Alternative titles; symbols
HGNC Approved Gene Symbol: USP7
Cytogenetic location: 16p13.2 Genomic coordinates (GRCh38) : 16:8,892,097-8,963,906 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 16p13.2 | Hao-Fountain syndrome | 616863 | Autosomal dominant | 3 |
The USP7 gene encodes a deubiquitinating enzyme that is an integral component of the MAGEL2 (605283)/TRIM27 (602165) ubiquitin ligase complex and is essential for WASH (613632)-mediated endosomal actin assembly and protein recycling (summary by Hao et al., 2015).
Herpes simplex virus type 1 (HSV-1) immediate-early protein Vmw110 is a nonspecific activator of gene expression and is required for efficient initiation of the viral lytic cycle. Vmw110 has been shown to bind to PML (102578)-containing nuclear bodies (ND10) and a 135-kD cellular protein. By screening a HeLa cell cDNA library with oligonucleotides based on the amino acid sequence of the purified 135-kD protein, Everett et al. (1997) cloned a cDNA encoding Vmw110-associated 135-kD protein, called herpesvirus-associated ubiquitin-specific protease (HAUSP) by them. The 1,102-amino acid HAUSP protein contains the 2 highly conserved active site domains of ubiquitin-specific proteases (USPs), a polyglutamine tract near the N terminus, and several regions predicted to form alpha helices. The authors showed that HAUSP can cleave model substrates of USPs. By immunofluorescence, they found that HAUSP is a predominantly nuclear protein that is present in a minority of ND10. Expression of Vmw110 early in virus infection increases the proportion of ND10 that contain HAUSP. Everett et al. (1997) stated that these results implicate a novel ubiquitin-dependent pathway in both the function of ND10 and the control of viral gene expression. Northern blot analysis of HeLa cell poly(A)+ RNA detected 2 low-level transcripts, 1 approximately 4.5 kb and the other slightly larger and of lower abundance. The NCBI dbEST database contains expressed sequence tags that match the HAUSP sequence and are derived from brain, liver, placenta, lung, and melanocyte cDNA libraries, suggesting that HAUSP is expressed in a wide variety of cell types.
Zapata et al. (2001) identified an N-terminal TRAF (see 601711)-like domain in USP7. USP7 localized predominantly to the nucleus in transfected COS-7 cells, and localization required the TRAF-like domain.
In USP7, Holowaty et al. (2003) identified an N-terminal p53 (191170)-binding domain, a catalytic domain, and 2 C-terminal domains. The p53-binding domain is identical to the TRAF-like domain described by Zapata et al. (2001).
Hao et al. (2015) found expression of the Usp7 gene in mouse hypothalamus.
By mass spectrometry of affinity-purified p53-associated factors, Li et al. (2002) identified HAUSP as a novel p53-interacting protein. HAUSP strongly stabilizes p53 even in the presence of excess MDM2 (164785), and also induces p53-dependent cell growth repression and apoptosis. HAUSP has an intrinsic enzymatic activity that specifically deubiquitinates p53 both in vivo and in vitro. Expression of a catalytically inactive point mutation of HAUSP in cells increased the levels of p53 ubiquitination and also destabilized p53. Li et al. (2002) concluded that their findings revealed an important mechanism by which p53 can be stabilized by direct deubiquitination and also implied that HAUSP may function as a tumor suppressor in vivo through the stabilization of p53.
Zapata et al. (2001) found that the TRAF-like domain of USP7 could interact in vitro with all TRAF proteins tested. The TRAF-like domain also suppressed NFKB (see 164011) induction by TRAF2 (601895), TRAF6 (602355), and some TRAF-binding TNF receptors (see 191190).
Holowaty et al. (2003) determined that in vitro translated USP7 could hydrolyze a linear ubiquitin fusion protein. Biochemical characterization indicated that deubiquitination by USP7 was resistant to high salt concentrations and high pH, but it was inactivated by a thiol-blocking reagent. USP7 also removed ubiquitin from a high molecular mass polyubiquitinated Epstein-Barr virus protein, EBNA1. By mutation analysis, proteolysis protection assays, and several protein binding assays, Holowaty et al. (2003) determined that the N-terminal p53-binding domain of USP7 interacted with EBNA1. The binding affinity between USP7 and EBNA1 was 10-fold higher than that between p53 and USP7. Holowaty et al. (2003) also determined that a C-terminal domain of USP7 interacted with the HSV-1 protein ICP0.
