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Cellosaurus SNU-398 (CVCL_0077)

[Text version]
Cell line name SNU-398
Synonyms SNU398; NCI-SNU-398
Accession CVCL_0077
Resource Identification Initiative To cite this cell line use: SNU-398 (RRID:CVCL_0077)
Comments Part of: Cancer Dependency Map project (DepMap) (includes Cancer Cell Line Encyclopedia - CCLE).
Part of: COSMIC cell lines project.
Part of: Liver Cancer Model Repository (LIMORE).
Part of: MD Anderson Cell Lines Project.
Part of: Seoul National University (SNU) cell line collection.
Population: Korean.
Doubling time: 39 hours (PubMed=7543080); 25.49 hours (PubMed=31378681).
Karyotypic information: Has lost chromosome Y.
Microsatellite instability: Stable (MSS) (Sanger).
Transformant: NCBI_TaxID; 10407; Hepatitis B virus (HBV).
Omics: Deep exome analysis.
Omics: Deep quantitative proteome analysis.
Omics: DNA methylation analysis.
Omics: Genome sequenced.
Omics: miRNA expression profiling.
Omics: Protein expression by reverse-phase protein arrays.
Omics: SNP array analysis.
Omics: Transcriptome analysis by microarray.
Omics: Transcriptome analysis by RNAseq.
Derived from site: In situ; Liver; UBERON=UBERON_0002107.
Sequence variations
  • Mutation; HGNC; 2514; CTNNB1; Simple; p.Ser37Cys (c.110C>G); ClinVar=VCV000017579; Zygosity=Heterozygous (PubMed=31378681; Cosmic-CLP=1240217; DepMap=ACH-000221).
  • Mutation; HGNC; 11998; TP53; Simple; p.Ser215Ile (c.644G>T); ClinVar=VCV000376660; Zygosity=Heterozygous (PubMed=8824565).
HLA typing Source: PubMed=26589293
Class I
HLA-AA*02:01,24:02
HLA-BB*15:32,40:02
HLA-CC*01:02,04:01
Genome ancestry Source: PubMed=30894373

Origin% genome
African1.33
Native American0.85
East Asian, North66.35
East Asian, South28.86
South Asian0
European, North0
European, South2.61
Disease Adult hepatocellular carcinoma (NCIt: C7956)
Adult hepatocellular carcinoma (ORDO: Orphanet_210159)
Species of origin Homo sapiens (Human) (NCBI Taxonomy: 9606)
Hierarchy Children:
CVCL_E1CC (Ubigene SNU-398 LZTR1 KO)
Sex of cell Male
Age at sampling 42Y
Category Cancer cell line
STR profile Source(s): ATCC=CRL-2233; Cosmic-CLP=1240217; KCLB=00398; PubMed=25877200; PubMed=31378681

Markers:
AmelogeninX,Y
CSF1PO13
D2S133819
D3S135817
D5S81812
D7S82010,11
D8S117912
D13S31711
D16S53910,14
D18S5115 (PubMed=25877200)
15,19 (ATCC=CRL-2233)
D19S43314,14.1
D21S1129
FGA22,23 (KCLB=00398)
23 (ATCC=CRL-2233; PubMed=25877200)
Penta D14
Penta E12
TH017,9 (ATCC=CRL-2233; Cosmic-CLP=1240217; PubMed=25877200)
8,9 (KCLB=00398)
9 (PubMed=31378681)
TPOX11
vWA17,18

Run an STR similarity search on this cell line
Web pages https://lccl.zucmanlab.com/hcc/cellLines/SNU398
https://tcpaportal.org/mclp/
Publications

PubMed=7543080; DOI=10.1002/ijc.2910620308
Park J.-G., Lee J.-H., Kang M.-S., Park K.-J., Jeon Y.-M., Lee H.-J., Kwon H.-S., Park H.-S., Yeo K.-S., Lee K.-U., Kim S.-T., Chung J.-K., Hwang Y.-J., Lee H.-S., Kim C.Y., Lee Y.I., Chen T.-R., Hay R.J., Song S.-Y., Kim W.-H., Ki C.-W., Kim Y.-I.
Characterization of cell lines established from human hepatocellular carcinoma.
Int. J. Cancer 62:276-282(1995)

PubMed=8824565; DOI=10.1002/(SICI)1097-0215(19960917)67:6<898::AID-IJC22>3.0.CO;2-X
Kang M.-S., Lee H.-J., Lee J.-H., Ku J.-L., Lee K.P., Kelley M.J., Won Y.-J., Kim S.-T., Park J.-G.
Mutation of p53 gene in hepatocellular carcinoma cell lines with HBX DNA.
Int. J. Cancer 67:898-902(1996)

PubMed=19956504; DOI=10.4143/crt.2005.37.1.1; PMCID=PMC2785416
Ku J.-L., Park J.-G.
Biology of SNU cell lines.
Cancer Res. Treat. 37:1-19(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=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=23505090; DOI=10.1002/hep.26402
Wang K., Lim H.Y., Shi S., Lee J., Deng S.-B., Xie T., Zhu Z., Wang Y.-L., Pocalyko D., Yang W.J., Rejto P.A., Mao M., Park C.-K., Xu J.-C.
Genomic landscape of copy number aberrations enables the identification of oncogenic drivers in hepatocellular carcinoma.
Hepatology 58:706-717(2013)

