Chemogenetic modulation of sensory neurons reveals their regulating role in melanoma progression

Costa, Pedro A. C.; Silva, Walison N.; Prazeres, Pedro H. D. M.; Picoli, Caroline C.; Guardia, Gabriela D. A.; Costa, Alinne C.; Oliveira, Mariana A.; Guimarães, Pedro P. G.; Gonçalves, Ricardo; Pinto, Mauro C. X.; Amorim, Jaime H.; Azevedo, Vasco A. C.; Resende, Rodrigo R.; Russo, Remo C.; Cunha, Thiago M.; Galante, Pedro A. F.; Mintz, Akiva; Birbrair, Alexander

doi:10.1186/s40478-021-01273-9

Acta Neuropathologica Communications

Table 2 Analyzes of genes from The Cancer Genome Atlas (TCGA) samples from 103 Skin Cutaneous Melanoma (SKCM) patients

From: Chemogenetic modulation of sensory neurons reveals their regulating role in melanoma progression

Up-regulated genes in alive × dead
Gene.symbol	log2FC	FDR
SLC5A4	4.35910	1.29E−09
VGF	3.26059	1.06E−05
NPPC	3.24826	2.60E−05
LINC00698	3.76414	3.90E−05
SPACA3	2.67598	1.97E−04
VCX3A	4.95714	2.21E−04
PRSS56	4.13411	4.15E−04
ARHGAP8	2.75929	4.15E−04
VCX	3.63292	4.28E−04
LINC01287	3.48781	7.19E−04
NGFR	1.99998	1.16E−03
NAT16	2.23940	1.16E−03
RP13-143G15.4	2.26728	1.34E−03
HLA-J	1.67323	1.38E−03
LHFPL4	2.80159	2.04E−03
RP11-376N17.4	2.27953	2.10E−03
ZNF689	1.08305	2.33E−03
DCD	6.91950	2.44E−03
SLITRK5	2.38821	2.59E−03
ARPP21	3.84108	2.67E−03
TFAP2B	2.73943	2.68E−03
VIT	2.42509	3.21E−03
HPCAL4	1.70772	3.30E−03
LINC00645	3.54408	4.05E−03
KLHL32	1.29974	4.09E−03
TRIML2	2.32595	4.80E−03
GFAP	2.04141	5.21E−03
MYOZ2	2.33172	6.94E−03
PPY	2.13167	7.88E−03
ARX	2.02055	8.39E−03
LRRTM2	1.75474	8.39E−03
C20orf203	1.95612	8.43E−03
LSMEM2	1.36377	8.43E−03
NRTN	1.74226	8.58E−03
RP11-809C18.3	1.54681	8.89E−03
FOSB	1.08702	9.10E−03
PASD1	4.57206	9.14E−03
UNC93B3	1.84987	9.14E−03
RP11-469H8.6	2.35144	9.14E−03
BCO1	2.17260	9.80E−03
