Written | 2014-08 | Erica Di Cesare, Patrizia Lavia |
Institute of Biology, Molecular Medicine, NanoBiotechnology (IBMN), National Research Council (CNR), c/o La Sapienza University, via degli Apuli 4, 00185 Rome, Italy |
Identity |
Alias (NCBI) | ADANE | ANE1 | NUP358 |
HGNC (Hugo) | RANBP2 |
HGNC Alias symb | NUP358 | ADANE |
HGNC Alias name | nucleoporin 358 |
HGNC Previous name | ANE1 |
HGNC Previous name | acute necrotizing encephalopathy 1 (autosomal dominant) |
LocusID (NCBI) | 5903 |
Atlas_Id | 483 |
Location | 2q12.3 [Link to chromosome band 2q12] |
Location_base_pair | Starts at 108719482 and ends at 108785809 bp from pter ( according to GRCh38/hg38-Dec_2013) [Mapping RANBP2.png] |
Fusion genes (updated 2017) | Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands) |
ALK (2p23.2) / RANBP2 (2q12.3) | RANBP2 (2q12.3) / ABL1 (9q34.12) | RANBP2 (2q12.3) / ALK (2p23.2) | |
RANBP2 (2q12.3) / BMP5 (6p12.1) | RANBP2 (2q12.3) / GCC2 (2q12.3) | RANBP2 (2q12.3) / INPP5B (1p34.3) | |
RANBP2 (2q12.3) / MAP2 (2q34) | RANBP2 (2q13) / ABL1 (9q34.12) | RANBP2 (2q13) / ALK (2p23.2) | |
RANBP2 (2q13) / BMP5 (6p12.1) | RPLP1 (15q23) / RANBP2 (2q12.3) |
Note | The human RANBP2 gene lies within a recombination "hot spot" genomic region on Chr 2q11-q13 (Krebber et al., 1997) as part of a gene "cluster" that contains the partially duplicated gene RANBP2L1, containing the RANBP2 5' gene portion (Nothwang et al., 1998). see also The nuclear pore complex: structure and function |
DNA/RNA |
Note | RANBP2 is an essential gene and RANBP2-null mice display early embryonic lethality (Aslanukov et al., 2006; Dawlaty et al., 2008). A single RANBP2 hypomorphic allele is, however, sufficient for viability. |
Description | The human RANBP2 gene comprises 31 exons and gives rise to one major mRNA encoding the RANBP2 protein, with at least 8 less represented alternative splicing variants (AceView; NCBI; GeneCards). |
Transcription | RANBP2 mRNA transcription is widespread in many though not all tissues (Fauser et al., 2001). In the mouse genome, the Ranbp2 promoter region lies in a CpG island, typical of "housekeeping" gene promoters and potentially subjected to epigenetic regulation. In silico analysis of the human RANBP2 gene promoter has identified potential binding sites for cell cycle- and cell proliferation-dependent transcription factors, some validated in chromatin immunoprecipitation (ChIP) assays (e.g., c-Fos, AP1 and others) (GeneCards). Binding sites for tissue-specific factors are also present, and RANBP2 mRNA transcript and protein product are highly expressed in certain tissues and cell types, e.g. neuronal cells (Fauser et al., 2001). Serial analysis of gene expression (SAGE) depicted aberrant up-regulation of RANBP2 in certain cancers, e.g. multiple myeloma (Felix et al., 2009). |
Protein |
Note | Biological overview: The RAN-binding protein 2 (RANBP2) or Nucleoporin 358 (NUP358, nucleoporin of 358 kDa) is the largest component of nuclear pore complexes (NPCs). The latter are highly complex structures composed of several orderly assembled proteins, called nucleoporins (NUPs), that represent gateways across the nuclear envelope (NE) for the exchange of macromolecules between the nucleus and the cytoplasm. This exchange is critical to many essential processes, e.g., DNA replication, DNA repair, DNA damage response, establishment of functional chromatin domains, replication checkpoint, transcriptional and epigenetic regulation of genes and genome function, mitotic entry. The RANBP2 nucleoporin is specific of higher eukaryotes and has a multimodular structure (Wu et al., 1995; Yokoyama et al., 1995; Wilken et al., 1995). It is unique among NUPs in that it is endowed with E3-type ligase activity for SUMO (small ubiquitin-related modifier) peptides (Pichler et al., 2002). This will be discussed in more depth below. RANBP2 operates in two major groups of cellular