aberrant proteins, thus ensuring cellular protein homeostasis, or proteostasis. Especially, continued proliferation and differentiation of stem cells require a high rate of translation; therefore, accurate PQC systems are essential to maintain stem cell function. Growing evidence suggested crucial roles of PQC systems in regulating the stemness and differentiation of stem cells. This review focuses on current knowledge regarding the components of the proteostasis network in stem cells, and the importance of proteostasis in maintaining stem cell identity and regenerative functions. A complete understanding of this process might uncover potential applications in aging intervention and aging-related diseases.
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Affiliation(s)
- Pengze Yan
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jie Ren
- University of Chinese Academy of Sciences, Beijing, 100049, China
- China National Center for Bioinformation, Beijing, 100101, China
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
| | - Weiqi Zhang
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- China National Center for Bioinformation, Beijing, 100101, China.
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
- Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Jing Qu
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Guang-Hui Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute for Brain Disorders, Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing, 100053, China.
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24
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Backlund M, Stein F, Rettel M, Schwarzl T, Perez-Perri JI, Brosig A, Zhou Y, Neu-Yilik G, Hentze MW, Kulozik AE. Plasticity of nuclear and cytoplasmic stress responses of RNA-binding proteins. Nucleic Acids Res 2020; 48:4725-4740. [PMID: 32313943 PMCID: PMC7229827 DOI: 10.1093/nar/gkaa256] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 04/01/2020] [Accepted: 04/04/2020] [Indexed: 02/07/2023] Open
Abstract
Cellular stress causes multifaceted reactions to trigger adaptive responses to environmental cues at all levels of the gene expression pathway. RNA-binding proteins (RBP) are key contributors to stress-induced regulation of RNA fate and function. Here, we uncover the plasticity of the RNA interactome in stressed cells, differentiating between responses in the nucleus and in the cytoplasm. We applied enhanced RNA interactome capture (eRIC) analysis preceded by nucleo-cytoplasmic fractionation following arsenite-induced oxidative stress. The data reveal unexpectedly compartmentalized RNA interactomes and their responses to stress, including differential responses of RBPs in the nucleus versus the cytoplasm, which would have been missed by whole cell analyses.
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Affiliation(s)
- Michael Backlund
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University, Im Neuenheimer Feld 350, 69120 Heidelberg, Germany & European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany & Hopp Children's Cancer Center, National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
- To whom correspondence should be addressed. Tel: +49 6221 564555;
| | - Frank Stein
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Mandy Rettel
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Thomas Schwarzl
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Joel I Perez-Perri
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Annika Brosig
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University, Im Neuenheimer Feld 350, 69120 Heidelberg, Germany & European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany & Hopp Children's Cancer Center, National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Collaboration for joint PhD degree between EMBL and Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Yang Zhou
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University, Im Neuenheimer Feld 350, 69120 Heidelberg, Germany & European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany & Hopp Children's Cancer Center, National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
| | - Gabriele Neu-Yilik
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University, Im Neuenheimer Feld 350, 69120 Heidelberg, Germany & European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany & Hopp Children's Cancer Center, National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
| | - Matthias W Hentze
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University, Im Neuenheimer Feld 350, 69120 Heidelberg, Germany & European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Correspondence may also be addressed to Matthias W. Hentze.
| | - Andreas E Kulozik
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University, Im Neuenheimer Feld 350, 69120 Heidelberg, Germany & European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany & Hopp Children's Cancer Center, National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
- Correspondence may also be addressed to Andreas E. Kulozik.
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25
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Evsen L, Li X, Zhang S, Razin S, Doetzlhofer A. let-7 miRNAs inhibit CHD7 expression and control auditory-sensory progenitor cell behavior in the developing inner ear. Development 2020; 147:147/15/dev183384. [PMID: 32816902 DOI: 10.1242/dev.183384] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 07/07/2020] [Indexed: 11/20/2022]
Abstract
The evolutionarily conserved lethal-7 (let-7) microRNAs (miRNAs) are well-known activators of proliferative quiescence and terminal differentiation. However, in the murine auditory organ, let-7g overexpression delays the differentiation of mechano-sensory hair cells (HCs). To address whether the role of let-7 in auditory-sensory differentiation is conserved among vertebrates, we manipulated let-7 levels within the chicken auditory organ: the basilar papilla. Using a let-7 sponge construct to sequester let-7 miRNAs, we found that endogenous let-7 miRNAs are essential for limiting the self-renewal of HC progenitor cells. Furthermore, let-7b overexpression experiments revealed that, similar to mice, higher than normal let-7 levels slow/delay HC differentiation. Finally, we identify CHD7, a chromatin remodeler, as a candidate for mediating the repressive function of let-7 in HC differentiation and inner ear morphogenesis. Our analysis uncovered an evolutionarily conserved let-7-5p-binding site within the chicken Chd7 gene and its human and murine homologs, and we show that let-7g overexpression in mice limits CHD7 expression in the developing inner ear, retina and brain. Haploinsufficiency of CHD7 in humans causes CHARGE syndrome and attenuation of let-7 function may be an effective method for treating CHD7 deficiency.
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Affiliation(s)
- Lale Evsen
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Xiaojun Li
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Shuran Zhang
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Sharjil Razin
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Angelika Doetzlhofer
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA .,Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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26
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Connacher RP, Goldstrohm AC. Molecular and biological functions of TRIM-NHL RNA-binding proteins. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1620. [PMID: 32738036 DOI: 10.1002/wrna.1620] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 06/17/2020] [Accepted: 06/19/2020] [Indexed: 01/02/2023]
Abstract
The TRIM-NHL family of proteins shares a conserved domain architecture and play crucial roles in stem cell biology, fertility, and development. This review synthesizes new insights that have revolutionized our understanding of the molecular and biological functions of TRIM-NHL proteins. Multiple TRIM-NHLs have been shown to bind specific RNA sequences and structures. X-ray crystal structures of TRIM-NHL proteins in complex with RNA ligands reveal versatile modes of RNA recognition by the NHL domain. Functional and genetic analyses show that TRIM-NHL RNA-binding proteins negatively regulate the protein expression from the target mRNAs that they bind. This repressive activity plays a crucial role in controlling stem cell fate in the developing brain and differentiating germline. To highlight these paradigms, we focus on several of the most-extensively studied TRIM-NHL proteins, specifically Drosophila and vertebrate TRIM71, among others. Brat is essential for development and regulates key target mRNAs to control differentiation of germline and neural stem cells. TRIM71 is also required for development and promotes stem cell proliferation while antagonizing differentiation. Moreover, TRIM71 can be utilized to help reprogram fibroblasts into induced pluripotent stem cells. Recently discovered mutations in TRIM71 cause the neurodevelopmental disease congenital hydrocephalus and emphasize the importance of its RNA-binding function in brain development. Further relevance of TRIM71 to disease pathogenesis comes from evidence linking it to several types of cancer, including liver and testicular cancer. Collectively, these advances demonstrate a primary role for TRIM-NHL proteins in the post-transcriptional regulation of gene expression in crucial biological processes. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications Translation > Translation Regulation RNA Turnover and Surveillance > Regulation of RNA Stability.
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Affiliation(s)
- Robert P Connacher
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
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27
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Liu J, Zhang C, Wang X, Hu W, Feng Z. Tumor suppressor p53 cross-talks with TRIM family proteins. Genes Dis 2020; 8:463-474. [PMID: 34179310 PMCID: PMC8209353 DOI: 10.1016/j.gendis.2020.07.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/06/2020] [Accepted: 07/07/2020] [Indexed: 12/11/2022] Open
Abstract
p53 is a key tumor suppressor. As a transcription factor, p53 accumulates in cells in response to various stress signals and selectively transcribes its target genes to regulate a wide variety of cellular stress responses to exert its function in tumor suppression. In addition to tumor suppression, p53 is also involved in many other physiological and pathological processes, e.g. anti-infection, immune response, development, reproduction, neurodegeneration and aging. To maintain its proper function, p53 is under tight and delicate regulation through different mechanisms, particularly the posttranslational modifications. The tripartite motif (TRIM) family proteins are a large group of proteins characterized by the RING, B-Box and coiled-coil (RBCC) domains at the N-terminus. TRIM proteins play important roles in regulation of many fundamental biological processes, including cell proliferation and death, DNA repair, transcription, and immune response. Alterations of TRIM proteins have been linked to many diseases including cancer, infectious diseases, developmental disorders, and neurodegeneration. Interestingly, recent studies have revealed that many TRIM proteins are involved in the regulation of p53, and at the same time, many TRIM proteins are also regulated by p53. Here, we review the cross-talk between p53 and TRIM proteins, and its impact upon cellular biological processes as well as cancer and other diseases.
