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Cellosaurus EB3 [Human Burkitt lymphoma] (CVCL_1185)

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Cell line name EB3 [Human Burkitt lymphoma]
Synonyms EB-3; Epstein-Barr-3; GM04679
Accession CVCL_1185
Resource Identification Initiative To cite this cell line use: EB3 [Human Burkitt lymphoma] (RRID:CVCL_1185)
Comments Problematic cell line: Partially contaminated. Some stocks (such as IFO50028) were contaminated by Daudi.
Part of: Cancer Dependency Map project (DepMap) (includes Cancer Cell Line Encyclopedia - CCLE).
Part of: COSMIC cell lines project.
Registration: International Cell Line Authentication Committee, Register of Misidentified Cell Lines; ICLAC-00380.
Population: African; Ugandan.
Doubling time: 48 hours (PubMed=5884338).
Microsatellite instability: Stable (MSS) (Sanger).
Transformant: NCBI_TaxID; 10376; Epstein-Barr virus (EBV).
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: In situ; Bone, jaw, maxilla; UBERON=UBERON_0002397.
Cell type: B-cell; CL=CL_0000236.
Sequence variations
  • Mutation; HGNC; 11998; TP53; Simple; p.Tyr163Cys (c.488A>G); ClinVar=VCV000127814; Zygosity=Heterozygous (Cosmic-CLP=906847; DepMap=ACH-002236).
  • Mutation; HGNC; 11998; TP53; Simple; p.Asn345Argfs*24 (c.1034_1037del); Zygosity=Heterozygous (Cosmic-CLP=906847; DepMap=ACH-002236).
  • Mutation; HGNC; 11998; TP53; Simple; c.1101-2A>G; ClinVar=VCV000141332; Zygosity=Heterozygous; Note=Splice acceptor mutation (Cosmic-CLP=906847; DepMap=ACH-002236).
HLA typing Source: PubMed=26589293
Class I
HLA-AA*03:01,30:02
HLA-BB*15:03,47:03
HLA-CC*02:02,07:01
Genome ancestry Source: PubMed=30894373

Origin% genome
African83.99
Native American0.51
East Asian, North5.96
East Asian, South0
South Asian0
European, North0
European, South9.53
Disease EBV-related Burkitt lymphoma (NCIt: C27694)
Burkitt lymphoma (ORDO: Orphanet_543)
Species of origin Homo sapiens (Human) (NCBI Taxonomy: 9606)
Sex of cell Male
Age at sampling 3Y
Category Cancer cell line
STR profile Source(s): ATCC=CCL-85; CCRID=1101HUM-PUMC000343; CLS=300373; Cosmic-CLP=906847; ECACC=90121003; PubMed=25877200

Markers:
AmelogeninX,Y
CSF1PO12,15
D2S133817,22
D3S135815,16
D5S8189,10
D6S104311,13
D7S82011
D8S117914
D12S39115
D13S31712,14
D16S53910,12
D18S5115,17
D19S43312.2,16.2
D21S1129
FGA22
Penta D10,11
Penta E14,16
TH017
TPOX6,9
vWA16,17,19 (Cosmic-CLP=906847)
17,19 (ATCC=CCL-85; CCRID=1101HUM-PUMC000343; CLS=300373; ECACC=90121003; PubMed=25877200)

Run an STR similarity search on this cell line
Web pages https://iclac.org/wp-content/uploads/Cross-Contaminations_v13_distribution.xlsx
https://cellbank.nibiohn.go.jp/legacy/cellbank/qualitycontrol/identification/summary.htm
Publications

PubMed=5884338
Epstein M.A., Barr Y.M., Achong B.G.
Studies with Burkitt's lymphoma.
Wistar Inst. Symp. Monogr. 4:69-82(1965)

PubMed=4169243; DOI=10.1093/jnci/39.5.1027
Klein G., Clifford P., Klein E., Smith R.T., Minowada J., Kourilsky F.M., Burchenal J.H.
Membrane immunofluorescence reactions of Burkitt lymphoma cells from biopsy specimens and tissue cultures.
J. Natl. Cancer Inst. 39:1027-1044(1967)

PubMed=6018567
Miles C.P., O'Neill F.
Chromosome studies of 8 in vitro lines of Burkitt's lymphoma.
Cancer Res. 27:392-402(1967)

PubMed=4894370; DOI=10.1002/1097-0142(196908)24:2<211::AID-CNCR2820240202>3.0.CO;2-3
Southam C.M., Burchenal J.H., Clarkson B.D. Sr., Tanzi A., Mackey R., McComb V.
Heterotransplantability of human cell lines derived from leukemia and lymphomas into immunologically tolerant rats.
Cancer 24:211-222(1969)

DOI=10.1007/BF02618370
Stulberg C.S., Coriell L.L., Kniazeff A.J., Shannon J.E.
The animal cell culture collection.
In Vitro 5:1-16(1970)

PubMed=4342611; DOI=10.1136/jcp.25.8.701; PMCID=PMC477481
Marston S.D., Almond E.J.P., Bishun N.P., Maunsell E.D., Sutton R.N.P.
A 'virus-free' cell line derived from a patient with infectious mononucleosis.
J. Clin. Pathol. 25:701-704(1972)

PubMed=4736620; DOI=10.1111/j.1469-1809.1973.tb00588.x
Povey S., Gardiner S.E., Watson B., Mowbray S., Harris H., Arthur E., Steel C.M., Blenkinsop C., Evans H.J.
Genetic studies on human lymphoblastoid lines: isozyme analysis on cell lines from forty-one different individuals and on mutants produced following exposure to a chemical mutagen.
Ann. Hum. Genet. 36:247-266(1973)

