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Cellosaurus LN-229 (CVCL_0393)

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Cell line name LN-229
Synonyms LN 229; LN229; LNT-229
Accession CVCL_0393
Resource Identification Initiative To cite this cell line use: LN-229 (RRID:CVCL_0393)
Comments Part of: Cancer Dependency Map project (DepMap) (includes Cancer Cell Line Encyclopedia - CCLE).
Part of: COSMIC cell lines project.
Population: Caucasian.
Doubling time: 24 hours (PubMed=9842975); 31 hours (PubMed=25984343).
Microsatellite instability: Stable (MSS) (Sanger).
Omics: Cell surface proteome.
Omics: CNV analysis.
Omics: CRISPR phenotypic screen.
Omics: Deep exome analysis.
Omics: Deep proteome analysis.
Omics: Deep quantitative proteome analysis.
Omics: DNA methylation analysis.
Omics: HLA class I peptidome analysis by proteomics.
Omics: shRNA library screening.
Omics: SNP array analysis.
Omics: Transcriptome analysis by microarray.
Omics: Transcriptome analysis by RNAseq.
Misspelling: LN22; Cosmic=2580915.
Derived from site: In situ; Brain, right frontal parieto-occipital cortex.
Sequence variations
  • Gene deletion; HGNC; 1787; CDKN2A; Zygosity=Homozygous (PubMed=9842975).
  • Mutation; HGNC; 6597; LIFR; Simple; p.Pro1060Ala (c.3178C>G); Zygosity=Heterozygous (Cosmic-CLP=1240169).
  • Mutation; HGNC; 9811; RAD21; Simple; p.Gln132Ter (c.394C>T); Zygosity=Heterozygous (Cosmic-CLP=1240169).
  • Mutation; HGNC; 11730; TERT; Simple; c.1-124C>T (c.228C>T) (C228T); Zygosity=Unspecified; Note=In promoter (PubMed=31068700).
  • Mutation; HGNC; 11998; TP53; Simple; p.Pro98Leu (c.293C>T); ClinVar=VCV000528236; Zygosity=Homozygous (PubMed=10416987; Cosmic-CLP=1240169).
HLA typing Source: PubMed=27412690
Class I
HLA-AA*03:01:01
HLA-BB*35:01
HLA-CC*04:01:01

Source: PubMed=26589293
Class I
HLA-AA*03:01,03:01
HLA-BB*35:01,35:01
HLA-CC*04:01,04:01
Class II
HLA-DQDQA1*01:01,01:01
DQB1*05:01,05:01
HLA-DRDRB1*01:01,11:19
Genome ancestry Source: PubMed=30894373

Origin% genome
African0
Native American0
East Asian, North2.23
East Asian, South0
South Asian0.02
European, North59.47
European, South38.27
Disease Glioblastoma (NCIt: C3058)
Glioblastoma (ORDO: Orphanet_360)
Species of origin Homo sapiens (Human) (NCBI Taxonomy: 9606)
Hierarchy Children:
CVCL_D7FE (LN-229-EGFP)CVCL_D7FD (LN-229-Luc)CVCL_WS33 (LN-229_indWIF1)
CVCL_D2RW (LN229/CD133)CVCL_D2TH (LN229/CD19)CVCL_D2TI (LN229/CD19ec)
CVCL_A8V5 (LN229/CD20)CVCL_D2TV (LN229/ectodomain-PODXL)CVCL_D2SN (LN229/EGFR)
CVCL_D2T3 (LN229/HER2)CVCL_D2S5 (LN229/hPD-L1)CVCL_D2U6 (LN229/hPDPN)
CVCL_D2R8 (LN229/mCCR3)CVCL_D2RM (LN229/mCD39)CVCL_D2SJ (LN229/mEGFR)
CVCL_D2SR (LN229/mHER2)CVCL_D2TU (LN229/PODXL)CVCL_D2TP (PDIS-13)
CVCL_E0XD (Ubigene LN-229 PICALM KO)CVCL_E0XE (Ubigene LN-229 RSRP1 KO)
Sex of cell Female
Age at sampling 60Y
Category Cancer cell line
STR profile Source(s): AddexBio=C0005017/4993; ATCC=CRL-2611; Cosmic-CLP=1240169; PubMed=22570425; PubMed=25877200; Technion Genomics Center