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Affiliation(s)
- Juan Liu
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, Rutgers-State University of New Jersey, 195 Little Albany Street, New Brunswick, NJ 08903, USA
| | - Cen Zhang
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, Rutgers-State University of New Jersey, 195 Little Albany Street, New Brunswick, NJ 08903, USA
| | - Xue Wang
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, Rutgers-State University of New Jersey, 195 Little Albany Street, New Brunswick, NJ 08903, USA
| | - Wenwei Hu
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, Rutgers-State University of New Jersey, 195 Little Albany Street, New Brunswick, NJ 08903, USA
| | - Zhaohui Feng
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, Rutgers-State University of New Jersey, 195 Little Albany Street, New Brunswick, NJ 08903, USA
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28
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Hao Q, Chen Y, Zhou X. The Janus Face of p53-Targeting Ubiquitin Ligases. Cells 2020; 9:cells9071656. [PMID: 32660118 PMCID: PMC7407405 DOI: 10.3390/cells9071656] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/03/2020] [Accepted: 07/06/2020] [Indexed: 12/11/2022] Open
Abstract
The tumor suppressor p53 prevents tumorigenesis and cancer progression by maintaining genomic stability and inducing cell growth arrest and apoptosis. Because of the extremely detrimental nature of wild-type p53, cancer cells usually mutate the TP53 gene in favor of their survival and propagation. Some of the mutant p53 proteins not only lose the wild-type activity, but also acquire oncogenic function, namely “gain-of-function”, to promote cancer development. Growing evidence has revealed that various E3 ubiquitin ligases are able to target both wild-type and mutant p53 for degradation or inactivation, and thus play divergent roles leading to cancer cell survival or death in the context of different p53 status. In this essay, we reviewed the recent progress in our understanding of the p53-targeting E3 ubiquitin ligases, and discussed the potential clinical implications of these E3 ubiquitin ligases in cancer therapy.
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Affiliation(s)
- Qian Hao
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China;
| | - Yajie Chen
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai 200032, China;
| | - Xiang Zhou
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China;
- Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai 200032, China
- Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
- Correspondence: ; Tel.: +86-21-54237325
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Torres-Fernández LA, Jux B, Bille M, Port Y, Schneider K, Geyer M, Mayer G, Kolanus W. The mRNA repressor TRIM71 cooperates with Nonsense-Mediated Decay factors to destabilize the mRNA of CDKN1A/p21. Nucleic Acids Res 2020; 47:11861-11879. [PMID: 31732746 PMCID: PMC7145526 DOI: 10.1093/nar/gkz1057] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 10/22/2019] [Accepted: 11/10/2019] [Indexed: 12/30/2022] Open
Abstract
Nonsense-mediated decay (NMD) plays a fundamental role in the degradation of premature termination codon (PTC)-containing transcripts, but also regulates the expression of functional transcripts lacking PTCs, although such 'non-canonical' functions remain ill-defined and require the identification of factors targeting specific mRNAs to the NMD machinery. Our work identifies the stem cell-specific mRNA repressor protein TRIM71 as one of these factors. TRIM71 plays an essential role in embryonic development and is linked to carcinogenesis. For instance, TRIM71 has been correlated with advanced stages and poor prognosis in hepatocellular carcinoma. Our data shows that TRIM71 represses the mRNA of the cell cycle inhibitor and tumor suppressor CDKN1A/p21 and promotes the proliferation of HepG2 tumor cells. CDKN1A specific recognition involves the direct interaction of TRIM71 NHL domain with a structural RNA stem-loop motif within the CDKN1A 3'UTR. Importantly, CDKN1A repression occurs independently of miRNA-mediated silencing. Instead, the NMD factors SMG1, UPF1 and SMG7 assist TRIM71-mediated degradation of CDKN1A mRNA, among other targets. Our data sheds light on TRIM71-mediated target recognition and repression mechanisms and uncovers a role for this stem cell-specific factor and oncogene in non-canonical NMD, revealing the existence of a novel mRNA surveillance mechanism which we have termed the TRIM71/NMD axis.
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Affiliation(s)
- Lucia A Torres-Fernández
- Molecular Immunology and Cell Biology, Life & Medical Sciences Institute (LIMES), University of Bonn, 53115 Bonn, Germany
| | - Bettina Jux
- Molecular Immunology and Cell Biology, Life & Medical Sciences Institute (LIMES), University of Bonn, 53115 Bonn, Germany
| | - Maximilian Bille
- Molecular Immunology and Cell Biology, Life & Medical Sciences Institute (LIMES), University of Bonn, 53115 Bonn, Germany
| | - Yasmine Port
- Molecular Immunology and Cell Biology, Life & Medical Sciences Institute (LIMES), University of Bonn, 53115 Bonn, Germany
| | - Karin Schneider
- Molecular Immunology and Cell Biology, Life & Medical Sciences Institute (LIMES), University of Bonn, 53115 Bonn, Germany
| | - Matthias Geyer
- Institute of Structural Biology, University Clinics Bonn, University of Bonn, 53127 Bonn, Germany
| | - Günter Mayer
- Center of Aptamer Research & Development; Chemical Biology & Chemical Genetics, Life & Medical Sciences Institute (LIMES). University of Bonn, 53121 Bonn, Germany
| | - Waldemar Kolanus
- Molecular Immunology and Cell Biology, Life & Medical Sciences Institute (LIMES), University of Bonn, 53115 Bonn, Germany
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Guan B, Qi F, Tian Y. Comprehensive analysis of competing endogenous RNA network in Wilms tumor based on the TARGET database. Transl Androl Urol 2020; 9:473-484. [PMID: 32420153 PMCID: PMC7214997 DOI: 10.21037/tau.2020.01.34] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Background Wilms tumor (WT) was the most common malignant tumor of urinary system in children. With the advances in gene sequencing, research of molecular mechanism of WT tumor was gradually increasing. However, few studies have explored the influence of competing endogenous RNA (ceRNA) in WT. Accordingly, we aimed to explore the mechanisms of ceRNA co-expression network in WT. Methods A total of 6 non-tumor controls and 127 WT patients’ RNA-seq data combined with clinical data was acquired from Therapeutically Applicable Research to Generate Effective Treatments (TARGET) database. Differentially expressed lncRNA, miRNA and mRNA between WT tissues and normal tissues were analyzed using “edgeR” package in R software. Weighted gene co-expression network analysis (WGCNA) was utilized to construct the ceRNA co-expression network while Molecular Complex Detection (MCODE) algorithm was used to extract the pivotal sub-network. Function annotation of mRNA was performed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). Survival analysis was then conducted based on long-rank test and Kaplan-Meier curves using the survival package. Results By applying the “edgeR” package in R, the transcriptome expression data of 127 WT tissues with 6 normal tissues were normalized. Moreover, 146 DElncRNAs, 62 DEmiRNAs, 287 DEmRNAs of them were involved in ceRNA network after applying WGCNA. According to MCODE, we identified that the interactions between LINC002253 (lncRNA) and TRIM71 (mRNA) was mediated by hsa-mir-301a and hsa-mir-301b (miRNA). Furthermore, we detected 13 DElncRNAs which were significantly associated with the progression of WT. Conclusions We used WGCNA method to construct the WT ceRNA network for the first time. TRIM71 was identified to be the most closely related genes involved in hub sub-network by MCDOE, suggesting it might act as a new drug target and prognostic factor based on our comprehensive results.
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Affiliation(s)
- Bo Guan
- Department of Urology, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
| | - Feng Qi
- Department of Urology, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Ye Tian
- Department of Urology, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
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Williams FP, Haubrich K, Perez-Borrajero C, Hennig J. Emerging RNA-binding roles in the TRIM family of ubiquitin ligases. Biol Chem 2020; 400:1443-1464. [PMID: 31120853 DOI: 10.1515/hsz-2019-0158] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 04/11/2019] [Indexed: 12/14/2022]
Abstract
TRIM proteins constitute a large, diverse and ancient protein family which play a key role in processes including cellular differentiation, autophagy, apoptosis, DNA repair, and tumour suppression. Mostly known and studied through the lens of their ubiquitination activity as E3 ligases, it has recently emerged that many of these proteins are involved in direct RNA binding through their NHL or PRY/SPRY domains. We summarise the current knowledge concerning the mechanism of RNA binding by TRIM proteins and its biological role. We discuss how RNA-binding relates to their previously described functions such as E3 ubiquitin ligase activity, and we will consider the potential role of enrichment in membrane-less organelles.