processes: - NPC- and NE-dependent processes ensuring nuclear functions in interphase (e.g., nuclear positioning, recruitment of motor proteins at the NE, centrosome anchoring to the NE, import and export of macromolecules in and out of the nucleus, including transcription and regulatory factors governing genome function); and - cell division events (NE breakdown, centrosome migration, assembly of the mitotic apparatus, chromosome segregation). In many of these processes, RANBP2 stimulates the conjugation of SUMO peptides (SUMO-1 to -4) to various target proteins at specific intracellular sites: the nuclear rim in interphase, and microtubules (MTs) as well as kinetochores (KTs) in mitosis. SUMO conjugation is emerging as a protein post-translational modification that modulates the localization and interactions of several proteins (reviewed by Lomelí and Vázquez, 2011; Flotho and Melchior, 2013). The protein-modifying and transport-regulating activities of RANBP2 target specific substrates in many tissues and cell types. As a result, RANBP2 acts as a cell context-dependent pleiotropic protein in a variety of physiological and pathological processes, including tumor suppression, neuroprotection and familial necrotic encephalopathy. |
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Figure 1. A Schematic of RANBP2 domains. Boxes 1-4 identify four RAN-binding domains, Cy indicates a cyclophilin-like domain, vertical dashes mark the position of FG-repeats that interact with transport receptors (modified from Werner et al., 2012). | |
Description | The human RANBP2 protein is composed of 3224 aminoacidic residues, with a molecular weight of 358 KDa, hence its name (Wu et al., 1995; Yokoyama et al., 1995). The alternative name RANBP2 derives from the presence of four RAN-binding domains (RBD), through which it binds the GTPase RAN. RANBP2 contains several more structural domains: - An N-terminal leucine-rich region anchors RANBP2 to the NPC. This region is also implicated in binding interphase microtubules (MTs) and regulating their dynamics (Joseph and Dasso, 2008). The structure of this region reveals an alpha-helical domain harboring three central tetratricopeptide repeats (TPRs) capable to bind single-stranded RNA in solution and thought to contribute to messenger ribonucleoprotein (mRNP) remodeling at the cytoplasmic face of the NPC (Kassube et al., 2012). - Four RAN binding domains (RBD1-4) (Yokoyama et al., 1995), 46-60% identical to the prototype RAN-binding domain (Pfam) in the first cloned RAN-binding partner, RANBP1 (Bressan et al., 1991; Coutavas et al., 1993). The RBDs act as coactivators of GTP hydrolysis on RAN with a dual purpose: a) to assist nuclear protein import, by preventing the accumulation of RANGTP at the NPC cytoplasmic side and avoid that RANGTP prematurely dissociates import complexes while traversing the NPC to reach the nucleus (Yaseen and Blobel, 1999a); b) to facilitate the export of nuclear cargos by assisting the dissociation of RANGTP from exportin-cargo complexes (Bernad et al., 2004). - Eight zinc-finger motifs (Cys2-Cys2 type) in the central portion of RANBP2; they provide a binding platform for exportin-1/CRM1 (Singh et al., 1999) and help CRM1 recycling into the nucleus (Bernad et al., 2004). These motifs can also interact with RanGDP (Yaseen and Blobel, 1999a). - Phenylalanine-glycine (FG) and FxFG repeats (the nucleoporin "signature" motif; x is any aminoacid) present on the fibril-like structures projecting from the NPC into the cytoplasm. These repeats provide multiple binding sites for nuclear transport receptors (karyopherin beta/ importin beta and exportin-1/CRM1. The interaction of FG-rich fibrils with transport vectors facilitates their passage across the NPC. - A domain endowed with SUMO E3 ligase activity, the first enzymatic activity identified for RANBP2 (Pichler et al., 2002), residing between RBDs 