Markers:
AmelogeninX
CSF1PO12
D1S165614,17
D2S44110,11
D2S133819,20
D3S135816,17
D5S81811 (PubMed=25877200)
11,12 (AddexBio=C0005017/4993; ATCC=CRL-2611; Cosmic-CLP=1240169; PubMed=22570425; Technion Genomics Center)
D7S82011 (PubMed=25877200)
8,11 (AddexBio=C0005017/4993; ATCC=CRL-2611; Cosmic-CLP=1240169; PubMed=22570425; Technion Genomics Center)
D8S117913,14
D10S124816
D12S39120,22
D13S31710,11
D16S53912
D18S5113,15
D19S43312,17.2
D21S1129,30
D22S104515,16
FGA23
Penta D10,11
Penta E7,16
TH019.3
TPOX8
vWA16,19

Run an STR similarity search on this cell line
Publications

PubMed=7693337
Li H., Hamou M.-F., de Tribolet N., Jaufeerally R., Hofmann M., Diserens A.-C., Van Meir E.G.
Variant CD44 adhesion molecules are expressed in human brain metastases but not in glioblastomas.
Cancer Res. 53:5345-5349(1993)

PubMed=8509230; DOI=10.1002/ijc.2910540329
Rimoldi D., Romero P., Carrel S.
The human melanoma antigen-encoding gene, MAGE-1, is expressed by other tumour cells of neuroectodermal origin such as glioblastomas and neuroblastomas.
Int. J. Cancer 54:527-528(1993)

PubMed=9842975; DOI=10.1002/(SICI)1097-0215(19981218)79:6<640::AID-IJC15>3.0.CO;2-z
Weller M., Rieger J., Grimmel C., Van Meir E.G., De Tribolet N., Krajewski S., Reed J.C., von Deimling A., Dichgans J.
Predicting chemoresistance in human malignant glioma cells: the role of molecular genetic analyses.
Int. J. Cancer 79:640-644(1998)

DOI=10.1007/0-306-46861-1_11
Ali-Osman F.
Brain tumors.
(In book chapter) Human cell culture. Vol. 2. Cancer cell lines part 2; Masters J.R.W., Palsson B.O. (eds.); pp.167-184; Kluwer Academic Publishers; New York; USA (1999)

PubMed=10416987; DOI=10.1111/j.1750-3639.1999.tb00536.x; PMCID=PMC8098486
Ishii N., Maier D., Merlo A., Tada M., Sawamura Y., Diserens A.-C., Van Meir E.G.
Frequent co-alterations of TP53, p16/CDKN2A, p14ARF, PTEN tumor suppressor genes in human glioma cell lines.
Brain Pathol. 9:469-479(1999)

PubMed=14614447; DOI=10.1038/sj.onc.1207198
Wischhusen J., Naumann U., Ohgaki H., Rastinejad F., Weller M.
CP-31398, a novel p53-stabilizing agent, induces p53-dependent and p53-independent glioma cell death.
Oncogene 22:8233-8245(2003)

PubMed=14655754; DOI=10.1111/j.1750-3639.2003.tb00479.x; PMCID=PMC8095903
Bahr O., Rieger J., Duffner F., Meyermann R., Weller M., Wick W.
P-glycoprotein and multidrug resistance-associated protein mediate specific patterns of multidrug resistance in malignant glioma cell lines, but not in primary glioma cells.
Brain Pathol. 13:482-494(2003)

