USP8

Summary

USP8 (ubiquitin specific peptidase 8, HGNC:12631) is a protein-coding gene on chromosome 15q21.2, encoding Ubiquitin carboxyl-terminal hydrolase 8 (P40818). Hydrolase that can remove conjugated ubiquitin from proteins and therefore plays an important regulatory role at the level of protein turnover by preventing degradation. It is a selective cancer dependency (DepMap: 85.1% of cell lines).

This gene encodes a protein that belongs to the ubiquitin-specific processing protease family of proteins. The encoded protein is thought to regulate the morphology of the endosome by ubiquitination of proteins on this organelle and is involved in cargo sorting and membrane trafficking at the early endosome stage. This protein is required for the cell to enter the S phase of the cell cycle and also functions as a positive regulator in the Hedgehog signaling pathway in development. Pseudogenes of this gene are present on chromosomes 2 and 6. Alternate splicing results in multiple transcript variants.

Source: NCBI Gene 9101 — RefSeq curated summary.

At a glance

• Gene–disease (curated): hereditary spastic paraplegia (Moderate, GenCC) — +3 more curated relationships
• GWAS associations: 6
• Clinical variants (ClinVar): 184 total — 4 pathogenic
• Phenotypes (HPO): 90
• Druggable target: yes
• Cancer driver (intOGen): activating (oncogene-like) across 3 cancer types
• Cancer dependency (DepMap): dependent in 85.1% of screened cell lines
• MANE Select transcript: NM_005154

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:12631
Approved symbol	USP8
Name	ubiquitin specific peptidase 8
Location	15q21.2
Locus type	gene with protein product
Status	Approved
Aliases	HumORF8, KIAA0055, UBPY, SPG59
Ensembl gene	ENSG00000138592
Ensembl biotype	protein_coding
OMIM	603158
Entrez	9101

Gene structure

Transcript identifiers

Ensembl transcripts: 34 — 22 protein_coding, 4 protein_coding_CDS_not_defined, 4 nonsense_mediated_decay, 3 retained_intron, 1 non_stop_decay

ENST00000307179, ENST00000396444, ENST00000419830, ENST00000425032, ENST00000558091, ENST00000558892, ENST00000559242, ENST00000559329, ENST00000560297, ENST00000560379, ENST00000560527, ENST00000560730, ENST00000560885, ENST00000560954, ENST00000560982, ENST00000561206, ENST00000561211, ENST00000561330, ENST00000882495, ENST00000882496, ENST00000882497, ENST00000919048, ENST00000919049, ENST00000919050, ENST00000919051, ENST00000919052, ENST00000919053, ENST00000956757, ENST00000956758, ENST00000956759, ENST00000956760, ENST00000956761, ENST00000956762, ENST00000956763

RefSeq mRNA: 3 — MANE Select: NM_005154 NM_001128610, NM_001283049, NM_005154

CCDS: CCDS10137, CCDS61632

Canonical transcript exons

ENST00000307179 — 20 exons

Exon	Start	End
ENSE00000931373	50476849	50476993
ENSE00000931375	50481481	50482065
ENSE00000931376	50484275	50484361
ENSE00000931377	50489801	50489881
ENSE00000931378	50490263	50490525
ENSE00000931379	50492701	50492913
ENSE00000931380	50494070	50494280
ENSE00002555209	50498903	50514421
ENSE00003493729	50497089	50497231
ENSE00003527621	50477276	50477499
ENSE00003528983	50459000	50459162
ENSE00003529348	50462280	50462322
ENSE00003532812	50441349	50441493
ENSE00003572398	50465047	50465191
ENSE00003603152	50498596	50498728
ENSE00003631388	50449400	50449485
ENSE00003640783	50471633	50471795
ENSE00003656405	50495848	50496084
ENSE00003682922	50439009	50439177
ENSE00003847028	50424405	50424514

Expression profiles

Bgee: expression breadth ubiquitous, 284 present calls, max score 97.38.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 24.1280 / max 574.1446, expressed in 1804 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
146612	17.9574	1795
146614	4.5560	1527
146613	1.5692	950
146611	0.0453	10

Top tissues by expression

295 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
calcaneal tendon	UBERON:0003701	97.38	gold quality
sural nerve	UBERON:0015488	97.07	gold quality
colonic epithelium	UBERON:0000397	96.49	gold quality
adrenal tissue	UBERON:0018303	96.06	gold quality
ventricular zone	UBERON:0003053	94.89	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	94.14	gold quality
rectum	UBERON:0001052	93.84	gold quality
monocyte	CL:0000576	93.69	gold quality
caput epididymis	UBERON:0004358	93.37	gold quality
mononuclear cell	CL:0000842	93.36	gold quality
leukocyte	CL:0000738	93.21	gold quality
corpus epididymis	UBERON:0004359	92.81	gold quality
gall bladder	UBERON:0002110	92.77	gold quality
islet of Langerhans	UBERON:0000006	92.71	gold quality
stromal cell of endometrium	CL:0002255	92.50	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	92.33	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	92.32	gold quality
cauda epididymis	UBERON:0004360	92.28	gold quality
jejunal mucosa	UBERON:0000399	92.07	gold quality
buccal mucosa cell	CL:0002336	91.79	silver quality
tonsil	UBERON:0002372	91.43	gold quality
popliteal artery	UBERON:0002250	91.25	gold quality
corpus callosum	UBERON:0002336	91.25	gold quality
tibial artery	UBERON:0007610	91.24	gold quality
descending thoracic aorta	UBERON:0002345	91.19	gold quality
endocervix	UBERON:0000458	90.96	gold quality
ganglionic eminence	UBERON:0004023	90.93	gold quality
left adrenal gland	UBERON:0001234	90.91	gold quality
adrenal gland	UBERON:0002369	90.88	gold quality
metanephros cortex	UBERON:0010533	90.88	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	13.08

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

115 targeting USP8, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-4682	100.00	68.89	1258
HSA-MIR-518D-5P	100.00	67.51	979
HSA-MIR-518E-5P	100.00	67.66	954
HSA-MIR-518F-5P	100.00	67.51	979
HSA-MIR-519A-5P	100.00	67.66	954
HSA-MIR-519B-5P	100.00	67.66	954
HSA-MIR-519C-5P	100.00	67.66	954
HSA-MIR-520C-5P	100.00	67.51	979
HSA-MIR-522-5P	100.00	67.66	954
HSA-MIR-523-5P	100.00	67.66	954
HSA-MIR-526A-5P	100.00	67.51	979
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-4789-3P	99.99	70.75	2484
HSA-MIR-520G-5P	99.99	66.76	658
HSA-MIR-19A-3P	99.98	75.33	2762
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-4666A-3P	99.96	71.71	3434
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-3143	99.93	71.96	3104
HSA-MIR-338-5P	99.92	72.34	2951
HSA-MIR-10523-5P	99.91	69.22	2038
HSA-MIR-5680	99.91	69.83	3421
HSA-MIR-454-3P	99.91	74.01	1925

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 85.1% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 40)

