Multiomics characterization of pyroptosis in the tumor microenvironment and therapeutic relevance in metastatic melanoma

Chen, Wenqiong; He, Yi; Zhou, Guowei; Chen, Xiang; Ye, Youqiong; Zhang, Guanxiong; Liu, Hong

doi:10.1186/s12916-023-03175-0

Table 1 Pyroptosis-related genes used in this study

From: Multiomics characterization of pyroptosis in the tumor microenvironment and therapeutic relevance in metastatic melanoma

Symbol ID	Aliase or full name	Gene ID	Ensembl ID	Known functions reported by previous studies	Source	PMID
NOD2	NLRC2	64,127	ENSG00000167207	Activation of inflammasome	Literature	25,879,280
TNFRSF1A	TNFR1	7132	ENSG00000067182	Activation of inflammasome	Literature	25,879,280
TNFRSF1B	TNFR2	7133	ENSG00000028137	Activation of inflammasome	Literature	25,879,280
TLR4		7099	ENSG00000136869	Activation of inflammasome	Literature	25,879,280
AIM2		9447	ENSG00000163568	Inflammasome	Literature; MSigDB-GOBP_PYROPTOSIS	33,692,549
NLRP1		22,861	ENSG00000091592	Inflammasome	Literature; MSigDB-GOBP_PYROPTOSIS	33,692,549
NLRP3		114,548	ENSG00000162711	Inflammasome	Literature; MSigDB-GOBP_PYROPTOSIS	33,692,549
ZBP1		81,030	ENSG00000124256	Inflammasome	Literature; MSigDB-GOBP_PYROPTOSIS	32,729,116; 34,471,287
NLRC4		58,484	ENSG00000091106	Inflammasome	Literature; MSigDB-GOBP_PYROPTOSIS	33,692,549
NAIP	BIRC1; NLRB1; psiNAIP	4671	ENSG00000249437	Inflammasome	Literature; MSigDB-GOBP_PYROPTOSIS	31,662,274
NLRP6		171,389	ENSG00000174885	Inflammasome	Literature; MSigDB-GOBP_PYROPTOSIS	35,138,947
NLRP7		199,713	ENSG00000167634	Inflammasome	Literature	22,361,007
NLRP9		338,321	ENSG00000185792	Inflammasome	Literature; MSigDB-GOBP_PYROPTOSIS	35,138,947; 28,636,595; 28,731,031
DHX9		1660	ENSG00000135829	Inflammasome	Literature; MSigDB-GOBP_PYROPTOSIS	28,636,595; 28,731,031
NLRP12		91,662	ENSG00000142405	Inflammasome	Literature	32,838,963; 32,295,623
MEFV		4210	ENSG00000103313	Inflammasome	Literature; MSigDB-GOBP_PYROPTOSIS	25,879,280
PYCARD	ASC	29,108	ENSG00000103490	Adaptor protein	Literature; MSigDB-GOBP_PYROPTOSIS	33,692,549
CASP1		834	ENSG00000137752	Cleavage protein	Literature; MSigDB-GOBP_PYROPTOSIS; MSigDB-REACTOME_PYROPTOSIS	32,553,275; 32,109,412; 31,216,460
CASP4		837	ENSG00000196954	Cleavage protein	Literature; MSigDB-GOBP_PYROPTOSIS; MSigDB-REACTOME_PYROPTOSIS	32,109,412; 31,216,460; 22,895,188; 25,119,034
CASP5		838	ENSG00000137757	Cleavage protein	Literature; MSigDB-REACTOME_PYROPTOSIS	32,109,412; 31,216,460; 25,119,034
CASP3		836	ENSG00000164305	Cleavage protein	Literature; MSigDB-REACTOME_PYROPTOSIS	28,459,430; 32,188,940; 28,392,147
CASP6		839	ENSG00000138794	Cleavage protein	MSigDB-GOBP_PYROPTOSIS