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Affiliation(s)
- Felix Preston Williams
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Kevin Haubrich
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Cecilia Perez-Borrajero
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Janosch Hennig
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany, e-mail:
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Du G, Wang X, Luo M, Xu W, Zhou T, Wang M, Yu L, Li L, Cai L, Wang PJ, Zhong Li J, Oatley JM, Wu X. mRBPome capture identifies the RNA-binding protein TRIM71, an essential regulator of spermatogonial differentiation. Development 2020; 147:dev184655. [PMID: 32188631 PMCID: PMC10679512 DOI: 10.1242/dev.184655] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 02/23/2020] [Indexed: 12/15/2022]
Abstract
Continual spermatogenesis relies on the actions of an undifferentiated spermatogonial population that is composed of stem cells and progenitors. Here, using mouse models, we explored the role of RNA-binding proteins (RBPs) in regulation of the biological activities of this population. Proteins bound to polyadenylated RNAs in primary cultures of undifferentiated spermatogonia were captured with oligo (dT)-conjugated beads after UV-crosslinking and profiled by proteomics (termed mRBPome capture), yielding a putative repertoire of 473 RBPs. From this database, the RBP TRIM71 was identified and found to be expressed by stem and progenitor spermatogonia in prepubertal and adult mouse testes. Tissue-specific deletion of TRIM71 in the male germline led to reduction of the undifferentiated spermatogonial population and a block in transition to the differentiating state. Collectively, these findings demonstrate a key role of the RBP system in regulation of the spermatogenic lineage and may provide clues about the influence of RBPs on the biology of progenitor cell populations in other lineages.
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Affiliation(s)
- Guihua Du
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Center for Reproductive Biology, School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
| | - Xinrui Wang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Key Laboratory of Rare Metabolic Diseases & Jiangsu Province Key Laboratory of Human Functional Genomics, Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing 211166, China
| | - Mengcheng Luo
- Department of Tissue and Embryology, School of Basic Medical Sciences, Wuhan University, and Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan 430071, China
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA 19104, USA
| | - Weiya Xu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Tao Zhou
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Mei Wang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Luping Yu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Lufan Li
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Li'e Cai
- Key Laboratory of Rare Metabolic Diseases & Jiangsu Province Key Laboratory of Human Functional Genomics, Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing 211166, China
| | - P Jeremy Wang
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA 19104, USA
| | - John Zhong Li
- Key Laboratory of Rare Metabolic Diseases & Jiangsu Province Key Laboratory of Human Functional Genomics, Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing 211166, China
| | - Jon M Oatley
- Center for Reproductive Biology, School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
| | - Xin Wu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China
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Yang X, Zhou Z, Mao Z, Shen M, Chen N, Miao D. Role of p53 deficiency in socket healing after tooth extractions. J Mol Histol 2020; 51:55-65. [PMID: 32006186 DOI: 10.1007/s10735-020-09856-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 01/26/2020] [Indexed: 12/17/2022]
Abstract
p53 is known to advance the cell arrest and cell senescence in human tumors. In this study, we displayed that osteogenic ability of p53-knockout (p53-/-) mice was significantly increased in the tooth extraction socket compared with wild-type (WT) counterparts. Bone marrow mesenchymal stem cells (BM-MSCs) from mandibular were collected and exhibited with elevated proliferation potential and colony-forming units compared with the control, as well as stronger mineral deposits and osteogenic markers. Besides, the bone mass and bone parameter in p53-/- mice were markedly enhanced compared with the counterpart after extractions by micro-CT. Masson's trichrome staining and immunohistochemistry also revealed that new bone filling and osterix/osteocalcin (Osx/OCN)-immunopositive staining in p53-/- mice were remarkably increased at each time point. Furthermore, consistent with the enhanced osteogenic markers, the angiogenic marker of blood vessels (alpha smooth muscle actin, α-SMA) was significantly elevated in p53-/- mice in contrast to WT mice. Importantly, we found that the osteoclast numbers exhibited an increased trend in p53-/- mice compared with WT mice during socket healing. Collectively, our result suggest that p53 deficiency could promote the osteogenesis and angiogenesis in the tooth extraction socket and might lend possibility for p53-based therapeutic approaches in acceleration of extraction bone healing.
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Affiliation(s)
- Xiaohan Yang
- The Research Center for Bone and Stem Cells, Nanjing Medical University, Nanjing, China.,Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, No. 140, Han Zhong Road, Nanjing, 210029, People's Republic of China.,Department of Stomatology, The Second Affiliated Hospital of Nanjing Medical University, No. 262, Zhong Shan North Road, Nanjing, 210003, People's Republic of China
| | - Zhixuan Zhou
- Department of Polyclinic, Affiliated Hospital of Stomatology, Nanjing Medical University, No. 136, Han Zhong Road, Nanjing, 210029, People's Republic of China
| | - Zhiyuan Mao
- The Research Center for Bone and Stem Cells, Nanjing Medical University, Nanjing, China.,Department of Stomatology, The Second Affiliated Hospital of Nanjing Medical University, No. 262, Zhong Shan North Road, Nanjing, 210003, People's Republic of China
| | - Ming Shen
- Department of Polyclinic, Affiliated Hospital of Stomatology, Nanjing Medical University, No. 136, Han Zhong Road, Nanjing, 210029, People's Republic of China
| | - Ning Chen
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, No. 140, Han Zhong Road, Nanjing, 210029, People's Republic of China. .,Department of Dental Implant, Affiliated Hospital of Stomatology, Nanjing Medical University, No. 136, Han Zhong Road, Nanjing, 210029, People's Republic of China.
| | - Dengshun Miao
- The Research Center for Bone and Stem Cells, Nanjing Medical University, Nanjing, China. .,Department of Stomatology, The Second Affiliated Hospital of Nanjing Medical University, No. 262, Zhong Shan North Road, Nanjing, 210003, People's Republic of China.
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Kaid C, Assoni A, Marçola M, Semedo-Kuriki P, Bortolin RH, Carvalho VM, Okamoto OK. Proteome and miRNome profiling of microvesicles derived from medulloblastoma cell lines with stem-like properties reveals biomarkers of poor prognosis. Brain Res 2020; 1730:146646. [PMID: 31917138 DOI: 10.1016/j.brainres.2020.146646] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 11/23/2019] [Accepted: 01/02/2020] [Indexed: 01/13/2023]
Abstract
Primary central nervous system (CNS) tumors are the most common deadly childhood cancer. Several patients with medulloblastoma experience local or metastatic recurrences after standard treatment, a condition associated with very poor prognosis. Current neuroimaging techniques do not accurately detect residual stem-like medulloblastoma cells promoting tumor relapses. In attempt to identify candidate tumor markers that could be circulating in blood or cerebrospinal (CSF) fluid of patients, we evaluated the proteome and miRNome content of extracellular microvesicles (MVs) released by highly-aggressive stem-like medulloblastoma cells overexpressing the pluripotent factor OCT4A. These cells display enhanced tumor initiating capability and resistance to chemotherapeutic agents. A common set of 464 proteins and 10 microRNAs were exclusively detected in MVs of OCT4A-overexpressing cells from four distinct medulloblastoma cell lines, DAOY, CHLA-01-MED, D283-MED, and USP13-MED. The interactome mapping of these exclusive proteins and miRNAs revealed ERK, PI3K/AKT/mTOR, EGF/EGFR, and stem cell self-renewal as the main oncogenic signaling pathways altered in these aggressive medulloblastoma cells. Of these MV cargos, four proteins (UBE2M, HNRNPCL2, HNRNPCL3, HNRNPCL4) and five miRNAs (miR-4449, miR-500b, miR-3648, miR-1291, miR-3607) have not been previously reported in MVs from normal tissues and in CSF. These proteins and miRNAs carried within MVs might serve as biomarkers of aggressive stem-like medulloblastoma cells to improve clinical benefit by helping refining diagnosis, patient stratification, and early detection of relapsed disease.
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Affiliation(s)
- Carolini Kaid
- Centro de Pesquisa sobre o Genoma Humano e Células-Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, CEP: 05508-090, Cidade Universitária, São Paulo, SP, Brazil
| | - Amanda Assoni
- Centro de Pesquisa sobre o Genoma Humano e Células-Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, CEP: 05508-090, Cidade Universitária, São Paulo, SP, Brazil
| | - Marina Marçola
- Centro de Pesquisa sobre o Genoma Humano e Células-Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, CEP: 05508-090, Cidade Universitária, São Paulo, SP, Brazil
| | - Patricia Semedo-Kuriki
- Centro de Pesquisa sobre o Genoma Humano e Células-Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, CEP: 05508-090, Cidade Universitária, São Paulo, SP, Brazil
| | - Raul Hernandes Bortolin
- Department of Clinical and Toxicological Analysis, School of Pharmaceutical Sciences, University of São Paulo, Brazil
| | | | - Oswaldo Keith Okamoto
- Centro de Pesquisa sobre o Genoma Humano e Células-Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, CEP: 05508-090, Cidade Universitária, São Paulo, SP, Brazil; Hemotherapy and Cellular Therapy Department, Hospital Israelita Albert Einstein, Sao Paulo, SP, Brazil.
