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Li RF, Wang YS, Lu FI, Huang YS, Chiu CC, Tai MH, Wu CY. Identification of Novel Vascular Genes Downstream of Islet2 and Nr2f1b Transcription Factors. Biomedicines 2022; 10:biomedicines10061261. [PMID: 35740282 PMCID: PMC9220758 DOI: 10.3390/biomedicines10061261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 05/21/2022] [Accepted: 05/22/2022] [Indexed: 12/10/2022] Open
Abstract
The genetic regulation of vascular development is not elucidated completely. We previously characterized the transcription factors Islet2 (Isl2) and Nr2f1b as being critical for vascular growth. In this study, we further performed combinatorial microarrays to identify genes that are potentially regulated by these factors. We verified the changed expression of several targets in isl2/nr2f1b morphants. Those genes expressed in vessels during embryogenesis suggested their functions in vascular development. We selectively assayed a potential target follistatin a (fsta). Follistatin is known to inhibit BMP, and BMP signaling has been shown to be important for angiogenesis. However, the fsta’s role in vascular development has not been well studied. Here, we showed the vascular defects in ISV growth and CVP patterning while overexpressing fsta in the embryo, which mimics the phenotype of isl2/nr2f1b morphants. The vascular abnormalities are likely caused by defects in migration and proliferation. We further observed the altered expression of vessel markers consistent with the vascular defects in (fli:fsta) embryos. We showed that the knockdown of fsta can rescue the vascular defects in (fli:fsta) fish, suggesting the functional specificity of fsta. Moreover, the decreased expression of fsta rescues abnormal vessel growth in isl2 and nr2f1b morphants, indicating that fsta functions downstream of isl2/nr2f1b. Lastly, we showed that Isl2/Nr2f1b control vascular development, via Fsta–BMP signaling in part. Collectively, our microarray data identify many interesting genes regulated by isl2/nr2f1b, which likely function in the vasculature. Our research provides useful information on the genetic control of vascular development.
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Affiliation(s)
- Ru-Fang Li
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung 804, Taiwan; (R.-F.L.); (Y.-S.W.); (Y.-S.H.); (C.-C.C.); (M.-H.T.)
| | - Yi-Shan Wang
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung 804, Taiwan; (R.-F.L.); (Y.-S.W.); (Y.-S.H.); (C.-C.C.); (M.-H.T.)
- Doctoral Degree Program in Marine Biotechnology, National Sun Yat-sen University, Kaohsiung 804, Taiwan
- Doctoral Degree Program in Marine Biotechnology, Academia Sinica, Taipei 115, Taiwan
| | - Fu-I Lu
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan 701, Taiwan;
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung 402, Taiwan
| | - Yi-Shan Huang
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung 804, Taiwan; (R.-F.L.); (Y.-S.W.); (Y.-S.H.); (C.-C.C.); (M.-H.T.)
- Doctoral Degree Program in Marine Biotechnology, National Sun Yat-sen University, Kaohsiung 804, Taiwan
| | - Chien-Chih Chiu
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung 804, Taiwan; (R.-F.L.); (Y.-S.W.); (Y.-S.H.); (C.-C.C.); (M.-H.T.)
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Ming-Hong Tai
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung 804, Taiwan; (R.-F.L.); (Y.-S.W.); (Y.-S.H.); (C.-C.C.); (M.-H.T.)
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung 804, Taiwan
| | - Chang-Yi Wu
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung 804, Taiwan; (R.-F.L.); (Y.-S.W.); (Y.-S.H.); (C.-C.C.); (M.-H.T.)
- Doctoral Degree Program in Marine Biotechnology, National Sun Yat-sen University, Kaohsiung 804, Taiwan
- Doctoral Degree Program in Marine Biotechnology, Academia Sinica, Taipei 115, Taiwan
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 804, Taiwan
- Correspondence: ; Tel.: +886-7-5252000 (ext. 3627)
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LNX1 Contributes to Cell Cycle Progression and Cisplatin Resistance. Cancers (Basel) 2021; 13:cancers13164066. [PMID: 34439220 PMCID: PMC8394373 DOI: 10.3390/cancers13164066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 08/09/2021] [Indexed: 12/13/2022] Open
Abstract
Simple Summary The ligand of numb-protein X1 (LNX1) is reported to be upregulated in various cancers, however the cellular function of LNX1 is not clearly characterized. The aim of the present study was to elucidate the regulation of LNX1 expression and clarify the role of LNX1 in cell-cycle progression and resistance to the cancer therapeutic agent, cisplatin. We found that LNX1 expression is decreased by DNA damage including cisplatin treatment and the levels of S and G2/M populations were correlated with LNX1 expression. We also showed that the upregulation of LNX1 contributes to cell-cycle progression and cisplatin resistance. Our data suggest that LNX1 is the important regulator of the cell cycle, and contributes to tumor progression. Abstract The ligand of numb-protein X1 (LNX1) acts as a proto-oncogene by inhibiting p53 stability; however, the regulation of LNX1 expression has not been investigated. In this study, we screened chemicals to identify factors that potentially regulate LNX1 expression. We found that LNX1 expression levels were decreased by DNA damage, including that by cisplatin. Upon treatment with lipopolysaccharide (LPS) and phorbol 12-myristate 13-acetate (PMA), LNX1 expression levels increased. In addition, cell-cycle progression increased upon LNX1 expression; the levels of S and G2/M populations were correlated with LNX1 expression. Moreover, in CRISPR-Cas9-mediated LNX1 knockout cells, we observed a delay in cell-cycle progression and a downregulation of genes encoding the cell-cycle markers cyclin D1 and cyclin E1. Finally, the upregulation of LNX1-activated cell-cycle progression and increased resistance to cisplatin-mediated cell death. Taken together, these results suggest that LNX1 contributes to cell-cycle progression and cisplatin resistance.
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Hong J, Won M, Ro H. The Molecular and Pathophysiological Functions of Members of the LNX/PDZRN E3 Ubiquitin Ligase Family. Molecules 2020; 25:E5938. [PMID: 33333989 PMCID: PMC7765395 DOI: 10.3390/molecules25245938] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/10/2020] [Accepted: 12/10/2020] [Indexed: 12/27/2022] Open
Abstract
The ligand of Numb protein-X (LNX) family, also known as the PDZRN family, is composed of four discrete RING-type E3 ubiquitin ligases (LNX1, LNX2, LNX3, and LNX4), and LNX5 which may not act as an E3 ubiquitin ligase owing to the lack of the RING domain. As the name implies, LNX1 and LNX2 were initially studied for exerting E3 ubiquitin ligase activity on their substrate Numb protein, whose stability was negatively regulated by LNX1 and LNX2 via the ubiquitin-proteasome pathway. LNX proteins may have versatile molecular, cellular, and developmental functions, considering the fact that besides these proteins, none of the E3 ubiquitin ligases have multiple PDZ (PSD95, DLGA, ZO-1) domains, which are regarded as important protein-interacting modules. Thus far, various proteins have been isolated as LNX-interacting proteins. Evidence from studies performed over the last two decades have suggested that members of the LNX family play various pathophysiological roles primarily by modulating the function of substrate proteins involved in several different intracellular or intercellular signaling cascades. As the binding partners of RING-type E3s, a large number of substrates of LNX proteins undergo degradation through ubiquitin-proteasome system (UPS) dependent or lysosomal pathways, potentially altering key signaling pathways. In this review, we highlight recent and relevant findings on the molecular and cellular functions of the members of the LNX family and discuss the role of the erroneous regulation of these proteins in disease progression.