PubMed=16697959; DOI=10.1016/j.ccr.2006.03.030
Lee J., Kotliarova S., Kotliarov Y., Li A.-G., Su Q., Donin N.M., Pastorino S., Purow B.W., Christopher N., Zhang W., Park J.K., Fine H.A.
Tumor stem cells derived from glioblastomas cultured in bFGF and EGF more closely mirror the phenotype and genotype of primary tumors than do serum-cultured cell lines.
Cancer Cell 9:391-403(2006)

PubMed=17595512; DOI=10.1159/000104150
Rieger J., Frank B., Weller M., Wick W.
Mechanisms of resistance of human glioma cells to Apo2 ligand/TNF-related apoptosis-inducing ligand.
Cell. Physiol. Biochem. 20:23-34(2007)

PubMed=19365568; DOI=10.1371/journal.pone.0005209; PMCID=PMC2666263
Bax D.A., Little S.E., Gaspar N., Perryman L., Marshall L., Viana-Pereira M., Jones T.A., Williams R.D., Grigoriadis A., Vassal G., Workman P., Sheer D., Reis R.M., Pearson A.D.J., Hargrave D., Jones C.
Molecular and phenotypic characterisation of paediatric glioma cell lines as models for preclinical drug development.
PLoS ONE 4:E5209-E5209(2009)

PubMed=20504876; DOI=10.1093/neuonc/noq051; PMCID=PMC2940700
Berger B., Capper D., Lemke D., Pfenning P.-N., Platten M., Weller M., von Deimling A., Wick W., Weiler M.
Defective p53 antiangiogenic signaling in glioblastoma.
Neuro-oncol. 12:894-907(2010)

PubMed=21406405; DOI=10.1158/0008-5472.CAN-10-3112
Grzmil M., Morin P. Jr., Lino M.M., Merlo A., Frank S., Wang Y.-H., Moncayo G., Hemmings B.A.
MAP kinase-interacting kinase 1 regulates SMAD2-dependent TGF-beta signaling pathway in human glioblastoma.
Cancer Res. 71:2392-2402(2011)

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=22570425; DOI=10.1093/neuonc/nos072; PMCID=PMC3367844
Bady P., Diserens A.-C., Castella V., Kalt S., Heinimann K., Hamou M.-F., Delorenzi M., Hegi M.E.
DNA fingerprinting of glioma cell lines and considerations on similarity measurements.
Neuro-oncol. 14:701-711(2012)

PubMed=25984343; DOI=10.1038/sdata.2014.35; PMCID=PMC4432652
Cowley G.S., Weir B.A., Vazquez F., Tamayo P., Scott J.A., Rusin S., East-Seletsky A., Ali L.D., Gerath W.F.J., Pantel S.E., Lizotte P.H., Jiang G.-Z., Hsiao J., Tsherniak A., Dwinell E., Aoyama S., Okamoto M., Harrington W., Gelfand E.T., Green T.M., Tomko M.J., Gopal S., Wong T.C., Li H.-B., Howell S., Stransky N., Liefeld T., Jang D., Bistline J., Meyers B.H., Armstrong S.A., Anderson K.C., Stegmaier K., Reich M., Pellman D., Boehm J.S., Mesirov J.P., Golub T.R., Root D.E., Hahn W.C.
Parallel genome-scale loss of function screens in 216 cancer cell lines for the identification of context-specific genetic dependencies.
Sci. Data 1:140035-140035(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=25894527; DOI=10.1371/journal.pone.0121314; PMCID=PMC4404347
Bausch-Fluck D., Hofmann A., Bock T., Frei A.P., Cerciello F., Jacobs A., Moest H., Omasits U., Gundry R.L., Yoon C., Schiess R., Schmidt A., Mirkowska P., Hartlova A.S., Van Eyk J.E., Bourquin J.-P., Aebersold R., Boheler K.R., Zandstra P.W., Wollscheid B.
A mass spectrometric-derived cell surface protein atlas.
PLoS ONE 10:E0121314-E0121314(2015)