3 and 4, that regulates sumoylation of target proteins (more detail below). - A C-terminal domain with peptidyl-prolyl isomerase activity, the second enzymatic activity ascribed to RANBP2 (Lin et al., 2013). - A cyclophilin A-like domain, harbouring an active site cavity that facilitates the binding to the HIV-1 capsid proteins during viral infection (Lin et al., 2013). Thus far, the SUMO E3 ligase domain, two RBDs, the N-terminal TPR domain and the C-terminal domain have been crystallized and structurally characterized (Vetter et al., 1999; Reverter and Lima, 2005; Geyer et al., 2005; Kassube et al., 2012; Lin et al., 2013). The SUMO E3 ligase activity of RANBP2 and the RANBP2/RANGAP1*SUMO1/Ubc9 (RRSU) complex |
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Figure 2. The localization of RANBP2 (red) in human Hela cells. Top row: note the punctuate red staining around the nucleus, which identifies the regular distribution of NPCs. Bottom row: a metaphase cell with aligned chromosomes (left panel). RANBP2 co-localizes with mitotic MTs with an accumulation at poles and at the kinetochore level, appearing as red spots proximal to the MT growing ends. | |
Localisation | Intracellular localization: In interphase cells, RANBP2 localizes at the cytoplasmic face of the NPCs (Wu et al., 1995; Yokoyama et al., 1995; Wilken et al., 1995; Walther et al., 2002): RANBP2-containing filaments are anchored to the NPC via interaction with a complex of nucleoporins containing Nup214 and Nup88 (Bernad et al., 2004) and project into the cytoplasm. Joseph et al. (2002 and 2004) first reported that, at the onset of mitosis, when the NE breaks down and NPCs disassemble, RANBP2 localizes to the microtubules (MTs) of the forming mitotic spindle, with an accumulation at poles; a fraction is recruited to chromosomal KTs when the latter become attached to MTs (Figure 2, bottom row). This localization underlies RANBP2's mitotic functions (see below). In early telophase RANBP2 is recruited back around chromatin of the reforming nuclei as the NE and NPCs reorganize. |
Function | RANBP2 in interphase nucleocytoplasmic transport As anticipated above, RANBP2 localization at cytoplasmic fibrils emanating from the NPC underlies its function in nucleocytoplasmic transport. - Nuclear protein import RANBP2 serves as a docking site for import complexes (the latter are of two main types: either composed of importin vectors interacting with proteins marked by a nuclear localization signal, NLS, or composed of transportin bound to ribonucleoproteins marked by the so-called M9 signal sequence, originally described in hnRNPs). The docking of import complex at RANBP2 cytoplasmic fibrils of the NPC aids the earliest step in nuclear import (Melchior et al., 1995; Delphin et al., 1997; Mahajan et al., 1997; Yaseen and Blobel, 1999b). RANBP2 itself does not directly participate in import, but facilitates it. In RANBP2-depleted HeLa cells, in vivo nuclear import by either Importin alpha/beta (Hutten et al., 2008) or transportin (Hutten et al., 2009) still occurs, but at substantially reduced rates. In a screening for nuclear proteins that accumulate in the cytoplasm upon RANBP2 depletion, Wälde and coworkers (2012) have also identified direct RANBP2 interactors: they found that an N-terminal fragment of RANBP2, harboring the NPC-binding domain, three FG motifs and RBD1, was sufficient to promote protein import, while neither the interaction with RANGAP1 nor the SUMO E3 ligase activity were required (Wälde et al., 2012). This is consistent with functional mapping data from Hamada and coworkers (2011) using various RANBP2-derived regions to complement RANBP2 knockout MEF cells, in which the RANBP2 N-terminal fragment restored import to RANBP2-null cells; the authors demonstrated a crucial role of this domain in aiding the recycling of RAN and importin beta complexes for nuclear import (Hamada et