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Affiliation(s)
- Jeongkwan Hong
- Department of Biological Sciences, College of Bioscience and Biotechnology, Chungnam National University, Daejeon 305-764, Korea;
| | - Minho Won
- Biotechnology Process Engineering Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), 30 Yeongudanji-ro, Cheongwon-gu, Cheongju 28116, Korea
| | - Hyunju Ro
- Department of Biological Sciences, College of Bioscience and Biotechnology, Chungnam National University, Daejeon 305-764, Korea;
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Abstract
Nasopharyngeal carcinoma (NPC) is the most common malignant tumor with a remarkable racial and geographical distribution including people in southern China, South East Asia, and the Middle East/North Africa. DNA methylation is an important manifestation of epigenetic modification, has been studied over several decades, and by regulating and controlling the expression of cancer-related genesits, abnormal DNA methylation can influence in a variety of human malignancy tumors.Until now, there is no analysis focus on differentially methylated, differential expressed genes (MDEGs) study, so we make a joint analysis for both gene methylation profiling microarray and gene expression profiling microarray in NPC. Two gene expression datasets (GSE64634 and GSE12452) and gene methylation profiling data set (GSE62336) were downloaded from GEO and analyzed using the online tool GEO2R to identify MDEGs. Gene ontology (GO) functional analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of the differentially methylated genes were performed. The STRING database was used to evaluate the interactions of MDEGs and to construct a protein-protein interaction (PPI) network using Cytoscape software. Hub genes were validated with the cBioPortal database.The overlap among the 3 datasets contained 135 hypermethylation genes and 541 hypomethylation genes between NPC and non-NPC samples. A total of 4 genes (TROAP, PCOLCE2, HOXA4, and C1QB) in Hyper-LGs and 14 genes (DYNC1H1, LNX1, RAB37, ALDH3A1, SLC24A4, CP, CEP250, ANK2, DNAI2, MUC13, ACACB, GABRP, STX7, and TTC9) in Hypo-HGs were identified as hub genes.The study of DNA methylation and gene expression provides us a strong support as well as new comprehensive information of MDEGs to the revelation of nasopharyngeal carcinoma's complex pathogenesis. However, further studies are needed to elucidate the biological function of these genes in NPC in the future.
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Affiliation(s)
- Zeng-hong Wu
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tao Zhou
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Hai-Ying Sun
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA
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MicroRNA-325-3p Facilitates Immune Escape of Mycobacterium tuberculosis through Targeting LNX1 via NEK6 Accumulation to Promote Anti-Apoptotic STAT3 Signaling. mBio 2020; 11:mBio.00557-20. [PMID: 32487755 PMCID: PMC7267881 DOI: 10.1128/mbio.00557-20] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Intracellular survival of Mycobacterium tuberculosis results in bacterial proliferation and the spread of infection in lungs, consequently deteriorating the conditions of tuberculosis (TB) patients. This research discovers a new immune escape pathway of M. tuberculosis by modulating host miR-325-3p expression, thus leading to the intracellular survival of M. tuberculosis. These findings make a contribution to the understanding of the immune escape of M. tuberculosis, and they provide a theoretical basis for the development of therapeutic approaches for drug-resistant TB. Tuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis that poses threats to the public. M. tuberculosis survives in macrophages by escaping from immune surveillance and clearance, which exacerbates the bacterial proliferation. However, the molecular mechanisms of this immune escape have not yet been fully understood. Using multiple cell and mouse models, we found that microRNA-325-3p (miR-325-3p) is upregulated after M. tuberculosis infection and Mir325-deficient mice show resistance to M. tuberculosis. We demonstrated that miR-325-3p directly targets LNX1, an E3 ubiquitin ligase of NEK6, and that this hampers the proteasomal degradation of NEK6 in macrophages. The abnormal accumulation of NEK6 leads to the activation of STAT3 signaling, thus inhibiting the process of apoptosis and promoting the intracellular survival of M. tuberculosis. Our findings not only reveal a new immune escape pathway of M. tuberculosis but also may provide new insights into the development of therapeutic approaches for drug-resistant TB.
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de la Rocha-Muñoz A, Núñez E, Arribas-González E, López-Corcuera B, Aragón C, de Juan-Sanz J. E3 ubiquitin ligases LNX1 and LNX2 are major regulators of the presynaptic glycine transporter GlyT2. Sci Rep 2019; 9:14944. [PMID: 31628376 PMCID: PMC6802383 DOI: 10.1038/s41598-019-51301-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 09/27/2019] [Indexed: 12/15/2022] Open
Abstract
The neuronal glycine transporter GlyT2 is an essential regulator of glycinergic neurotransmission that recaptures glycine in presynaptic terminals to facilitate transmitter packaging in synaptic vesicles. Alterations in GlyT2 expression or activity result in lower cytosolic glycine levels, emptying glycinergic synaptic vesicles and impairing neurotransmission. Lack of glycinergic neurotransmission caused by GlyT2 loss-of-function mutations results in Hyperekplexia, a rare neurological disease characterized by generalized stiffness and motor alterations that may cause sudden infant death. Although the importance of GlyT2 in pathology is known, how this transporter is regulated at the molecular level is poorly understood, limiting current therapeutic strategies. Guided by an unbiased screening, we discovered that E3 ubiquitin ligase Ligand of Numb proteins X1/2 (LNX1/2) modulate the ubiquitination status of GlyT2. The N-terminal RING-finger domain of LNX1/2 ubiquitinates a cytoplasmic C-terminal lysine cluster in GlyT2 (K751, K773, K787 and K791), and this process regulates the expression levels and transport activity of GlyT2. The genetic deletion of endogenous LNX2 in spinal cord primary neurons causes an increase in GlyT2 expression and we find that LNX2 is required for PKC-mediated control of GlyT2 transport. This work identifies, to our knowledge, the first E3 ubiquitin-ligases acting on GlyT2, revealing a novel molecular mechanism that controls presynaptic glycine availability. Providing a better understanding of the molecular regulation of GlyT2 may help future investigations into the molecular basis of human disease states caused by dysfunctional glycinergic neurotransmission, such as hyperekplexia and chronic pain.
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Affiliation(s)
- A de la Rocha-Muñoz
- Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid, Consejo Superior de Investigaciones Científicas, 28049, Madrid, Spain
- IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
| | - E Núñez
- Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid, Consejo Superior de Investigaciones Científicas, 28049, Madrid, Spain
- IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
| | - E Arribas-González
- Instituto Cajal, Consejo Superior de Investigaciones Científicas, 28002, Madrid, Spain
| | - B López-Corcuera
- Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid, Consejo Superior de Investigaciones Científicas, 28049, Madrid, Spain
- IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
| | - C Aragón
- Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid, Consejo Superior de Investigaciones Científicas, 28049, Madrid, Spain.
- IdiPAZ, Hospital Universitario La Paz, Madrid, Spain.
| | - J de Juan-Sanz
- Sorbonne Université and Institut du Cerveau et de la Moelle Epinière (ICM) - Hôpital Pitié-Salpêtrière, Inserm, CNRS, Paris, France.
