TISIDB

Summary
Symbol	SPTLC2
Name	serine palmitoyltransferase, long chain base subunit 2
Aliases	KIAA0526; LCB2; LCB2A; hLCB2a; HSN1C; NSAN1C; LCB 2; SPT 2; long chain base biosynthesis protein 2a; serine ......
Chromosomal Location	14q24.3
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Basic function annotation. > Subcellular Location, Domain and Function > Gene Ontology > KEGG and Reactome Pathway

> Subcellular Location, Domain and Function [ TOP ]
Subcellular Location	Endoplasmic reticulum membrane Single-pass membrane protein
Domain	PF00155 Aminotransferase class I and II
Function	Serine palmitoyltransferase (SPT). The heterodimer formed with LCB1/SPTLC1 constitutes the catalytic core. The composition of the serine palmitoyltransferase (SPT) complex determines the substrate preference. The SPTLC1-SPTLC2-SPTSSA complex shows a strong preference for C16-CoA substrate, while the SPTLC1-SPTLC2-SPTSSB complex displays a preference for C18-CoA substrate.

> Gene Ontology [ TOP ]
Biological Process	GO:0006066 alcohol metabolic process GO:0006643 membrane lipid metabolic process GO:0006644 phospholipid metabolic process GO:0006665 sphingolipid metabolic process GO:0006667 sphinganine metabolic process GO:0006670 sphingosine metabolic process GO:0006672 ceramide metabolic process GO:0006684 sphingomyelin metabolic process GO:0006686 sphingomyelin biosynthetic process GO:0006914 autophagy GO:0008654 phospholipid biosynthetic process GO:0009894 regulation of catabolic process GO:0009896 positive regulation of catabolic process GO:0010506 regulation of autophagy GO:0010508 positive regulation of autophagy GO:0016042 lipid catabolic process GO:0016236 macroautophagy GO:0016239 positive regulation of macroautophagy GO:0016241 regulation of macroautophagy GO:0019216 regulation of lipid metabolic process GO:0019751 polyol metabolic process GO:0030148 sphingolipid biosynthetic process GO:0031329 regulation of cellular catabolic process GO:0031331 positive regulation of cellular catabolic process GO:0034311 diol metabolic process GO:0034312 diol biosynthetic process GO:0044242 cellular lipid catabolic process GO:0044283 small molecule biosynthetic process GO:0045834 positive regulation of lipid metabolic process GO:0046165 alcohol biosynthetic process GO:0046173 polyol biosynthetic process GO:0046467 membrane lipid biosynthetic process GO:0046511 sphinganine biosynthetic process GO:0046512 sphingosine biosynthetic process GO:0046513 ceramide biosynthetic process GO:0046519 sphingoid metabolic process GO:0046520 sphingoid biosynthetic process GO:0050994 regulation of lipid catabolic process GO:0050996 positive regulation of lipid catabolic process GO:0061724 lipophagy GO:0097164 ammonium ion metabolic process GO:1901615 organic hydroxy compound metabolic process GO:1901617 organic hydroxy compound biosynthetic process GO:1904502 regulation of lipophagy GO:1904504 positive regulation of lipophagy
Molecular Function	GO:0004758 serine C-palmitoyltransferase activity GO:0016408 C-acyltransferase activity GO:0016409 palmitoyltransferase activity GO:0016454 C-palmitoyltransferase activity GO:0016746 transferase activity, transferring acyl groups GO:0016747 transferase activity, transferring acyl groups other than amino-acyl groups GO:0030170 pyridoxal phosphate binding GO:0043168 anion binding GO:0048037 cofactor binding
Cellular Component	GO:0002178 palmitoyltransferase complex GO:0017059 serine C-palmitoyltransferase complex GO:0031211 endoplasmic reticulum palmitoyltransferase complex