CASP8		841	ENSG00000064012	Cleavage protein	Literature; MSigDB-GOBP_PYROPTOSIS	30,381,458; 31,748,744; 31,723,262; 30,361,383; 34,012,073
GZMA		3001	ENSG00000145649	Cleavage protein	Literature; MSigDB-GOBP_PYROPTOSIS	32,299,851
GZMB		3002	ENSG00000100453	Cleavage protein	Literature; MSigDB-GOBP_PYROPTOSIS; MSigDB-REACTOME_PYROPTOSIS	32,188,940
ELANE		1991	ENSG00000197561; ENSG00000277571	Cleavage protein	Literature; MSigDB-GOBP_PYROPTOSIS; MSigDB-REACTOME_PYROPTOSIS	29,539,421
CTSG		1511	ENSG00000100448	Cleavage protein	Literature	33,692,549
GSDMA		284,110	ENSG00000167914	Executor	Literature; MSigDB-GOBP_PYROPTOSIS	29,362,479; 31,690,840; 29,695,864; 35,110,732
GSDMB		55,876	ENSG00000073605	Executor	Literature; MSigDB-GOBP_PYROPTOSIS	32,299,851; 29,362,479; 31,690,840
GSDMC		56,169	ENSG00000147697	Executor	Literature; MSigDB-GOBP_PYROPTOSIS	29,362,479
GSDMD		79,792	ENSG00000104518; ENSG00000278718	Executor	Literature; MSigDB-GOBP_PYROPTOSIS; MSigDB-REACTOME_PYROPTOSIS	32,553,275; 32,109,412; 26,375,003; 26,375,259; 26,611,636; 27,281,216; 27,383,986; 27,339,137; 27,418,190; 27,573,174; 29,195,811; 29,274,245; 29,362,479; 31,690,840
DFNA5	GSDME	1687	ENSG00000105928	Executor	Literature; MSigDB-GOBP_PYROPTOSIS; MSigDB-REACTOME_PYROPTOSIS	28,459,430; 32,188,940; 29,362,479; 31,690,840
DFNB59	PJVK	494,513	ENSG00000204311	Executor	Literature	29,362,479
PLCG1		5335	ENSG00000124181	Pore-forming	Literature	29,937,272
RRAGA	RAGA	10,670	ENSG00000155876	Pore-forming	Literature	34,289,345; 35,058,659
RRAGC	RAGC	64,121	ENSG00000116954	Pore-forming	Literature	34,289,345; 35,058,659
LAMTOR1	C11orf59	55,004	ENSG00000149357	Pore-forming	Literature	34,289,345; 35,058,659
LAMTOR2		28,956	ENSG00000116586	Pore-forming	Literature	34,289,345; 35,058,659
MAPKSP1	LAMTOR3	8649	ENSG00000109270	Pore-forming	Literature	34,289,345; 35,058,659
C7orf59	LAMTOR4	389,541	ENSG00000188186	Pore-forming	Literature	34,289,345; 35,058,659
HBXIP	LAMTOR5	10,542	ENSG00000134248	Pore-forming	Literature	34,289,345; 35,058,659
FNIP2		57,600	ENSG00000052795	Pore-forming	Literature	34,289,345; 35,058,659
FLCN	Folliculin	201,163	ENSG00000154803	Pore-forming	Literature	34,289,345; 35,058,659
NINJ1		4814	ENSG00000131669	Pore-forming	Literature	33,472,215
IL1A		3552	ENSG00000115008	Released substance	MSigDB-REACTOME_PYROPTOSIS
IL1B		3553	ENSG00000125538	Released substance	Literature; MSigDB-REACTOME_PYROPTOSIS	29,195,811; 29,274,245
IL18		3606	ENSG00000150782	Released substance	Literature; MSigDB-REACTOME_PYROPTOSIS	29,195,811; 29,274,245
HMGB1		3146	ENSG00000189403	Released substance	Literature; MSigDB-REACTOME_PYROPTOSIS	33,692,549