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TRIM E3 Ubiquitin Ligases in Rare Genetic Disorders. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1233:311-325. [PMID: 32274764 DOI: 10.1007/978-3-030-38266-7_14] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The TRIM family comprises proteins characterized by the presence of the tripartite motif composed of a RING domain, one or two B-box domains and a coiled-coil region. The TRIM shared domain structure underscores a common biochemical function as E3 ligase within the ubiquitination cascade. The TRIM proteins represent one of the largest E3 ligase families counting in human more than 70 members. These proteins are implicated in a plethora of cellular processes such as apoptosis, cell cycle regulation, muscular physiology, and innate immune response. Consistently, their alteration results in several pathological conditions emphasizing their medical relevance. Here, the genetic and pathogenetic mechanisms of rare disorders directly caused by mutations in TRIM genes will be reviewed. These diseases fall into different pathological areas, from malformation birth defects due to developmental abnormalities, to neurological disorders and progressive teenage neuromuscular disorders. In many instances, TRIM E3 ligases act on several substrates thus exerting pleiotropic activities: the need of unraveling disease-specific TRIM pathways for a precise targeting therapy avoiding dramatic side effects will be discussed.
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Bang S, Kaur S, Kurokawa M. Regulation of the p53 Family Proteins by the Ubiquitin Proteasomal Pathway. Int J Mol Sci 2019; 21:E261. [PMID: 31905981 PMCID: PMC6981958 DOI: 10.3390/ijms21010261] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 12/24/2019] [Indexed: 12/25/2022] Open
Abstract
The tumor suppressor p53 and its homologues, p63 and p73, play a pivotal role in the regulation of the DNA damage response, cellular homeostasis, development, aging, and metabolism. A number of mouse studies have shown that a genetic defect in the p53 family could lead to spontaneous tumor development, embryonic lethality, or severe tissue abnormality, indicating that the activity of the p53 family must be tightly regulated to maintain normal cellular functions. While the p53 family members are regulated at the level of gene expression as well as post-translational modification, they are also controlled at the level of protein stability through the ubiquitin proteasomal pathway. Over the last 20 years, many ubiquitin E3 ligases have been discovered that directly promote protein degradation of p53, p63, and p73 in vitro and in vivo. Here, we provide an overview of such E3 ligases and discuss their roles and functions.
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Affiliation(s)
| | | | - Manabu Kurokawa
- Department of Biological Sciences, Kent State University, Kent, OH 44242, USA; (S.B.); (S.K.)
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Wang L, Su Y, Huang C, Yin Y, Chu A, Knupp A, Tang Y. NANOG and LIN28 dramatically improve human cell reprogramming by modulating LIN41 and canonical WNT activities. Biol Open 2019; 8:8/12/bio047225. [PMID: 31806618 PMCID: PMC6918770 DOI: 10.1242/bio.047225] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Human cell reprogramming remains extremely inefficient and the underlying mechanisms by different reprogramming factors are elusive. We found that NANOG and LIN28 (NL) synergize to improve OCT4, SOX2, KLF4 and MYC (OSKM)-mediated reprogramming by ∼76-fold and shorten reprogramming latency by at least 1 week. This synergy is inhibited by GLIS1 but reinforced by an inhibitor of the histone methyltransferase DOT1L (iDOT1L) to a ∼127-fold increase in TRA-1-60-positive (+) iPSC colonies. Mechanistically, NL serve as the main drivers of reprogramming in cell epithelialization, the expression of Let-7 miRNA target LIN41, and the activation of canonical WNT/β-CATENIN signaling, which can be further enhanced by iDOT1L treatment. LIN41 overexpression in addition to OSKM similarly promoted cell epithelialization and WNT activation in reprogramming, and a dominant-negative LIN41 mutation significantly blocked NL- and iDOT1L-enhanced reprogramming. We also found that NL- and iDOT1L-induced canonical WNT activation facilitates the initial development kinetics of iPSCs. However, a substantial increase in more mature, homogeneous TRA-1-60+ colony formation was achieved by inhibiting WNT activity at the middle-to-late-reprogramming stage. We further found that LIN41 can replace LIN28 to synergize with NANOG, and that the coexpression of LIN41 with NL further enhanced the formation of mature iPSCs under WNT inhibition. Our study established LIN41 and canonical WNT signaling as the key downstream effectors of NL for the dramatic improvement in reprogramming efficiency and kinetics, and optimized a condition for the robust formation of mature human iPSC colonies from primary cells.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Ling Wang
- Department of Animal Science, Institute for Systems Genomics, University of Connecticut, 1390 Storrs Rd, Storrs, CT 06269, USA
| | - Yue Su
- Department of Animal Science, Institute for Systems Genomics, University of Connecticut, 1390 Storrs Rd, Storrs, CT 06269, USA
| | - Chang Huang
- Department of Animal Science, Institute for Systems Genomics, University of Connecticut, 1390 Storrs Rd, Storrs, CT 06269, USA
| | - Yexuan Yin
- Department of Animal Science, Institute for Systems Genomics, University of Connecticut, 1390 Storrs Rd, Storrs, CT 06269, USA
| | - Alexander Chu
- Department of Animal Science, Institute for Systems Genomics, University of Connecticut, 1390 Storrs Rd, Storrs, CT 06269, USA
| | - Alec Knupp
- Department of Animal Science, Institute for Systems Genomics, University of Connecticut, 1390 Storrs Rd, Storrs, CT 06269, USA
| | - Young Tang
- Department of Animal Science, Institute for Systems Genomics, University of Connecticut, 1390 Storrs Rd, Storrs, CT 06269, USA
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Nenasheva VV, Tarantul VZ. Many Faces of TRIM Proteins on the Road from Pluripotency to Neurogenesis. Stem Cells Dev 2019; 29:1-14. [PMID: 31686585 DOI: 10.1089/scd.2019.0152] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Tripartite motif (TRIM) proteins participate in numerous biological processes. They are the key players in immune system and are involved in the oncogenesis. Moreover, TRIMs are the highly conserved regulators of developmental pathways in both vertebrates and invertebrates. In particular, numerous data point to the participation of TRIMs in the determination of stem cell fate, as well as in the neurogenesis. TRIMs apply various mechanisms to perform their functions. Their common feature is the ability to ubiquitinate proteins mediated by the Really Interesting New Gene (RING) domain. Different C-terminal domains of TRIMs are involved in DNA and RNA binding, protein/protein interactions, and chromatin-mediated transcriptional regulation. Mutations and alterations of TRIM expression cause significant disturbances in the stem cells' self-renewal and neurogenesis, which result in the various pathologies of the nervous system (neurodegeneration, neuroinflammation, and malignant transformation). This review discusses the diverse molecular mechanisms of participation of TRIMs in stem cell maintenance and self-renewal as well as in neural differentiation processes and neuropathology.
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Affiliation(s)
- Valentina V Nenasheva
- Department of Viral and Cellular Molecular Genetics, Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Vyacheslav Z Tarantul
- Department of Viral and Cellular Molecular Genetics, Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
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Li R, Weng L, Liu B, Zhu L, Zhang X, Tian G, Hu L, Li Q, Jiang S, Shang M. TRIM59 predicts poor prognosis and promotes pancreatic cancer progression via the PI3K/AKT/mTOR-glycolysis signaling axis. J Cell Biochem 2019; 121:1986-1997. [PMID: 31693252 DOI: 10.1002/jcb.29433] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 10/04/2019] [Indexed: 12/18/2022]
Abstract
Aberrant expression of the tripartite motif containing 59 (TRIM59) has been reported to participate in the development and progression of various human cancers. However, its expression pattern and cellular roles in pancreatic cancer (PC) remains unclear. In our study, we found that TRIM59 expression was significantly increased in PC tissues and was positively correlated with several malignant behaviors and poor overall survival of PC patients based on bioinformatics analysis and immunohistochemistry staining. Functionally, small interfering RNA-mediated TRIM59 depletion inhibited cell proliferation and migration in vitro, while TRIM59 overexpression promoted cell proliferation and migration in vitro and drove tumor growth and liver metastasis in vivo. Mechanically, TRIM59 was found to enhance glycolysis through activating the PI3K/AKT/mTOR pathway, ultimately contributing to PC progression. Taken together, our results demonstrate that TRIM59 may be a potential predictor for PC and promotes PC progression via the PI3K/AKT/mTOR-glycolysis signaling pathway, which establishes the rationale for targeting the TRIM59-related pathways to treat PC.