al., 2011). In summary, RANBP2 aids nuclear import by at least two mechanisms: i) by "capturing" transport receptors through the FG-repeats, it conveys them towards the NPC and reduces the effective concentration of import receptors required for efficient transport, while ii) by interacting with selected cargos in a receptor-independent manner, through the RANBP2 N-ter domain, it increases the overall efficiency of nuclear import. Interestingly, RANBP2 is also implicated in the nuclear delivery and integration of certain human viruses, including Herpes simplex (Copeland et al., 2009) and immunodeficiency virus-1 (HIV-1) (Zhang et al., 2010; Ocwieja et al., 2011; Schaller et al., 2011). - Nuclear export RANBP2 also plays roles in mRNA export. Poly(A)+ mRNA accumulates in nuclei of RANBP2-null MEFs (Hamada et al., 2011), although the intracellular distribution of poly(A)+ mRNA is not affected in RANBP2 hypomorphic mice-derived MEF cells (Dawlaty et al., 2008): thus, mRNA export requires RANBP2, but can proceed, albeit being impaired, in the presence of significantly decreased abundance. These data suggest that RANBP2 facilitates the export pathway, yet is not an indispensable component. Overall, RANBP2 affects the rate of nucleo-cytoplasmic transport of many proteins, including transcriptional and epigenetic factors. The latter are often mislocalized in tumor cells and in other cellular contexts in which RANBP2 expression is altered, with a global impact on genome functions. An emerging concept is that tumor cells exploit specific properties of NUPs to deregulate gene transcription, chromatin boundaries and essential transport-dependent regulatory circuits (Xu and Powers, 2009; Köhler and Hurt, 2010). Structural functions at the nuclear rim and NPCs Cell differentiation-associated functions Mitosis Regulation of the SUMO conjugation pathway in mitosis RANBP2 in cell viability |
Homology | RANBP2 is conserved among metazoa but absent in Saccharomyces cerevisiae. |
Mutations |
Note | An autosomal dominant mutation of RANBP2 (1880C-->T, yielding the Thr585Met missense mutation in the leucine-rich domain required for binding to both the NPC and to MTs) has been identified in the familial predisposition to acute necrotizing encephalopathy (ANE), arising in otherwise healthy children after common viral infections, such as influenza (Neilson et al., 2009; Loh and Appleton, 2010). Fusions of the RANBP2 gene with the gene encoding anaplastic lymphoma kinase (ALK) are associated with inflammatory myofibroblastic tumors (see below). RANBP2 mutants (i.e. point mutations or deletion mutants) have been engineered in several laboratories to study the role of different domains in various cellular processes. |
Implicated in |
Note | |
Entity | Various cancers |
Note | RANBP2 is implicated in many cancer types. It is difficult to draw a single unifying mechanism, yet two recurrent features are worth noting: a) the SUMO ligase and SUMO-stabilizing activity of RANBP2 targets many mitotic factors, as explained above, which can contribute to genetic instability and tumorigenesis when dysregulated (e.g., RANGAP1 and hence the functional state of RAN at KTs, Topo II, Borealin). Mouse models created by crossing RANBP2 hypomorphic (RANBP2H) and null (RANBP2-) alleles, displaying gradual degrees of RANBP2 insufficiency, are prone to carcinogen-induced and spontaneous tumors: the incidence of skin tumors dramatically increased in mice with reduced compared to wild-type RANBP2 expression and lung adenocarcinomas developed in virtually all insufficient mice (Dawlaty et al., 2008). b) generally, a striking link exists between some NUPs, their propensity to undergo translocation and fusion with other gene partners and neoplastic diseases (reviewed in Köhler and Hurt, 2010). RANBP2 shares this tendency with some other NUPs: residing in a chromosomal recombination "hot spot", is involved in several instances of translocation; signalling molecules involved in the resulting fusion protein become aberrantly concentrated at the NE, with tumorigenic consequences (see below). |
