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Cellosaurus OCUM-1 (CVCL_3084)

[Text version]
Cell line name OCUM-1
Synonyms OCUM1; Osaka City University Medical school-1
Accession CVCL_3084
Resource Identification Initiative To cite this cell line use: OCUM-1 (RRID:CVCL_3084)
Comments Part of: Cancer Dependency Map project (DepMap) (includes Cancer Cell Line Encyclopedia - CCLE).
Part of: COSMIC cell lines project.
Population: Japanese.
Doubling time: 33.2 hours (PubMed=1961183); 33 hours (PubMed=29435981); ~38 hours (Note=Lot 12222004), 49 hours (Note=Lot 09162009), ~64 hours (Note=Lot 11282012), ~26 hours (Note=Lot 08172016), ~34 hours (Note=Lot 06252018) (JCRB=JCRB0192).
Microsatellite instability: Instable (MSI-low) (Sanger).
Omics: Array-based CGH.
Omics: Deep exome analysis.
Omics: Deep quantitative proteome analysis.
Omics: DNA methylation analysis.
Omics: SNP array analysis.
Omics: Transcriptome analysis by microarray.
Omics: Transcriptome analysis by RNAseq.
Derived from site: Metastatic; Pleural effusion; UBERON=UBERON_0000175.
Sequence variations
  • Mutation; HGNC; 6840; MAP2K1; Simple; p.Gln56Pro (c.167A>C); ClinVar=VCV000375978; Zygosity=Hemizygous (PubMed=22327936).
HLA typing Source: PubMed=26589293
Class I
HLA-AA*24:02,31:01
HLA-BB*07:02,52:01
HLA-CC*07:02,12:02
Class II
HLA-DQDQB1*06:04,06:04
Genome ancestry Source: PubMed=30894373

Origin% genome
African0
Native American0.6
East Asian, North77.58
East Asian, South21.82
South Asian0
European, North0
European, South0
Disease Gastric signet ring cell adenocarcinoma (NCIt: C5250)
Species of origin Homo sapiens (Human) (NCBI Taxonomy: 9606)
Sex of cell Female
Age at sampling 38Y
Category Cancer cell line
STR profile Source(s): Cosmic-CLP=1298358; JCRB=JCRB0192; PubMed=25877200

Markers:
AmelogeninX
CSF1PO10,12
D3S135817
D5S8189,10
D7S82012
D8S117911,12
D13S31710,11
D16S53911
D18S5112,13
D21S1130
FGA19,23
Penta D12,13
Penta E12,19
TH019
TPOX8,11
vWA14,16,17 (JCRB=JCRB0192)
14,17 (Cosmic-CLP=1298358; PubMed=25877200)

Run an STR similarity search on this cell line
Publications

PubMed=1961183
Kubo T.
Establishment and characterization of a new gastric cancer cell line (OCUM-1), derived from Borrmann type IV tumor.
Nihon Geka Gakkai Zasshi 92:1451-1460(1991)

DOI=10.1016/B978-0-12-333530-2.50014-9
Sekiguchi M., Suzuki T.
Gastric tumor cell lines.
(In book chapter) Atlas of human tumor cell lines; Hay R.J., Park J.-G., Gazdar A.F. (eds.); pp.287-316; Academic Press; New York; USA (1994)

PubMed=15723654; DOI=10.1111/j.1349-7006.2005.00016.x; PMCID=PMC11160020
Takada H., Imoto I., Tsuda H., Sonoda I., Ichikura T., Mochizuki H., Okanoue T., Inazawa J.
Screening of DNA copy-number aberrations in gastric cancer cell lines by array-based comparative genomic hybridization.
Cancer Sci. 96:100-110(2005)

PubMed=20215515; DOI=10.1158/0008-5472.CAN-09-3458; PMCID=PMC2881662
Rothenberg S.M., Mohapatra G., Rivera M.N., Winokur D., Greninger P., Nitta M., Sadow P.M., Sooriyakumar G., Brannigan B.W., Ulman M.J., Perera R.M., Wang R., Tam A., Ma X.-J., Erlander M., Sgroi D.C., Rocco J.W., Lingen M.W., Cohen E.E.W., Louis D.N., Settleman J., Haber D.A.
A genome-wide screen for microdeletions reveals disruption of polarity complex genes in diverse human cancers.
Cancer Res. 70:2158-2164(2010)

PubMed=21115893
Kuramitsu Y., Baron B., Yoshino S., Zhang X.-L., Tanaka T., Yashiro M., Hirakawa K., Oka M., Nakamura K.
Proteomic differential display analysis shows up-regulation of 14-3-3 sigma protein in human scirrhous-type gastric carcinoma cells.
Anticancer Res. 30:4459-4465(2010)

PubMed=22327936; DOI=10.1093/carcin/bgs099
Choi Y.L., Soda M., Ueno T., Hamada T., Haruta H., Yamato A., Fukumura K., Ando M., Kawazu M., Yamashita Y., Mano H.
Oncogenic MAP2K1 mutations in human epithelial tumors.
Carcinogenesis 33:956-961(2012)