PubMed=7316467; DOI=10.1111/j.1469-1809.1980.tb00953.x
Povey S., Jeremiah S., Arthur E., Steel M., Klein G.
Differences in genetic stability between human cell lines from patients with and without lymphoreticular malignancy.
Ann. Hum. Genet. 44:119-133(1980)

PubMed=6286763; DOI=10.4049/jimmunol.129.3.1336
Benjamin D., Magrath I.T., Maguire R.T., Janus C., Todd-Kulikowsk H.D., Parsons R.G.
Immunoglobulin secretion by cell lines derived from African and American undifferentiated lymphomas of Burkitt's and non-Burkitt's type.
J. Immunol. 129:1336-1342(1982)

PubMed=2985879; DOI=10.1016/0145-2126(85)90084-0
Drexler H.G., Gaedicke G., Minowada J.
Isoenzyme studies in human leukemia-lymphoma cell lines -- 1 carboxylic esterase.
Leuk. Res. 9:209-229(1985)

PubMed=2998993
Steel C.M., Morten J.E.N., Foster E.
The cytogenetics of human B lymphoid malignancy: studies in Burkitt's lymphoma and Epstein-Barr virus-transformed lymphoblastoid cell lines.
IARC Sci. Publ. 60:265-292(1985)

PubMed=3159941; DOI=10.1016/0145-2126(85)90134-1
Drexler H.G., Gaedicke G., Minowada J.
Isoenzyme studies in human leukemia-lymphoma cell lines -- III Beta-hexosaminidase (E.C. 3.2.1.30).
Leuk. Res. 9:549-559(1985)

PubMed=3874327; DOI=10.1016/0145-2126(85)90133-x
Drexler H.G., Gaedicke G., Minowada J.
Isoenzyme studies in human leukemia-lymphoma cells lines -- II. Acid phosphatase.
Leuk. Res. 9:537-548(1985)

PubMed=3518877; DOI=10.3109/07357908609038260
Fogh J.
Human tumor lines for cancer research.
Cancer Invest. 4:157-184(1986)

PubMed=2052620; DOI=10.1073/pnas.88.12.5413; PMCID=PMC51883
Gaidano G., Ballerini P., Gong J.Z., Inghirami G., Neri A., Newcomb E.W., Magrath I.T., Knowles D.M., Dalla-Favera R.
p53 mutations in human lymphoid malignancies: association with Burkitt lymphoma and chronic lymphocytic leukemia.
Proc. Natl. Acad. Sci. U.S.A. 88:5413-5417(1991)

CLPUB00447
Mulivor R.A., Suchy S.F.
1992/1993 catalog of cell lines. NIGMS human genetic mutant cell repository. 16th edition. October 1992.
(In misc. document) Institute for Medical Research (Camden, N.J.) NIH 92-2011; pp.1-918; National Institutes of Health; Bethesda; USA (1992)

PubMed=8515068; DOI=10.4049/jimmunol.150.12.5418
Jain V.K., Judde J.-G., Max E.E., Magrath I.T.
Variable IgH chain enhancer activity in Burkitt's lymphomas suggests an additional, direct mechanism of c-myc deregulation.
J. Immunol. 150:5418-5428(1993)

PubMed=20164919; DOI=10.1038/nature08768; PMCID=PMC3145113
Bignell G.R., Greenman C.D., Davies H.R., Butler A.P., Edkins S., Andrews J.M., Buck G., Chen L., Beare D., Latimer C., Widaa S., Hinton J., Fahey C., Fu B.-Y., Swamy S., Dalgliesh G.L., Teh B.T., Deloukas P., Yang F.-T., Campbell P.J., Futreal P.A., Stratton M.R.
Signatures of mutation and selection in the cancer genome.
Nature 463:893-898(2010)

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=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=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=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; CCL-85
CLS; 300373
Coriell; GM04679
ECACC; 90121003
JCRB; IFO50028 - Discontinued
Cell line databases/resources CLO; CLO_0002874
CLO; CLO_0019013
cancercelllines; CVCL_1185
CCRID; 1101HUM-PUMC000343
Cell_Model_Passport; SIDM00793
CGH-DB; 9198-4
Cosmic-CLP; 906847
DepMap; ACH-002236
IGRhCellID; EB3
LINCS_LDP; LCL-2032
Biological sample resources BioSample; SAMN03473119
Chemistry resources ChEMBL-Cells; CHEMBL3308824
ChEMBL-Targets; CHEMBL2366369
GDSC; 906847
PharmacoDB; EB3_312_2019
PubChem_Cell_line; CVCL_1185
Encyclopedic resources Wikidata; Q54831748
Experimental variables resources EFO; EFO_0002174
Gene expression databases ArrayExpress; E-MTAB-38
ArrayExpress; E-MTAB-783
ArrayExpress; E-MTAB-2706
ArrayExpress; E-MTAB-3610
GEO; GSM1669748
Polymorphism and mutation databases Cosmic; 687840
Cosmic; 906847
Cosmic; 1818343
IARC_TP53; 155
IARC_TP53; 21145
Progenetix; CVCL_1185
Proteomic databases PRIDE; PXD030304
Sequence databases EGA; EGAS00001000610
EGA; EGAS00001000978
EGA; EGAS00001002554
Entry history
Entry creation04-Apr-2012
Last entry update02-May-2024
Version number43