Entity | Inflammatory myofibroblastic tumors |
Note | RANBP2 is implicated in a subset of inflammatory myofibroblastic tumors (IMT), rare soft tissue tumors involving mesenchymal cell types, with a prominent inflammatory component. IMTs rarely metastasize, yet often recur rapidly with fatal outcomes in some cases. Some 50% of IMTs harbor rearrangements of the ALK gene (encoding the anaplastic lymphoma kinase ALK), located at 2p23, with diverse partners, and overexpress the ALK protein, mostly in the cytoplasm. In several IMT cases, ALK is fused to RANBP2 and acquires a perinuclear localization. These cases generally have a more aggressive clinical course, suggesting that the RANBP2-dependent ALK perinuclear localization may be prognostic of malignant behavior. The first two IMT cases with a RANBP2-ALK fusion were described by Ma et al. (2003). By sequence analysis, the N-terminal 867 residues of RANBP2 were fused to the cytoplasmic segment of ALK, originating an 1430-amino acid chimeric protein. In both cases, the RANBP2-ALK fusion was present in myofibroblasts and was nuclear membrane-associated, attributable to the presence of the NPC-binding domain of RANBP2 in the fusion. Patel et al. (2007) reported on an IMT in a young boy (karyotype 45,XY,der(2)inv(2)(p23q12)del(2)(p11.1p11.2),-22) with an ALK-RANBP2 fusion, identified by FISH and confirmed by cloning and sequencing of the breakpoints. Chen and Lee (2008) described a hepatic IMT with a RANBP2-ALK rearrangement. PCR product sequencing revealed the presence of exon 18 from RANBP2 and exon 20 from ALK. Tumor cells showed a round cell phenotype with nuclear membrane accumulation of ALK protein. Mariño-Enríquez et al. (2011) characterized 11 cases of intra-abdominal IMT with epithelioid morphology. Nine showed perinuclear ALK staining, three of which harbored a RANBP2-ALK fusion. These patients experienced rapid recurrence. The authors suggest that the epithelioid variant of IMT with nuclear membrane or perinuclear ALK represents an aggressive form of sarcoma, with rapid recurrences and frequently fatal. Li et al. (2013) reported two more cases of IMT with RANBP2-ALK fusions, with epithelioid and rounded tumor cell morphology, from the pelvic and peritoneal cavities respectively, both associated with quick recurrence and poor prognosis. In 2014 the first case of a large tumor appearing in the pleural cavity was described (Kozu et al., 2014) in a patient with massive pleural effusion. The tumor showed the presence of a RANBP2-ALK fusion, rounded cells with an epithelioid shape, and a prominent inflammatory infiltrate, which led the authors to diagnose an epithelioid inflammatory myofibroblastic sarcoma (EIMS) and recognize it as an IMT variant. An EIMS case arising in the pelvic cavity was also described by Kimbara et al. (2014) as an aggressive variant of IMT. The tumor cells displayed epithelioid morphology and ALK staining on the nuclear membrane, associated with RANBP2-ALK fusion identified by RT-PCR. The patient experienced rapid local recurrence after surgery. The tumor was resistant to doxorubicin, but underwent shrinkage after treatment with the ALK inhibitor crizotinib. |
Entity | Multiple myeloma |
Note | Felix et al. (2009) generated SAGE libraries from normal and neoplastic plasma cells to identify differentially expressed genes in multiple myeloma (MM). They identified 46 upregulated genes in the MM library and validated them by qRT-PCR. RANBP2 belongs to a group of upregulated genes in >50% of tested MM cases and in meta-analyses (ONCOMINE database) of MM compared to normal plasma cells. The authors proposed that RANBP2 might be a potential therapeutic target in myeloma. |
Entity | Acute myelomonocytic leukemia |