PubMed=22460905; DOI=10.1038/nature11003; PMCID=PMC3320027
Barretina J.G., Caponigro G., Stransky N., Venkatesan K., Margolin A.A., Kim S., Wilson C.J., Lehar J., Kryukov G.V., Sonkin D., Reddy A., Liu M., Murray L., Berger M.F., Monahan J.E., Morais P., Meltzer J., Korejwa A., Jane-Valbuena J., Mapa F.A., Thibault J., Bric-Furlong E., Raman P., Shipway A., Engels I.H., Cheng J., Yu G.-Y.K., Yu J.-J., Aspesi P. Jr., de Silva M., Jagtap K., Jones M.D., Wang L., Hatton C., Palescandolo E., Gupta S., Mahan S., Sougnez C., Onofrio R.C., Liefeld T., MacConaill L.E., Winckler W., Reich M., Li N.-X., Mesirov J.P., Gabriel S.B., Getz G., Ardlie K., Chan V., Myer V.E., Weber B.L., Porter J., Warmuth M., Finan P., Harris J.L., Meyerson M.L., Golub T.R., Morrissey M.P., Sellers W.R., Schlegel R., Garraway L.A.
The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity.
Nature 483:603-607(2012)

PubMed=24807215; DOI=10.1038/ncomms4830; PMCID=PMC4024760
Liu J.-F., McCleland M.L., Stawiski E.W., Gnad F., Mayba O., Haverty P.M., Durinck S., Chen Y.-J., Klijn C., Jhunjhunwala S., Lawrence M., Liu H.-B., Wan Y.-N., Chopra V.S., Yaylaoglu M.B., Yuan W.-L., Ha C., Gilbert H.N., Reeder J., Pau G., Stinson J., Stern H.M., Manning G., Wu T.D., Neve R.M., de Sauvage F.J., Modrusan Z., Seshagiri S., Firestein R., Zhang Z.-M.
Integrated exome and transcriptome sequencing reveals ZAK isoform usage in gastric cancer.
Nat. Commun. 5:3830.1-3830.8(2014)

PubMed=25343454; DOI=10.1371/journal.pone.0111146; PMCID=PMC4208810
Choong M.-L., Tan S.-H., Tan T.-Z., Manesh S., Ngo A., Yong J.W.-Y., Yang H.H., Lee M.A.
Molecular integrative clustering of Asian gastric cell lines revealed two distinct chemosensitivity clusters.
PLoS ONE 9:E111146-E111146(2014)

PubMed=25485619; DOI=10.1038/nbt.3080
Klijn C., Durinck S., Stawiski E.W., Haverty P.M., Jiang Z.-S., Liu H.-B., Degenhardt J., Mayba O., Gnad F., Liu J.-F., Pau G., Reeder J., Cao Y., Mukhyala K., Selvaraj S.K., Yu M.-M., Zynda G.J., Brauer M.J., Wu T.D., Gentleman R.C., Manning G., Yauch R.L., Bourgon R., Stokoe D., Modrusan Z., Neve R.M., de Sauvage F.J., Settleman J., Seshagiri S., Zhang Z.-M.
A comprehensive transcriptional portrait of human cancer cell lines.
Nat. Biotechnol. 33:306-312(2015)

PubMed=25877200; DOI=10.1038/nature14397
Yu M., Selvaraj S.K., Liang-Chu M.M.Y., Aghajani S., Busse M., Yuan J., Lee G., Peale F.V., Klijn C., Bourgon R., Kaminker J.S., Neve R.M.
A resource for cell line authentication, annotation and quality control.
Nature 520:307-311(2015)

PubMed=26589293; DOI=10.1186/s13073-015-0240-5; PMCID=PMC4653878
Scholtalbers J., Boegel S., Bukur T., Byl M., Goerges S., Sorn P., Loewer M., Sahin U., Castle J.C.
TCLP: an online cancer cell line catalogue integrating HLA type, predicted neo-epitopes, virus and gene expression.
Genome Med. 7:118.1-118.7(2015)

PubMed=27397505; DOI=10.1016/j.cell.2016.06.017; PMCID=PMC4967469
Iorio F., Knijnenburg T.A., Vis D.J., Bignell G.R., Menden M.P., Schubert M., Aben N., Goncalves E., Barthorpe S., Lightfoot H., Cokelaer T., Greninger P., van Dyk E., Chang H., de Silva H., Heyn H., Deng X.-M., Egan R.K., Liu Q.-S., Mironenko T., Mitropoulos X., Richardson L., Wang J.-H., Zhang T.-H., Moran S., Sayols S., Soleimani M., Tamborero D., Lopez-Bigas N., Ross-Macdonald P., Esteller M., Gray N.S., Haber D.A., Stratton M.R., Benes C.H., Wessels L.F.A., Saez-Rodriguez J., McDermott U., Garnett M.J.
A landscape of pharmacogenomic interactions in cancer.
Cell 166:740-754(2016)