> KEGG and Reactome Pathway [ TOP ]
KEGG	hsa04071 Sphingolipid signaling pathway hsa00600 Sphingolipid metabolism hsa01100 Metabolic pathways
Reactome	R-HSA-1430728: Metabolism R-HSA-556833: Metabolism of lipids and lipoproteins R-HSA-1660661: Sphingolipid de novo biosynthesis R-HSA-428157: Sphingolipid metabolism

Summary
Symbol	SPTLC2
Name	serine palmitoyltransferase, long chain base subunit 2
Aliases	KIAA0526; LCB2; LCB2A; hLCB2a; HSN1C; NSAN1C; LCB 2; SPT 2; long chain base biosynthesis protein 2a; serine ......
Chromosomal Location	14q24.3
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Literatures that report relations between SPTLC2 and anti-tumor immunity. The specific mechanism were also collected if the literature reports that a gene specifically promotes or inhibits the infiltration or function of T/NK cells.

> Text Mining [ TOP ]
There is no record.

Summary
Symbol	SPTLC2
Name	serine palmitoyltransferase, long chain base subunit 2
Aliases	KIAA0526; LCB2; LCB2A; hLCB2a; HSN1C; NSAN1C; LCB 2; SPT 2; long chain base biosynthesis protein 2a; serine ......
Chromosomal Location	14q24.3
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	High-throughput screening data (e.g. CRISPR-Cas9, shRNA and RNAi) for T cell-mediated killing. Genetic screen techniques can identify mechanisms of tumor cell resistance (e.g., PTPN2) and sensitivity (e.g., APLNR) to killing by cytotoxic T cells, the central effectors of anti-tumor immunity. After comprehensively searching, eight groups of screening data sets were collected in the current database. In this tab, users can check whether their selected genes cause resistance or increase sensitivity to T cell-mediated killing in various data sets.

> High-throughput Screening

[ TOP ]

Statistical results of SPTLC2 in screening data sets for detecting immune reponses.

PMID	Screening System	Cancer Type	Cell Line	Data Set	Statistical Results	Relation to immunity
29301958	CRISPR-Cas9	melanoma	B16F10	Pmel-1 T cell	NA/NS	NA/NS
29301958	CRISPR-Cas9	melanoma	B16F10	OT-1 T cell	logFC: -2.62; FDR: 0.00722	Resistant to T cell-mediated killing
28783722	CRISPR-Cas9	melanoma	Mel624	2CT-CRISPR	NA/NS	NA/NS
28723893	CRISPR-Cas9	melanoma	B16	GVAX+Anti-PD1	NA/NS	NA/NS
28723893	CRISPR-Cas9	melanoma	B16	GVAX	NA/NS	NA/NS
25691366	RNAi	Breast cancer	MCF7	Luc-CTL assay	NA/NS	NA/NS
24476824	shRNA	melanoma	B16	Primary screen	NA/NS	NA/NS
24476824	shRNA	melanoma	B16	Secondary screen	NA/NS	NA/NS

Summary
Symbol	SPTLC2
Name	serine palmitoyltransferase, long chain base subunit 2
Aliases	KIAA0526; LCB2; LCB2A; hLCB2a; HSN1C; NSAN1C; LCB 2; SPT 2; long chain base biosynthesis protein 2a; serine ......
Chromosomal Location	14q24.3
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Transcriptomic and genomic profiling of pre-treated tumor biopsies from responders and non-responders to immunotherapy. These data were used to identify signatures and mechanisms of response to checkpoint blockade (e.g., anti-PDL1 and anti-PD1). One example is that mutations in the gene PBRM1 benefit clinical survival of patients with clear cell renal cell carcinoma. After comprehensively searching, we collected 5 and 6 of transcriptomic and genomic data sets, respectively. In this tab, users can check whether their selected genes have significant difference of expression or mutation between responders and non-responders in various data sets. > Expression difference between responders and non-responders > Mutation difference between responders and non-responders

> Expression difference between responders and non-responders

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Points in the above scatter plot represent the expression difference of SPTLC2 in various data sets.