• The cellular functions of UBPY are complex but clearly distinct from those of the Lys-63-ubiquitin-specific protease, AMSH, with which it shares a binding site on the SH3 domain of STAM (PMID:16520378)
• UBPY regulates the level of protein ubiquitination on endosomes, which is required for maintaining the morphology of the organelle (PMID:16771824)
• The USP8 recognition domain of NRDP1 has a novel protein fold that interacts with a conserved peptide loop of the rhodanese domain. (PMID:17035239)
• UBPY-mediated EGFR de-ubiquitination promotes EGFR degradation (PMID:17121848)
• UBPY MIT domain and another ubiquitin isopeptidase, AMSH, reveals common interactions with CHMP1A and CHMP1B but a distinct selectivity of AMSH for CHMP3/VPS24, a core subunit of the ESCRT-III complex, and UBPY for CHMP7. (PMID:17711858)
• Data suggest that AMSH and UBPY are essential for trafficking and down-regulation of PAR(2) but not for regulating PAR(2) dissociation from beta-arrestin2 or PAR(2)-mediated ERK2 activation. (PMID:19684015)
• USP8 promotes trafficking and degradation of CXCR4 at the sorting endosome. (PMID:20876529)
• Studies indicate that USP8/Ubpy and AMSH interact with ESCRT components to modulate the ubiquitination status of receptors and relevant sorting proteins. (PMID:21448666)
• USP8 is a positive regulator in Hh signaling by down-regulating Smo ubiquitination and thereby mediating Smo intracellular trafficking. (PMID:22253573)
• a UBPY-derived peptide can outcompete ubiquitin for STAM2 SH3 domain binding (PMID:22841719)
• Ubiquitin-specific peptidase 8 (USP8) regulates endosomal trafficking of the epithelial Na+ channel (PMID:23297398)
• Usp8 is a target for SRC-mediated tyrosine phosphorylation in the N-terminal 504 amino acids upon EGF stimulation of EGFR. (PMID:23333852)
• The ESCRT accessory protein HD-PTP/PTPN23 associates with epidermal growth factor receptor (EGFR) and combines with the deubiquitinating enzyme UBPY/USP8 to transfer EGFR from ESCRT-0 to ESCRT-III and drive EGFR sorting to intralumenal vesicles. (PMID:23477725)
• Knockdown of ubiquitin-specific peptidase 8 (USP8) selectively kills gefitinib-resistant non-small lung cancer cells. (PMID:23748694)
• Balanced reciprocal cross-regulation of RNF41 and USP8 determines whether receptors are sorted for lysosomal degradation or recycling, this way regulating basal cytokine receptor levels. (PMID:23750007)
• No relationship was found in serum XIAP and USP8 levels with clinical parameters, response to chemotherapy, and survival in patients with advanced stages of non-small cell lung cancer. (PMID:24344018)
• USP8 maintains a basal expression of HIF1alpha and HIF transcriptional output in normoxia. (PMID:24378640)
• UBE2E3 and UBPY participate in the regulation of TDP-43 ubiquitination, solubility, and neurodegeneration (PMID:24825905)
• USP8 is involved in deubiquitination of LRIG1, influencing the efficiency of Met degradation. (PMID:24828152)
• USP8 is required for ci-M6PR endosomal localisation. (PMID:24894536)
• USP8, and the endosomal sorting protein, VPS28, are the negative regulators of NOD2-induced IL-8 secretion. (PMID:25170077)
• This work uncovers a novel role for USP8-mediated deubiquitination of K6-linked ubiquitin conjugates from parkin in mitochondrial quality control. (PMID:25216678)
• Somatic USP8 mutations in corticotroph adenomas clustered in the 14-3-3 protein binding motif and enhanced catalysis and proteolytic cleavage, which increased EGF receptor deubiqutination and signaling. USP8 mutants enhanced POMC promoter activity. (PMID:25485838)
• In surgically resected primary USP8-mutated tumor cells, USP8 knockdown or blocking EGFR effectively attenuates ACTH secretion. Inhibition of USP8 or EGFR is promising for treating USP8-mutated corticotrophin adenoma. (PMID:25675982)
• these findings implicate a novel role for K6-linked Ub conjugates and USP8-mediated deubiquitination in the regulation of PARK2 in mitochondrial quality control (PMID:25700639)
• BRUCE acts as a scaffold, bridging the ubiquitin-specific peptidase 8 (USP8) and BRIT1 in a complex to coordinate USP8-catalyzed deubiquitination of BRIT1. (PMID:25733871)
• Haplotype CAAG may be a down-regulating factor for the risk of non-obstructive azoospermia. (PMID:25863102)
• The identification of USP8 mutations as contributors to the pathogenesis of ACTH-secreting pituitary adenomas represents an exciting advance in our understanding of Cushing’s disease and its potential treatment into the of precision medicine. (PMID:25930709)
• USP8 is frequently mutated in adenomas causing Cushing’s disease, especially in those from female adult patients diagnosed at a younger age. (PMID:25942478)
• Studies indicate that ubiquitin specific protease 8 protein (USP8) mutations contribute to adrenocorticotropic hormone (ACTH) overproduction in Cushing’s disease (CD). (PMID:26285834)
• USP8 regulates VEGFR2 trafficking, signaling and proteolysis. (PMID:26459808)
• Ubpy loss of function results in the accumulation of autophagosomes due to a blockade of the autophagy flux. (PMID:26571504)
• The presence of USP8 mutations may predict favorable responses to the somatostatin analog pasireotide in corticotroph adenomas of Cushing’s disease. (PMID:26578638)
• Results show that in addition to the scaffolding function in complex formation, BRUCE has an E3 ligase function to promote BRIT1 deubiquitination by USP8 leading to accumulation of BRIT1 at DNA double-strand break. (PMID:26683461)
• No somatic mutations were observed in USP8 in a cohort of GH-secreting pituitary adenomas. (PMID:26701869)
• findings demonstrate that USP8 plays a key role in the trafficking and degradation of BACE1 by deubiquitinating lysine 501. (PMID:27302062)
• Data indicate that USP8 functions as a novel deubiquitylase of FLIPL and inhibits extrinsic apoptosis by stabilizing FLIPL. (PMID:27321185)
• in human cells, Usp8 knockdown increased the lysosomal degradation of alpha-synuclein. (PMID:27444016)
• Somatic USP8 gene mutations are a common cause of pediatric Cushing disease due to pituitary adenoma. (PMID:28505279)
• Overexpression of USP8 in lung adenocarcinoma is an early event during the course of tumor progression, and is related to EGFR expression. (PMID:28544031)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	usp8	ENSDARG00000063719
mus_musculus	Usp8	ENSMUSG00000027363
rattus_norvegicus	Usp8	ENSRNOG00000010729
drosophila_melanogaster	Usp8	FBGN0038862

Paralogs (71): USP2 (ENSG00000036672), USP28 (ENSG00000048028), USP36 (ENSG00000055483), USP13 (ENSG00000058056), USP33 (ENSG00000077254), USP40 (ENSG00000085982), USP48 (ENSG00000090686), USP14 (ENSG00000101557), USP11 (ENSG00000102226), USP10 (ENSG00000103194), USP31 (ENSG00000103404), USP42 (ENSG00000106346), USP5 (ENSG00000111667), USP4 (ENSG00000114316), USP9Y (ENSG00000114374), USP34 (ENSG00000115464), USP35 (ENSG00000118369), USP45 (ENSG00000123552), USP22 (ENSG00000124422), USP9X (ENSG00000124486), USP6 (ENSG00000129204), USP29 (ENSG00000131864), USP26 (ENSG00000134588), USP30 (ENSG00000135093), USP15 (ENSG00000135655), USP37 (ENSG00000135913), USP44 (ENSG00000136014), USP20 (ENSG00000136878), USP3 (ENSG00000140455), USP21 (ENSG00000143258), USP43 (ENSG00000154914), USP25 (ENSG00000155313), USP16 (ENSG00000156256), USP24 (ENSG00000162402), USP1 (ENSG00000162607), USP49 (ENSG00000164663), USP38 (ENSG00000170185), USP50 (ENSG00000170236), USP47 (ENSG00000170242), USP32 (ENSG00000170832)

Protein

Protein identifiers

Ubiquitin carboxyl-terminal hydrolase 8 — P40818 (reviewed: P40818)

Alternative names: Deubiquitinating enzyme 8, Ubiquitin isopeptidase Y, Ubiquitin thioesterase 8, Ubiquitin-specific-processing protease 8

All UniProt accessions (8): P40818, A0A075B720, H0YKV1, H0YLH2, H0YLS3, H0YM17, H0YM47, H0YNL5

UniProt curated annotations — full annotation on UniProt →

Function. Hydrolase that can remove conjugated ubiquitin from proteins and therefore plays an important regulatory role at the level of protein turnover by preventing degradation. Converts both ‘Lys-48’ an ‘Lys-63’-linked ubiquitin chains. Catalytic activity is enhanced in the M phase. Involved in cell proliferation. Required to enter into S phase in response to serum stimulation. May regulate T-cell anergy mediated by RNF128 via the formation of a complex containing RNF128 and OTUB1. Probably regulates the stability of STAM2 and RASGRF1. Regulates endosomal ubiquitin dynamics, cargo sorting, membrane traffic at early endosomes, and maintenance of ESCRT-0 stability. The level of protein ubiquitination on endosomes is essential for maintaining the morphology of the organelle. Deubiquitinates EPS15 and controls tyrosine kinase stability. Removes conjugated ubiquitin from EGFR thus regulating EGFR degradation and downstream MAPK signaling. Involved in acrosome biogenesis through interaction with the spermatid ESCRT-0 complex and microtubules. Deubiquitinates BIRC6/bruce and KIF23/MKLP1. Deubiquitinates BACE1 which inhibits BACE1 lysosomal degradation and modulates BACE-mediated APP cleavage and amyloid-beta formation.

Subunit / interactions. Forms a ternary complex with RNF128 and OTUB1. Interacts (via C-terminal UCH catalytic domain) with OTUB1 isoform 1. Interacts with STAM2 (via SH3 domain). Interacts with DNAJB3, EGFR, EPS15, RASGRF1, RNF41, YWHAE, YWHAG and YWHAZ. Interacts with NBR1, RASGRF1, RNF41 and IST1. Associates with the ESCRT-0 complex and with microtubules. Interacts with BIRC6/bruce and KIF23/MKLP1. (Microbial infection) Interacts with Zika virus non-structural protein 1.

Subcellular location. Cytoplasm. Nucleus. Endosome membrane. Cell membrane.

