Sarcoma

Research Article

Molecular Analysis of a Recurrent Sarcoma Identifies a Mutation in FAF1

Table 3

Deregulation of genes for drug disposition. Analysis of RNASeq for at least twofold overexpression (italic font) or underexpression (bold font) of genes for (a) transport and (b) metabolism in tumor compared to muscle and bone. For the export transporters (ABC transporters), only overexpression is considered relevant for drug resistance. Not shown in the table are the underexpressed genes (ABCA7, ABCA8, ABCA13, ABCB6, ABCB10, ABCC6, ABCC6P1, ABCC6P2, ABCC8, ABCC11, ABCD2, ABCG2, and ABCG5).

(a) Transport


Gene ID	Symbol	Name	Tumor bone	Tumor muscle
Gene ID	Symbol	Name	log₂-fold change	log₂-fold change

650655	ABCA17P	ATP-binding cassette, subfamily A (ABC1), member 17, pseudogene	1.360	2.116
24	ABCA4	ATP-binding cassette, subfamily A (ABC1), member 4	2.038	2.802

6555	SLC10A2	Solute carrier family 10 (sodium/bile acid cotransporter family), member 2	−1.962	−2.112
345274	SLC10A6	Solute carrier family 10 (sodium/bile acid cotransporter family), member 6	2.623	3.240
6563	SLC14A1	Solute carrier family 14 (urea transporter), member 1 (Kidd blood group)	−3.074	−3.152
6565	SLC15A2	Solute carrier family 15 (H+/peptide transporter), member 2	−2.027	−2.152
6566	SLC16A1	Solute carrier family 16, member 1 (monocarboxylic acid transporter 1)	1.401	2.170
117247	SLC16A10	Solute carrier family 16, member 10 (aromatic amino acid transporter)	2.113	2.848
6567	SLC16A2	Solute carrier family 16, member 2 (monocarboxylic acid transporter 8)	3.242	3.848
10786	SLC17A3	Solute carrier family 17 (sodium phosphate), member 3	−2.868	−2.959
6571	SLC18A2	Solute carrier family 18 (vesicular monoamine), member 2	−2.087	−2.194
6573	SLC19A1	Solute carrier family 19 (folate transporter), member 1	−2.099	−2.203
10560	SLC19A2	Solute carrier family 19 (thiamine transporter), member 2	1.820	2.548
80704	SLC19A3	Solute carrier family 19, member 3	−3.331	−3.478
387775	SLC22A10	Solute carrier family 22, member 10	5.711	6.085
9390	SLC22A13	Solute carrier family 22 (organic anion transporter), member 13	2.623	3.217
85413	SLC22A16	Solute carrier family 22 (organic cation/carnitine transporter), member 16	−8.101	−7.299
51310	SLC22A17	Solute carrier family 22, member 17	1.475	2.175
5002	SLC22A18	Solute carrier family 22, member 18	2.038	2.722
6582	SLC22A2	Solute carrier family 22 (organic cation transporter), member 2	4.793	5.216
6581	SLC22A3	Solute carrier family 22 (extraneuronal monoamine transporter), member 3	2.554	3.182
6583	SLC22A4	Solute carrier family 22 (organic cation/ergothioneine transporter), member 4	−3.603	−3.776
151295	SLC23A3	Solute carrier family 23 (nucleobase transporters), member 3	2.109	2.848
10478	SLC25A17	Solute carrier family 25 (mitochondrial carrier), member 17	1.311	2.077
83733	SLC25A18	Solute carrier family 25 (mitochondrial carrier), member 18	1.846	2.570
788	SLC25A20	Solute carrier family 25 (carnitine/acylcarnitine translocase), member 20	−2.105	−2.207
89874	SLC25A21	Solute carrier family 25 (mitochondrial oxodicarboxylate carrier), member 21	−2.962	−3.105
51312	SLC25A37	Solute carrier family 25, member 37	−4.633	−4.866
51629	SLC25A39	Solute carrier family 25, member 39	−2.585	−2.737
203427	SLC25A43	Solute carrier family 25, member 43	1.325	2.088
65012	SLC26A10	Solute carrier family 26, member 10	3.896	4.472
115111	SLC26A7	Solute carrier family 26, member 7	3.431	4.018
116369	SLC26A8	Solute carrier family 26, member 8	−5.354	−5.536
115019	SLC26A9	Solute carrier family 26, member 9	1.623	2.419
11001	SLC27A2	Solute carrier family 27 (fatty acid transporter), member 2	−4.278	−4.487
64078	SLC28A3	Solute carrier family 28 (sodium-coupled nucleoside transporter), member 3	−4.543	−4.812
222962	SLC29A4	Solute carrier family 29 (nucleoside transporters), member 4	−1.962	−2.045
81031	SLC2A10	Solute carrier family 2 (facilitated glucose transporter), member 10	2.532	3.170
6518	SLC2A5	Solute carrier family 2 (facilitated glucose/fructose transporter), member 5	−3.647	−3.821
55532	SLC30A10	Solute carrier family 30, member 10	−3.547	−3.725