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Park R, Kim H, Jang M, Jo D, Park YI, Namkoong S, Lee JI, Jang IS, Park J. LNX1 contributes to tumor growth by down-regulating p53 stability. FASEB J 2019; 33:13216-13227. [PMID: 31533005 DOI: 10.1096/fj.201900366r] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The well-known tumor suppressor p53 inhibits the formation of various cancers by inducing cell cycle arrest and apoptosis. Although p53 mutations are commonly found in many cancers, p53 is functionally inactivated in tumor cells that retain wild-type p53. Here, we show that the ligand of numb protein X1 (LNX1) inhibited p53-dependent transcription by decreasing the half-life of p53. We generated LNX1 knockout (KO) cells in p53 wild-type cancer cells (A549, HCT116, and MCF7) using the clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 gene-editing system. LNX1 KO activated p53-dependent transcription by increasing the stability of p53. Moreover, lentivirus-mediated overexpression of LNX1 decreased p53 protein levels and inhibited p53-dependent transcription. LNX1 interacted with p53 and mouse double minute 2 (MDM2) and increased the ubiquitination of p53 in an MDM2-dependent manner. Finally, we demonstrated that LNX1 was required for efficient tumor growth both in cell culture and in a mouse tumor xenograft model. These results collectively indicated that LNX1 contributed to tumor growth by inhibiting p53-dependent signaling in p53 wild-type cancer cells.-Park, R., Kim, H., Jang, M., Jo, D., Park, Y.-I., Namkoong, S., Lee, J. I., Jang, I.-S., Park, J. LNX1 contributes to tumor growth by down-regulating p53 stability.
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Affiliation(s)
- Rackhyun Park
- Division of Biological Science and Technology, Yonsei University, Wonju, South Korea
| | - Hyunju Kim
- Division of Biological Science and Technology, Yonsei University, Wonju, South Korea
| | - Minsu Jang
- Division of Biological Science and Technology, Yonsei University, Wonju, South Korea
| | - Daum Jo
- Division of Biological Science and Technology, Yonsei University, Wonju, South Korea
| | - Yea-In Park
- Division of Biological Science and Technology, Yonsei University, Wonju, South Korea
| | - Sim Namkoong
- Department of Biochemistry, Kangwon National University, Chuncheon, South Korea
| | - Jin I Lee
- Division of Biological Science and Technology, Yonsei University, Wonju, South Korea
| | - Ik-Soon Jang
- Division of Bioconvergence Analysis, Korea Basic Science Institute, Daejeon, South Korea
| | - Junsoo Park
- Division of Biological Science and Technology, Yonsei University, Wonju, South Korea
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LNX1/LNX2 proteins: functions in neuronal signalling and beyond. Neuronal Signal 2018; 2:NS20170191. [PMID: 32714586 PMCID: PMC7373230 DOI: 10.1042/ns20170191] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 05/02/2018] [Accepted: 05/08/2018] [Indexed: 12/16/2022] Open
Abstract
Ligand of NUMB Protein X1 and X2 (LNX1 and LNX2) are E3 ubiquitin ligases, named for their ability to interact with and promote the degradation of the cell fate determinant protein NUMB. On this basis they are thought to play a role in modulating NUMB/NOTCH signalling during processes such as cortical neurogenesis. However, LNX1/2 proteins can bind, via their four PDZ (PSD95, DLGA, ZO-1) domains, to an extraordinarily large number of other proteins besides NUMB. Many of these interactions suggest additional roles for LNX1/2 proteins in the nervous system in areas such as synapse formation, neurotransmission and regulating neuroglial function. Twenty years on from their initial discovery, I discuss here the putative neuronal functions of LNX1/2 proteins in light of the anxiety-related phenotype of double knockout mice lacking LNX1 and LNX2 in the central nervous system (CNS). I also review what is known about non-neuronal roles of LNX1/2 proteins, including their roles in embryonic patterning and pancreas development in zebrafish and their possible involvement in colorectal cancer (CRC), osteoclast differentiation and immune function in mammals. The emerging picture places LNX1/2 proteins as potential regulators of multiple cellular signalling processes, but in many cases the physiological significance of such roles remains only partly validated and needs to be considered in the context of the tight control of LNX1/2 protein levels in vivo.
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Nayak D, Sivaraman J. Structure of LNX1:Ubc13~Ubiquitin Complex Reveals the Role of Additional Motifs for the E3 Ligase Activity of LNX1. J Mol Biol 2018; 430:1173-1188. [PMID: 29496391 DOI: 10.1016/j.jmb.2018.02.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 02/17/2018] [Accepted: 02/19/2018] [Indexed: 10/17/2022]
Abstract
LNX1 (ligand of numb protein-X1) is a RING and PDZ domain-containing E3 ubiquitin ligase that ubiquitinates human c-Src kinase. Here, we report the identification and structure of the ubiquitination domain of LNX1, the identification of Ubc13/Ube2V2 as a functional E2 in vitro, and the structural and functional studies of the Ubc13~Ub intermediate in complex with the ubiquitination domain of LNX1. The RING domain of LNX1 is embedded between two zinc-finger motifs (Zn-RING-Zn), both of which are crucial for its ubiquitination activity. In the heterodimeric complex, the ubiquitin of one monomer shares more buried surface area with LNX1 of the other monomer and these interactions are unique and essential for catalysis. This study reveals how the LNX1 RING domain is structurally and mechanistically dependent on other motifs for its E3 ligase activity, and describes how dimeric LNX1 recruits ubiquitin-loaded Ubc13 for Ub transfer via E3 ligase-mediated catalysis.
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Affiliation(s)
- Digant Nayak
- Department of Biological Sciences, 14 Science Drive 4, National University of Singapore, Singapore 117543
| | - J Sivaraman
- Department of Biological Sciences, 14 Science Drive 4, National University of Singapore, Singapore 117543.
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Talukdar S, Das SK, Pradhan AK, Emdad L, Shen XN, Windle JJ, Sarkar D, Fisher PB. Novel function of MDA-9/Syntenin (SDCBP) as a regulator of survival and stemness in glioma stem cells. Oncotarget 2018; 7:54102-54119. [PMID: 27472461 PMCID: PMC5342330 DOI: 10.18632/oncotarget.10851] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 07/07/2016] [Indexed: 12/27/2022] Open
Abstract
Glioblastoma multiforme (GBM) is an aggressive cancer with current therapies only marginally impacting on patient survival. Glioma stem cells (GSCs), a subpopulation of highly tumorigenic cells, are considered major contributors to glioma progression and play seminal roles in therapy resistance, immune evasion and increased invasion. Despite clinical relevance, effective/selective therapeutic targeting strategies for GSCs do not exist, potentially due to the lack of a definitive understanding of key regulators of GSCs. Consequently, there is a pressing need to identify therapeutic targets and novel options to effectively target this therapy-resistant cell population. The precise roles of GSCs in governing GBM development, progression and prognosis are under intense scrutiny, but key upstream regulatory genes remain speculative. MDA-9/Syntenin (SDCBP), a scaffold protein, regulates tumor pathogenesis in multiple cancers. Highly aggressive cancers like GBM express elevated levels of MDA-9 and contain increased populations of GSCs. We now uncover a unique function of MDA-9 as a facilitator and determinant of glioma stemness and survival. Mechanistically, MDA-9 regulates multiple stemness genes (Nanog, Oct4 and Sox2) through activation of STAT3. MDA-9 controls survival of GSCs by activating the NOTCH1 pathway through phospho-Src and DLL1. Once activated, cleaved NOTCH1 regulates C-Myc expression through RBPJK, thereby facilitating GSC growth and proliferation. Knockdown of MDA-9 affects the NOTCH1/C-Myc and p-STAT3/Nanog pathways causing a loss of stemness and initiation of apoptosis in GSCs. Our data uncover a previously unidentified relationship between MDA-9 and GSCs, reinforcing relevance of this gene as a potential therapeutic target in GBM.