Post-translational modifications. Phosphorylation of Ser-718 is essential for interaction with YWHAE and for cytosol localization. Undergoes dephosphorylation at Ser-718 in the M phase. Tyrosine-phosphorylated in its N-terminal half in an EGFR-dependent manner. Ubiquitinated. Inactive form is mostly monoubiquitinated, but polyubiquitination happens too. Ubiquitination is increased in EGF-stimulated cells. Ubiquitination of active form is undetectable, suggesting a possibility that USP8 deubiquitinates itself, thereby regulating its own function.

Disease relevance. Pituitary adenoma 4, ACTH-secreting (PITA4) [MIM:219090] A form of pituitary adenoma, a neoplasm of the pituitary gland and one of the most common neuroendocrine tumors. Pituitary adenomas are clinically classified as functional and non-functional tumors, and manifest with a variety of features, including local invasion of surrounding structures and excessive hormone secretion. Functional pituitary adenomas are further classified by the type of hormone they secrete. PITA4 results in excessive production of adrenocorticotropic hormone. This leads to hypersecretion of cortisol by the adrenal glands and ACTH-dependent Cushing syndrome. Clinical manifestations of Cushing syndrome include facial and truncal obesity, abdominal striae, muscular weakness, osteoporosis, arterial hypertension, diabetes. The disease is caused by variants affecting the gene represented in this entry.

Domain organisation. The MIT domain is required for endosomal localization, CHMP1B-binding, maintenance of ESCRT-0 stability and EGFR degradation. The rhodanese domain is sufficient for RNF41-binding.

Induction. Upon growth stimulation in starved human fibroblasts. Decreases in response to growth arrest induced by cell-cell contact.

Similarity. Belongs to the peptidase C19 family.

Isoforms (2)

UniProt ID	Names	Canonical?
P40818-1	1	yes
P40818-2	2

RefSeq proteins (3): NP_001122082, NP_001269978, NP_005145* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001394	Peptidase_C19_UCH	Domain
IPR001763	Rhodanese-like_dom	Domain
IPR015063	USP8_dimer	Domain
IPR018200	USP_CS	Conserved_site
IPR028889	USP	Domain
IPR036873	Rhodanese-like_dom_sf	Homologous_superfamily
IPR038765	Papain-like_cys_pep_sf	Homologous_superfamily
IPR048498	WW_USP8	Domain
IPR050185	Ub_carboxyl-term_hydrolase	Family

Pfam: PF00443, PF00581, PF08969, PF20625

Enzyme classification (BRENDA):

• EC 3.4.19.12 — ubiquitinyl hydrolase 1 (BRENDA: 30 organisms, 328 substrates, 173 inhibitors, 70 Km, 58 kcat entries)

Substrate kinetics (BRENDA)

29 substrates with measured Km, best-characterized 15. Km ranges are aggregated across organisms/conditions.

Substrate	Km (mM)	Measurements
UBIQUITIN-7-AMIDO-4-METHYLCOUMARIN	—	7
DABCYL-FKKKGGGDVKE-EDANS	0.0142–0.0616	6
UBIQUITIN 7-AMIDO-4-METHYLCOUMARIN	—	5
UBIQUITIN ETHYL ESTER	0.0006–0.03	5
DABCYL-FRLKGGAPIKGV-EDANS	0.0048–0.0217	3
UBIQUITIN-W-G75A	0.0001–0.0004	2
UBIQUITIN-W-G76A	0.0011–0.002	2
UBIQUITIN-W-H68A	0.0005	2
UBIQUITIN-W-I44A	0.0003–0.0004	2
UBIQUITIN-W-K11A	0.0011–0.0023	2
UBIQUITIN-W-K48A	0.0003–0.0007	2
UBIQUITIN-W-K63A	0.0004–0.0008	2
UBIQUITIN-W-K6A	0.0009–0.0014	2
UBIQUITIN-W-L71A	0.008–0.0198	2
UBIQUITIN-W-L73A	0.0058–0.0104	2

UniProt features (103 total): helix 31, strand 25, sequence variant 9, modified residue 8, turn 7, compositionally biased region 6, region of interest 4, domain 3, sequence conflict 3, active site 2, splice variant 2, chain 1, mutagenesis site 1, short sequence motif 1

Structure

Experimental structures (PDB)

9 structures.

PDB	Method	Resolution (Å)
6F09	X-RAY DIFFRACTION	1.59
8ADM	X-RAY DIFFRACTION	1.7
2GFO	X-RAY DIFFRACTION	2
2A9U	X-RAY DIFFRACTION	2.1
8XPN	X-RAY DIFFRACTION	2.1
2GWF	X-RAY DIFFRACTION	2.3
3N3K	X-RAY DIFFRACTION	2.6
8Y9A	X-RAY DIFFRACTION	3.1
1WHB	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P40818-F1	71.98	0.37

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (2): 786 (nucleophile); 1067 (proton acceptor)

Post-translational modifications (8): 160, 392, 400, 452, 577, 718, 719, 945

Mutagenesis-validated functional residues (1):

Position	Phenotype
786	impairs deubiquitination activity and leads to endosome membrane accumulation.

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

ID	Pathway
R-HSA-1358803	Downregulation of ERBB2:ERBB3 signaling
R-HSA-4641263	Regulation of FZD by ubiquitination
R-HSA-5689880	Ub-specific processing proteases
R-HSA-6807004	Negative regulation of MET activity

MSigDB gene sets: 436 (showing top): GOBP_MITOTIC_CYTOKINESIS, YAGI_AML_WITH_INV_16_TRANSLOCATION, GOBP_ENDOSOME_ORGANIZATION, RORA1_01, GOBP_CELLULAR_RESPONSE_TO_LIPID, GOCC_SECRETORY_GRANULE, GOBP_RESPONSE_TO_CORTICOSTEROID, GOBP_VESICLE_ORGANIZATION, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GOBP_REGULATION_OF_WNT_SIGNALING_PATHWAY, WONG_PROTEASOME_GENE_MODULE, GOBP_CELLULAR_RESPONSE_TO_OXYGEN_CONTAINING_COMPOUND, GOBP_PROTEIN_MODIFICATION_BY_SMALL_PROTEIN_REMOVAL, GOBP_NEGATIVE_REGULATION_OF_PROTEIN_CATABOLIC_PROCESS, GOBP_CELL_CELL_SIGNALING

GO Biological Process (15): mitotic cytokinesis (GO:0000281), proteolysis (GO:0006508), endosome organization (GO:0007032), Ras protein signal transduction (GO:0007265), protein deubiquitination (GO:0016579), regulation of protein stability (GO:0031647), regulation of protein localization (GO:0032880), protein K63-linked deubiquitination (GO:0070536), protein K48-linked deubiquitination (GO:0071108), cellular response to dexamethasone stimulus (GO:0071549), positive regulation of canonical Wnt signaling pathway (GO:0090263), regulation of protein catabolic process at postsynapse, modulating synaptic transmission (GO:0099576), negative regulation of lysosomal protein catabolic process (GO:1905166), positive regulation of amyloid fibril formation (GO:1905908), cellular response to nerve growth factor stimulus (GO:1990090)

GO Molecular Function (10): cysteine-type endopeptidase activity (GO:0004197), cysteine-type deubiquitinase activity (GO:0004843), SH3 domain binding (GO:0017124), cadherin binding (GO:0045296), K63-linked deubiquitinase activity (GO:0061578), K48-linked deubiquitinase activity (GO:1990380), protein binding (GO:0005515), peptidase activity (GO:0008233), cysteine-type peptidase activity (GO:0008234), hydrolase activity (GO:0016787)

GO Cellular Component (12): acrosomal membrane (GO:0002080), nucleus (GO:0005634), cytoplasm (GO:0005737), early endosome (GO:0005769), cytosol (GO:0005829), plasma membrane (GO:0005886), endosome membrane (GO:0010008), postsynaptic density (GO:0014069), midbody (GO:0030496), glutamatergic synapse (GO:0098978), endosome (GO:0005768), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-4 pathways:

Category	Pathways
Downregulation of ERBB2 signaling	1
TCF dependent signaling in response to WNT	1
Deubiquitination	1
Signaling by MET	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	4
deubiquitinase activity	3
protein deubiquitination	2
cysteine-type peptidase activity	2
endosome	2
mitotic cell cycle	1
cytoskeleton-dependent cytokinesis	1
mitotic cell cycle process	1
protein metabolic process	1
endomembrane system organization	1
vesicle organization	1
small GTPase-mediated signal transduction	1
cysteine-type deubiquitinase activity	1
protein modification by small protein removal	1
regulation of biological quality	1
intracellular protein localization	1
regulation of localization	1
cellular response to glucocorticoid stimulus	1
response to dexamethasone	1
cellular response to ketone	1
positive regulation of Wnt signaling pathway	1
canonical Wnt signaling pathway	1
regulation of canonical Wnt signaling pathway	1
chemical synaptic transmission	1
regulation of protein catabolic process	1
postsynapse	1
postsynaptic modulation of chemical synaptic transmission	1
negative regulation of protein catabolic process in the vacuole	1
lysosomal protein catabolic process	1
regulation of lysosomal protein catabolic process	1
positive regulation of protein metabolic process	1
positive regulation of supramolecular fiber organization	1
regulation of amyloid fibril formation	1
amyloid fibril formation	1
cellular response to growth factor stimulus	1
response to nerve growth factor	1
endopeptidase activity	1
protein domain specific binding	1
cell adhesion molecule binding	1
binding	1