XKR7	1.93913	1.00E−02
RDH5	1.36688	1.04E−02
PAGE1	3.69526	1.10E−02
RP5-907D15.4	1.73346	1.10E−02
AC003092.1	2.31155	1.20E−02
IGHV1-58	3.09550	1.20E−02
FOXG1	3.56195	1.36E−02
GBA3	2.67229	1.39E−02
FKSG51	1.89383	1.39E−02
BTNL8	1.87248	1.46E−02
ACHE	1.18749	1.52E−02
KCNJ11	1.81031	1.52E−02
ENPP7P2	1.45231	1.64E−02
CCKBR	2.06353	1.73E−02
PCSK1N	1.87835	1.76E−02
RP11-114G11.5	3.04186	1.76E−02
EFTUD1P1	2.13819	1.77E−02
OR2N1P	5.08848	1.83E−02
CA10	2.21148	1.85E−02
SLCO5A1	1.55420	1.88E−02
IBSP	1.81676	1.91E−02
RP11-88I21.1	3.56590	1.94E−02
MAGEA9	5.10603	1.96E−02
SYP	1.03514	2.15E−02
NBEAP1	1.55393	2.17E−02
RP5-965G21.4	1.14894	2.18E−02
MPZ	1.95997	2.22E−02
RP11-299H22.3	2.95030	2.22E−02
FBXO2	1.34819	2.31E−02
LGSN	2.41190	2.31E−02
RDH8	2.14341	2.32E−02
AC073325.2	1.90901	2.38E−02
GAGE1	3.92238	2.44E−02
MYB	1.16344	2.55E−02
AATK	1.23997	2.63E−02
DOK7	1.48390	2.72E−02
AC068580.7	2.45353	2.72E−02
RP11-36D19.9	1.99056	2.72E−02
HAPLN2	1.51979	2.73E−02
TDRD12	2.24362	3.09E−02
RP11-159H10.3	1.83751	3.18E−02
CHGB	1.62908	3.32E−02
RCN3	1.25033	3.32E−02
RP5-1171I10.5	1.33948	3.32E−02
NMRK2	2.15724	3.33E−02
TNNI3	1.50305	3.33E−02
DPEP3	1.81124	3.33E−02
DPYSL5	2.12990	3.33E−02
ZNF365	1.53513	3.39E−02
KCNQ2	1.98246	3.51E−02
PMP2	2.27248	3.53E−02
HAVCR1	2.17185	3.56E−02
RP1-140K8.5	1.72113	3.72E−02
ROR1-AS1	2.03339	3.75E−02
C1QTNF1-AS1	1.82857	3.75E−02
WFDC1	1.74139	3.99E−02
DEFB126	2.40171	3.99E−02
LBP	1.71514	3.99E−02
CDH12	2.39970	3.99E−02
FABP7	2.11963	3.99E−02
MAGEB17	1.73309	3.99E−02
MYBPC1	1.99301	3.99E−02
RP4-764D2.1	1.03824	4.07E−02
CD5L	1.77129	4.21E−02
CPN2	1.81842	4.21E−02
ZNF727	2.20430	4.21E−02
CST1	2.16587	4.35E−02
RP11-9G1.3	2.55148	4.48E−02
LL22NC03-22D1.1	2.49624	4.50E−02
NPFFR1	1.60868	4.54E−02
MYRIP	1.45769	4.67E−02
RP11-369C8.1	2.61906	4.95E−02