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Affiliation(s)
- Rongkun Li
- Department of Interventional Radiology, Tongren Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Li Weng
- Department of Interventional Radiology, Tongren Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Bingyan Liu
- Department of Interventional Radiology, Tongren Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lili Zhu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoxin Zhang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Guangang Tian
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lipeng Hu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Qing Li
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shuheng Jiang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Mingyi Shang
- Department of Interventional Radiology, Tongren Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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Yang Z, Liu C, Wu H, Xie Y, Gao H, Zhang X. CSB affected on the sensitivity of lung cancer cells to platinum-based drugs through the global decrease of let-7 and miR-29. BMC Cancer 2019; 19:948. [PMID: 31615563 PMCID: PMC6792260 DOI: 10.1186/s12885-019-6194-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 09/24/2019] [Indexed: 12/16/2022] Open
Abstract
Background Transcription-coupled nucleotide excision repair (TC-NER) plays a prominent role in the removal of DNA adducts induced by platinum-based chemotherapy reagents. Cockayne syndrome protein B (CSB), the master sensor of TCR, is also involved in the platinum resistant. Let-7 and miR-29 binding sites are highly conserved in the proximal 3′UTR of CSB. Methods We conducted immunohistochemisty to examine the expression of CSB in NSCLC. To determine whether let-7 family and miR-29 family directly interact with the putative target sites in the 3′UTR of CSB, we used luciferase reporter gene analysis. To detect the sensitivity of non-small cell lung cancer (NSCLC) cells to platinum-based drugs, CCK analysis and apoptosis analysis were performed. Results We found that let-7 and miR-29 negatively regulate the expression of CSB by directly targeting to the 3′UTR of CSB. The endogenous CSB expression could be suppressed by let-7 and miR-29 in lung cancer cells. The suppression of CSB activity by endogenous let-7 and miR-29 can be robustly reversed by their sponges. Down-regulation of CSB induced apoptosis and increased the sensitivity of NSCLC cells to cisplatin and carboplatin drugs. Let-7 and miR-29 directly effect on cisplatin and carboplatin sensitivity in NSCLC. Conclusions In conclusion, the platinum-based drug resistant of lung cancer cells may involve in the regulation of let-7 and miR-29 to CSB.
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Affiliation(s)
- Zhenbang Yang
- Institute of Molecular Genetics, College of Life Science, North China University of Science and Technology, Tangshan, China.,Hebei Key Laboratory of Basic Medicine for Chronic Disease, School of Basic Medical Sciences, North China University of Science and Technology, Tangshan, China
| | - Chunling Liu
- Department of Pathology, Affiliated Tangshan Renmin Hospital North China University of Science and Technology, Tangshan, China
| | - Hongjiao Wu
- Institute of Molecular Genetics, College of Life Science, North China University of Science and Technology, Tangshan, China
| | - Yuning Xie
- Institute of Molecular Genetics, College of Life Science, North China University of Science and Technology, Tangshan, China.,Institute of Epidemiology, School of Public Health, North China University of Science and Technology, Tangshan, China
| | - Hui Gao
- Institute of Molecular Genetics, College of Life Science, North China University of Science and Technology, Tangshan, China.,Institute of Epidemiology, School of Public Health, North China University of Science and Technology, Tangshan, China
| | - Xuemei Zhang
- Institute of Molecular Genetics, College of Life Science, North China University of Science and Technology, Tangshan, China.
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41
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Ubiquitin ligase TRIM71 suppresses ovarian tumorigenesis by degrading mutant p53. Cell Death Dis 2019; 10:737. [PMID: 31570706 PMCID: PMC6769007 DOI: 10.1038/s41419-019-1977-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 08/14/2019] [Accepted: 09/04/2019] [Indexed: 11/17/2022]
Abstract
Hotspot p53 mutants augment cancer cell proliferation, metastasis and metabolism through their gain-of-function (GOF). Ovarian cancer sustains the highest frequency of TP53 mutations, but the mechanisms underlying regulation of mutant p53s’ GOF in this type of cancer remain incompletely understood. Herein, we identified the E3-ubiquitin ligase TRIM71 as a novel mutant p53-binding protein. Ectopic TRIM71-induced ubiquitination and proteasomal degradation of mutant p53 by binding to its transactivation (TA) domain, and inhibited the expression of a broad spectrum of mutant p53 target genes. Ectopic TRIM71 also restrained, whereas ablation of TRIM71 endorsed, ovarian carcinoma cell growth in vitro and in vivo. Significantly, TRIM71 overexpression is highly associated with favorable prognosis, particularly, in TP53-mutated ovarian carcinomas. Altogether, our findings unveil the anti-tumor function of TRIM71 in ovarian cancer development and prognosis by downregulating mutant p53s.
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42
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Cao L, Zhang Y, Qian M, Wang X, Shuai Q, Gao C, Lang R, Yang J. Construction of multicellular aggregate by E-cadherin coated microparticles enhancing the hepatic specific differentiation of mesenchymal stem cells. Acta Biomater 2019; 95:382-394. [PMID: 30660779 DOI: 10.1016/j.actbio.2019.01.030] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 01/10/2019] [Accepted: 01/15/2019] [Indexed: 12/22/2022]
Abstract
The differentiation of human mesenchymal stem cells (hMSCs) into hepatocyte-like cells in vitroprovides a promising candidate for cell therapy of liver diseases, and cell aggregates have been proposed to improve the efficiency of expansion and differentiation. Previously, we engineered multicellular aggregates incorporating human E-cadherin fusion protein (hE-cad-Fc)-coated poly(lactic-co-glycolic acid) (PLGA) microparticles (hE-cad-PLGAs), and a significant improvement was obtained in both cellular proliferation of and cytokine secretion by hMSCs. In this study, hepatic differentiation of hMSCs was induced by a biomimetic microenvironment consisting of these engineered aggregates and a cocktail of specific cytokines. The ratio of hE-cad-PLGAs to hMSCs in engineered hMSCs aggregates was optimized to 1:3 for hepatic differentiation. The expressions of hepatic-specific markers were significantly promoted, and cell polarity and activated drug metabolism enzymes were established in MSC/hE-cad-PLGA aggregates compared with MSC and MSC/PLGA aggregates. Moreover, the expressions of stemness and definitive endoderm markers confirmed effectively induced endoderm differentiation in MSC/hE-cad-PLGA aggregates, which was consistent with the pattern of embryonic development. After pre-differentiation for 1 week, the MSC/hE-cad-PLGA aggregates continuously progressed the hepatic phenotype expression in healthy rat peritoneum. Therefore, the biomimetic microenvironment constructed by hE-cad-PLGAs in engineered multicellular aggregates was able to promote the process of endoderm differentiation and the subsequent hepatic differentiation of hMSCs. It would be appropriate for applied research in hepatotoxic drug screening and cell-based treatment of liver diseases. By optimizing with other cytokine cocktail, the engineered multicellular aggregates can be applied to the construction of other endoderm-derived organs. STATEMENT OF SIGNIFICANCE: The differentiation of mesenchymal stem cells (MSCs) into hepatocyte-like cells in vitroprovides a promising for cell therapy for liver diseases, and cell aggregates have been proposed to improve the expansion and differentiation efficiency. Here, engineered multicellular aggregates were constructed by E-cadherin modified microparticles (hE-cad-PLGAs) construct a biomimetic microenvironment to promote the process of endoderm differentiation and the subsequent hepatic differentiation of hMSCs. Furthermore, after pre-differentiation for 1 week, the MSC/hE-cad-PLGA aggregates continuously progressed the hepatic phenotype expression in healthy rat peritoneum. Therefore, engineered multicellular aggregates with hE-cad-PLGAs would be appropriate for applied research in hepatotoxic drug screening and cell-based treatment of liver diseases, and provide a promising method in the construction of other endoderm-derived organs.
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Affiliation(s)
- Lei Cao
- The Key Laboratory of Bioactive Materials, Ministry of Education, College of Life Science, Nankai University, Tianjin 300071, China
| | - Yan Zhang
- The Key Laboratory of Bioactive Materials, Ministry of Education, College of Life Science, Nankai University, Tianjin 300071, China; State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, China
| | - Mengyuan Qian
- The Key Laboratory of Bioactive Materials, Ministry of Education, College of Life Science, Nankai University, Tianjin 300071, China
| | - Xueping Wang
- The Key Laboratory of Bioactive Materials, Ministry of Education, College of Life Science, Nankai University, Tianjin 300071, China
| | - Qizhi Shuai
- The Key Laboratory of Bioactive Materials, Ministry of Education, College of Life Science, Nankai University, Tianjin 300071, China
| | - Chao Gao
- The Key Laboratory of Bioactive Materials, Ministry of Education, College of Life Science, Nankai University, Tianjin 300071, China
| | - Ren Lang
- Department of Hepatobiliary Surgery, Beijing Chaoyang Hospital, Capital Medical University, Beijing 100020, China
| | - Jun Yang
- The Key Laboratory of Bioactive Materials, Ministry of Education, College of Life Science, Nankai University, Tianjin 300071, China.