PubMed=26496030; DOI=10.18632/oncotarget.6171; PMCID=PMC4791243
Patil V., Pal J., Somasundaram K.
Elucidating the cancer-specific genetic alteration spectrum of glioblastoma derived cell lines from whole exome and RNA sequencing.
Oncotarget 6:43452-43471(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=25772239; DOI=10.1038/onc.2015.61
Vassallo I., Zinn P.O., Lai M., Rajakannu P., Hamou M.-F., Hegi M.E.
WIF1 re-expression in glioblastoma inhibits migration through attenuation of non-canonical WNT signaling by downregulating the lncRNA MALAT1.
Oncogene 35:12-21(2016)

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=27412690; DOI=10.1074/mcp.M116.060350; PMCID=PMC5013317
Shraibman B., Kadosh D.M., Barnea E., Admon A.
Human leukocyte antigen (HLA) peptides derived from tumor antigens induced by inhibition of DNA methylation for development of drug-facilitated immunotherapy.
Mol. Cell. Proteomics 15:3058-3070(2016)

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=30971826; DOI=10.1038/s41586-019-1103-9
Behan F.M., Iorio F., Picco G., Goncalves E., Beaver C.M., Migliardi G., Santos R., Rao Y., Sassi F., Pinnelli M., Ansari R., Harper S., Jackson D.A., McRae R., Pooley R., Wilkinson P., van der Meer D.J., Dow D., Buser-Doepner C.A., Bertotti A., Trusolino L., Stronach E.A., Saez-Rodriguez J., Yusa K., Garnett M.J.
Prioritization of cancer therapeutic targets using CRISPR-Cas9 screens.
Nature 568:511-516(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) AddexBio; C0005017/4993
ATCC; CRL-2611
CLS; 305043
Ubigene; YC-A021
Cell line databases/resources CLO; CLO_0007363
MCCL; MCC:0000288
cancercelllines; CVCL_0393
Cell_Model_Passport; SIDM00684
Cosmic-CLP; 1240169
DepMap; ACH-000595
LINCS_LDP; LCL-1354
Lonza; 1322
Anatomy/cell type resources BTO; BTO:0002004
Biological sample resources BioSample; SAMN03471191
BioSample; SAMN03471692
BioSample; SAMN10987619
CRISP screens repositories BioGRID_ORCS_Cell_line; 929
Chemistry resources ChEMBL-Cells; CHEMBL4295402
ChEMBL-Targets; CHEMBL4296459
GDSC; 1240169
PharmacoDB; LN229_841_2019
PubChem_Cell_line; CVCL_0393
Encyclopedic resources Wikidata; Q54902771
Experimental variables resources EFO; EFO_0006637
Gene expression databases ArrayExpress; E-MTAB-2706
ArrayExpress; E-MTAB-2770
ArrayExpress; E-MTAB-3610
GEO; GSM101615
GEO; GSM101616
GEO; GSM326200
GEO; GSM397665
GEO; GSM397666
GEO; GSM481416
GEO; GSM887270
GEO; GSM888345
GEO; GSM1374621
GEO; GSM1670049
GEO; GSM2113428
GEO; GSM2113429
GEO; GSM2113430
GEO; GSM2113431
Polymorphism and mutation databases Cosmic; 849861
Cosmic; 1746958
Cosmic; 1995485
Cosmic; 2302323
Cosmic; 2367492
Cosmic; 2491102
Cosmic; 2516025
Cosmic; 2580915
IARC_TP53; 30212
LiGeA; CCLE_871
Progenetix; CVCL_0393
Proteomic databases PRIDE; PXD000589
PRIDE; PXD003790
PRIDE; PXD030304
Sequence databases EGA; EGAS00001000610
EGA; EGAS00001000978
Entry history
Entry creation04-Apr-2012
Last entry update10-Sep-2024
Version number41