Correlation of gene expression and associated mutation profiles of APOBEC3A, APOBEC3B, REV1, UNG, and FHIT with chemosensitivity of cancer cell lines to drug treatment

Vural, Suleyman; Simon, Richard; Krushkal, Julia

doi:10.1186/s40246-018-0150-x

Human Genomics

Table 6 Strongest significant correlations between candidate gene expression and drug sensitivity

From: Correlation of gene expression and associated mutation profiles of APOBEC3A, APOBEC3B, REV1, UNG, and FHIT with chemosensitivity of cancer cell lines to drug treatment

Cancer category	Gene	Agent	n	ρ	p	p _adj	Drug action/alternative name	Reference
PAAD	APOBEC3A	JQ1^a	28	− 0.819	9.70 × 10⁻⁸	0.0001	BET inhibitor	[78]
PRAD	APOBEC3A	PD-0332991^a	5	− 1.000	1.40 × 10⁻²⁴	1.75 × 10⁻²¹	Palbociclib; CDK 4/6 inhibitor	[100]
PRAD	APOBEC3B	GDC0941^a	5	− 1.000	1.40 × 10⁻²⁴	1.75 × 10⁻²¹	Pictilisib; pan-class I PI3K inhibitor	[101]
PRAD	APOBEC3B	KIN001-260^a	5	− 1.000	1.40 × 10⁻²⁴	1.75 × 10⁻²¹	IKKb inhibitor	[36]
PRAD	APOBEC3B	EHT 1864^a	5	− 1.000	1.40 × 10⁻²⁴	1.75 × 10⁻²¹	Rac inhibitor	[102]
PRAD	APOBEC3B	Nutlin-3a^a	5	− 1.000	1.40 × 10⁻²⁴	1.75 × 10⁻²¹	Inhibitor of MDM2-p53 interaction	[87]
CESC	APOBEC3B	ZM-447439^a	5	− 1.000	1.40 × 10⁻²⁴	1.75 × 10⁻²¹	Aurora kinase inhibitor	[103]
MM	APOBEC3B	QL-VIII-58^a	5	− 1.000	1.40 × 10⁻²⁴	1.75 × 10⁻²¹	Inhibitor of mTOR and ATR signaling	[36]
MM	APOBEC3B	ZG-10^a	5	− 1.000	1.40 × 10⁻²⁴	1.75 × 10⁻²¹	Inhibitor of JNK1 and p38 signaling	[36]
SAR	APOBEC3B	TGX221^a	6	− 1.000	< 4.95 × 10⁻³²⁴	< 4.95 × 10⁻³²⁴	PI3Kβ inhibitor	[36]
CESC	REV1	MLN4924^a	5	− 1.000	1.40 × 10⁻²⁴	1.75 × 10⁻²¹	Pevodenistat; NAE inhibitor	[36]
RCC	REV1	XMD8-92^a	6	− 1.000	< 4.95 × 10⁻³²⁴	< 4.95 × 10⁻³²⁴	BMK1/ERK5 inhibitor	[104]
NSCLC	REV1	RDEA119^a	123	0.381	1.35 × 10⁻⁵	0.0153	Refametinib; BAY 86-9766; MEK inhibitor	[83]
NSCLC	REV1	PD-0325901^a	106	0.405	1.64 × 10⁻⁵	0.0179	MEK inhibitor	[81]
NSCLC	REV1	AKT inhibitor VIII^a	121	0.373	2.51 × 10⁻⁵	0.0262	AKT inhibitor	[36]
NSCLC	REV1	Embelin^a	121	0.366	3.61 × 10⁻⁵	0.0349	XIAP inhibitor	[36]
NSCLC	REV1	Trametinib^a	121	0.361	4.71 × 10⁻⁵	0.0436	MEK inhibitor	[84]
NSCLC	REV1	AZD6482^a	130	0.348	4.84 × 10⁻⁵	0.0436	PI3Kβ inhibitor	[36]
NSCLC	REV1	PD-0332991^a	100	0.392	5.41 × 10⁻⁵	0.0471	Palbociclib; CDK 4/6 inhibitor	[100]
PRAD	REV1	NSC-207895^a	5	1.000	1.40 × 10⁻²⁴	1.75 × 10⁻²¹	MDMX inhibitor	[105]
PRAD	REV1	Piperlongumine^a	5	1.000	1.40 × 10⁻²⁴	1.75 × 10⁻²¹	Piplartine; ROS induction	[36]
PRAD	UNG	ZM-447439^a	5	1.000	1.40 × 10⁻²⁴	1.75 × 10⁻²¹	Aurora kinase inhibitor	[103]
PRAD	UNG	NU-7441^a	5	1.000	1.40 × 10⁻²⁴	1.75 × 10⁻²¹	DNA-PK inhibitor	[36]
PRAD	UNG	CCT007093^a	5	− 1.000	1.40 × 10⁻²⁴	1.75 × 10⁻²¹	PPM1D inhibitor	[36]
PRAD	UNG	JQ1^a	5	− 1.000	1.40 × 10⁻²⁴	1.75 × 10⁻²¹	BET inhibitor	[78]
PRAD	FHIT	NVP-BHG712^a	5	− 1.000	1.40 × 10^− 24	1.75 × 10⁻²¹	EphB4 inhibitor	[36]
CESC	FHIT	MK-2206^a	5	− 1.000	1.40 × 10⁻²⁴	1.75 × 10⁻²¹	AKT inhibitor	[36]
MEL	FHIT	TAE684^b	38	0.621	3.24 × 10⁻⁵	0.0325	ALK inhibitor	[36]
SCLC	FHIT	ABT-869^a	6	− 1.000	< 4.95 × 10⁻³²⁴	< 4.95 × 10⁻³²⁴	Linifanib; VEGFR/PDGFR family receptor inhibitor	[106]
SCLC	FHIT	Mitomycin C^a	6	− 1.000	< 4.95 × 10⁻³²⁴	< 4.95 × 10⁻³²⁴	DNA cross-linking/monoalkylating agent	[36, 107]
Pan-cancer	APOBEC3B	17-AAG^a	536	− 0.293	4.25 × 10⁻¹²	5.85 × 10⁻⁹	HSP90 inhibitor	[85]

Shown are statistically significant correlations satisfying |ρ| > 0.25, p_adj < 0.05. The p values were adjusted for false discovery rate accounting for 5 genes and 255 agents with 275 drug sensitivity measures from CCLE or GDSC resources (N_tests = 1375 for pan-cancer analysis). Among individual cancer categories, FDR adjustment also accounted for 26 cancer categories with ≥ 5 available cell lines in each category with both gene expression and drug sensitivity data for correlation analysis (N_tests = 26,110). Abbreviations of cancer categories are provided in the legend of Table 1
n sample size for correlation analysis, ρ Spearman correlation coefficient, p p value prior to FDR adjustment, p_adj FDR-adjusted p value, BET bromodomain and extraterminal family of proteins, BRAF v-raf murine sarcoma viral oncogene homolog B, CDK cyclin-dependent kinase, DNA-PK DNA-dependent protein kinase, HDAC histone deacetylase, HSP90 molecular chaperone heat shock protein 90, MEK mitogen-activated protein kinase kinases, NAE NEDD8-activating enzyme E1, PI3K phosphatidylinositol-3-kinase, ROS reactive oxygen species, XIAP X-linked inhibitor of apoptosis
^aDrug sensitivity data from GDSC [30, 35]
^bDrug sensitivity data from Cancer Cell Line Encyclopedia (CCLE) [33]

Back to article page

ISSN: 1479-7364

Contact us

General enquiries: journalsubmissions@springernature.com