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Welte T, Tuck AC, Papasaikas P, Carl SH, Flemr M, Knuckles P, Rankova A, Bühler M, Großhans H. The RNA hairpin binder TRIM71 modulates alternative splicing by repressing MBNL1. Genes Dev 2019; 33:1221-1235. [PMID: 31371437 PMCID: PMC6719626 DOI: 10.1101/gad.328492.119] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 06/19/2019] [Indexed: 01/19/2023]
Abstract
In this study, Welte et al. investigated the dual roles of mammalian TRIM71, a phylogenetically conserved regulator of development, in the control of stem cell fate. They demonstrate that TRIM71 shapes the transcriptome of mESCs predominantly through its RNA-binding activity and identify a set of primary targets consistently regulated in various human and mouse cell lines, including MBNL1/Muscleblind. TRIM71/LIN-41, a phylogenetically conserved regulator of development, controls stem cell fates. Mammalian TRIM71 exhibits both RNA-binding and protein ubiquitylation activities, but the functional contribution of either activity and relevant primary targets remain poorly understood. Here, we demonstrate that TRIM71 shapes the transcriptome of mouse embryonic stem cells (mESCs) predominantly through its RNA-binding activity. We reveal that TRIM71 binds targets through 3′ untranslated region (UTR) hairpin motifs and that it acts predominantly by target degradation. TRIM71 mutations implicated in etiogenesis of human congenital hydrocephalus impair target silencing. We identify a set of primary targets consistently regulated in various human and mouse cell lines, including MBNL1 (Muscleblind-like protein 1). MBNL1 promotes cell differentiation through regulation of alternative splicing, and we demonstrate that TRIM71 promotes embryonic splicing patterns through MBNL1 repression. Hence, repression of MBNL1-dependent alternative splicing may contribute to TRIM71's function in regulating stem cell fates.
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Affiliation(s)
- Thomas Welte
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Alex C Tuck
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Panagiotis Papasaikas
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.,Swiss Institute of Bioinformatics, 4058 Basel, Switzerland.,These authors contributed equally to this work
| | - Sarah H Carl
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.,Swiss Institute of Bioinformatics, 4058 Basel, Switzerland.,These authors contributed equally to this work
| | - Matyas Flemr
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Philip Knuckles
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Aneliya Rankova
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.,University of Basel, 4056 Basel, Switzerland
| | - Marc Bühler
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.,University of Basel, 4056 Basel, Switzerland
| | - Helge Großhans
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.,University of Basel, 4056 Basel, Switzerland
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Oncogenic lncRNA downregulates cancer cell antigen presentation and intrinsic tumor suppression. Nat Immunol 2019; 20:835-851. [PMID: 31160797 PMCID: PMC6619502 DOI: 10.1038/s41590-019-0400-7] [Citation(s) in RCA: 234] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 04/12/2019] [Indexed: 12/12/2022]
Abstract
The mechanisms through which tumor cells genetically lose antigenicity and evade immune checkpoints remain largely elusive. Here, we report that tissue-specific expression of the human long-noncoding RNA LINK-A in mouse mammary glands initiated metastatic mammary gland tumors, which phenotypically resembled human triple-negative breast cancer (TNBC). LINK-A expression facilitated crosstalk between phosphatidylinositol-(3,4,5)-trisphosphate and inhibitory G-protein–coupled receptor (GPCR) pathways, attenuating protein kinase A (PKA)-mediated phosphorylation of the E3 ubiquitin ligase TRIM71. Consequently, LINK-A expression enhanced K48–polyubiquitination-mediated degradation of the antigen peptide-loading complex (PLC) and intrinsic tumor suppressors Rb and p53. Treatment with LINK-A-locked nucleic acids or GPCR antagonists stabilized the PLC components, Rb, and p53, and sensitized mammary gland tumors to immune checkpoint blockers (ICBs). Importantly, PD-1 blockade-resistant TNBC patients exhibited elevated LINK-A levels and downregulated PLC components. Hence, we demonstrated lncRNA-dependent downregulation of antigenicity and intrinsic tumor suppression, which may provide the basis for developing a therapeutic regimen of combinational immunotherapy and effective early prevention for TNBCs.
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45
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Yao Z, Guo Z, Wang Y, Li W, Fu Y, Lin Y, Lin W, Lin X. Integrated Succinylome and Metabolome Profiling Reveals Crucial Role of S-Ribosylhomocysteine Lyase in Quorum Sensing and Metabolism of Aeromonas hydrophila. Mol Cell Proteomics 2019; 18:200-215. [PMID: 30352804 PMCID: PMC6356075 DOI: 10.1074/mcp.ra118.001035] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 09/27/2018] [Indexed: 01/21/2023] Open
Abstract
Protein modification by lysine succinylation is a newly identified post-translational modification (PTM) of lysine residues and plays an important role in diverse physiological functions, although their associated biological characteristics are still largely unknown. Here, we investigated the effects of lysine succinylation on the physiological regulation within a well-known fish pathogen, Aeromonas hydrophila A high affinity purification method was used to enrich peptides with lysine succinylation in A. hydrophila ATCC 7966, and a total of 2,174 lysine succinylation sites were identified on 666 proteins using LC-MS/MS. Gene ontology analysis indicated that these succinylated proteins are involved in diverse metabolic pathways and biological processes, including translation, protein export, and central metabolic pathways. The modifications of several selected candidates were further validated by Western blotting. Using site-directed mutagenesis, we observed that the succinylation of lysines on S-ribosylhomocysteine lyase (LuxS) at the K23 and K30 sites positively regulate the production of the quorum sensing autoinducer AI-2, and that these PTMs ultimately alter its competitiveness with another pathogen, Vibrio alginolyticus Moreover, subsequent metabolomic analyses indicated that K30 succinylation on LuxS may suppress the activated methyl cycle (AMC) and that both the K23 and K30 sites are involved in amino acid metabolism. Taken together, the results from this study provide significant insights into the functions of lysine succinylation and its critical roles on LuxS in regulating the cellular physiology of A. hydrophila.
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Affiliation(s)
- Zujie Yao
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring (School of Life Sciences, Fujian Agriculture and Forestry University), Fuzhou, PR China;; Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, PR China;; Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, PR China
| | - Zhuang Guo
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring (School of Life Sciences, Fujian Agriculture and Forestry University), Fuzhou, PR China;; Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, PR China
| | - Yuqian Wang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring (School of Life Sciences, Fujian Agriculture and Forestry University), Fuzhou, PR China;; Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, PR China
| | - Wanxin Li
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring (School of Life Sciences, Fujian Agriculture and Forestry University), Fuzhou, PR China;; Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, PR China
| | - Yuying Fu
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring (School of Life Sciences, Fujian Agriculture and Forestry University), Fuzhou, PR China;; Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, PR China
| | - Yuexu Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring (School of Life Sciences, Fujian Agriculture and Forestry University), Fuzhou, PR China;; Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, PR China
| | - Wenxiong Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring (School of Life Sciences, Fujian Agriculture and Forestry University), Fuzhou, PR China;; Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, PR China
| | - Xiangmin Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring (School of Life Sciences, Fujian Agriculture and Forestry University), Fuzhou, PR China;; Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, PR China;.