7782	SLC30A4	Solute carrier family 30 (zinc transporter), member 4	2.832	3.372
6569	SLC34A1	Solute carrier family 34 (sodium phosphate), member 1	−4.716	−4.941
340146	SLC35D3	Solute carrier family 35, member D3	−5.662	−5.906
54733	SLC35F2	Solute carrier family 35, member F2	1.433	2.170
206358	SLC36A1	Solute carrier family 36 (proton/amino acid symporter), member 1	−2.265	−2.345
285641	SLC36A3	Solute carrier family 36 (proton/amino acid symporter), member 3	−2.284	−2.393
54020	SLC37A1	Solute carrier family 37 (glycerol-3-phosphate transporter), member 1	−2.112	−2.212
2542	SLC37A4	Solute carrier family 37 (glucose-6-phosphate transporter), member 4	−2.117	−2.219
151258	SLC38A11	Solute carrier family 38, member 11	2.410	3.085
55089	SLC38A4	Solute carrier family 38, member 4	1.837	2.548
92745	SLC38A5	Solute carrier family 38, member 5	−1.994	−2.152
91252	SLC39A13	Solute carrier family 39 (zinc transporter), member 13	1.301	2.070
23516	SLC39A14	Solute carrier family 39 (zinc transporter), member 14	2.569	3.188
29985	SLC39A3	Solute carrier family 39 (zinc transporter), member 3	−2.032	−2.152
283375	SLC39A5	Solute carrier family 39 (metal ion transporter), member 5	1.623	2.370
7922	SLC39A7	Solute carrier family 39 (zinc transporter), member 7	1.273	2.058
30061	SLC40A1	Solute carrier family 40 (iron-regulated transporter), member 1	−3.612	−3.796
84102	SLC41A2	Solute carrier family 41, member 2	1.293	2.070
8501	SLC43A1	Solute carrier family 43, member 1	−2.013	−2.152
57153	SLC44A2	Solute carrier family 44, member 2	−2.047	−2.152
50651	SLC45A1	Solute carrier family 45, member 1	2.038	2.722
146802	SLC47A2	Solute carrier family 47, member 2	−1.962	−2.026
6521	SLC4A1	Solute carrier family 4, anion exchanger, member 1	−6.513	−6.453
57282	SLC4A10	Solute carrier family 4, sodium bicarbonate transporter, member 10	−2.640	−2.753
83959	SLC4A11	Solute carrier family 4, sodium borate transporter, member 11	1.846	2.569
6508	SLC4A3	Solute carrier family 4, anion exchanger, member 3	1.261	2.045
8671	SLC4A4	Solute carrier family 4, sodium bicarbonate cotransporter, member 4	2.445	3.113
9497	SLC4A7	Solute carrier family 4, sodium bicarbonate cotransporter, member 7	2.717	3.307
6523	SLC5A1	Solute carrier family 5 (sodium/glucose cotransporter), member 1	−2.547	−2.705
159963	SLC5A12	Solute carrier family 5 (sodium/glucose cotransporter), member 12	4.753	5.206
6527	SLC5A4	Solute carrier family 5 (low affinity glucose cotransporter), member 4	−3.969	−4.249
6540	SLC6A13	Solute carrier family 6 (neurotransmitter transporter, GABA), member 13	1.328	2.092
55117	SLC6A15	Solute carrier family 6 (neutral amino acid transporter), member 15	1.623	2.333
388662	SLC6A17	Solute carrier family 6, member 17	2.038	2.728
54716	SLC6A20	Solute carrier family 6 (proline IMINO transporter), member 20	1.697	2.433
6532	SLC6A4	Solute carrier family 6 (neurotransmitter transporter, serotonin), member 4	−2.512	−2.611
6534	SLC6A7	Solute carrier family 6 (neurotransmitter transporter, L-proline), member 7	2.623	3.228
56301	SLC7A10	Solute carrier family 7, (neutral amino acid transporter, y+ system) member 10	−3.421	−3.603
6547	SLC8A3	Solute carrier family 8 (sodium/calcium exchanger), member 3	−2.204	−2.309
285335	SLC9A10	Solute carrier family 9, member 10	1.208	2.000
6549	SLC9A2	Solute carrier family 9 (sodium/hydrogen exchanger), member 2	2.038	2.706
9368	SLC9A3R1	Solute carrier family 9 (sodium/hydrogen exchanger), member 3 regulator 1	−2.760	−2.846
9351	SLC9A3R2	Solute carrier family 9 (sodium/hydrogen exchanger), member 3 regulator 2	1.889	2.619
84679	SLC9A7	Solute carrier family 9 (sodium/hydrogen exchanger), member 7	3.347	3.935
10599	SLCO1B1	Solute carrier organic anion transporter family, member 1B1	3.360	3.977
28234	SLCO1B3	Solute carrier organic anion transporter family, member 1B3	9.760	9.569
6578	SLCO2A1	Solute carrier organic anion transporter family, member 2A1	2.432	3.096
28232	SLCO3A1	Solute carrier organic anion transporter family, member 3A1	−2.032	−2.152
353189	SLCO4C1	Solute carrier organic anion transporter family, member 4C1	−6.850	−6.611