Down-regulated genes in alive × dead
Gene.symbol	log2FC	FDR
AVPR1A	− 2.06066	8.65E−08
KRT16P2	− 5.08308	1.00E−07
CHST8	− 3.38063	7.38E−07
ST6GAL2	− 2.68516	1.74E−06
PRSS35	− 3.35395	4.71E−6
SLC8A3	− 3.18840	9.15E−06
CRABP1	− 3.07142	9.15E−6
HSPB3	− 3.24770	2.15E−05
TREX2	− 2.43750	2.15E−05
B3GNT4	− 1.77784	2.26E−05
NPTX1	− 2.61603	1.97E−04
PI3	− 3.60121	2.70E−04
HEYL	-1.67534	2.99E−04
ID3	− 1.32736	3.67E−04
ADRB2	− 1.81924	3.91E−04
C6orf223	− 2.13191	4.15E−04
AJAP1	− 1.92423	4.56E−04
CHRNA4	− 2.95110	4.69E−04
RHCG	− 2.92093	5.10E−04
PART1	− 2.14901	5.50E−04
ALOX12	− 1.23574	5.50E−04
RSPO3	− 1.48997	6.13E−04
GDPD3	− 1.74062	7.38E−04
CNFN	− 2.84236	8.27E−04
ANO2	− 1.70534	9.14E−04
OVOL1	− 2.75293	9.14E−04
CLDN4	− 2.52180	9.56E−04
GREB1L	− 2.35313	1.12E−03
IGLV9-49	− 3.84182	1.20E−03
TGM1	− 2.85878	1.28E−03
CYSRT1	− 2.10472	1.34E−03
LYPD5	− 2.27815	1.34E−03
CYP19A1	− 1.84923	1.41E−03
ACTG2	− 1.63424	1.41E−03
ABCG4	− 2.12582	1.41E−03
FAM3D	− 2.12972	1.41E−03
PAPSS2	− 1.50601	1.41E−03
AC124789.1	− 2.07689	1.41E−03
RASL11B	− 1.54784	1.43E−03
MAFB	− 1.28214	1.43E−03
NGF	− 1.73693	2.01E−03
AC006116.20	− 1.47472	2.01E−03
S100A12	− 2.64402	2.10E−03
KLK14	− 2.29647	2.39E−03
IL1RN	− 2.09008	2.39E−03
B3GNT8	− 1.78028	2.39E−03
GPX3	− 1.88978	2.39E−03
CDA	− 2.22423	2.68E−03
CHN1	− 1.30585	2.68E−03
PRSS27	− 1.71351	2.68E−03
TMEM79	− 1.43989	3.52E−03
NOTCH3	− 1.22297	3.57E−03
FGF18	− 1.35348	3.80E−03
HGF	− 1.19158	4.28E−03
SH3RF3	− 1.23159	4.49E−03
KRT37	− 4.22818	4.57E−03
SH3RF3-AS1	− 1.31293	4.57E−03
ZC3H12A	− 1.35742	4.67E−03
TBX4	− 1.84817	5.39E−03
CLIC3	− 2.31078	5.58E−03
LRRC43	− 1.34142	5.69E−03
NRARP	− 1.42862	5.97E−03
B3GNT3	− 1.97566	6.61E−03
ELF3	− 2.07351	6.73E−03
LRRN2	− 1.90993	6.80E−03
NFE4	− 2.76901	6.80E−03
KLK10	− 2.72909	6.94E−03
LINC01121	− 1.68460	7.15E−03
SDCBP2	− 1.48707	7.88E−03
FAM83G	− 1.50253	7.88E−03
ZNF469	− 1.06394	7.88E−03
ROR2	− 1.15831	7.92E−03
LYNX1	− 1.75074	7.92E−03
VSIG10L	− 1.54237	7.92E−03
PITX1	− 2.50531	8.39E−03
PNMA5	− 2.07397	8.43E−03
LTB4R2	− 1.38009	8.43E−03
GTSF1	− 1.95376	8.89E−03
RP3-449H6.1	− 2.80745	8.89E−03
PKDCC	− 1.47224	9.03E−03
C11orf87	− 1.86276	9.10E−03
C9orf47	− 1.63063	9.10E−03
KLK12	− 3.43996	9.10E−03
SPNS2	− 1.33949	9.43E−03
TCHH	− 1.56077	1.00E−02
ADRA1D	− 1.45232	1.01E−02
LINC00675	− 2.28274	1.01E−02
GLP1R	− 1.93142	1.04E−02
DLX5	− 1.61403	1.05E−02
JUP	− 1.81687	1.10E−02
GREM1	− 1.36182	1.10E−02
FUT2	− 1.65558	1.10E−02
FLJ43879	− 1.73000	1.10E−02
RP4-530I15.9	− 1.37950	1.10E−02
ADAMTSL4	− 1.15965	1.10E−02
LGALS9C	− 1.74166	1.11E−02
RP11-145A3.1	− 1.28593	1.20E−02
LINC00689	− 2.44100	1.20E−02
RP11-57C13.6	− 2.13756	1.20E−02