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Affiliation(s)
- Sarmistha Talukdar
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, VA, USA.,VCU Institute of Molecular Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Swadesh K Das
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, VA, USA.,VCU Institute of Molecular Medicine, Virginia Commonwealth University, Richmond, VA, USA.,VCU Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA
| | - Anjan K Pradhan
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, VA, USA.,VCU Institute of Molecular Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Luni Emdad
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, VA, USA.,VCU Institute of Molecular Medicine, Virginia Commonwealth University, Richmond, VA, USA.,VCU Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA
| | - Xue-Ning Shen
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, VA, USA.,VCU Institute of Molecular Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Jolene J Windle
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, VA, USA.,VCU Institute of Molecular Medicine, Virginia Commonwealth University, Richmond, VA, USA.,VCU Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA
| | - Devanand Sarkar
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, VA, USA.,VCU Institute of Molecular Medicine, Virginia Commonwealth University, Richmond, VA, USA.,VCU Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA
| | - Paul B Fisher
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, VA, USA.,VCU Institute of Molecular Medicine, Virginia Commonwealth University, Richmond, VA, USA.,VCU Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA
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Suppression of cancer stemness by upregulating Ligand-of-Numb protein X1 in colorectal carcinoma. PLoS One 2017; 12:e0188665. [PMID: 29190716 PMCID: PMC5708683 DOI: 10.1371/journal.pone.0188665] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 11/10/2017] [Indexed: 01/27/2023] Open
Abstract
Cancer stem-like cells (CSCs) have been reported to play major roles in tumorigenesis, tumor relapse, and metastasis after therapy against colorectal carcinoma (CRC). Therefore, identification of colorectal CSC regulators could provide promising targets for CRC. Ligand-of-Numb protein X1 (LNX1) is one E3 ubiquitin ligase which mediates the ubiquitination and degradation of Numb. Although several studies indicate LNX1 could be a potential suppressor of cancer diseases, the functions of LNX1 in mediating cancer stemness remain poorly understood. In this study, LNX1 was identified as a negative regulator of cancer stemness in CRC, which was downregulated in colonospheres or side population (SP) cells. Furthermore, the coxsackievirus and adenovirus receptor (CXADR) was found to be one critical downstream mediator of cancer stemness regulated by LNX1. Interestingly, the anti-breast cancer drug tamoxifen was found to be an agonist of LNX1 and suppress cancer stemness in CRC. In sum, this study provided the evidences that LNX1 signaling plays important roles in regulating the stemness of colon cancer cells.
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12
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Lenihan JA, Saha O, Young PW. Proteomic analysis reveals novel ligands and substrates for LNX1 E3 ubiquitin ligase. PLoS One 2017; 12:e0187352. [PMID: 29121065 PMCID: PMC5679597 DOI: 10.1371/journal.pone.0187352] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 10/18/2017] [Indexed: 11/25/2022] Open
Abstract
Ligand of Numb protein X1 (LNX1) is an E3 ubiquitin ligase that contains a catalytic RING (Really Interesting New Gene) domain and four PDZ (PSD-95, DlgA, ZO-1) domains. LNX1 can ubiquitinate Numb, as well as a number of other ligands. However, the physiological relevance of these interactions in vivo remain unclear. To gain functional insights into the LNX family, we have characterised the LNX1 interactome using affinity purification and mass spectrometry. This approach identified a large number of novel LNX1-interacting proteins, as well as confirming known interactions with NUMB and ERC2. Many of the novel interactions mapped to the LNX PDZ domains, particularly PDZ2, and many showed specificity for LNX1 over the closely related LNX2. We show that PPFIA1 (liprin-α1), KLHL11, KIF7 and ERC2 are substrates for ubiquitination by LNX1. LNX1 ubiquitination of liprin-α1 is dependent on a PDZ binding motif containing a carboxyl terminal cysteine that binds LNX1 PDZ2. Surprisingly, the neuronally-expressed LNX1p70 isoform, that lacks the RING domain, was found to promote ubiquitination of PPFIA1 and KLHL11, albeit to a lesser extent than the longer RING-containing LNX1p80 isoform. Of several E3-ligases identified in the LNX1 interactome we confirm interactions of LNX1 with MID2/TRIM1 and TRIM27. On this basis we propose a model whereby LNX1p70, despite lacking a catalytic RING domain, may function as a scaffold to promote ubiquitination of its ligands through recruitment of other E3-ligases. These findings provide functional insights into the LNX protein family, particularly the neuronal LNX1p70 isoform.
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Affiliation(s)
- Joan A. Lenihan
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Orthis Saha
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Paul W. Young
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
- * E-mail:
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13
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Lenihan JA, Saha O, Heimer-McGinn V, Cryan JF, Feng G, Young PW. Decreased Anxiety-Related Behaviour but Apparently Unperturbed NUMB Function in Ligand of NUMB Protein-X (LNX) 1/2 Double Knockout Mice. Mol Neurobiol 2016; 54:8090-8109. [DOI: 10.1007/s12035-016-0261-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 10/25/2016] [Indexed: 10/20/2022]
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14
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Broecker F, Hardt C, Herwig R, Timmermann B, Kerick M, Wunderlich A, Schweiger MR, Borsig L, Heikenwalder M, Lehrach H, Moelling K. Transcriptional signature induced by a metastasis-promoting c-Src mutant in a human breast cell line. FEBS J 2016; 283:1669-88. [PMID: 26919036 DOI: 10.1111/febs.13694] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 01/20/2016] [Accepted: 02/23/2016] [Indexed: 01/06/2023]
Abstract
UNLABELLED Deletions at the C-terminus of the proto-oncogene protein c-Src kinase are found in the viral oncogene protein v-Src as well as in some advanced human colon cancers. They are associated with increased kinase activity and cellular invasiveness. Here, we analyzed the mRNA expression signature of a constitutively active C-terminal mutant of c-Src, c-Src(mt), in comparison with its wild-type protein, c-Src(wt), in the human non-transformed breast epithelial cell line MCF-10A. We demonstrated previously that the mutant altered migratory and metastatic properties. Genome-wide transcriptome analysis revealed that c-Src(mt) de-regulated the expression levels of approximately 430 mRNAs whose gene products are mainly involved in the cellular processes of migration and adhesion, apoptosis and protein synthesis. 82.9% of these genes have previously been linked to cellular migration, while the others play roles in RNA transport and splicing processes, for instance. Consistent with the transcriptome data, cells expressing c-Src(mt), but not those expressing c-Src(wt), showed the capacity to metastasize into the lungs of mice in vivo. The mRNA expression profile of c-Src(mt)-expressing cells shows significant overlap with that of various primary human tumor samples, possibly reflecting elevated Src activity in some cancerous cells. Expression of c-Src(mt) led to elevated migratory potential. We used this model system to analyze the transcriptional changes associated with an invasive cellular phenotype. These genes and pathways de-regulated by c-Src(mt) may provide suitable biomarkers or targets of therapeutic approaches for metastatic cells. DATABASE This project was submitted to the National Center for Biotechnology Information BioProject under ID PRJNA288540. The Illumina RNA-Seq reads are available in the National Center for Biotechnology Information Sequence Read Archive under study ID SRP060008 with accession numbers SRS977414 for MCF-10A cells, SRS977717 for mock cells, SRS978053 for c-Src(wt) cells and SRS978046 for c-Src(mt) cells.