No	PMID	Cancer type	Group	Drug	# Res	# NRes	Log2 (Fold Change)	P value
1	26997480	Melanoma	all	Anti-PD-1 (pembrolizumab and nivolumab)	14	12	0.221	0.327
2	26997480	Melanoma	MAPKi	Anti-PD-1 (pembrolizumab and nivolumab)	6	5	0.421	0.787
3	26997480	Melanoma	non-MAPKi	Anti-PD-1 (pembrolizumab and nivolumab)	8	7	0.077	0.945
4	28552987	Urothelial cancer	all	Anti-PD-L1 (atezolizumab)	9	16	0.043	0.868
5	28552987	Urothelial cancer	smoking	Anti-PD-L1 (atezolizumab)	5	9	-0.062	0.974
6	28552987	Urothelial cancer	non-smoking	Anti-PD-L1 (atezolizumab)	4	7	0.178	0.943
7	29033130	Melanoma	all	Anti-PD-1 (nivolumab)	26	23	0.142	0.727
8	29033130	Melanoma	NIV3-PROG	Anti-PD-1 (nivolumab)	15	11	0.483	0.787
9	29033130	Melanoma	NIV3-NAIVE	Anti-PD-1 (nivolumab)	11	12	-0.272	0.894
10	29301960	Clear cell renal cell carcinoma (ccRCC)	all	Anti-PD-1 (nivolumab)	4	8	0.388	0.774
11	29301960	Clear cell renal cell carcinoma (ccRCC)	VEGFRi	Anti-PD-1 (nivolumab)	2	0	0	1
12	29301960	Clear cell renal cell carcinoma (ccRCC)	non-VEGFRi	Anti-PD-1 (nivolumab)	2	8	0.791	0.683
13	29443960	Urothelial cancer	all	Anti-PD-L1 (atezolizumab)	68	230	-0.028	0.658

> Mutation difference between responders and non-responders

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Points in the above scatter plot represent the mutation difference of SPTLC2 in various data sets.

No	PMID	Cancer type	Group	Drug	# Res	# NRes	% Mut/Res	% Mut/NRes	% Diff (R vs NR)	Pval
1	25765070	Non-small cell lung cancer (NSCLC)	all	Anti-PD-1 (pembrolizumab)	14	17	0	0	0	1
2	25765070	Non-small cell lung cancer (NSCLC)	smoking	Anti-PD-1 (pembrolizumab)	10	3	0	0	0	1
3	25765070	Non-small cell lung cancer (NSCLC)	non-smoking	Anti-PD-1 (pembrolizumab)	4	14	0	0	0	1
4	26359337	Melanoma	all	Anti-CTLA-4 (ipilimumab)	27	73	0	2.7	-2.7	1
5	26359337	Melanoma	BRAFi	Anti-CTLA-4 (ipilimumab)	0	14	0	0	0	1
6	26359337	Melanoma	non-BRAFi	Anti-CTLA-4 (ipilimumab)	27	59	0	3.4	-3.4	1
7	26997480	Melanoma	all	Anti-PD-1 (pembrolizumab and nivolumab)	21	17	0	0	0	1
8	26997480	Melanoma	MAPKi	Anti-PD-1 (pembrolizumab and nivolumab)	8	6	0	0	0	1
9	26997480	Melanoma	non-MAPKi	Anti-PD-1 (pembrolizumab and nivolumab)	13	11	0	0	0	1
10	28552987	Urothelial cancer	all	Anti-PD-L1 (atezolizumab)	9	16	11.1	0	11.1	0.36
11	28552987	Urothelial cancer	smoking	Anti-PD-L1 (atezolizumab)	5	9	20	0	20	0.357
12	28552987	Urothelial cancer	non-smoking	Anti-PD-L1 (atezolizumab)	4	7	0	0	0	1
13	29033130	Melanoma	all	Anti-PD-1 (nivolumab)	38	27	0	3.7	-3.7	0.415
14	29033130	Melanoma	NIV3-PROG	Anti-PD-1 (nivolumab)	22	13	0	7.7	-7.7	0.371
15	29033130	Melanoma	NIV3-NAIVE	Anti-PD-1 (nivolumab)	16	14	0	0	0	1
16	29301960	Clear cell renal cell carcinoma (ccRCC)	all	Anti-PD-1 (nivolumab)	11	13	0	7.7	-7.7	1
17	29301960	Clear cell renal cell carcinoma (ccRCC)	VEGFRi	Anti-PD-1 (nivolumab)	6	1	0	0	0	1
18	29301960	Clear cell renal cell carcinoma (ccRCC)	non-VEGFRi	Anti-PD-1 (nivolumab)	5	12	0	8.3	-8.3	1