WNT11	− 1.67218	1.23E−02
SOX11	− 1.31510	1.27E−02
SMCO2	− 1.86262	1.29E−02
AC104654.2	− 1.54674	1.34E−02
RP11-715H19.2	− 2.54830	1.45E−02
MALL	− 1.65870	1.50E−02
SLPI	− 2.56276	1.50E−02
ZNF385B	− 1.82165	1.52E−02
AC079305.10	− 1.07337	1.52E−02
RARRES1	− 1.09119	1.56E−02
C1orf177	− 1.80915	1.64E−02
MIR4635	− 1.81095	1.68E−02
KCNK12	− 1.74033	1.70E−02
CTC-525D6.2	− 3.65998	1.75E−02
FGF7	− 1.14265	1.76E−02
KRT82	− 2.71344	1.76E−02
CTD-2554C21.3	− 2.09957	1.76E−02
VNN3	− 1.87348	1.94E−02
KRT17P6	− 2.54509	1.94E−02
CD36	− 1.47332	1.98E−02
ALDH1L1	− 1.84277	1.99E−02
KRT25	− 3.64328	2.04E−02
GLIS3	− 1.24797	2.06E−02
SPRR2D	− 2.65861	2.06E−02
CEACAM19	− 1.48405	2.11E−02
ZNF154	− 1.19730	2.12E−02
FBLIM1	− 1.00682	2.15E−02
OR7E11P	− 3.14060	2.15E−02
ZNF185	− 1.43741	2.27E−02
MYOC	− 3.14651	2.30E−02
SULT2B1	− 2.16618	2.31E−02
PLA2G4E−AS1	− 1.49669	2.32E−02
IL36G	− 2.54342	2.39E−02
IGKV2-29	− 3.58127	2.43E−02
PADI3	− 1.60173	2.45E−02
WDR87	− 2.67496	2.45E−02
CTD-2555C10.3	− 1.62741	2.45E−02
SMPD3	− 1.51129	2.63E−02
LYPD3	− 2.15151	2.63E−02
SPINK9	− 2.18753	2.63E−02
RP3-405J10.2	− 1.89008	2.63E−02
KRT17	− 2.51044	2.65E−02
RP11-845M18.6	− 2.34005	2.70E−02
CPXM2	− 1.33321	2.72E−02
GDPD2	− 1.69177	2.79E−02
LINC01482	− 1.58713	2.84E−02
KRT8P13	− 2.24864	3.07E−02
ANGPT2	− 1.42767	3.23E−02
TMEM45B	− 1.81149	3.23E−02
KLK13	-2.41601	3.23E−02
IGHE	− 2.55145	3.23E−02
SPRR2A	− 2.94281	3.23E−02
RP11-91J3.3	− 1.87453	3.23E−02
CTC-490G23.2	− 2.34066	3.32E−02
ADAMTS15	− 1.20759	3.33E−02
RHOD	− 1.51767	3.33E−02
COL28A1	− 1.56903	3.33E−02
RP11-752L20.3	− 1.07531	3.33E−02
AC133785.1	− 2.02852	3.47E−02
GNA15	− 1.37100	3.49E−02
FAM46B	− 1.22702	3.53E−02
KRT80	− 2.07094	3.53E−02
TWIST2	− 1.11079	3.53E−02
KRT42P	− 2.45179	3.53E−2
PRSS50	− 1.86776	3.64E−02
TBX1	− 1.26122	3.69E−2
KRT81	− 1.69382	3.75E−02
ALOX12B	− 2.41352	3.75E−02
KCNMA1-AS1	− 1.82562	3.79E−02
HS3ST3A1	− 1.28721	3.84E−02
USP2	− 1.07928	3.99E−02
BMP4	− 1.23615	3.99E−02
G6PC2	− 2.36196	3.99E−02
RP11-169K16.4	− 1.98903	3.99E−02
COL8A1	− 1.22669	4.09E−02
SIX2	− 1.02697	4.09E−02
KRT17P2	− 2.21877	4.21E−02
BDKRB1	− 1.22248	4.35E−02
LINC00857	− 1.30729	4.35E−02
CREB3L1	− 1.04632	4.44E−02
CCBE1	− 1.04094	4.44E−02
PRR15L	− 1.31182	4.48E−02
ST8SIA2	− 1.70296	4.50E−02
S100A9	− 2.02615	4.55E−02
SIK1	− 1.83293	4.60E−02
EPN3	− 1.93269	4.65E−02
ZBTB16	− 1.22227	4.67E−02
ATP8B5P	− 1.00252	4.76E−02
DUOX1	− 1.72011	4.78E−02
TRIM53CP	− 2.79481	4.80E−02
C6orf132	− 1.81165	4.87E−02
MDFI	− 1.36942	4.91E−02
CATSPERB	− 1.85527	4.94E−02
HSPE1P5	− 1.47888	4.94E−02
DEFB4A	− 3.10613	4.95E−02
SDC1	− 1.36628	4.96E−02

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