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Affiliation(s)
- Felix Broecker
- Max Planck Institute for Molecular Genetics, Berlin, Germany.,University of Zurich, Switzerland
| | | | - Ralf Herwig
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | | | - Martin Kerick
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | | | | | - Lubor Borsig
- Institute of Physiology, Zurich Center for Integrative Human Physiology, University of Zurich, Switzerland
| | - Mathias Heikenwalder
- Institute of Virology, Technische Universität München, Germany.,Institute of Virology, Helmholtz Zentrum Munich, Germany.,Department Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hans Lehrach
- Max Planck Institute for Molecular Genetics, Berlin, Germany.,Dahlem Centre for Genome Research and Medical Systems Biology, Berlin, Germany.,Alacris Theranostics GmbH, Berlin, Germany
| | - Karin Moelling
- Max Planck Institute for Molecular Genetics, Berlin, Germany.,University of Zurich, Switzerland
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The Roles of RNase-L in Antimicrobial Immunity and the Cytoskeleton-Associated Innate Response. Int J Mol Sci 2016; 17:ijms17010074. [PMID: 26760998 PMCID: PMC4730318 DOI: 10.3390/ijms17010074] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 12/21/2015] [Accepted: 01/04/2016] [Indexed: 12/26/2022] Open
Abstract
The interferon (IFN)-regulated endoribonuclease RNase-L is involved in multiple aspects of the antimicrobial innate immune response. It is the terminal component of an RNA cleavage pathway in which dsRNA induces the production of RNase-L-activating 2-5A by the 2′-5′-oligoadenylate synthetase. The active nuclease then cleaves ssRNAs, both cellular and viral, leading to downregulation of their expression and the generation of small RNAs capable of activating retinoic acid-inducible gene-I (RIG-I)-like receptors or the nucleotide-binding oligomerization domain-like receptor 3 (NLRP3) inflammasome. This leads to IFNβ expression and IL-1β activation respectively, in addition to broader effects on immune cell function. RNase-L is also one of a growing number of innate immune components that interact with the cell cytoskeleton. It can bind to several cytoskeletal proteins, including filamin A, an actin-binding protein that collaborates with RNase-L to maintain the cellular barrier to viral entry. This antiviral activity is independent of catalytic function, a unique mechanism for RNase-L. We also describe here the interaction of RNase-L with the E3 ubiquitin ligase and scaffolding protein, ligand of nump protein X (LNX), a regulator of tight junction proteins. In order to better understand the significance and context of these novel binding partners in the antimicrobial response, other innate immune protein interactions with the cytoskeleton are also discussed.
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16
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Hu T, Yang H, Han ZG. PDZRN4 acts as a suppressor of cell proliferation in human liver cancer cell lines. Cell Biochem Funct 2015; 33:443-9. [PMID: 26486104 DOI: 10.1002/cbf.3130] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 07/12/2015] [Accepted: 08/03/2015] [Indexed: 11/11/2022]
Abstract
Recently, some reports show that Ligand of Numb Protein-X 1 (LNX1) could be a suppressor gene in gliomas, while our current research has firstly shown that PDZ domain containing ring finger 4 (PDZRN4), another member of LNX family, could also be a potential suppressor in hepatocellular carcinoma (HCC). PDZRN4, also named LNX4 (Ligand of Numb Protein-X 4), is a member of the LNX family. We recently found that PDZRN4, but not LNX1, was down-regulated in HCC samples, and the role of PDZRN4 in the progression of HCC had not been studied before. To address this question, firstly, we evaluated the expression of PDZRN4 in HCC samples and adjacent non-cancerous tissues. Semi-quantitative polymerase chain reaction showed that PDZRN4 was down-regulated in 24/36 (66.7%) HCC samples separately. In addition, our research shows that PDZRN4 is silenced in all of the 12 HCC cell lines tested. Subsequently, cell-based functional assay exhibited that ectopic expression of PDZRN4 inhibits the proliferation, plate colony formation and anchorage-independent colony formation of HCC cells. Collectively, our results showed that PDZRN4 might be a potential tumour suppressor gene and had anti-proliferative effect on HCC cell proliferation, which would be of great significance to the researches on HCC.
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Affiliation(s)
- Taotao Hu
- Key Laboratory of Systems Biomedicine (Ministry of Education) of Rui-Jin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Shanghai-MOST Key Laboratory for Disease and Health Genomics, Chinese National Human Genome Center, Shanghai, Shanghai, China
| | - Hong Yang
- Key Laboratory of Systems Biomedicine (Ministry of Education) of Rui-Jin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.,School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Ze-Guang Han
- Key Laboratory of Systems Biomedicine (Ministry of Education) of Rui-Jin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University, Shanghai, China.,Shanghai-MOST Key Laboratory for Disease and Health Genomics, Chinese National Human Genome Center, Shanghai, Shanghai, China
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17
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Lenihan JA, Saha O, Mansfield LM, Young PW. Tight, cell type-specific control of LNX expression in the nervous system, at the level of transcription, translation and protein stability. Gene 2014; 552:39-50. [PMID: 25200495 DOI: 10.1016/j.gene.2014.09.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2014] [Revised: 09/01/2014] [Accepted: 09/04/2014] [Indexed: 11/19/2022]
Abstract
LNX1 and LNX2 are E3 ubiquitin ligases that can interact with Numb - a key regulator of neurogenesis and neuronal differentiation. LNX1 can target Numb for proteasomal degradation, and Lnx mRNAs are prominently expressed in the nervous system, suggesting that LNX proteins play a role in neural development. This hypothesis remains unproven, however, largely because LNX proteins are present at very low levels in vivo. Here, we demonstrate expression of both LNX1 and LNX2 proteins in the brain for the first time. We clarify the cell-type specific expression of LNX isoforms in both the CNS and PNS, and identify a novel LNX1 isoform. Using luciferase reporter assays, we show that the 5' untranslated region of the Lnx1_variant 2 mRNA, that generates the LNX1p70 isoform, strongly suppresses protein production. This effect is mediated in part by the presence of upstream open reading frames (uORFs), but also by a sequence element that decreases both mRNA levels and translational efficiency. By contrast, uORFs do not negatively regulate LNX1p80 or LNX2 expression. Instead, we find some evidence that protein turnover via proteasomal degradation may influence LNX1p80 levels in cells. These observations provide plausible explanations for the low levels of LNX1 proteins detected in vivo.
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Affiliation(s)
- Joan A Lenihan
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Orthis Saha
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Louise M Mansfield
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Paul W Young
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland.
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18
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Georgess D, Mazzorana M, Terrado J, Delprat C, Chamot C, Guasch RM, Pérez-Roger I, Jurdic P, Machuca-Gayet I. Comparative transcriptomics reveals RhoE as a novel regulator of actin dynamics in bone-resorbing osteoclasts. Mol Biol Cell 2013; 25:380-96. [PMID: 24284899 PMCID: PMC3907278 DOI: 10.1091/mbc.e13-07-0363] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Two-step transcriptomic profiling of bone-resorbing OCs versus nonresorbing MGCs generated a list of 115 genes potentially involved in bone resorption. Of these, RhoE was investigated. Its role in podosome dynamics is central for OC migration, SZ formation, and, ultimately, bone resorption. The function of osteoclasts (OCs), multinucleated giant cells (MGCs) of the monocytic lineage, is bone resorption. To resorb bone, OCs form podosomes. These are actin-rich adhesive structures that pattern into rings that drive OC migration and into “sealing-zones” (SZs) that confine the resorption lacuna. Although changes in actin dynamics during podosome patterning have been documented, the mechanisms that regulate these changes are largely unknown. From human monocytic precursors, we differentiated MGCs that express OC degradation enzymes but are unable to resorb the mineral matrix. We demonstrated that, despite exhibiting bona fide podosomes, these cells presented dysfunctional SZs. We then performed two-step differential transcriptomic profiling of bone-resorbing OCs versus nonresorbing MGCs to generate a list of genes implicated in bone resorption. From this list of candidate genes, we investigated the role of Rho/Rnd3. Using primary RhoE-deficient OCs, we demonstrated that RhoE is indispensable for OC migration and bone resorption by maintaining fast actin turnover in podosomes. We further showed that RhoE activates podosome component cofilin by inhibiting its Rock-mediated phosphorylation. We conclude that the RhoE-Rock-cofilin pathway, by promoting podosome dynamics and patterning, is central for OC migration, SZ formation, and, ultimately, bone resorption.