The p53 tumor suppressor protein has a major role in protecting the integrity of the genome, and a balance between the ubiquitin ligase activity of proteins such as HDM2 (164785) and ubiquitin protease activity of USP7 determines the half-life of p53. Meulmeester et al. (2005) demonstrated that USP7 also indirectly affected p53 stability by deubiquitinating HDMX (602704), a regulator of HDM2. In addition, the deubiquitination activity of USP7 toward both HDMX and HDM2 was impaired following DNA damage, although the general activity of USP7 was not affected.
Song et al. (2008) found that PTEN (601728) was aberrantly localized in acute promyelocytic leukemia (APL; 612376) in which PML function was disrupted by the PML-RARA (180240) fusion oncoprotein. Treatment with drugs that triggered PML-RARA degradation restored nuclear PTEN. PML opposed the activity of HAUSP towards PTEN through a mechanism involving DAXX (603186). Confocal microscopy and immunohistochemistry demonstrated that HAUSP was overexpressed in prostate cancer and that levels of HAUSP directly correlated with tumor aggressiveness and with PTEN nuclear exclusion. Song et al. (2008) concluded that a PML-HAUSP network controls PTEN deubiquitinylation and subcellular localization, which is perturbed in human cancers.
Independently, Zhang et al. (2012) and Schwertman et al. (2012) showed that UVSSA (614632) stabilized the transcription-coupled nucleotide excision repair (NER) organizing protein ERCC6 (609413) by delivering USP7 to the NER complex. They concluded that UVSSA-USP7-mediated stabilization of ERCC6 is a critical regulatory mechanism of transcription-coupled NER, which removes transcription-blocking DNA damage.
Hao et al. (2015) found that the USP7 deubiquitinating enzyme is an integral component of the MAGEL2 (605283)/TRIM27 (602165) ubiquitin ligase complex and is essential for WASH (613632)-mediated endosomal actin assembly and protein recycling. USP7 acts as a molecular rheostat to fine-tune endosomal F-actin levels by counteracting TRIM27 autoubiquitination and degradation and preventing overactivation of WASH by directly deubiquitinating it. Partial knockdown of USP7 resulted in decreased TRIM27 protein levels, decreased F-actin assembly, and impaired endosomal protein recycling.
Turnbull et al. (2017) reported that 2 compounds, FT671 and FT827, inhibit USP7 with high affinity and specificity in vitro and within human cells. Cocrystal structures revealed that both compounds target a dynamic pocket near the catalytic center of the autoinhibited apo form of USP7, which differs from other USP deubiquitinases. Consistent with USP7 target engagement in cells, FT671 destabilizes USP7 substrates including MDM2, increases levels of p53 (191170), and results in the transcription of p53 target genes, induction of the tumor suppressor p21 (CDKN1A; 116899), and inhibition of tumor growth in mice.
Kategaya et al. (2017) used nuclear magnetic resonance-based screening and structure-based design to develop selective USP7 inhibitors GNE-6640 and GNE-6776. These compounds induced tumor cell death and enhanced cytotoxicity with chemotherapeutic agents and targeted compounds, including PIM kinase (see 164960) inhibitors. Structural studies revealed that GNE-6640 and GNE-6776 noncovalently targeted USP7 12 angstroms distant from the catalytic cysteine. The compounds attenuate ubiquitin binding and thus inhibit USP7 deubiquitinase activity. GNE-6640 and GNE-6776 interact with acidic residues that mediate hydrogen-bond interactions with the ubiquitin lys48 side chain, suggesting that USP7 preferentially interacts with and cleaves ubiquitin moieties that have free lys48 side chains.
By immunoprecipitation and mass spectrometric analysis in HEK293A cells, Manea et al. (2023) identified USP7 as an interacting partner of NGN3 (NEUROG3; 604882). USP7 deubiquitinated and stabilized NGN3 by preventing its proteasomal degradation. Database analysis indicated that USP7 expression preceded NGN3 expression during human pancreas development, similar to its role in murine pancreas development (see ANIMAL MODEL). Moreover, USP7 inhibition impaired beta-cell differentiation in human induced-pluripotent stem cell-derived pancreas organoids, similar to findings in mice with pancreas-specific deletion of Usp7.