Note | Maesako et al. (2014) identified a RANBP2-ALK fusion mRNA transcript in a case of myeloid leukemia, associated with the chromosomal inversion inv(2)(p23q13), and resulting in nuclear membrane association of ALK. Another rearrangement involving RANBP2 and ALK was reported by Lim et al. (2014) in an acute myelomonocytic leukemia (AML) in a 31-year-old woman with a karyotype of 45,XX,inv(2)(p23q21),-7[20], associated with a RANBP2-ALK fusion transcript and strong staining of the fusion protein around the nuclear membrane in leukemic cells. The patient had an unfavorable clinical course. |
Entity | Colorectal cancer |
Note | Gylfe et al. (2013) highlighted another type of recombination tumorigenic events involving RANBP2. Because microsatellite instability occurs in some 15% of all colorectal cancers, the authors sequenced the exomes of 25 colorectal tumors and respective healthy colon tissue. They confirmed potential mutation hot spots in 15 genes, among which RANBP2; these were validated in tumors with microsatellite instability and showed that RANBP2 also contains hot spot mutations in the validation set. |
Entity | Proposed tumor-promoting mechanisms of RANBP2 via SUMO-conjugation and stimulation of tumorigenic signaling |
Note | The data discussed above indicate some major routes through which RANBP2 can contribute to cancer onset and progression: increasing their genetic instability during mitosis and impairing global nuclear functions in interphase. An increasing implication of SUMO conjugation in the function of proteins relevant to cancer is emerging, particularly in DNA damage and repair. Among the growing instances of RANBP2-dependent protein SUMOylation, some proteins have established roles in tumorigenic signaling pathways. Miyauchi et al. (2012) demonstrated a role of RANBP2 in SUMOylation and localization of MDM2, a major regulator of p53 stability, suggesting therefore a possible indirect implication of RANBP2 in p53 functions. Packham et al. (2014) showed that RANBP2 is implicated in the pro-tumorigenic activity of the insulin-like growth factor-1 receptor (IGF-1R), an activator of the PI3K/Akt pathway with key roles in tumorigenesis. The biological activity of IGF-1R depends on its nuclear translocation, which in turn depends on SUMOylation. Packham et al. (2014) characterized spatially regulated interactions of IGF-1R, first with dynactin, which transports IGF-1R to NPCs, and therein with importin-β and RANBP2. RANBP2 interacts with and stabilizes sumoylated IGF-1R, enabling its nuclear accumulation and hence the activation of tumorigenic pathways that depend on it. Interestingly, RANBP2 levels are abnormally elevated in transgenic mouse models of prostate cancer constitutively expressing a PI3K catalytic subunit (PIK3CA), and treating the animals with a PI3K inhibitor decreases RANBP2 protein abundance (Renner et al., 2007). These data converge to suggest functional cross-talks between RANBP2 and tumorigenic pathways. |
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Citation |
This paper should be referenced as such : |
Erica Di Cesare, Patrizia Lavia |
RANBP2 (RAN binding protein 2) |
Atlas Genet Cytogenet Oncol Haematol. 2015;19(6):390-400. |
Free journal version : [ pdf ] [ DOI ] |
Other Leukemias implicated (Data extracted from papers in the Atlas) [ 5 ] |
inv(2)(p23q13) RANBP2/ALK::t(2;2)(p23;q13) RANBP2/ALK
Juvenile myelomonocytic leukemia (JMML) t(2;8)(q12;p11) RANBP2/FGFR1 t(2;9)(q12;q34) RANBP2/ABL1 t(4;10)(q12;p11) KIF5B/PDGFRA |
Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 4 ] |
Soft Tissues: Inflammatory myofibroblastic tumor
Soft tissue tumors: an overview Soft Tissues: Inflammatory myofibroblastic tumor with t(2;2)(p23;q13)ALK/RANBP2 t(2;6)(q13;p12) RANBP2/BMP5 |
External links |
REVIEW articles | automatic search in PubMed |
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