PubMed=29435981; DOI=10.1002/ijc.31304
Kim H.J., Kang S.K., Kwon W.S., Kim T.S., Jeong I., Jeung H.-C., Kragh M., Horak I.D., Chung H.C., Rha S.Y.
Forty-nine gastric cancer cell lines with integrative genomic profiling for development of c-MET inhibitor.
Int. J. Cancer 143:151-159(2018)

PubMed=30894373; DOI=10.1158/0008-5472.CAN-18-2747; PMCID=PMC6445675
Dutil J., Chen Z.-H., Monteiro A.N.A., Teer J.K., Eschrich S.A.
An interactive resource to probe genetic diversity and estimated ancestry in cancer cell lines.
Cancer Res. 79:1263-1273(2019)

PubMed=31068700; DOI=10.1038/s41586-019-1186-3; PMCID=PMC6697103
Ghandi M., Huang F.W., Jane-Valbuena J., Kryukov G.V., Lo C.C., McDonald E.R. 3rd, Barretina J.G., Gelfand E.T., Bielski C.M., Li H.-X., Hu K., Andreev-Drakhlin A.Y., Kim J., Hess J.M., Haas B.J., Aguet F., Weir B.A., Rothberg M.V., Paolella B.R., Lawrence M.S., Akbani R., Lu Y.-L., Tiv H.L., Gokhale P.C., de Weck A., Mansour A.A., Oh C., Shih J., Hadi K., Rosen Y., Bistline J., Venkatesan K., Reddy A., Sonkin D., Liu M., Lehar J., Korn J.M., Porter D.A., Jones M.D., Golji J., Caponigro G., Taylor J.E., Dunning C.M., Creech A.L., Warren A.C., McFarland J.M., Zamanighomi M., Kauffmann A., Stransky N., Imielinski M., Maruvka Y.E., Cherniack A.D., Tsherniak A., Vazquez F., Jaffe J.D., Lane A.A., Weinstock D.M., Johannessen C.M., Morrissey M.P., Stegmeier F., Schlegel R., Hahn W.C., Getz G., Mills G.B., Boehm J.S., Golub T.R., Garraway L.A., Sellers W.R.
Next-generation characterization of the Cancer Cell Line Encyclopedia.
Nature 569:503-508(2019)

PubMed=31978347; DOI=10.1016/j.cell.2019.12.023; PMCID=PMC7339254
Nusinow D.P., Szpyt J., Ghandi M., Rose C.M., McDonald E.R. 3rd, Kalocsay M., Jane-Valbuena J., Gelfand E.T., Schweppe D.K., Jedrychowski M.P., Golji J., Porter D.A., Rejtar T., Wang Y.K., Kryukov G.V., Stegmeier F., Erickson B.K., Garraway L.A., Sellers W.R., Gygi S.P.
Quantitative proteomics of the Cancer Cell Line Encyclopedia.
Cell 180:387-402.e16(2020)

PubMed=35839778; DOI=10.1016/j.ccell.2022.06.010; PMCID=PMC9387775
Goncalves E., Poulos R.C., Cai Z.-X., Barthorpe S., Manda S.S., Lucas N., Beck A., Bucio-Noble D., Dausmann M., Hall C., Hecker M., Koh J., Lightfoot H., Mahboob S., Mali I., Morris J., Richardson L., Seneviratne A.J., Shepherd R., Sykes E., Thomas F., Valentini S., Williams S.G., Wu Y.-X., Xavier D., MacKenzie K.L., Hains P.G., Tully B., Robinson P.J., Zhong Q., Garnett M.J., Reddel R.R.
Pan-cancer proteomic map of 949 human cell lines.
Cancer Cell 40:835-849.e8(2022)

Cross-references
Cell line collections (Providers) JCRB; JCRB0192
Cell line databases/resources CLO; CLO_0037145
cancercelllines; CVCL_3084
Cell_Model_Passport; SIDM00568
CGH-DB; 131-1
Cosmic-CLP; 1298358
DepMap; ACH-000247
LINCS_LDP; LCL-2002
Anatomy/cell type resources BTO; BTO:0005918
Biological sample resources BioSample; SAMN03471652
BioSample; SAMN03473049
BioSample; SAMN10987922
Chemistry resources GDSC; 1298358
PharmacoDB; OCUM1_1193_2019
Encyclopedic resources Wikidata; Q54931820
Experimental variables resources EFO; EFO_0006714
Gene expression databases ArrayExpress; E-MTAB-2706
ArrayExpress; E-MTAB-2770
ArrayExpress; E-MTAB-3610
GEO; GSM552369
GEO; GSM827576
GEO; GSM887474
GEO; GSM888554
GEO; GSM1374795
GEO; GSM1670301
Polymorphism and mutation databases Cosmic; 1889265
Cosmic; 2009531
Cosmic; 2443794
Cosmic; 2484967
Cosmic; 2807640
LiGeA; CCLE_111
Progenetix; CVCL_3084
Proteomic databases PRIDE; PXD030304
Sequence databases EGA; EGAS00001000610
EGA; EGAS00001000978
Entry history
Entry creation04-Apr-2012
Last entry update10-Sep-2024
Version number38