Crystal Structure
Hu et al. (2002) reported the crystal structures of the 40-kD catalytic core domain of HAUSP in isolation and in complex with ubiquitin aldehyde. These studies revealed that ubiquitin-specific processing protease (UBP) deubiquitinating enzymes such as HAUSP exhibit a conserved 3-domain architecture, comprising 'fingers,' 'palm,' and 'thumb.' The leaving ubiquitin moiety is specifically coordinated by the fingers, with its C terminus placed in the active site between the palm and the thumb. Binding by ubiquitin aldehyde induces a drastic conformational change in the active site that realigns the catalytic triad residues for catalysis.
Turnbull et al. (2017) determined cocrystal structures of USP7 with the USP7 inhibiting compounds FT671 and FT827 at 2.35- and 2.33-angstrom resolution, respectively. The USP7 catalytic domain adopts the well characterized hand-like structure with thumb, fingers, and palm subdomains, and the compounds bind the inactive apo USP7 in the thumb-palm cleft that guides the ubiquitin C terminus into the active site.
Based on 197 bp of sequence similarity between the HAUSP gene and a genomic clone (GenBank Z94768), Kashuba et al. (1997) tentatively mapped the HAUSP gene to 3p21. By fluorescence in situ hybridization, Robinson et al. (1998) mapped the HAUSP gene to 16p13.3.
In a 13-year-old girl with Hao-Fountain syndrome (HAFOUS; 616863), Hao et al. (2015) identified a de novo heterozygous nonsense mutation in the USP7 gene (Y143X; 602519.0001). Direct functional studies of the variant and studies of patient cells were not performed, but it was predicted to result in haploinsufficiency. However, in vitro knockdown of USP7 in cells resulted in a decrease in TRIM27 (602165) protein levels and impaired endosomal protein recycling with decreased F-actin accumulation.
In 11 patients (patients 10-17, 21-23), including 2 sibs, with HAFOUS, Fountain et al. (2019) identified de novo heterozygous point mutations in the USP7 gene (see, e.g., 602519.0002-602519.0005). The patients were ascertained from several different laboratories or institutions through collaborative efforts, including the USP7-Related Diseases contact page and GeneMatcher, after clinical genome or exome sequencing identified putative pathogenic USP7 mutations. There were 1 nonsense, 2 frameshift, 2 splice site, and 5 missense mutations; the mutations occurred throughout the gene. Three additional patients (patients 18, 19, and 20) with a similar phenotype had de novo missense variants in the USP7 gene, but each had additional genetic variants that may have contributed to the phenotype. Two more patients (patients 7 and 8) had larger de novo heterozygous deletions affecting USP7. Functional studies of the variants and studies of patient cells were not performed, but the authors postulated a loss-of-function effect with haploinsufficiency, since several patients had nonsense, frameshift, or deletion mutations. There were no apparent genotype/phenotype correlations.
Manea et al. (2023) found that mice with conditional pancreas-specific deletion of Usp7 were viable. Mutant mice had reduced body weight compared with wildtype, but they had no significant difference in pancreas/total body weight ratio, and they had reduced endocrine lineage specification and diabetes. The phenotype of mutant mice was due to defective pancreatic development during Ngn3 expression, as Usp7 regulated Ngn3-mediated endocrine formation during development. Consequently, Usp7 loss severely impacted the endocrine compartment in mutant mice, but not the exocrine compartment.
In a 13-year-old girl with Hao-Fountain syndrome (HAFOUS; 616863), Hao et al. (2015) identified a de novo heterozygous c.429C-G transversion in the USP7 gene, resulting in a tyr143-to-ter (Y143X) substitution and predicted to result in haploinsufficiency. Direct functional studies of the variant and studies of patient cells were not performed. However, in vitro knockdown of USP7 in cells resulted in a decrease in TRIM27 (602165) protein levels and impaired endosomal protein recycling with decreased F-actin accumulation.
In a patient (patient 10) with Hao-Fountain syndrome (HAFOUS; 616863), Fountain et al. (2019) identified a de novo heterozygous c.1728T-A transversion (c.1728T-A, NM_003470.2) in the USP7 gene, predicted to result in a cys576-to-ter (C576X) substitution. The mutation was found by clinical exome or genome sequencing. Functional studies of the variant and studies of patient cells were not performed, but the authors postulated a loss-of-function effect and haploinsufficiency as the pathogenetic mechanism.