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46
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Li P, Wu M, Lin Q, Wang S, Chen T, Jiang H. Key genes and integrated modules in hematopoietic differentiation of human embryonic stem cells: a comprehensive bioinformatic analysis. Stem Cell Res Ther 2018; 9:301. [PMID: 30409225 PMCID: PMC6225692 DOI: 10.1186/s13287-018-1050-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 08/07/2018] [Accepted: 10/16/2018] [Indexed: 12/30/2022] Open
Abstract
Background The generation of hematopoietic stem cells (HSCs) and blood cells from human embryonic stem cells (hESCs) is a major goal for regenerative medicine; however, the differentiation mechanisms are largely undefined. Here, we aimed to identify the regulated genes and functional modules related to the early differentiation of the endothelial-to-hematopoietic transition (EHT) using comprehensive bioinformatics analyses. Methods Undifferentiated hESCs (hESC-H9), CD34+ cells from 10-day differentiated hESC-H9 cells, and CD34+ cells from umbilical cord cells were isolated and collected. Cells from these three groups were subjected to RNA extraction and microarray analysis by which differentially expressed genes (DEGs) and time-series profiles were analyzed by significance analysis of microarray (SAM) and short time-series expression miner (STEM) algorithms. Gene enrichment analysis was performed by ClusterProfiler Package in Rstudio, while a protein-protein interaction (PPI) network was constructed by search tool for the retrieval of interacting genes (STRING) and visualized in Cytoscape. Hub genes were further identified with the MCODE algorithm in Cytoscape. Results In the present study, we identified 11,262 DEGs and 16 time-series profiles that were enriched in biological processes of chromosome segregation, cell cycle, and leukocyte activation and differentiation, as well as hematopoiesis. Analysis using the MCODE algorithm further identified six integrated modules that might play an important role in the EHT process, including mitosis/cell cycle, mitochondrial process, splicing, ubiquitination, ribosome, and apoptosis. Conclusions The study identified potential genes and integrated functional modules associated with the hematopoietic and endothelial differentiation of human ESCs. Electronic supplementary material The online version of this article (10.1186/s13287-018-1050-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pengfei Li
- Department of Hematology, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Mengyao Wu
- Department of Hematology, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Qiwang Lin
- Department of Gynecology, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, 200011, China
| | - Shu Wang
- Department of Hematology, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Tong Chen
- Department of Hematology, Huashan Hospital, Fudan University, Shanghai, 200040, China.
| | - Hua Jiang
- Department of Gynecology, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, 200011, China.
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Wang Y, Ding Q, Lu YC, Cao SY, Liu QX, Zhang L. Interferon-stimulated gene 15 enters posttranslational modifications of p53. J Cell Physiol 2018; 234:5507-5518. [PMID: 30317575 DOI: 10.1002/jcp.27347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 08/17/2018] [Indexed: 12/27/2022]
Abstract
The tumor suppressor protein p53 is a central governor of various cellular signals. It is well accepted that ubiquitination as well as ubiquitin-like (UBL) modifications of p53 protein is critical in the control of its activity. Interferon-stimulated gene 15 (ISG15) is a well-known UBL protein with pleiotropic functions, serving both as a free intracellular molecule and as a modifier by conjugating to target proteins. Initially, attentions have historically focused on the antiviral effects of ISG15 pathway. Remarkably, a significant role in the processes of autophagy, DNA repair, and protein translation provided considerable insight into the new functions of ISG15 pathway. Despite the deterministic revelation of the relation between ISG15 and p53, the functional consequence of p53 ISGylation appears somewhat confused. More important, more recent studies have hinted p53 ubiquitination or other UBL modifications that might interconnect with its ISGylation. Here, we aim to summarize the current knowledge of p53 ISGylation and the differences in other significant modifications, which would be beneficial for the development of p53-based cancer therapy.
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Affiliation(s)
- Yang Wang
- School of Pharmacy, Anhui Medical University, Hefei, China.,Institute for Liver Diseases of Anhui Medical University, Anhui Medical University, Hefei, China.,The Key Laboratory of Major Autoimmune Disease, School of Pharmacy, Anhui Medical University, Hefei, China.,The Key Laboratory of Anti-inflammatory and Immune Medicines, Ministry of Education, Anhui Medical University, Hefei, China
| | - Qi Ding
- School of Pharmacy, Anhui Medical University, Hefei, China.,Institute for Liver Diseases of Anhui Medical University, Anhui Medical University, Hefei, China.,The Key Laboratory of Major Autoimmune Disease, School of Pharmacy, Anhui Medical University, Hefei, China.,The Key Laboratory of Anti-inflammatory and Immune Medicines, Ministry of Education, Anhui Medical University, Hefei, China
| | - Yu-Chen Lu
- School of Pharmacy, Anhui Medical University, Hefei, China.,Institute for Liver Diseases of Anhui Medical University, Anhui Medical University, Hefei, China.,The Key Laboratory of Major Autoimmune Disease, School of Pharmacy, Anhui Medical University, Hefei, China.,The Key Laboratory of Anti-inflammatory and Immune Medicines, Ministry of Education, Anhui Medical University, Hefei, China
| | - Shi-Yang Cao
- School of Pharmacy, Anhui Medical University, Hefei, China.,Institute for Liver Diseases of Anhui Medical University, Anhui Medical University, Hefei, China.,The Key Laboratory of Major Autoimmune Disease, School of Pharmacy, Anhui Medical University, Hefei, China.,The Key Laboratory of Anti-inflammatory and Immune Medicines, Ministry of Education, Anhui Medical University, Hefei, China
| | - Qing-Xue Liu
- School of Pharmacy, Anhui Medical University, Hefei, China.,Institute for Liver Diseases of Anhui Medical University, Anhui Medical University, Hefei, China.,The Key Laboratory of Major Autoimmune Disease, School of Pharmacy, Anhui Medical University, Hefei, China.,The Key Laboratory of Anti-inflammatory and Immune Medicines, Ministry of Education, Anhui Medical University, Hefei, China
| | - Lei Zhang
- School of Pharmacy, Anhui Medical University, Hefei, China.,Institute for Liver Diseases of Anhui Medical University, Anhui Medical University, Hefei, China.,The Key Laboratory of Major Autoimmune Disease, School of Pharmacy, Anhui Medical University, Hefei, China.,The Key Laboratory of Anti-inflammatory and Immune Medicines, Ministry of Education, Anhui Medical University, Hefei, China
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Furey CG, Choi J, Jin SC, Zeng X, Timberlake AT, Nelson-Williams C, Mansuri MS, Lu Q, Duran D, Panchagnula S, Allocco A, Karimy JK, Khanna A, Gaillard JR, DeSpenza T, Antwi P, Loring E, Butler WE, Smith ER, Warf BC, Strahle JM, Limbrick DD, Storm PB, Heuer G, Jackson EM, Iskandar BJ, Johnston JM, Tikhonova I, Castaldi C, López-Giráldez F, Bjornson RD, Knight JR, Bilguvar K, Mane S, Alper SL, Haider S, Guclu B, Bayri Y, Sahin Y, Apuzzo MLJ, Duncan CC, DiLuna ML, Günel M, Lifton RP, Kahle KT. De Novo Mutation in Genes Regulating Neural Stem Cell Fate in Human Congenital Hydrocephalus. Neuron 2018; 99:302-314.e4. [PMID: 29983323 PMCID: PMC7839075 DOI: 10.1016/j.neuron.2018.06.019] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 04/03/2018] [Accepted: 06/12/2018] [Indexed: 12/30/2022]
Abstract
Congenital hydrocephalus (CH), featuring markedly enlarged brain ventricles, is thought to arise from failed cerebrospinal fluid (CSF) homeostasis and is treated with lifelong surgical CSF shunting with substantial morbidity. CH pathogenesis is poorly understood. Exome sequencing of 125 CH trios and 52 additional probands identified three genes with significant burden of rare damaging de novo or transmitted mutations: TRIM71 (p = 2.15 × 10-7), SMARCC1 (p = 8.15 × 10-10), and PTCH1 (p = 1.06 × 10-6). Additionally, two de novo duplications were identified at the SHH locus, encoding the PTCH1 ligand (p = 1.2 × 10-4). Together, these probands account for ∼10% of studied cases. Strikingly, all four genes are required for neural tube development and regulate ventricular zone neural stem cell fate. These results implicate impaired neurogenesis (rather than active CSF accumulation) in the pathogenesis of a subset of CH patients, with potential diagnostic, prognostic, and therapeutic ramifications.