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Affiliation(s)
- Dan Georgess
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Lyon 1, CNRS, Ecole Normale Supérieure de Lyon, Lyon Cedex 07, France Laboratoire de Biologie Moléculaire de la Cellule, Université de Lyon, Université Lyon 1, CNRS, Ecole Normale Supérieure de Lyon, Lyon Cedex 07, France Departamento Medicina y Cirugía Animal, Facultad de Veterinaria, Universidad CEU Cardenal Herrera, 46115 Alfara del Patriarca, Valencia, Spain Plateau Technique Imagerie/Microscopie Facility, SFR Biosciences (UMS3444/US8), Ecole Normale Supérieure de Lyon, Lyon Cedex 07, France Laboratory of Cellular Pathology, 46012 Valencia, Spain Departamento Ciencias Biomédicas-Seminario Salud, 46113 Moncada, Valencia, Spain
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Das SK, Bhutia SK, Sokhi UK, Azab B, Su ZZ, Boukerche H, Anwar T, Moen EL, Chatterjee D, Pellecchia M, Sarkar D, Fisher PB. Raf kinase inhibitor RKIP inhibits MDA-9/syntenin-mediated metastasis in melanoma. Cancer Res 2012; 72:6217-26. [PMID: 23066033 DOI: 10.1158/0008-5472.can-12-0402] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Melanoma differentiation associated gene-9 (MDA-9), also known as syntenin, functions as a positive regulator of melanoma progression and metastasis. In contrast, the Raf kinase inhibitor, RKIP, a negative modulator of RAF-stimulated MEKK activation, is strongly downregulated in metastatic melanoma cells. In this study, we explored a hypothesized inverse relationship between MDA-9 and RKIP in melanoma. Tumor array and cell line analyses confirmed an inverse relationship between expression of MDA-9 and RKIP during melanoma progression. We found that MDA-9 transcriptionally downregulated RKIP in support of a suggested cross-talk between these two proteins. Furthermore, MDA-9 and RKIP physically interacted in a manner that correlated with a suppression of FAK and c-Src phosphorylation, crucial steps necessary for MDA-9 to promote FAK/c-Src complex formation and initiate signaling cascades that drive the MDA-9-mediated metastatic phenotype. Finally, ectopic RKIP expression in melanoma cells overrode MDA-9-mediated signaling, inhibiting cell invasion, anchorage-independent growth, and in vivo dissemination of tumor cells. Taken together, these findings establish RKIP as an inhibitor of MDA-9-dependent melanoma metastasis, with potential implications for targeting this process therapeutically.
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Affiliation(s)
- Swadesh K Das
- Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, USA
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20
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Guo Z, Song E, Ma S, Wang X, Gao S, Shao C, Hu S, Jia L, Tian R, Xu T, Gao Y. Proteomics strategy to identify substrates of LNX, a PDZ domain-containing E3 ubiquitin ligase. J Proteome Res 2012; 11:4847-62. [PMID: 22889411 DOI: 10.1021/pr300674c] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Ubiquitin ligases (E3s) confer specificity to ubiquitination by recognizing target substrates. However, the substrates of most E3s have not been extensively discovered, and new methods are needed to efficiently and comprehensively identify these substrates. Mostly, E3s specifically recognize substrates via their protein interaction domains. We developed a novel integrated strategy to identify substrates of E3s containing protein interaction domains on a proteomic scale. The binding properties of the protein interaction domains were characterized by screening a random peptide library using a yeast two-hybrid system. Artificial degrons, consisting of a preferential ubiquitination sequence and particular interaction domain-binding motifs, were tested as potential substrates by in vitro ubiquitination assays. Using this strategy, not only substrates but also nonsubstrate regulators can be discovered. The detailed substrate recognition mechanisms, which are useful for drug discovery, can also be characterized. We used the Ligand of Numb protein X (LNX) family of E3s, a group of PDZ domain-containing RING-type E3 ubiquitin ligases, to demonstrate the feasibility of this strategy. Many potential substrates of LNX E3s were identified. Eight of the nine selected candidates were ubiquitinated in vitro, and two novel endogenous substrates, PDZ-binding kinase (PBK) and breakpoint cluster region protein (BCR), were confirmed in vivo. We further revealed that the LNX1-mediated ubiquitination and degradation of PBK inhibited cell proliferation and enhanced sensitivity to doxorubicin-induced apoptosis. The substrate recognition mechanism of LNX E3s was also characterized; this process involves the recognition of substrates via their specific PDZ domains by binding to the C-termini of the target proteins. This strategy can potentially be extended to a variety of E3s that contain protein interaction domain(s), thereby serving as a powerful tool for the comprehensive identification of their substrates on a proteomic scale.
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Affiliation(s)
- Zhengguang Guo
- National Key Laboratory of Medical Molecular Biology, Department of Physiology and Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences/School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
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21
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Wolting CD, Griffiths EK, Sarao R, Prevost BC, Wybenga-Groot LE, McGlade CJ. Biochemical and computational analysis of LNX1 interacting proteins. PLoS One 2011; 6:e26248. [PMID: 22087225 PMCID: PMC3210812 DOI: 10.1371/journal.pone.0026248] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2011] [Accepted: 09/23/2011] [Indexed: 12/18/2022] Open
Abstract
PDZ (Post-synaptic density, 95 kDa, Discs large, Zona Occludens-1) domains are protein interaction domains that bind to the carboxy-terminal amino acids of binding partners, heterodimerize with other PDZ domains, and also bind phosphoinositides. PDZ domain containing proteins are frequently involved in the assembly of multi-protein complexes and clustering of transmembrane proteins. LNX1 (Ligand of Numb, protein X 1) is a RING (Really Interesting New Gene) domain-containing E3 ubiquitin ligase that also includes four PDZ domains suggesting it functions as a scaffold for a multi-protein complex. Here we use a human protein array to identify direct LNX1 PDZ domain binding partners. Screening of 8,000 human proteins with isolated PDZ domains identified 53 potential LNX1 binding partners. We combined this set with LNX1 interacting proteins identified by other methods to assemble a list of 220 LNX1 interacting proteins. Bioinformatic analysis of this protein list was used to select interactions of interest for future studies. Using this approach we identify and confirm six novel LNX1 binding partners: KCNA4, PAK6, PLEKHG5, PKC-alpha1, TYK2 and PBK, and suggest that LNX1 functions as a signalling scaffold.