In a patient (patient 12) with Hao-Fountain syndrome (HAFOUS; 616863), Fountain et al. (2019) identified a de novo heterozygous 2-bp deletion (c.2169_2170delAG, NM_003470.2) in the USP7 gene, predicted to result in a frameshift and premature termination (Arg723fs). The mutation was found by clinical exome or genome sequencing. Functional studies of the variant and studies of patient cells were not performed, but the authors postulated a loss-of-function effect and haploinsufficiency as the pathogenetic mechanism.
In a patient (patient 14) with Hao-Fountain syndrome (HAFOUS; 616863), Fountain et al. (2019) identified a de novo heterozygous c.675G-A transition (c.675G-A, NM_003470.2) in the USP7 gene, resulting in a met225-to-ile (M225I) substitution. The mutation was found by clinical exome or genome sequencing. Functional studies of the variant and studies of patient cells were not performed, but the authors postulated a loss-of-function effect and haploinsufficiency as the pathogenetic mechanism.
In 2 sibs (patients 21 and 22) with Hao-Fountain syndrome (HAFOUS; 616863), Fountain et al. (2019) identified a de novo heterozygous G-to-T transversion in the USP7 gene (c.3202+1G-T, NM_003470.2), predicted to result in a splicing abnormality. The mutation was found by clinical exome or genome sequencing. Functional studies of the variant and studies of patient cells were not performed, but the authors postulated a loss-of-function effect with haploinsufficiency.
Everett, R. D., Meredith, M., Orr, A., Cross, A., Kathoria, M., Parkinson, J. A novel ubiquitin-specific protease is dynamically associated with the PML nuclear domain and binds to a herpesvirus regulatory protein. EMBO J. 16: 1519-1530, 1997. Note: Corrected republication of EMBO J. 16: 566-577, 1997. [PubMed: 9130697] [Full Text: https://doi.org/10.1093/emboj/16.7.1519]
Fountain, M. D., Oleson, D. S., Rech, M. E., Segebrecht, L., Hunter, J. V., McCarthy, J. M., Lupo, P. J., Holtgrewe, M., Moran, R., Rosenfeld, J. A., Isidor, B., Le Caignec, C., and 44 others. Pathogenic variants in USP7 cause a neurodevelopmental disorder with speech delays, altered behavior, and neurologic anomalies. Genet. Med. 21: 1797-1807, 2019. [PubMed: 30679821] [Full Text: https://doi.org/10.1038/s41436-019-0433-1]
Hao, Y.-H., Fountain, M. D., Jr., Fon Tacer, K., Xia, F., Bi, W., Kang, S.-H. L., Patel, A., Rosenfeld, J. A., Le Caignec, C., Isidor, B., Krantz, I. D., Noon, S. E., Pfotenhauer, J. P., Morgan, T. M., Moran, R., Pedersen, R. C., Saenz, M. S., Schaaf, C. P., Potts, P. R. USP7 acts as a molecular rheostat to promote WASH-dependent endosomal protein recycling and is mutated in a human neurodevelopmental disorder. Molec. Cell 59: 956-969, 2015. [PubMed: 26365382] [Full Text: https://doi.org/10.1016/j.molcel.2015.07.033]
Holowaty, M. N., Sheng, Y., Nguyen, T., Arrowsmith, C., Frappier, L. Protein interaction domains of the ubiquitin-specific protease, USP7/HAUSP. J. Biol. Chem. 278: 47753-47761, 2003. [PubMed: 14506283] [Full Text: https://doi.org/10.1074/jbc.M307200200]
Hu, M., Li, P., Li, M., Li, W., Yao, T., Wu, J.-W., Gu, W., Cohen, R. E., Shi, Y. Crystal structure of a UBP-family deubiquitinating enzyme in isolation and in complex with ubiquitin aldehyde. Cell 111: 1041-1054, 2002. [PubMed: 12507430] [Full Text: https://doi.org/10.1016/s0092-8674(02)01199-6]