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Affiliation(s)
- Charuta Gavankar Furey
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Jungmin Choi
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Sheng Chih Jin
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Xue Zeng
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Andrew T Timberlake
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Carol Nelson-Williams
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - M Shahid Mansuri
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Qiongshi Lu
- Department of Biostatistics & Medical Informatics, University of Wisconsin, Madison, WI 53706, USA
| | - Daniel Duran
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Shreyas Panchagnula
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, USA
| | - August Allocco
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Jason K Karimy
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Arjun Khanna
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Jonathan R Gaillard
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Tyrone DeSpenza
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Prince Antwi
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Erin Loring
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - William E Butler
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Edward R Smith
- Department of Neurosurgery, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Benjamin C Warf
- Department of Neurosurgery, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jennifer M Strahle
- Department of Neurological Surgery and Pediatrics, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - David D Limbrick
- Department of Neurological Surgery and Pediatrics, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Phillip B Storm
- Department of Neurosurgery, Hospital of the University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Gregory Heuer
- Department of Neurosurgery, Hospital of the University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Eric M Jackson
- Department of Neurosurgery, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - Bermans J Iskandar
- Department of Neurological Surgery, University of Wisconsin Medical School, Madison, WI 53726, USA
| | - James M Johnston
- Department of Neurosurgery, University of Alabama School of Medicine, Birmingham, AL 35233, USA
| | - Irina Tikhonova
- Yale Center for Genome Analysis, Yale University, New Haven, CT 06510, USA
| | | | | | - Robert D Bjornson
- Yale Center for Genome Analysis, Yale University, New Haven, CT 06510, USA
| | - James R Knight
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Yale Center for Genome Analysis, Yale University, New Haven, CT 06510, USA
| | - Kaya Bilguvar
- Yale Center for Genome Analysis, Yale University, New Haven, CT 06510, USA
| | - Shrikant Mane
- Yale Center for Genome Analysis, Yale University, New Haven, CT 06510, USA
| | - Seth L Alper
- Division of Nephrology and Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Department of Medicine, Harvard Medical School, Boston, MA 02215, USA
| | - Shozeb Haider
- Department of Pharmaceutical and Biological Chemistry, University College London School of Pharmacy, London WC1N 1AX, UK
| | - Bulent Guclu
- Kartal Dr. Lutfi Kirdar Research and Training Hospital, Istanbul 34860, Turkey
| | - Yasar Bayri
- Acibadem Mehmet Ali Aydinlar University, School of Medicine, Department of Neurosurgery, Division of Pediatric Neurosurgery, Istanbul 34752, Turkey
| | - Yener Sahin
- Acibadem Mehmet Ali Aydinlar University, School of Medicine, Department of Neurosurgery, Division of Pediatric Neurosurgery, Istanbul 34752, Turkey
| | - Michael L J Apuzzo
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Charles C Duncan
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Michael L DiLuna
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Murat Günel
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Richard P Lifton
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY 10065, USA
| | - Kristopher T Kahle
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, USA; Department of Cellular & Molecular Physiology, Yale University School of Medicine, New Haven, CT 06510, USA.
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49
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Ma X, Ma X, Qiu Y, Zhu L, Lin Y, You Y, Ma D, Qin Z, Sun C, Zhao Y, Sun Y, Han L. TRIM50 suppressed hepatocarcinoma progression through directly targeting SNAIL for ubiquitous degradation. Cell Death Dis 2018; 9:608. [PMID: 29789583 PMCID: PMC5964248 DOI: 10.1038/s41419-018-0644-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Revised: 04/30/2018] [Accepted: 05/02/2018] [Indexed: 02/07/2023]
Abstract
Tripartite motif-containing 50 (TRIM50) belongs to the tripartite motif (TRIM) protein family, which has been implicated in the pathogenesis of multiple cancers. However, the role of TRIM50 in hepatocellular carcinoma (HCC) remains to be clarified. Here we showed that TRIM50 expression was significantly decreased in liver cancer tissues compared with corresponding non-cancerous liver tissues, and its decreased expression was significantly correlated with advanced disease progression. Gain-of-function assay by exogenous overexpression of TRIM50 in HCC cells showed that proliferation, colony formation, migration and invasion of HCC cells were significantly inhibited, whereas loss-of-function assay by TRIM50 knockdown showed that these malignant behaviors of HCC cells were significantly increased. Further investigation showed that TRIM50 could directly bind with SNAIL and induced K-48 linked poly-ubiquitous degradation of SNAIL protein, which further reversed SNAIL-mediated epithelial-to-mesenchymal transition (EMT) process of HCC cells. In vivo assay by xenograft tumor model verified the antitumor effect of TRIM50 on HCC. Taken together, these results showed that TRIM50 acted as a tumor suppressor in HCC cells by directly targeting SNAIL and reversing EMT, which further indicated that positive modulation of TRIM50 might be a novel therapeutic strategy for SNAIL overexpressed HCC cells.
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Affiliation(s)
- Xiaoxiao Ma
- Department of Immunology, Shandong Provincial Key Laboratory of Infection & Immunology, Shandong University School of Basic Medical Sciences, 250012, Jinan, China
| | - Xiaomin Ma
- Department of Immunology, Shandong Provincial Key Laboratory of Infection & Immunology, Shandong University School of Basic Medical Sciences, 250012, Jinan, China
| | - Yumin Qiu
- Department of Immunology, Shandong Provincial Key Laboratory of Infection & Immunology, Shandong University School of Basic Medical Sciences, 250012, Jinan, China
| | - Lihui Zhu
- Department of Immunology, Shandong Provincial Key Laboratory of Infection & Immunology, Shandong University School of Basic Medical Sciences, 250012, Jinan, China
| | - Yueke Lin
- Department of Immunology, Shandong Provincial Key Laboratory of Infection & Immunology, Shandong University School of Basic Medical Sciences, 250012, Jinan, China
| | - Yajing You
- Department of Immunology, Shandong Provincial Key Laboratory of Infection & Immunology, Shandong University School of Basic Medical Sciences, 250012, Jinan, China
| | - Dapeng Ma
- Department of Immunology, Shandong Provincial Key Laboratory of Infection & Immunology, Shandong University School of Basic Medical Sciences, 250012, Jinan, China
| | - Zhenzhi Qin
- Department of Immunology, Shandong Provincial Key Laboratory of Infection & Immunology, Shandong University School of Basic Medical Sciences, 250012, Jinan, China
| | - Caiyu Sun
- Department of Immunology, Shandong Provincial Key Laboratory of Infection & Immunology, Shandong University School of Basic Medical Sciences, 250012, Jinan, China
| | - Yunxue Zhao
- Department of Pharmacology, Shandong University School of Basic Medical Sciences, 250012, Jinan, China
| | - Yanlin Sun
- Department of Pathology, Shandong University School of Basic Medical Sciences, 250012, Jinan, China
| | - Lihui Han
- Department of Immunology, Shandong Provincial Key Laboratory of Infection & Immunology, Shandong University School of Basic Medical Sciences, 250012, Jinan, China.
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50
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Kumari P, Aeschimann F, Gaidatzis D, Keusch JJ, Ghosh P, Neagu A, Pachulska-Wieczorek K, Bujnicki JM, Gut H, Großhans H, Ciosk R. Evolutionary plasticity of the NHL domain underlies distinct solutions to RNA recognition. Nat Commun 2018; 9:1549. [PMID: 29674686 PMCID: PMC5908797 DOI: 10.1038/s41467-018-03920-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 03/21/2018] [Indexed: 11/28/2022] Open
Abstract
RNA-binding proteins regulate all aspects of RNA metabolism. Their association with RNA is mediated by RNA-binding domains, of which many remain uncharacterized. A recently reported example is the NHL domain, found in prominent regulators of cellular plasticity like the C. elegans LIN-41. Here we employ an integrative approach to dissect the RNA specificity of LIN-41. Using computational analysis, structural biology, and in vivo studies in worms and human cells, we find that a positively charged pocket, specific to the NHL domain of LIN-41 and its homologs (collectively LIN41), recognizes a stem-loop RNA element, whose shape determines the binding specificity. Surprisingly, the mechanism of RNA recognition by LIN41 is drastically different from that of its more distant relative, the fly Brat. Our phylogenetic analysis suggests that this reflects a rapid evolution of the domain, presenting an interesting example of a conserved protein fold that acquired completely different solutions to RNA recognition. The C. elegans LIN-41 and its homologs, including human TRIM71/LIN41, contain the RNA binding NHL domain. Here the authors combine computational analysis, structural biology and in vivo studies, to explain how these proteins bind RNA and how rapid evolution of NHL domains resulted in different solutions to RNA recognition.
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Affiliation(s)
- Pooja Kumari
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058, Basel, Switzerland
| | - Florian Aeschimann
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058, Basel, Switzerland
| | - Dimos Gaidatzis
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058, Basel, Switzerland.,Swiss Institute of Bioinformatics, 4058, Basel, Switzerland
| | - Jeremy J Keusch
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058, Basel, Switzerland
| | - Pritha Ghosh
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109, Warsaw, Poland
| | - Anca Neagu
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058, Basel, Switzerland
| | | | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109, Warsaw, Poland.,Faculty of Biology, Institute of Biotechnology and Moleular Biology, Adam Mickiewicz University, ul. Umultowska 89, 61-614, Poznan, Poland
| | - Heinz Gut
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058, Basel, Switzerland.
| | - Helge Großhans
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058, Basel, Switzerland.,University of Basel, Petersplatz 1, 4001, Basel, Switzerland
| | - Rafal Ciosk
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058, Basel, Switzerland. .,Institute of Bioorganic Chemistry, Polish Academy of Sciences, ul. Noskowskiego 12/14, 61-704, Poznan, Poland.
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