Protein interactions and networks

STRING

2298 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
USP8	RNF41	Q9H4P4	992
USP8	OTUB1	Q96FW1	921
USP8	STAM2	O75886	913
USP8	ZUP1	Q96AP4	885
USP8	STAMBP	O95630	824
USP8	QTRT1	Q9BXR0	769
USP8	USP28	Q96RU2	752
USP8	PIK3R2	O00459	746
USP8	STAM	Q92783	727
USP8	BIRC6	Q9NR09	722
USP8	RNF128	Q8TEB7	721
USP8	NTRK1	P04629	714
USP8	CHMP1A	Q9HD42	713
USP8	OTUB2	Q96DC9	705
USP8	GRAP2	O75791	703

IntAct

128 interactions, top by confidence:

A	B	Type	Score
YWHAZ	USP8	psi-mi:“MI:0915”(physical association)	0.900
YWHAB	USP8	psi-mi:“MI:0915”(physical association)	0.900
USP8	YWHAZ	psi-mi:“MI:0915”(physical association)	0.900
USP8	YWHAQ	psi-mi:“MI:0915”(physical association)	0.870
USP8	YWHAG	psi-mi:“MI:0915”(physical association)	0.830
GRAP2	STAMBP	psi-mi:“MI:0914”(association)	0.810
YWHAH	ABLIM1	psi-mi:“MI:0914”(association)	0.800
YWHAB	WDR62	psi-mi:“MI:0914”(association)	0.770
USP8	Grap2	psi-mi:“MI:0407”(direct interaction)	0.750
Grap2	USP8	psi-mi:“MI:0915”(physical association)	0.750
Grap2	USP8	psi-mi:“MI:0407”(direct interaction)	0.750
USP8	CHMP1B	psi-mi:“MI:0915”(physical association)	0.700
CHMP1B	USP8	psi-mi:“MI:0915”(physical association)	0.700
USP8	CHMP1B	psi-mi:“MI:0407”(direct interaction)	0.700
USP8	CHMP1A	psi-mi:“MI:0915”(physical association)	0.670
CHMP1A	USP8	psi-mi:“MI:0915”(physical association)	0.670
USP8	CHMP1A	psi-mi:“MI:0407”(direct interaction)	0.670
YWHAG	BLTP3B	psi-mi:“MI:0914”(association)	0.640
YWHAG	BLTP3B	psi-mi:“MI:2364”(proximity)	0.640
SFN	USP8	psi-mi:“MI:0915”(physical association)	0.630
USP8		psi-mi:“MI:0204”(deubiquitination reaction)	0.620
	USP8	psi-mi:“MI:0204”(deubiquitination reaction)	0.620
YWHAH	PLEKHG3	psi-mi:“MI:0914”(association)	0.610
CHMP4C	USP8	psi-mi:“MI:0915”(physical association)	0.610
YWHAB	BLTP3B	psi-mi:“MI:2364”(proximity)	0.610

BioGRID (311): PLA2G2A (Biochemical Activity), UBC (Biochemical Activity), USP8 (Affinity Capture-Western), USP8 (Affinity Capture-Western), SCNN1B (Affinity Capture-Western), SCNN1G (Affinity Capture-Western), EPS15 (Biochemical Activity), UBC (Co-crystal Structure), Rasgrf1 (Affinity Capture-Western), USP8 (Affinity Capture-MS), USP8 (Affinity Capture-Western), BIRC6 (Affinity Capture-Western), MCPH1 (Affinity Capture-Western), USP8 (Affinity Capture-Western), MCPH1 (Co-localization)

ESM2 similar proteins: A0A0R4IXF6, A1A5R8, A9ZLX4, D3YXJ0, E9PUQ8, G3UZ78, O00750, O15164, O54828, P30052, P40818, P48984, P52963, P59997, P97496, Q02225, Q08AX9, Q08BR4, Q08D35, Q16760, Q1LUC3, Q2I6J1, Q3UWM4, Q498F0, Q5JSH3, Q5JTW2, Q5RHD1, Q60665, Q64398, Q68FF0, Q6INA9, Q6NSI8, Q6NVE8, Q6PDG5, Q6ZMT4, Q7ZVP1, Q80U87, Q86XP1, Q8C5W4, Q8N7X0

Diamond homologs: A0A0R4IB93, A1CIL1, A1CW53, A2Q9N1, A4FUN7, A5D9H7, A5PJS6, A5WWB0, A6QR55, B0Y4P5, B2GUZ1, B3LGK1, B8NSV5, C0HB46, D0RB01, E2RK09, E7F6T8, E9Q9U0, F1M625, F1N5V1, G5E8G2, G5E8I7, O22207, O24454, O57429, O60079, O75317, O94966, P34547, P35123, P35125, P38187, P39967, P40818, P50102, P51784, P52479, P62068, P62069, Q01988

SIGNOR signaling

11 interactions.

A	Effect	B	Mechanism
USP8	“up-regulates quantity by stabilization”	BACE1	deubiquitination
USP8	“up-regulates quantity by stabilization”	EGFR	deubiquitination
USP8	“up-regulates quantity by stabilization”	RNF41	deubiquitination
RNF41	“down-regulates quantity by destabilization”	USP8	ubiquitination
USP8	“down-regulates quantity”	EGFR	destabilization
USP8	“down-regulates quantity”	MET	destabilization
USP8	“up-regulates quantity”	STAM	binding
USP8	“up-regulates quantity”	BACE1	deubiquitination
EGFR	“up-regulates activity”	USP8	phosphorylation

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 88 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Activation of BAD and translocation to mitochondria	7	87.4×	1e-10
Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex	7	77.1×	2e-10
SARS-CoV-1 targets host intracellular signalling and regulatory pathways	7	77.1×	2e-10
Activation of BH3-only proteins	7	57.0×	1e-09
Budding and maturation of HIV virion	7	46.8×	5e-09
Endosomal Sorting Complex Required For Transport (ESCRT)	7	42.3×	9e-09
Pyroptosis	6	41.6×	1e-07
Sealing of the nuclear envelope (NE) by ESCRT-III	7	39.7×	1e-08

GO biological processes:

GO term	Partners	Fold	FDR
nuclear membrane reassembly	9	114.4×	2e-15
late endosome to lysosome transport	9	114.4×	2e-15
midbody abscission	10	93.9×	6e-16
viral budding via host ESCRT complex	9	92.6×	2e-14
multivesicular body sorting pathway	9	92.6×	2e-14
regulation of mitotic spindle assembly	9	84.5×	4e-14
regulation of centrosome duplication	8	75.2×	4e-12
multivesicular body assembly	10	67.5×	2e-14

Disease & clinical

Cancer significance

From intOGen — cancer-driver classification: activating (oncogene-like) across 3 cancer types — HCC, LUSC, PCM.

Clinical variants and AI predictions

ClinVar

184 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	4
Likely pathogenic	0
Uncertain significance	79
Likely benign	53
Benign	23

Top pathogenic / likely-pathogenic (4)

Variant ID	HGVS	Classification
161991	NM_005154.5(USP8):c.2152TCC[1] (p.Ser719del)	Pathogenic
161992	NM_005154.5(USP8):c.2152T>C (p.Ser718Pro)	Pathogenic
161993	NM_005154.5(USP8):c.2153C>G (p.Ser718Cys)	Pathogenic
161995	NM_005154.5(USP8):c.2159C>G (p.Pro720Arg)	Pathogenic

SpliceAI

3587 predictions. Top by Δscore:

Variant	Effect	Δscore
15:50439001:T:TA	acceptor_gain	1.0000
15:50439003:TTTCA:T	acceptor_loss	1.0000
15:50439004:TTCA:T	acceptor_loss	1.0000
15:50439005:TCA:T	acceptor_loss	1.0000
15:50439006:CA:C	acceptor_loss	1.0000
15:50439007:A:AG	acceptor_gain	1.0000
15:50439007:AG:A	acceptor_gain	1.0000
15:50439008:G:GA	acceptor_gain	1.0000
15:50439008:G:T	acceptor_loss	1.0000
15:50439008:GG:G	acceptor_gain	1.0000
15:50439008:GGAAA:G	acceptor_gain	1.0000
15:50439174:AGAG:A	donor_loss	1.0000
15:50439175:GAG:G	donor_gain	1.0000
15:50439176:AGG:A	donor_loss	1.0000
15:50439177:GGT:G	donor_loss	1.0000
15:50439178:G:GA	donor_loss	1.0000
15:50441340:A:AG	acceptor_gain	1.0000
15:50441346:A:AG	acceptor_gain	1.0000
15:50441347:A:G	acceptor_gain	1.0000
15:50441348:G:GG	acceptor_gain	1.0000
15:50441348:GT:G	acceptor_gain	1.0000
15:50441348:GTT:G	acceptor_gain	1.0000
15:50441348:GTTA:G	acceptor_gain	1.0000
15:50441348:GTTAT:G	acceptor_gain	1.0000
15:50441414:A:T	donor_gain	1.0000
15:50441418:GGCC:G	donor_gain	1.0000
15:50441489:AGCAG:A	donor_loss	1.0000
15:50441490:GCAG:G	donor_gain	1.0000
15:50441490:GCAGG:G	donor_loss	1.0000
15:50441491:CAG:C	donor_loss	1.0000

AlphaMissense

7368 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
15:50489873:T:A	W655R	1.000
15:50489873:T:C	W655R	1.000
15:50490293:T:G	Y668D	1.000
15:50492802:T:C	L779P	1.000
15:50492809:C:A	N781K	1.000
15:50492809:C:G	N781K	1.000
15:50492818:T:A	N784K	1.000
15:50492818:T:G	N784K	1.000
15:50492822:T:C	C786R	1.000
15:50492823:G:A	C786Y	1.000
15:50492824:T:G	C786W	1.000
15:50492833:C:A	N789K	1.000
15:50492833:C:G	N789K	1.000
15:50494224:G:C	D868H	1.000
15:50494225:A:C	D868A	1.000
15:50494225:A:T	D868V	1.000
15:50494249:T:C	L876P	1.000
15:50494254:G:C	D878H	1.000
15:50494255:A:T	D878V	1.000
15:50494261:T:C	L880P	1.000
15:50494269:G:C	D883H	1.000
15:50494273:T:C	L884P	1.000
15:50495948:C:T	S920F	1.000
15:50495971:G:C	G928R	1.000
15:50495972:G:A	G928D	1.000
15:50495982:A:C	K931N	1.000
15:50495982:A:T	K931N	1.000
15:50495983:T:C	S932P	1.000
15:50495995:T:A	C936S	1.000
15:50495995:T:C	C936R	1.000

dbSNP variants (sampled 300 via entrez): RS1000026126 (15:50442153 T>G), RS1000040659 (15:50461775 C>G,T), RS1000086580 (15:50443538 C>T), RS1000087294 (15:50448794 A>G), RS1000094384 (15:50493159 G>A,C,T), RS1000135239 (15:50499683 A>G), RS1000169749 (15:50497998 A>G), RS1000181642 (15:50448528 T>A), RS1000193660 (15:50493242 A>G), RS1000224488 (15:50493627 C>G), RS1000250720 (15:50444899 A>G), RS1000343804 (15:50445114 A>G), RS1000368022 (15:50479238 G>A,T), RS1000384895 (15:50499387 T>C), RS1000457550 (15:50438890 A>G)

Disease associations

OMIM: gene MIM:603158 | disease phenotypes: MIM:303350, MIM:219090

GenCC curated gene-disease

Disease	Classification	Inheritance
hereditary spastic paraplegia	Moderate	Autosomal recessive
autosomal recessive spastic paraplegia type 59	Supportive	Autosomal recessive
complex neurodevelopmental disorder	Limited	Autosomal dominant
genetic developmental and epileptic encephalopathy	Limited	Autosomal dominant

Mondo (5): hereditary spastic paraplegia (MONDO:0019064), Cushing disease due to pituitary adenoma (MONDO:0009050), autosomal recessive spastic paraplegia type 59 (MONDO:0018416), complex neurodevelopmental disorder (MONDO:0100038), genetic developmental and epileptic encephalopathy (MONDO:0100062)

Orphanet (3): Hereditary spastic paraplegia (Orphanet:685), Cushing disease (Orphanet:96253), Autosomal recessive spastic paraplegia type 59 (Orphanet:401795)

HPO phenotypes

90 total (30 of 90 shown, HPO-id order):

HPO	Term
HP:0000006	Autosomal dominant inheritance
HP:0000007	Autosomal recessive inheritance
HP:0000141	Amenorrhea
HP:0000639	Nystagmus
HP:0000708	Atypical behavior
HP:0000709	Psychosis
HP:0000712	Emotional lability
HP:0000716	Depression
HP:0000725	Psychotic episodes
HP:0000726	Dementia
HP:0000787	Nephrolithiasis
HP:0000819	Diabetes mellitus
HP:0000822	Hypertension
HP:0000869	Secondary amenorrhea
HP:0000876	Oligomenorrhea
HP:0000939	Osteoporosis
HP:0000953	Hyperpigmentation of the skin
HP:0000963	Thin skin
HP:0000969	Edema
HP:0000978	Bruising susceptibility
HP:0000979	Purpura
HP:0001007	Hirsutism
HP:0001041	Facial erythema
HP:0001050	Plethora
HP:0001058	Poor wound healing
HP:0001061	Acne
HP:0001065	Striae distensae
HP:0001123	Visual field defect
HP:0001249	Intellectual disability
HP:0001258	Spastic paraplegia

GWAS associations

6 associations (top):

Study	Trait	p-value
GCST006979_1020	Heel bone mineral density	1.000000e-17
GCST007844_3	Ankylosing spondylitis	1.000000e-13
GCST010796_1577	Electrocardiogram morphology (amplitude at temporal datapoints)	2.000000e-08
GCST010796_1578	Electrocardiogram morphology (amplitude at temporal datapoints)	3.000000e-08
GCST90002394_491	Monocyte percentage of white cells	3.000000e-14
GCST90002396_632	Mean reticulocyte volume	7.000000e-10

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0009270	heel bone mineral density
EFO:0004327	electrocardiography
EFO:0007989	monocyte percentage of leukocytes
EFO:0010701	mean reticulocyte volume

MeSH disease descriptors (2)

Descriptor	Name	Tree numbers
D049913	ACTH-Secreting Pituitary Adenoma	C04.557.470.035.012; C04.588.322.609.145; C10.228.140.617.738.675.149; C19.344.609.145; C19.700.734.145
D015419	Spastic Paraplegia, Hereditary	C10.500.300.820; C10.574.500.495.820; C10.668.829.800.300.820; C16.131.666.300.820; C16.320.400.375.820

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (2): CHEMBL2157854 (SINGLE PROTEIN), CHEMBL4742277 (PROTEIN-PROTEIN INTERACTION)

PharmGKB: 1 entry (VIP=true, CPIC=false)

GtoPdb / IUPHAR curated pharmacology

(IUPHAR/BPS Guide to Pharmacology — expert-curated)

Target class: enzyme — C19: Ubiquitin-specific protease

Most potent curated ligand interactions (1 total), top 1:

Ligand	Action	Affinity	Parameter
compound 61 [PMID: 36221183]	Inhibition	9.55	pIC50

ChEMBL bioactivities

55 potent at pChembl≥5 of 88 total, top 48 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
9.55	IC50	0.28	nM	CHEMBL5185273
8.90	IC50	1.27	nM	CHEMBL5196686
8.70	IC50	2	nM	CHEMBL5173239
8.57	IC50	2.7	nM	CHEMBL5172138
7.02	IC50	96	nM	CHEMBL2398212
6.88	IC50	133	nM	CHEMBL3407548
6.60	IC50	250	nM	CHEMBL5281075
6.55	IC50	280	nM	CHEMBL5180195
6.55	IC50	280	nM	CHEMBL5532263
6.54	IC50	290	nM	CHEMBL5170305
6.54	IC50	290	nM	CHEMBL4569978
6.50	IC50	316	nM	CHEMBL5269711
6.28	IC50	520	nM	CHEMBL5523555
6.25	IC50	560	nM	CHEMBL5202404
6.15	IC50	710	nM	CHEMBL5276040
6.09	IC50	810	nM	CHEMBL4515695
6.07	IC50	850	nM	CHEMBL5208383
6.07	IC50	850	nM	CHEMBL5723334
6.03	IC50	930	nM	CHEMBL4584162
6.02	IC50	960	nM	CHEMBL2398212
6.02	IC50	950	nM	CHEMBL3392741
5.92	IC50	1200	nM	CHEMBL5184337
5.92	IC50	1200	nM	CHEMBL5630265
5.85	IC50	1400	nM	CHEMBL5180195
5.82	IC50	1500	nM	CHEMBL5542690
5.80	IC50	1600	nM	CHEMBL5561761
5.68	IC50	2100	nM	CHEMBL4580655
5.66	IC50	2200	nM	CHEMBL5176518
5.60	IC50	2500	nM	CHEMBL4550273
5.58	IC50	2600	nM	CHEMBL5171659
5.55	IC50	2800	nM	CHEMBL5523445
5.54	IC50	2900	nM	CHEMBL5560776
5.51	IC50	3100	nM	CHEMBL5272836
5.46	IC50	3500	nM	CHEMBL5197403
5.42	IC50	3800	nM	CHEMBL5562765
5.40	IC50	4000	nM	CHEMBL4442330
5.37	IC50	4300	nM	CHEMBL5557100
5.33	Kd	4700	nM	CHEMBL5184337
5.33	IC50	4700	nM	CHEMBL3392741
5.32	IC50	4800	nM	CHEMBL5532378
5.31	EC50	4900	nM	CHEMBL4303622
5.29	IC50	5100	nM	CHEMBL5206972
5.28	IC50	5300	nM	CHEMBL5559268
5.17	IC50	6700	nM	CHEMBL5560773
5.09	IC50	8200	nM	CHEMBL5559526
5.08	IC50	8400	nM	CHEMBL5282532
5.05	IC50	9000	nM	CHEMBL5557814
5.01	IC50	9700	nM	CHEMBL5566850