Kashuba, V. I., Gizatullin, R. Z., Protopopov, A. I., Allikmets, R., Korolev, S., Li, J., Boldog, F., Tory, K., Zabarovska, V., Marcsek, Z., Sumegi, J., Klein, G., Zabarovsky, E. R., Kisselev, L. NotI linking/jumping clones of human chromosome 3: mapping of the TFRC, RAB7 and HAUSP genes to regions rearranged in leukemia and deleted in solid tumors. FEBS Lett. 419: 181-185, 1997. [PubMed: 9428630] [Full Text: https://doi.org/10.1016/s0014-5793(97)01449-x]
Kategaya, L., Di Lello, P., Rouge, L., Pastor, R., Clark, K. R., Drummond, J., Kleinheinz, T., Lin, E., Upton, J.-P., Prakash, S., Heideker, J., McCleland, M., and 32 others. USP7 small-molecule inhibitors interfere with ubiquitin binding. Nature 550: 534-538, 2017. [PubMed: 29045385] [Full Text: https://doi.org/10.1038/nature24006]
Li, M., Chen, D., Shiloh, A., Luo, J., Nikolaev, A. Y., Qin, J., Gu, W. Deubiquitination of p53 by HAUSP is an important pathway for p53 stabilization. Nature 416: 648-653, 2002. [PubMed: 11923872] [Full Text: https://doi.org/10.1038/nature737]
Manea, T., Nelson, J. K., Garrone, C. M., Hansson, K., Evans, I., Behrens, A., Sancho, R. USP7 controls NGN3 stability and pancreatic endocrine lineage development. Nature Commun. 14: 2457, 2023. [PubMed: 37117185] [Full Text: https://doi.org/10.1038/s41467-023-38146-9]
Meulmeester, E., Maurice, M. M., Boutell, C., Teunisse, A. F. A. S., Ovaa, H., Abraham, T. E., Dirks, R. W., Jochemsen, A. G. Loss of HAUSP-mediated deubiquitination contributes to DNA damage-induced destabilization of Hdmx and Hdm2. Molec. Cell 18: 565-576, 2005. Note: Erratum: Molec. Cell 19: 143-144, 2005. [PubMed: 15916963] [Full Text: https://doi.org/10.1016/j.molcel.2005.04.024]
Robinson, P. A., Lomonte, P., Leek, J. P., Markham, A. F., Everett, R. D. Assignment of herpesvirus-associated ubiquitin-specific protease gene HAUSP to human chromosome band 16p13.3 by in situ hybridization. Cytogenet. Cell Genet. 83: 100 only, 1998. [PubMed: 9925944] [Full Text: https://doi.org/10.1159/000015142]
Schwertman, P., Lagarou, A., Dekkers, D. H. W., Raams, A., van der Hoek, A. C., Laffeber, C., Hoeijmakers, J. H. J., Demmers, J. A. A., Fousteri, M., Vermeulen, W., Marteijn, J. A. UV-sensitive syndrome protein UVSSA recruits USP7 to regulate transcription-coupled repair. Nature Genet. 44: 598-602, 2012. [PubMed: 22466611] [Full Text: https://doi.org/10.1038/ng.2230]
Song, M. S., Salmena, L., Carracedo, A., Egia, A., Lo-Coco, F., Teruya-Feldstein, J., Pandolfi, P. P. The deubiquitinylation and localization of PTEN are regulated by a HAUSP-PML network. Nature 455: 813-817, 2008. [PubMed: 18716620] [Full Text: https://doi.org/10.1038/nature07290]
Turnbull, A. P., Ioannidis, S., Krajewski, W. W., Pinto-Fernandez, A., Heride, C., Martin, A. C. L., Tonkin, L. M., Townsend, E. C., Buker, S. M., Lancia, D. R., Caravella, J. A., Toms, A. V., and 31 others. Molecular basis of USP7 inhibition by selective small-molecule inhibitors. Nature 550: 481-486, 2017. [PubMed: 29045389] [Full Text: https://doi.org/10.1038/nature24451]
Zapata, J. M., Pawlowski, K., Haas, E., Ware, C. F., Godzik, A., Reed, J. C. A diverse family of proteins containing tumor necrosis factor receptor-associated factor domains. J. Biol. Chem. 276: 24242-24252, 2001. [PubMed: 11279055] [Full Text: https://doi.org/10.1074/jbc.M100354200]
Zhang, X., Horibata, K., Saijo, M., Ishigami, C., Ukai, A., Kanno, S., Tahara, H., Neilan, E. G., Honma, M., Nohmi, T., Yasui, A., Tanaka, K. Mutations in UVSSA cause UV-sensitive syndrome and destabilize ERCC6 in transcription-coupled DNA repair. Nature Genet. 44: 593-597, 2012. [PubMed: 22466612] [Full Text: https://doi.org/10.1038/ng.2228]