(b) Metabolism


Gene ID	Symbol	Name	Tumor bone	Tumor muscle
Gene ID	Symbol	Name	log₂-fold change	log₂-fold Cchange

1583	CYP11A1	Cytochrome P450, family 11, subfamily A, polypeptide 1	1.623	2.396
1589	CYP21A2	Cytochrome P450, family 21, subfamily A, polypeptide 2	−1.962	−2.036
1591	CYP24A1	Cytochrome P450, family 24, subfamily A, polypeptide 1	5.208	5.577
1592	CYP26A1	Cytochrome P450, family 26, subfamily A, polypeptide 1	2.623	3.257
1594	CYP27B1	Cytochrome P450, family 27, subfamily B, polypeptide 1	1.846	2.585
339761	CYP27C1	Cytochrome P450, family 27, subfamily C, polypeptide 1	3.585	4.178
1553	CYP2A13	Cytochrome P450, family 2, subfamily A, polypeptide 13	−1.962	−2.035
1580	CYP4B1	Cytochrome P450, family 4, subfamily B, polypeptide 1	−4.820	−5.065
66002	CYP4F12	Cytochrome P450, family 4, subfamily F, polypeptide 12	−6.070	−6.195
8529	CYP4F2	Cytochrome P450, family 4, subfamily F, polypeptide 2	−7.769	−7.060
4051	CYP4F3	Cytochrome P450, family 4, subfamily F, polypeptide 3	−8.244	−7.491
11283	CYP4F8	Cytochrome P450, family 4, subfamily F, polypeptide 8	−5.006	−5.270
260293	CYP4X1	Cytochrome P450, family 4, subfamily X, polypeptide 1	−2.476	−2.580
9420	CYP7B1	Cytochrome P450, family 7, subfamily B, polypeptide 1	2.502	3.170

2326	FMO1	Flavin containing monooxygenase 1	4.360	4.859
2327	FMO2	Flavin containing monooxygenase 2 (nonfunctional)	−4.074	−4.337
2328	FMO3	Flavin containing monooxygenase 3	−4.036	−4.309
388714	FMO6P	Flavin containing monooxygenase 6 pseudogene	−2.569	−2.737

493869	GPX8	Glutathione peroxidase 8 (putative)	2.814	3.371
2938	GSTA1	Glutathione S-transferase alpha 1	1.623	2.363
2939	GSTA2	Glutathione S-transferase alpha 2	2.038	2.741
2941	GSTA4	Glutathione S-transferase alpha 4	1.492	2.188
2953	GSTT2	Glutathione S-transferase theta 2	4.682	5.170
653689	GSTT2B	Glutathione S-transferase theta 2B (gene/pseudogene)	3.739	4.307

84779	NAA11	N(alpha)-acetyltransferase 11, NatA catalytic subunit	7.439	7.996
9027	NAT8	N-acetyltransferase 8 (GCN5-related, putative)	−2.769	−2.920

7358	UGDH	UDP-glucose 6-dehydrogenase	2.333	3.018
55757	UGGT2	UDP-glucose glycoprotein glucosyltransferase 2	1.604	2.271
10720	UGT2B11	UDP glucuronosyltransferase 2 family, polypeptide B11	−3.586	−3.768
7367	UGT2B17	UDP glucuronosyltransferase 2 family, polypeptide B17	−2.836	−2.959
54490	UGT2B28	UDP glucuronosyltransferase 2 family, polypeptide B28	−3.132	−3.284
167127	UGT3A2	UDP glycosyltransferase 3 family, polypeptide A2	−4.716	−4.907