PubChem BioAssay actives

53 with measured affinity, of 282 total; 44 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

Compound	Assay	Type	Value	Unit
2-[2-chloro-6-fluoro-3-[(3R)-1-methylpyrrolidin-3-yl]oxyphenyl]benzo[f][1,3]benzoxazole-4,9-dione	1857648: Inhibition of N-terminal His-6 tagged USP8 (734 to 1110 residues) (unknown origin) expressed in Escherichia coli BL21 (DE3) cells measured after 3 hrs by fluorescence based Plate reader method	ic50	0.0003	uM
2-[2-chloro-5-[(3R)-1-methylpyrrolidin-3-yl]oxyphenyl]benzo[f][1,3]benzoxazole-4,9-dione	1857648: Inhibition of N-terminal His-6 tagged USP8 (734 to 1110 residues) (unknown origin) expressed in Escherichia coli BL21 (DE3) cells measured after 3 hrs by fluorescence based Plate reader method	ic50	0.0013	uM
2-[6-chloro-2-fluoro-3-[(3R)-1-methylpyrrolidin-3-yl]oxyphenyl]benzo[f][1,3]benzoxazole-4,9-dione	1857648: Inhibition of N-terminal His-6 tagged USP8 (734 to 1110 residues) (unknown origin) expressed in Escherichia coli BL21 (DE3) cells measured after 3 hrs by fluorescence based Plate reader method	ic50	0.0020	uM
2-pyridin-3-ylbenzo[f][1,3]benzoxazole-4,9-dione	1857648: Inhibition of N-terminal His-6 tagged USP8 (734 to 1110 residues) (unknown origin) expressed in Escherichia coli BL21 (DE3) cells measured after 3 hrs by fluorescence based Plate reader method	ic50	0.0027	uM
7-chloro-9-oxoindeno[1,2-b]pyrazine-2,3-dicarbonitrile	1491533: Inhibition of human full-length His-tagged USP8 expressed baculovirus infected insect cells using Ub-AMC as substrate by fluorescence spectroscopic analysis	ic50	0.0960	uM
2,3-bis(butylsulfonylmethyl)benzo[g]quinoxaline-5,10-dione	2069641: Inhibition of USP8 (unknown origin) using Di-Ub IQF K48-02 as substrate preincubated for 30 mins followed by substrate addition by high-throughput assay	ic50	0.1000	uM
6-chloro-9-oxoindeno[1,2-b]pyrazine-2,3-dicarbonitrile	1930799: Inhibition of human USP8 using Ub-AMC as substrate	ic50	0.1330	uM
7-fluoro-9-oxoindeno[1,2-b]pyrazine-2,3-dicarbonitrile	1930799: Inhibition of human USP8 using Ub-AMC as substrate	ic50	0.2500	uM
(9E)-9-ethoxyiminoindeno[1,2-b]pyrazine-2,3-dicarbonitrile	2069638: Inhibition of human His tagged full-length USP8 expressed in baculovirus infected Sf9 cells using Ub-AMC as substrate by fluorescence spectroscopy	ic50	0.2800	uM
(9Z)-9-ethoxyiminoindeno[1,2-b]pyrazine-2,3-dicarbonitrile	1881094: Inhibition of human full length USP8 overexpressed in baculovirus-infected insect cells using ubiquitin-C-terminal 7-amido-4-methylcoumarin as substrate by fluorescence spectroscopy	ic50	0.2800	uM
9-oxofluorene-2,3-dicarbonitrile	1881094: Inhibition of human full length USP8 overexpressed in baculovirus-infected insect cells using ubiquitin-C-terminal 7-amido-4-methylcoumarin as substrate by fluorescence spectroscopy	ic50	0.2900	uM
9-oxoindeno[1,2-b]pyrazine-2,3-dicarbonitrile	1930799: Inhibition of human USP8 using Ub-AMC as substrate	ic50	0.2900	uM
7-fluoro-8-methyl-9-oxoindeno[1,2-b]pyrazine-2,3-dicarbonitrile	1930799: Inhibition of human USP8 using Ub-AMC as substrate	ic50	0.3160	uM
4-methoxy-2-[[4-(5-methylthiophen-2-yl)phenyl]sulfonylamino]-N-(4-phenyl-1,3-thiazol-2-yl)benzamide	2069591: Inhibition of N-terminal His6 tagged USP8 (734 to 1110 residues) (unknown origin) expressed in Escherichia coli BL21 (DE3) cells using ubiquitin-rhodamine-110 as substrate preincubated with compound for 30 mins followed by substrate addition measured after 30 mins by fluorometric assay	ic50	0.5200	uM
(9E)-9-prop-2-enoxyiminoindeno[1,2-b]pyrazine-2,3-dicarbonitrile	1881094: Inhibition of human full length USP8 overexpressed in baculovirus-infected insect cells using ubiquitin-C-terminal 7-amido-4-methylcoumarin as substrate by fluorescence spectroscopy	ic50	0.5600	uM
7,8-dimethoxy-9-oxoindeno[1,2-b]pyrazine-2,3-dicarbonitrile	1930799: Inhibition of human USP8 using Ub-AMC as substrate	ic50	0.7100	uM
5,8-dimethoxy-9-oxoindeno[1,2-b]pyrazine-2,3-dicarbonitrile	1930799: Inhibition of human USP8 using Ub-AMC as substrate	ic50	0.8100	uM
(9E)-9-phenylmethoxyiminoindeno[1,2-b]pyrazine-2,3-dicarbonitrile	1881094: Inhibition of human full length USP8 overexpressed in baculovirus-infected insect cells using ubiquitin-C-terminal 7-amido-4-methylcoumarin as substrate by fluorescence spectroscopy	ic50	0.8500	uM
6-methyl-9-oxoindeno[1,2-b]pyrazine-2,3-dicarbonitrile	1930799: Inhibition of human USP8 using Ub-AMC as substrate	ic50	0.9300	uM
2-[(4-methylphenyl)sulfonylamino]-N-(4-phenyl-1,3-thiazol-2-yl)-4-(trifluoromethyl)benzamide	1930822: Inhibition of human USP8 using Di-Ub IQF as substrate incubated for 15 mins by K63-2 assay	ic50	0.9500	uM
3-[1-(4-bromophenyl)-5-phenylpyrazol-3-yl]pyridine	2131445: Inhibition of human USP8 expressed in Escherichia coli using K63-linked di-ubiquitin (ENZO BML-UW0730-0050) as substrate preincubated for 15 mins followed by substrate addition and measured after 20 mins by fluorescence based analysis	ic50	1.2000	uM
8-[(3,5-dimethyl-1H-pyrazol-4-yl)oxy]-5,7-dihydroxy-2-[4-(4-pyridin-2-ylpiperazin-1-yl)phenyl]chromen-4-one	1881098: Inhibition of N-terminal His6-tagged USP8 (unknown origin) catalytic domain (734 to 1110 residues) expressed in Escherichia coli BL21 (DE3) cells assessed as deubiquitinating activity using ubiquitin-rhodamine -110 as substrate incubated for 30 mins followed by substrate addition measured after 30 mins by ubiquitin-rhodamine-110 based fluorometric assay	ic50	1.2000	uM
2-[(4-phenylphenyl)sulfonylamino]-N-(4-phenyl-1,3-thiazol-2-yl)-4-(trifluoromethyl)benzamide	2069591: Inhibition of N-terminal His6 tagged USP8 (734 to 1110 residues) (unknown origin) expressed in Escherichia coli BL21 (DE3) cells using ubiquitin-rhodamine-110 as substrate preincubated with compound for 30 mins followed by substrate addition measured after 30 mins by fluorometric assay	ic50	1.5000	uM
4-methoxy-2-[(4-phenylphenyl)sulfonylamino]-N-(5-phenyl-1,3,4-thiadiazol-2-yl)benzamide	2069591: Inhibition of N-terminal His6 tagged USP8 (734 to 1110 residues) (unknown origin) expressed in Escherichia coli BL21 (DE3) cells using ubiquitin-rhodamine-110 as substrate preincubated with compound for 30 mins followed by substrate addition measured after 30 mins by fluorometric assay	ic50	1.6000	uM
7-methoxy-9-oxoindeno[1,2-b]pyrazine-2,3-dicarbonitrile	1930799: Inhibition of human USP8 using Ub-AMC as substrate	ic50	2.1000	uM