PubMed=23887712; DOI=10.1038/ncomms3218; PMCID=PMC3731665
Nault J.-C., Mallet M., Pilati C., Calderaro J., Bioulac-Sage P., Laurent C., Laurent A., Cherqui D., Balabaud C., Zucman-Rossi J.
High frequency of telomerase reverse-transcriptase promoter somatic mutations in hepatocellular carcinoma and preneoplastic lesions.
Nat. Commun. 4:2218.1-2218.7(2013)

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=25574106; DOI=10.3748/wjg.v21.i1.311; PMCID=PMC4284350
Cevik D., Yildiz G., Ozturk M.
Common telomerase reverse transcriptase promoter mutations in hepatocellular carcinomas from different geographical locations.
World J. Gastroenterol. 21:311-317(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=28196595; DOI=10.1016/j.ccell.2017.01.005; PMCID=PMC5501076
Li J., Zhao W., Akbani R., Liu W.-B., Ju Z.-L., Ling S.-Y., Vellano C.P., Roebuck P., Yu Q.-H., Eterovic A.K., Byers L.A., Davies M.A., Deng W.-L., Gopal Y.N.V., Chen G., von Euw E.M., Slamon D.J., Conklin D., Heymach J.V., Gazdar A.F., Minna J.D., Myers J.N., Lu Y.-L., Mills G.B., Liang H.
Characterization of human cancer cell lines by reverse-phase protein arrays.
Cancer Cell 31:225-239(2017)

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=31063779; DOI=10.1053/j.gastro.2019.05.001
Caruso S., Calatayud A.-L., Pilet J., La Bella T., Rekik S., Imbeaud S., Letouze E., Meunier L., Bayard Q., Rohr-Udilova N., Peneau C., Grasl-Kraupp B., de Koning L., Ouine B., Bioulac-Sage P., Couchy G., Calderaro J., Nault J.-C., Zucman-Rossi J., Rebouissou S.
Analysis of liver cancer cell lines identifies agents with likely efficacy against hepatocellular carcinoma and markers of response.
Gastroenterology 157:760-776(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=31378681; DOI=10.1016/j.ccell.2019.07.001; PMCID=PMC7505724
Qiu Z.-X., Li H., Zhang Z.-T., Zhu Z.-F., He S., Wang X.-J., Wang P.-C., Qin J.-J., Zhuang L.-P., Wang W., Xie F.-B., Gu Y., Zou K.-K., Li C., Li C., Wang C.-H., Cen J., Chen X.-T., Shu Y.-J., Zhang Z., Sun L.-L., Min L.-H., Fu Y., Huang X.-W., Lv H., Zhou H., Ji Y., Zhang Z.-G., Meng Z.-Q., Shi X.-L., Zhang H.-B., Li Y.-X., Hui L.-J.
A pharmacogenomic landscape in human liver cancers.
Cancer Cell 36:179-193.e11(2019)

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) ATCC; CRL-2233
KCLB; 00398
Cell line databases/resources CLO; CLO_0009098
MCCL; MCC:0000435
cancercelllines; CVCL_0077
Cell_Model_Passport; SIDM01181
Cosmic-CLP; 1240217
DepMap; ACH-000221
IGRhCellID; SNU398
LIMORE; SNU398
LINCS_LDP; LCL-1934
Anatomy/cell type resources BTO; BTO:0003170
Biological sample resources BioSample; SAMN03473191
BioSample; SAMN10987942
CRISP screens repositories BioGRID_ORCS_Cell_line; 368
Chemistry resources ChEMBL-Cells; CHEMBL3307619
ChEMBL-Targets; CHEMBL614454
GDSC; 1240217
PharmacoDB; SNU398_1458_2019
PubChem_Cell_line; CVCL_0077
Encyclopedic resources Wikidata; Q54955184
Experimental variables resources EFO; EFO_0002347
Gene expression databases ArrayExpress; E-MTAB-38
ArrayExpress; E-MTAB-2706
ArrayExpress; E-MTAB-2770
ArrayExpress; E-MTAB-3610
GEO; GSM481448
GEO; GSM565922
GEO; GSM827415
GEO; GSM887623
GEO; GSM888708
GEO; GSM936780
GEO; GSM1374890
GEO; GSM1670468
GEO; GSM2551587
Polymorphism and mutation databases Cosmic; 873393
Cosmic; 928143
Cosmic; 1187337
Cosmic; 1995640
Cosmic; 2009538
Cosmic; 2023868
Cosmic; 2162531
Cosmic; 2321036
Cosmic; 2771606
IARC_TP53; 6307
LiGeA; CCLE_422
Progenetix; CVCL_0077
Proteomic databases PRIDE; PXD030304
Sequence databases EGA; EGAS00001000610
EGA; EGAS00001000978
Entry history
Entry creation04-Apr-2012
Last entry update02-May-2024
Version number39