GPX4		2879	ENSG00000167468	Negative regulators	Literature	29,937,272
CHMP1A		5119	ENSG00000131165	Negative regulators	Literature	30,467,171; 32,669,618
CHMP1B		57,132	ENSG00000255112	Negative regulators	Literature	30,467,171; 32,669,618
CHMP2A		27,243	ENSG00000130724	Negative regulators	Literature; MSigDB-REACTOME_PYROPTOSIS	30,467,171; 32,669,618
CHMP2B		25,978	ENSG00000083937	Negative regulators	Literature; MSigDB-REACTOME_PYROPTOSIS	30,467,171; 32,669,618
VPS24	CHMP3	51,652	ENSG00000115561	Negative regulators	Literature; MSigDB-REACTOME_PYROPTOSIS	30,467,171; 32,669,618
CHMP4A		29,082	ENSG00000254505; ENSG00000285302	Negative regulators	Literature; MSigDB-REACTOME_PYROPTOSIS	30,467,171; 32,669,618
CHMP4B		128,866	ENSG00000101421	Negative regulators	Literature; MSigDB-REACTOME_PYROPTOSIS	30,467,171; 32,669,618
CHMP4C		92,421	ENSG00000164695	Negative regulators	Literature; MSigDB-REACTOME_PYROPTOSIS	30,467,171; 32,669,618
CHMP5		51,510	ENSG00000086065	Negative regulators	Literature	30,467,171; 32,669,618
CHMP6		79,643	ENSG00000176108	Negative regulators	Literature; MSigDB-REACTOME_PYROPTOSIS	30,467,171; 32,669,618
CHMP7		91,782	ENSG00000147457	Negative regulators	Literature; MSigDB-REACTOME_PYROPTOSIS	30,467,171; 32,669,618
KIAA0174	CHMP8; IST1	9798	ENSG00000182149	Negative regulators	Literature	30,467,171; 32,669,618
CFLAR	cFILP	8837	ENSG00000003402	Negative regulators	Literature	32,193,329
DDX3X		1654	ENSG00000215301	Negative regulators	Literature	31,511,697
MIR223	MicroRNA 223	407,008	ENSG00000284567	Negative regulators	Literature; MSigDB-GOBP_PYROPTOSIS	23,772,809
APIP		51,074	ENSG00000149089		MSigDB-GOBP_PYROPTOSIS
ZAK	MAP3K20	51,776	ENSG00000091436		MSigDB-GOBP_PYROPTOSIS
TREM2		54,209	ENSG00000095970		MSigDB-GOBP_PYROPTOSIS
DPP9		91,039	ENSG00000142002		MSigDB-GOBP_PYROPTOSIS
BAK1		578	ENSG00000030110		MSigDB-REACTOME_PYROPTOSIS
TP63		8626	ENSG00000073282		MSigDB-REACTOME_PYROPTOSIS
BAX		581	ENSG00000087088		MSigDB-REACTOME_PYROPTOSIS
IRF1		3659	ENSG00000125347		MSigDB-REACTOME_PYROPTOSIS
IRF2		3660	ENSG00000168310		MSigDB-REACTOME_PYROPTOSIS
TP53		7157	ENSG00000141510		MSigDB-REACTOME_PYROPTOSIS
CYCS		54,205	ENSG00000172115		MSigDB-REACTOME_PYROPTOSIS

1. MSigDB-GOBP_PYROPTOSIS: 28 genes
2. MSigDB-REACTOME_PYROPTOSIS: 27 genes
3. MSigDB-GOBP_PYROPTOSIS and MSigDB-REACTOME_PYROPTOSIS were downloaded from MSigDB, with the files named “MSigDB-GOBP_PYROPTOSIS.v2023.1.Hs.grp” and “MSigDB-REACTOME_PYROPTOSIS.v2023.1.Hs.grp”

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ISSN: 1741-7015

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