4-[4-(5,7-dihydroxy-8-methoxy-4-oxochromen-2-yl)phenyl]piperazine-1-carbaldehyde	1881098: Inhibition of N-terminal His6-tagged USP8 (unknown origin) catalytic domain (734 to 1110 residues) expressed in Escherichia coli BL21 (DE3) cells assessed as deubiquitinating activity using ubiquitin-rhodamine -110 as substrate incubated for 30 mins followed by substrate addition measured after 30 mins by ubiquitin-rhodamine-110 based fluorometric assay	ic50	2.2000	uM
6,7-dimethoxy-9-oxoindeno[1,2-b]pyrazine-2,3-dicarbonitrile	1930799: Inhibition of human USP8 using Ub-AMC as substrate	ic50	2.5000	uM
4-(2-amino-4-methoxyphenyl)-N-(4-nitrophenyl)piperazine-1-carbothioamide	1881097: Inhibition of N-terminal His6-tagged USP8 (unknown origin) expressed in Escherichia coli BL21 (DE3) cells using ubiquitin-rhodamine -110 as substrate incubated for 15 mins followed by substrate addition measured after 1 hrs by ubiquitin-rhodamine-110 based fluorometric assay	ic50	2.6000	uM
2-[(4-phenylphenyl)sulfonylamino]-N-(5-phenyl-1,3,4-thiadiazol-2-yl)-4-(trifluoromethyl)benzamide	2069591: Inhibition of N-terminal His6 tagged USP8 (734 to 1110 residues) (unknown origin) expressed in Escherichia coli BL21 (DE3) cells using ubiquitin-rhodamine-110 as substrate preincubated with compound for 30 mins followed by substrate addition measured after 30 mins by fluorometric assay	ic50	2.8000	uM
N-(1,3-benzothiazol-2-yl)-2-[(4-phenylphenyl)sulfonylamino]-4-(trifluoromethyl)benzamide	2069591: Inhibition of N-terminal His6 tagged USP8 (734 to 1110 residues) (unknown origin) expressed in Escherichia coli BL21 (DE3) cells using ubiquitin-rhodamine-110 as substrate preincubated with compound for 30 mins followed by substrate addition measured after 30 mins by fluorometric assay	ic50	2.9000	uM
8-methyl-9-oxoindeno[1,2-b]pyrazine-2,3-dicarbonitrile	1930799: Inhibition of human USP8 using Ub-AMC as substrate	ic50	3.1000	uM
8-[(3,5-dimethyl-1H-pyrazol-4-yl)oxy]-5,7-dihydroxy-2-[4-(4-phenylpiperazin-1-yl)phenyl]chromen-4-one	1881098: Inhibition of N-terminal His6-tagged USP8 (unknown origin) catalytic domain (734 to 1110 residues) expressed in Escherichia coli BL21 (DE3) cells assessed as deubiquitinating activity using ubiquitin-rhodamine -110 as substrate incubated for 30 mins followed by substrate addition measured after 30 mins by ubiquitin-rhodamine-110 based fluorometric assay	ic50	3.5000	uM
2-[(4-bromophenyl)sulfonylamino]-4-methoxy-N-(4-phenyl-1,3-thiazol-2-yl)benzamide	2069591: Inhibition of N-terminal His6 tagged USP8 (734 to 1110 residues) (unknown origin) expressed in Escherichia coli BL21 (DE3) cells using ubiquitin-rhodamine-110 as substrate preincubated with compound for 30 mins followed by substrate addition measured after 30 mins by fluorometric assay	ic50	3.8000	uM
6-methoxy-9-oxoindeno[1,2-b]pyrazine-2,3-dicarbonitrile	1930799: Inhibition of human USP8 using Ub-AMC as substrate	ic50	4.0000	uM
4-methoxy-N-(5-phenyl-1,3,4-thiadiazol-2-yl)-2-(pyridin-3-ylsulfonylamino)benzamide	2069591: Inhibition of N-terminal His6 tagged USP8 (734 to 1110 residues) (unknown origin) expressed in Escherichia coli BL21 (DE3) cells using ubiquitin-rhodamine-110 as substrate preincubated with compound for 30 mins followed by substrate addition measured after 30 mins by fluorometric assay	ic50	4.3000	uM
2-(naphthalen-1-ylsulfonylamino)-N-(4-phenyl-1,3-thiazol-2-yl)-4-(trifluoromethyl)benzamide	2069591: Inhibition of N-terminal His6 tagged USP8 (734 to 1110 residues) (unknown origin) expressed in Escherichia coli BL21 (DE3) cells using ubiquitin-rhodamine-110 as substrate preincubated with compound for 30 mins followed by substrate addition measured after 30 mins by fluorometric assay	ic50	4.8000	uM
(2,6-diamino-5-thiocyanato-3-pyridinyl) thiocyanate	1925875: Inhibition of USP8 (unknown origin)	ec50	4.9000	uM
8-[(3,5-dimethyl-1H-pyrazol-4-yl)oxy]-2-[4-[4-(furan-2-carbonyl)piperazin-1-yl]phenyl]-5,7-dihydroxychromen-4-one	1881098: Inhibition of N-terminal His6-tagged USP8 (unknown origin) catalytic domain (734 to 1110 residues) expressed in Escherichia coli BL21 (DE3) cells assessed as deubiquitinating activity using ubiquitin-rhodamine -110 as substrate incubated for 30 mins followed by substrate addition measured after 30 mins by ubiquitin-rhodamine-110 based fluorometric assay	ic50	5.1000	uM
4-methoxy-N-(4-phenyl-1,3-thiazol-2-yl)-2-(pyridin-3-ylsulfonylamino)benzamide	2069591: Inhibition of N-terminal His6 tagged USP8 (734 to 1110 residues) (unknown origin) expressed in Escherichia coli BL21 (DE3) cells using ubiquitin-rhodamine-110 as substrate preincubated with compound for 30 mins followed by substrate addition measured after 30 mins by fluorometric assay	ic50	5.3000	uM
4-methoxy-N-(4-phenyl-1,3-thiazol-2-yl)-2-[[2-(trifluoromethyl)phenyl]sulfonylamino]benzamide	2069591: Inhibition of N-terminal His6 tagged USP8 (734 to 1110 residues) (unknown origin) expressed in Escherichia coli BL21 (DE3) cells using ubiquitin-rhodamine-110 as substrate preincubated with compound for 30 mins followed by substrate addition measured after 30 mins by fluorometric assay	ic50	6.7000	uM
N-(4-phenyl-1,3-thiazol-2-yl)-2-(thiophen-2-ylsulfonylamino)-4-(trifluoromethyl)benzamide	2069591: Inhibition of N-terminal His6 tagged USP8 (734 to 1110 residues) (unknown origin) expressed in Escherichia coli BL21 (DE3) cells using ubiquitin-rhodamine-110 as substrate preincubated with compound for 30 mins followed by substrate addition measured after 30 mins by fluorometric assay	ic50	8.2000	uM
3,9-dioxo-4H-indeno[1,2-b]pyrazine-2-carbonitrile	1930799: Inhibition of human USP8 using Ub-AMC as substrate	ic50	8.4000	uM
2-[(4-fluorophenyl)sulfonylamino]-4-methoxy-N-(5-phenyl-1,3,4-thiadiazol-2-yl)benzamide	2069591: Inhibition of N-terminal His6 tagged USP8 (734 to 1110 residues) (unknown origin) expressed in Escherichia coli BL21 (DE3) cells using ubiquitin-rhodamine-110 as substrate preincubated with compound for 30 mins followed by substrate addition measured after 30 mins by fluorometric assay	ic50	9.0000	uM
N-(5-phenyl-1,3,4-thiadiazol-2-yl)-2-(pyridin-3-ylsulfonylamino)-4-(trifluoromethyl)benzamide	2069591: Inhibition of N-terminal His6 tagged USP8 (734 to 1110 residues) (unknown origin) expressed in Escherichia coli BL21 (DE3) cells using ubiquitin-rhodamine-110 as substrate preincubated with compound for 30 mins followed by substrate addition measured after 30 mins by fluorometric assay	ic50	9.7000	uM