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Affiliation(s)
- Cheryl D. Wolting
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Canada
| | - Emily K. Griffiths
- Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Canada
| | - Renu Sarao
- Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Canada
| | - Brittany C. Prevost
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Canada
| | - Leanne E. Wybenga-Groot
- Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Canada
| | - C. Jane McGlade
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Canada
- * E-mail:
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22
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Abstract
Over 250 PDZ (PSD95/Dlg/ZO-1) domain-containing proteins have been described in the human proteome. As many of these possess multiple PDZ domains, the potential combinations of associations with proteins that possess PBMs (PDZ-binding motifs) are vast. However, PDZ domain recognition is a highly specific process, and much less promiscuous than originally thought. Furthermore, a large number of PDZ domain-containing proteins have been linked directly to the control of processes whose loss, or inappropriate activation, contribute to the development of human malignancies. These regulate processes as diverse as cytoskeletal organization, cell polarity, cell proliferation and many signal transduction pathways. In the present review, we discuss how PBM–PDZ recognition and imbalances therein can perturb cellular homoeostasis and ultimately contribute to malignant progression.
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Flynn M, Saha O, Young P. Molecular evolution of the LNX gene family. BMC Evol Biol 2011; 11:235. [PMID: 21827680 PMCID: PMC3162930 DOI: 10.1186/1471-2148-11-235] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Accepted: 08/09/2011] [Indexed: 02/07/2023] Open
Abstract
Background LNX (Ligand of Numb Protein-X) proteins typically contain an amino-terminal RING domain adjacent to either two or four PDZ domains - a domain architecture that is unique to the LNX family. LNX proteins function as E3 ubiquitin ligases and their domain organisation suggests that their ubiquitin ligase activity may be targeted to specific substrates or subcellular locations by PDZ domain-mediated interactions. Indeed, numerous interaction partners for LNX proteins have been identified, but the in vivo functions of most family members remain largely unclear. Results To gain insights into their function we examined the phylogenetic origins and evolution of the LNX gene family. We find that a LNX1/LNX2-like gene arose in an early metazoan lineage by gene duplication and fusion events that combined a RING domain with four PDZ domains. These PDZ domains are closely related to the four carboxy-terminal domains from multiple PDZ domain containing protein-1 (MUPP1). Duplication of the LNX1/LNX2-like gene and subsequent loss of PDZ domains appears to have generated a gene encoding a LNX3/LNX4-like protein, with just two PDZ domains. This protein has novel carboxy-terminal sequences that include a potential modular LNX3 homology domain. The two ancestral LNX genes are present in some, but not all, invertebrate lineages. They were, however, maintained in the vertebrate lineage, with further duplication events giving rise to five LNX family members in most mammals. In addition, we identify novel interactions of LNX1 and LNX2 with three known MUPP1 ligands using yeast two-hybrid asssays. This demonstrates conservation of binding specificity between LNX and MUPP1 PDZ domains. Conclusions The LNX gene family has an early metazoan origin with a LNX1/LNX2-like protein likely giving rise to a LNX3/LNX4-like protein through the loss of PDZ domains. The absence of LNX orthologs in some lineages indicates that LNX proteins are not essential in invertebrates. In contrast, the maintenance of both ancestral LNX genes in the vertebrate lineage suggests the acquisition of essential vertebrate specific functions. The revelation that the LNX PDZ domains are phylogenetically related to domains in MUPP1, and have common binding specificities, suggests that LNX and MUPP1 may have similarities in their cellular functions.
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Affiliation(s)
- Michael Flynn
- Department of Biochemistry, University College Cork, Cork, Ireland
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Clemastine causes immune suppression through inhibition of extracellular signal-regulated kinase-dependent proinflammatory cytokines. J Allergy Clin Immunol 2011; 128:1286-94. [PMID: 21807405 DOI: 10.1016/j.jaci.2011.06.023] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2010] [Revised: 06/07/2011] [Accepted: 06/08/2011] [Indexed: 10/14/2022]
Abstract
BACKGROUND Antihistamines are considered safe and used worldwide against allergy, pruritus, nausea, and cough and as sleeping aids. Nonetheless, a growing number of reports suggest that antihistamines also have immunoregulatory functions. OBJECTIVE We examined the extent and by what potential mechanisms histamine-1-receptor (H1R) antagonists exert immune suppressive effects. METHODS Immune suppression by antihistamines and immunosuppressants was tested in mice infected with Listeria monocytogenes. Potential modes of action were studied in vitro by using murine and human cells. We also tested whether injection of clemastine in healthy volunteers affected the activation of peripheral macrophages and monocytes. Finally, therapeutic application of clemastine-mediated immune suppression was tested in a murine model of sepsis. RESULTS Clemastine and desloratadine strongly reduced innate responses to Listeria monocytogenes in mice as did dexamethasone. The immune suppression was MyD88 independent and characterized by inhibition of the mitogen-activated protein kinase-extracellular signal-regulated kinase signaling pathway, leading to overall impaired innate immunity with reduced TNF-α and IL-6 production. Surprisingly, the observed effects were H1R independent as demonstrated in H1R-deficient mice. Moreover, in a double-blind placebo-controlled clinical trial, 1 intravenous administration of clemastine reduced the TNF-α secretion potential of peripheral blood macrophages and monocytes. This inhibition could be exploited to treat sepsis in mice. CONCLUSIONS The safety profile of antihistamines may need to be revisited. However, antihistamine-mediated immune suppression may also be exploited and find applications in the treatment of inflammatory diseases.
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Zheng D, Sun Y, Gu S, Ji C, Zhao W, Xie Y, Mao Y. LNX (Ligand of Numb-protein X) interacts with RhoC, both of which regulate AP-1-mediated transcriptional activation. Mol Biol Rep 2009; 37:2431-7. [PMID: 19701800 DOI: 10.1007/s11033-009-9754-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2009] [Accepted: 08/06/2009] [Indexed: 10/20/2022]
Abstract
LNX (Ligand of Numb-protein X) was originally isolated as a binding partner to the cell-fate Determinant Numb during development, and then identified to act as a RING finger-type E3 ubiquitin ligase for the ubiquitylation and degradation of Numb. LNX contains 4 PDZ domains which are proved to play a central role in organizing diverse cell signaling assemblies. A yeast two-hybrid screening was used to identify LNX as a potential binding partner for RhoC. RhoC, a member of the Ras family of small GTPases, promotes reorganization of the actin cytoskeleton and regulation of cell shape, attachment, and motility. The interaction between LNX and RhoC in mammalian cells was identified by co-immunoprecipitation assays, and the efficient binding required the first PDZ domain of LNX. LNX and RhoC were further colocalized with each other in mammalian cells, in which RhoC changed its sublocalization from cytoplasm to nucleus when co-transferred with LNX. Furthermore, co-expression of RhoC reduced the transcriptional activity of AP-1, which was up-regulated by over-expression of LNX alone. These results suggest that LNX and RhoC might be part of a larger protein complex that would have important functions in signaling transduction about regulating the transcriptional activities of AP-1.
