The UBC-40 Urothelial Bladder Cancer cell line index: a genomic resource for functional studies

Earl, Julie; Rico, Daniel; Carrillo-de-Santa-Pau, Enrique; Rodríguez-Santiago, Benjamín; Méndez-Pertuz, Marinela; Auer, Herbert; Gómez, Gonzalo; Grossman, Herbert Barton; Pisano, David G; Schulz, Wolfgang A; Pérez-Jurado, Luis A; Carrato, Alfredo; Theodorescu, Dan; Chanock, Stephen; Valencia, Alfonso; Real, Francisco X

doi:10.1186/s12864-015-1450-3

BMC Genomics

Table 1 Genetic characterization and copy number analysis of the major oncogenes and tumor suppressor genes involved in UBC cell lines

From: The UBC-40 Urothelial Bladder Cancer cell line index: a genomic resource for functional studies

Name	Source	Grade	Sex	*FGFR3*	*PIK3CA*	*HRAS*	*KRAS2*	*NRAS*	*TERT*	*INK4A* CN status	*TP53* (Mutation/CN)	Genome instability group
253J	UCC	G4	F	WT^1,4	E545G^2,4	WT⁴	WT¹	WT⁴	WT¹¹	HD ^1,4	WT/N³	Intermediate
5637	UCC	G2	M	WT^1,4	WT^1,4	WT^1,4	WT⁴	WT¹	Mut¹¹	WT^1,4	c.839G > C/N^1,2,3	Intermediate
575A	UCC	G3	M	WT^1,4	WT⁴					WT	WT/LOH¹	Intermediate
639V	UCC	G3	M	WT^1,4/R248C²	A1066V^1,2,4	WT^1,4	WT¹/G12D²	WT^1/H131R²	Mut¹¹	LOH⁴	c.743G > A/N^1,2,3	High
92-1	UCC	G3	F	WT^1,4	WT⁴	WT⁴	WT⁴	WT⁴	Mut^11,12	WT^6,4	cd 158, 162, 228, 280 & 294/N^6,8	Intermediate
96-1	UCC	G2/3	M	WT^1,4	WT⁴	WT⁴	WT⁴	WT⁴	Mut^11,12	HD⁶	cd 175/N^6,8	Intermediate
97-1	UCC	G1/2	M	WT^1,4	WT⁴	WT⁴	WT⁴	WT⁴	WT¹¹	HD⁶	WT/LOH^6,8	LOW
97-18	UCC	G3	Y	WT^1,4	WT⁴	WT⁴	WT⁴	WT⁴	Mut^11,12	LOH⁴	cd 220/LOH⁸	High
97-24		G3	Y	WT^1,4	WT⁴	WT⁴	WT⁴	WT⁴	Mut^11,12	WT⁴	cd 275/N⁸	High
97-7	UCC	G2/3	Y	S249C¹	WT⁴	WT⁴	WT⁴	WT⁴	Mut¹¹	WT4	cd 128/N⁸	High
BC61	UCC	G2	Y	G372C^4,10	WT⁴	WT⁴	WT⁴	WT⁴		WT4	WT/N	Low
HT1197	UCC	G4	M	S249C^1,4	E545K^1,4	WT^1,4	WT¹	WT¹/Q61R⁴	Mut^11,12	WT¹	WT¹/c.1094A- > G³
HT1376	UCC	G3	F	WT^1,4	WT^1,4	WT^1,4	WT¹	WT¹	Mut¹¹	WT^1,4	c.749C > T/LOH^1,2,3	Low
HU456		G1	M			WT⁴	G12S⁴	WT⁴	WT¹²	HD⁴	WT/N⁷	Intermediate
J82	EC	G3	M	WT¹/K652E^2,4	P124L^1,2,4	WT^1,4	WT¹	WT¹	Mut¹¹	WT^1,4	c.960G- > C&c.820G- > T&c.811G- > A&c.783_919del137/N^1,2,3	Intermediate
JON	UCC			WT¹/S249C¹	WT⁴	WT⁴	WT⁴	WT⁴	Mut¹¹/WT¹²		Mut⁴
KK47		G1	M			WT⁴	WT⁴	WT⁴	WT¹²	WT⁴	N	High
LGWO1 G600				WT^1,4	WT⁴	WT⁴	G12C⁴	WT⁴	WT¹²	HD⁴	LOH	Low
MGH-U3	UCC	G1	M	Y375C⁴/Y373C¹	WT⁴	WT⁴	WT⁴	WT⁴	Mut^11,12	HD⁴	WT/N⁴	Low
MGH-U4	focal severe urothelial atypia	G1	M	WT^1,4	H1047R⁴				Mut¹²	HD⁴	WT/N⁴	Low
PSI	UCC	G3	M			WT⁴	WT⁴	WT⁴	Mut¹²		WT⁷
RT112	UCC	G2	F	WT^1,2,4/Amp⁴ /FGFR3-TACC3 fusion ¹³	WT^1,4	WT^1,4	WT¹	WT¹	Mut^11,12	HD^1,4	c.743G > A&c.548C- > G/LOH^1,2,3	Low