CTD chemical–gene interactions

29 total (human), top 29 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	increases expression	2
Particulate Matter	decreases expression, decreases reaction, increases abundance	2
FR900359	affects phosphorylation	1
bisphenol F	affects cotreatment, decreases expression	1
dicrotophos	decreases expression	1
coumarin	increases phosphorylation	1
bafilomycin A1	decreases activity, increases cleavage, increases reaction	1
di-n-butylphosphoric acid	affects expression	1
pifithrin	decreases reaction, increases cleavage, increases expression, decreases activity	1
K 7174	increases expression	1
2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amide	decreases reaction, decreases expression	1
jinfukang	decreases expression	1
Resveratrol	affects cotreatment, increases expression	1
Air Pollutants	increases abundance, decreases expression	1
Vehicle Emissions	decreases expression, decreases reaction	1
Benzo(a)pyrene	increases expression	1
Caffeine	decreases phosphorylation	1
Chloroquine	decreases activity, increases cleavage, increases reaction	1
Dexamethasone	affects cotreatment, decreases expression	1
Doxorubicin	decreases expression	1
Indomethacin	affects cotreatment, decreases expression	1
Methyl Methanesulfonate	increases expression	1
Plant Extracts	affects cotreatment, increases expression	1
Ribonucleotides	affects binding	1
Tobacco Smoke Pollution	increases expression	1
Valproic Acid	affects expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, decreases expression	1
Cysteine Proteinase Inhibitors	decreases activity, increases cleavage, increases reaction, decreases expression, increases expression (+2 more)	1
Lactic Acid	decreases expression	1

ChEMBL screening assays

54 unique, capped per target: 51 binding, 3 functional

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL2163021	Binding	Inhibition of USP8 by Ub-CHOP reporter assay	Selective Dual Inhibitors of the Cancer-Related Deubiquitylating Proteases USP7 and USP47. — ACS Med Chem Lett
CHEMBL5723231	Functional	Affinity Biochemical interaction: (enzymatic assay (cleavage of fluorogenic Ub-AMC substrate)) EUB0002563a USP8	Affinity Biochemical Literature for EUbOPEN Chemogenomic Library

Cellosaurus cell lines

6 cell lines: 6 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_B2KR	Abcam HeLa USP8 KO	Cancer cell line	Female
CVCL_B8RK	Abcam HCT 116 USP8 KO	Cancer cell line	Male
CVCL_B9CF	Abcam MCF-7 USP8 KO	Cancer cell line	Female
CVCL_B9U0	Abcam A-549 USP8 KO	Cancer cell line	Male
CVCL_TX14	HAP1 USP8 (-) 1	Cancer cell line	Male
CVCL_TX15	HAP1 USP8 (-) 2	Cancer cell line	Male

Clinical trials (associated diseases)

106 trials via MONDO — disease-level, not drug-specific.

Trial	Phase	Status	Title
NCT07542548	PHASE4	COMPLETED	D-Cycloserine for Serine Palmitoyltransferase Inhibition
NCT01794793	PHASE4	COMPLETED	Study to Allow Access to Pasireotide for Patients Benefiting From Pasireotide Treatment in Novartis-sponsored Studies
NCT02060383	PHASE4	COMPLETED	Study of Management of Pasireotide-induced Hyperglycemia in Adult Patients With Cushing’s Disease or Acromegaly
NCT03080181	PHASE4	COMPLETED	Adipokine Profile in Patients With Cushing’s Disease on Pasireotide Treatment
NCT06719141	PHASE3	RECRUITING	A Study to Investigate LP352 in Children and Adults With Developmental and Epileptic Encephalopathies (DEE)
NCT06908226	PHASE3	ENROLLING_BY_INVITATION	A Study to Investigate LP352 in Children and Adults With Developmental and Epileptic Encephalopathy (DEE)
NCT00434148	PHASE3	COMPLETED	Safety and Efficacy of Different Dose Levels of Pasireotide in Patients With de Novo, Persistent or Recurrent Cushing’s Disease
NCT00889525	PHASE3	COMPLETED	Study of Cabergoline in Treatment of Corticotroph Pituitary Tumor
NCT01371565	PHASE3	COMPLETED	Compassionate Use of CORLUX® (Mifepristone) in the Treatment of Signs and Symptoms of Endogenous Cushing’s Syndrome
NCT01374906	PHASE3	COMPLETED	Efficacy and Safety of Pasireotide Administered Monthly in Patients With Cushing’s Disease
NCT01582061	PHASE3	COMPLETED	An Open-label, Multi-center, Expanded Access Study of Pasireotide s.c. in Patients With Cushing’s Disease.
NCT01925092	PHASE3	WITHDRAWN	Mifepristone in Children With Refractory Cushing’s Disease
NCT02697734	PHASE3	COMPLETED	Efficacy and Safety Evaluation of Osilodrostat in Cushing’s Disease
NCT03621280	PHASE3	COMPLETED	Open-label Treatment in Cushing’s Syndrome
NCT03961906	PHASE2	COMPLETED	Physiotherapy in Hereditary Spastic Paraplegia
NCT04768166	PHASE2	COMPLETED	Testing Miglustat Administration in Subjects With Spastic Paraplegia 11
NCT05626634	PHASE2	COMPLETED	Open-label, Long-term Safety Study of LP352 in Subjects With Developmental and Epileptic Encephalopathy
NCT00171951	PHASE2	COMPLETED	Extension Study to Assess the Safety and Efficacy of Pasireotide in Participants With Cushing’s Disease
NCT00612066	PHASE2	TERMINATED	Rosiglitazone in Treating Patients With Newly Diagnosed ACTH-Secreting Pituitary Tumor (Cushing Disease)
NCT01331239	PHASE2	COMPLETED	Safety and Efficacy of LCI699 in Cushing’s Disease Patients
NCT02484755	PHASE2	UNKNOWN	Targeted Therapy With Gefitinib in Patients With USP8-mutated Cushing’s Disease
NCT03774446	PHASE2	RECRUITING	Multicenter Study of Seliciclib (R-roscovitine) for Cushing Disease
NCT04339751	PHASE2	WITHDRAWN	Effect of Vorinostat on ACTH Producing Pituitary Adenomas in Cushing s Disease
NCT05971758	PHASE2	RECRUITING	Fimepinostat, Combination HDAC and Pi3-kinase Inhibitor Tumor-Directed Therapy for Cushing Disease
NCT06471829	PHASE2	RECRUITING	A Trial of Lu AG13909 in Adult Participants With Cushing’s Disease
NCT06117020	PHASE1	COMPLETED	Single and Multiple Ascending Dose Study of MTR-601 in Healthy Individuals
NCT06700811	PHASE1	RECRUITING	Ketogenic Diet for Prevention of Epileptic Spasms in Infantile Onset Genetic Epilepsies
NCT02604186	PHASE2/PHASE3	COMPLETED	Effects of Botulinum Toxin Injections in Patients With Hereditary Spastic Paraplegia
NCT05518188	PHASE1/PHASE2	RECRUITING	Melpida: Recombinant Adeno-associated Virus (serotype 9) Encoding a Codon Optimized Human AP4M1 Transgene (hAP4M1opt)
NCT06948019	PHASE1/PHASE2	NOT_YET_RECRUITING	Safety and Efficacy of AAV9/AP4B1 (BFB-101) For Patients With AP4B1-related Hereditary Spastic Paraplegia Type 47 (SPG47)
NCT06478238	EARLY_PHASE1	RECRUITING	Calcium Folinate Treatment of Spastic Paraplegia 56
NCT00023075	Not specified	COMPLETED	Nuclear Magnetic Spectroscopy Imaging to Evaluate Primary Lateral Sclerosis, Hereditary Spastic Paraplegia and Amyotrophic Lateral Sclerosis
NCT00136630	Not specified	COMPLETED	Natural History, Genetic Bases and Phenotype-genotype Correlations in Autosomal Dominant Spinocerebellar Degenerations
NCT00140829	Not specified	COMPLETED	SPATAX: Clinical and Genetic Analysis of Cerebellar Ataxias and Spastic Paraplegias
NCT00677768	Not specified	COMPLETED	Validation of Biomarkers in Amyotrophic Lateral Sclerosis (ALS)
NCT01568658	Not specified	ACTIVE_NOT_RECRUITING	Genetic and Physical Study of Childhood Nerve and Muscle Disorders
NCT02327845	Not specified	ENROLLING_BY_INVITATION	Phenotype, Genotype & Biomarkers in ALS and Related Disorders
NCT02852278	Not specified	COMPLETED	A Patient Centric Motor Neuron Disease Activities of Daily Living Scale
NCT02859428	Not specified	TERMINATED	Disease Natural History and Biomarkers of SPG3A, SPG4A, and SPG31
NCT03104088	Not specified	COMPLETED	Studying Cognition in SPG4