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Affiliation(s)
- Dan Zheng
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, 200433 Shanghai, People's Republic of China
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Organizer restriction through modulation of Bozozok stability by the E3 ubiquitin ligase Lnx-like. Nat Cell Biol 2009; 11:1121-7. [PMID: 19668196 PMCID: PMC2759713 DOI: 10.1038/ncb1926] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2009] [Accepted: 05/20/2009] [Indexed: 12/18/2022]
Abstract
The organizer anchors the primary embryonic axis, and balance between dorsal (organizer) and ventral domains is fundamental to body patterning. LNX (ligand of Numb protein-X) is a RING finger and four PDZ domain-containing E3 ubiquitin ligase. LNX serves as a binding platform and may have a role in cell fate determination, but its in vivo functions are unknown. Here we show that Lnx-l (Lnx-like) functions as a critical regulator of dorso-ventral axis formation in zebrafish. Depletion of Lnx-l using specific antisense morpholinos (MOs) caused strong embryonic dorsalization. We identified Bozozok (Boz, also known as Dharma or Nieuwkoid) as a binding partner and substrate of Lnx-l. Boz is a homeodomain-containing transcriptional repressor induced by canonical Wnt signalling that is critical for dorsal organizer formation. Lnx-l induced K48-linked polyubiquitylation of Boz, leading to its proteasomal degradation in human 293T cells and in zebrafish embryos. Dorsalization induced by Boz overexpression was suppressed by raising the level of Lnx-l, but Lnx-l failed to counteract dorsalization caused by mutant Boz lacking a critical motif for Lnx-l binding. Furthermore, dorsalization induced by depletion of Lnx-l was alleviated by attenuation of Boz expression. We conclude that Lnx-l modulates Boz activity to prevent the invasion of ventral regions of the embryo by organizer tissue. These studies introduce a ubiquitin ligase, Lnx-l, as a balancing modulator of axial patterning in the zebrafish embryo.
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27
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Baumgartner M, Weiss A, Fritzius T, Heinrich J, Moelling K. The PDZ protein MPP2 interacts with c-Src in epithelial cells. Exp Cell Res 2009; 315:2888-98. [PMID: 19665017 DOI: 10.1016/j.yexcr.2009.07.028] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2008] [Revised: 07/21/2009] [Accepted: 07/31/2009] [Indexed: 01/15/2023]
Abstract
c-Src is a non-receptor tyrosine kinase involved in regulating cell proliferation, cell migration and cell invasion and is tightly controlled by reversible phosphorylation on regulatory sites and through protein-protein interactions. The interaction of c-Src with PDZ proteins was recently identified as novel mechanism to restrict c-Src function. The objective of this study was to identify and characterise PDZ proteins that interact with c-Src to control its activity. By PDZ domain array screen, we identified the interaction of c-Src with the PDZ protein Membrane Protein Palmitoylated 2 (MPP2), a member of the Membrane-Associated Guanylate Kinase (MAGUK) family, to which also the Discs large (Dlg) tumour suppressor protein belongs. The function of MPP2 has not been established and the functional significance of the MPP2 c-Src interaction is not known. We found that in non-transformed breast epithelial MCF-10A cells, endogenous MPP2 associated with the cytoskeleton in filamentous structures, which partially co-localised with microtubules and c-Src. MPP2 and c-Src interacted in cells, where c-Src kinase activity promoted increased interaction of c-Src with MPP2. We furthermore found that MPP2 was able to negatively regulate c-Src kinase activity in cells, suggesting that the functional significance of the MPP2-c-Src interaction is to restrict Src activity. Consequently, the c-Src-dependent disorganisation of the cortical actin cytoskeleton of epithelial cells expressing c-Src was suppressed by MPP2. In conclusion we demonstrate here that MPP2 interacts with c-Src in cells to control c-Src activity and morphological function.
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Affiliation(s)
- Martin Baumgartner
- Institute of Medical Virology, University of Zürich, Zürich, Switzerland.
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28
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Confalonieri S, Quarto M, Goisis G, Nuciforo P, Donzelli M, Jodice G, Pelosi G, Viale G, Pece S, Di Fiore PP. Alterations of ubiquitin ligases in human cancer and their association with the natural history of the tumor. Oncogene 2009; 28:2959-68. [PMID: 19543318 DOI: 10.1038/onc.2009.156] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Protein ubiquitination is critical for many cellular processes, through its ability to regulate protein degradation and various signaling mechanisms. In the ubiquitin (Ub) system, substrate specificity is achieved through the E3 family of Ub ligases. Because alterations of the ubiquitination machinery have been reported in human cancers, the selective interference with Ub ligases might represent a powerful therapeutic tool. Here, we report the first wide survey of misregulation of Ub ligases in cancer. We analysed 82 Ub ligases in nine types of cancer by in situ hybridization on tissue microarrays. We found 27 instances in which an Ub ligase was altered in a given type of tumor, when compared with normal tissues: 21 cases of overexpression and 6 cases of underexpression. We further analysed selected Ub ligases in large cohorts of breast and non-small-cell lung carcinomas. In five, of six, of these extended analyses (HUWE1, CCNB1IP1, SIAH1 and SIAH2 in breast cancer and CCNB1IP1 in lung cancer), we found that the levels of Ub ligases correlated significantly with relevant prognostic factors, and with clinical outcome. Our findings show that the alteration of Ub ligases is a frequent event in cancer and identify candidate targets for molecular therapies.
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Affiliation(s)
- S Confalonieri
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy.
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Takahashi S, Iwamoto N, Sasaki H, Ohashi M, Oda Y, Tsukita S, Furuse M. The E3 ubiquitin ligase LNX1p80 promotes the removal of claudins from tight junctions in MDCK cells. J Cell Sci 2009; 122:985-94. [DOI: 10.1242/jcs.040055] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The structural continuity of tight junctions (TJs) is consistently maintained even when epithelial cells divide and move within the cellular sheet. This process is associated with dynamic remodeling of TJs by coordinated internalization and generation of claudin-based TJ strands, but the molecular mechanism behind the regulated turnover of TJs remains largely unknown. In this study, we identified the p80 isoform of the E3 ubiquitin ligase ligand of Numb-protein X1 (LNX1p80) as a protein binding to claudin-1. Interestingly, the concentration of claudins in TJs was remarkably reduced when LNX1p80 was overexpressed in MDCK cells, and there was a reduction not only in the number of TJ strands but also in the amount of detergent-insoluble claudins. We also found that LNX1p80 promoted polyubiquitylation of claudins. This ubiquitylation is dependent on its RING-finger domain and is not mediated by Lys48 of ubiquitin, which is used for protein degradation by the proteasome. Furthermore, LNX1p80 was often colocalized with claudins in vesicular structures containing markers for late endosomes and lysosomes. These findings suggest that LNX1p80 is involved in the ubiquitylation, endocytosis and lysosomal degradation of claudins, and that the turnover of TJs is regulated by ubiquitylation.
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Affiliation(s)
- Senye Takahashi
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe, Sakyo-ku, Kyoto 606-8501, Japan
| | - Noriko Iwamoto
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe, Sakyo-ku, Kyoto 606-8501, Japan
- Division of Cell Biology, Department of Physiology and Cell Biology, Graduate School of Medicine, Kobe University, Kusunoki-cho 7-5-1, Chuo-ku, Kobe 650-0017, Japan
| | - Hiroyuki Sasaki
- Department of Molecular Cell Biology, Institute of DNA Medicine, The Jikei University School of Medicine, Nishi-Shinbashi, Minato-ku, Tokyo 105-8461, Japan
| | - Masato Ohashi
- Laboratory of Nano-Structure Physiology, Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, Higashiyama 5-1, Myodaiji-cho, Okazaki 444-8787, Japan
| | - Yukako Oda
- Division of Cell Biology, Department of Physiology and Cell Biology, Graduate School of Medicine, Kobe University, Kusunoki-cho 7-5-1, Chuo-ku, Kobe 650-0017, Japan
| | - Shoichiro Tsukita
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe, Sakyo-ku, Kyoto 606-8501, Japan
| | - Mikio Furuse
- Division of Cell Biology, Department of Physiology and Cell Biology, Graduate School of Medicine, Kobe University, Kusunoki-cho 7-5-1, Chuo-ku, Kobe 650-0017, Japan
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