RT4	UCC	G1	M	WT^1,4/Amp⁴/FGFR3-TACC3 fusion ¹³	WT¹	WT	WT¹	WT¹	Mut^11,12	HD^1,4	WT/LOH^1,3	Low
SCaBER	SCC		M	WT^1,2,4	WT	WT⁴	WT⁴	WT¹	Mut^11,12	LOH⁴	c.329G > T/LOH^2,3	Intermediate
SW-1710	UCC		F	WT^1,2,4	WT^1,4	WT^1,4	WT¹	WT	Mut^11,12	HD¹	c.817C > T/LOH^1,2,3	High
SW-800	UCC		M	WT^1,4	WT⁴	WT⁴	WT⁴	WT⁴	Mut¹²	HD⁴	WT/N⁴	Low
SW-850				WT⁴	WT⁴	G12V⁴	WT⁴	WT⁴
SW-780	UCC	G1	F	WT^1,2/S773F² /FGFR3-BAIAP2L1 fusion ¹³	WT^1,	WT¹	WT¹	WT¹	Mut¹²	HD⁴	WT/N¹	Low
T24	EC	G3	F	WT^1,4	WT^1,4	G12V^1,4	WT¹	WT¹	Mut^11,12	WT¹/LOH⁴	c.378C > G/N^1,3	Low
TCCSUP	UCC	G4	F	WT^1,4	E545K¹	WT^1,4	WT¹	WT¹	Mut^11,12	WT¹	c.1045G > T/LOH^1,3	Intermediate
UM-UC-1	UCC-LN	G2	M	WT¹	WT⁴	WT⁴	WT⁴	WT⁴		HD⁴	c.454C- > T/LOH^2,3,5	Intermediate
UMUC- 2	UCC	CIS	M	WT¹					Mut¹²		WT⁵
UM-UC-3	UCC		M	WT^1,4	WT^1,4	WT^1,4	G12C^1,2,4	WT¹	Mut¹¹	HD¹/WT⁴	c.338 T > G/N^1,3,5,9	High
UM-UC-4	UCC-LC		F	WT⁴	WT⁴					WT⁴	LOH	High
UM-UC-5			F	WT⁴	E545K⁴	WT⁴	WT⁴	WT⁴	Mut¹²	HD⁴	LOH	Intermediate
UM-UC-6	UCC		M	WT¹/R248C⁴	E545K⁴	WT⁴				HD⁴	WT/LOH^1,5,9	Low
UM-UC-7			M	WT⁴	WT⁴	WT⁴			Mut¹²	WT⁴	LOH	Intermediate
UM-UC-9	UCC			WT⁴	WT⁴	WT⁴			Mut¹²	LOH⁴	Mut/LOH^5,9	Intermediate
UM-UC-10	UCC			WT⁴	WT⁴	WT⁴	WT⁴	WT⁴	Mut¹²		Mut⁵
UM-UC-11	UCC			WT⁴	WT⁴	WT⁴	WT⁴	WT⁴	Mut¹²	HD⁴	WT/N⁵	High
UM-UC-12	UCC		Y	WT⁴	WT⁴	WT⁴	WT⁴	WT⁴		WT⁴	N	High
UM-UC-13	UCC-LN		Y	WT⁴	WT⁴	WT⁴	WT⁴	WT⁴	Mut¹²	LOH⁴	Mut/N⁵	High
UM-UC-14	UCC		Y	S249C¹	WT⁴				Mut^11,12	HD⁴	Mut/LOH^5,9	Low
UM-UC-15	UCC			Y375C⁴	E545K⁴	WT⁴	WT⁴	WT⁴	Mut¹²
UM-UC-17				S249C⁴	WT⁴					HD⁴	LOH	Intermediate
UM-UC-18				WT⁴	WT⁴	Q61K⁴	WT⁴	WT⁴	Mut¹²	WT⁴	N	High
VM-CUB-1	EC	G2	M	WT¹	WT¹/E542K + E674Q²	WT¹	WT¹	WT¹	Mut^11,12	c.322G > C¹/LOH⁴	c.524G > A&c.378C- > G/LOH^1,23	High
VM-CUB-2	EC		M	WT^1,4	WT⁴	WT⁴	WT⁴	WT⁴	Mut¹¹	HD^1,4	c.473G- > T&c.488A- > G/LOH³	High
VM-CUB-3	EC	G3	M	WT^1,4	E545K⁴	WT⁴	WT⁴	WT⁴	Mut¹¹	HD⁴	c.833C- > T/N³	Low

All TERT mutations were -124 bp(G > A) except the line marked as #-57 bp(T > G).
Amp, amplification; WT, wild type; Mut, mutant; LOH, loss of heterozygosity; HD, homozygous deletion; N, copy number neutral; Y, Y chromosome detected.
¹COSMIC database; ²CCLE database; ³IARC database1, COSMIC database; 2, CCLE database; 3, IARC database; ⁴our data; ⁵Specific TP53 mutation is not specified. [35]; ⁶ TP53 mutation determined by expression analysis [36]; ⁷[45]; ⁸specific mutation not reported [46], ⁹[47]; ¹⁰[48]; ¹¹[49]. ¹²[13]. ¹³[17].

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ISSN: 1471-2164

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