Summary
Symbol	SPTLC2
Name	serine palmitoyltransferase, long chain base subunit 2
Aliases	KIAA0526; LCB2; LCB2A; hLCB2a; HSN1C; NSAN1C; LCB 2; SPT 2; long chain base biosynthesis protein 2a; serine ......
Chromosomal Location	14q24.3
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Relations between abundance of tumor-infiltrating lymphocytes (TILs) and expression, copy number, methylation, or mutation of SPTLC2. The immune-related signatures of 28 TIL types from Charoentong's study, which can be viewed in the download page. For each cancer type, the relative abundance of TILs were inferred by using gene set variation analysis (GSVA) based on gene expression profile. In this tab, users can examine which kinds of TILs might be regulated by the current gene.

> Lymphocyte [ TOP ]

Summary
Symbol	SPTLC2
Name	serine palmitoyltransferase, long chain base subunit 2
Aliases	KIAA0526; LCB2; LCB2A; hLCB2a; HSN1C; NSAN1C; LCB 2; SPT 2; long chain base biosynthesis protein 2a; serine ......
Chromosomal Location	14q24.3
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Relations between three kinds of immunomodulators and expression, copy number, methylation, or mutation of SPTLC2. These immunomo-dulators were collected from Charoentong's study. In this tab, users can examine which immunomodulators might be regulated by SPTLC2. > Immunoinhibitor > Immunostimulator > MHC molecule

> Immunoinhibitor [ TOP ]

> Immunostimulator [ TOP ]

> MHC molecule [ TOP ]

Summary
Symbol	SPTLC2
Name	serine palmitoyltransferase, long chain base subunit 2
Aliases	KIAA0526; LCB2; LCB2A; hLCB2a; HSN1C; NSAN1C; LCB 2; SPT 2; long chain base biosynthesis protein 2a; serine ......
Chromosomal Location	14q24.3
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Relations between chemokines (or receptors) and expression, copy number, methylation, or mutation of SPTLC2. In this tab, users can examine which chemokines (or receptors) might be regulated by the current gene. > Chemokine > Receptor

> Chemokine [ TOP ]

> Receptor [ TOP ]

Summary
Symbol	SPTLC2
Name	serine palmitoyltransferase, long chain base subunit 2
Aliases	KIAA0526; LCB2; LCB2A; hLCB2a; HSN1C; NSAN1C; LCB 2; SPT 2; long chain base biosynthesis protein 2a; serine ......
Chromosomal Location	14q24.3
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Distribution of SPTLC2 expression across immune and molecular subtypes. > Immune subtype > Molecular subtype

> Immune subtype [ TOP ]

> Molecular subtype [ TOP ]

Summary
Symbol	SPTLC2
Name	serine palmitoyltransferase, long chain base subunit 2
Aliases	KIAA0526; LCB2; LCB2A; hLCB2a; HSN1C; NSAN1C; LCB 2; SPT 2; long chain base biosynthesis protein 2a; serine ......
Chromosomal Location	14q24.3
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Associations between SPTLC2 and clinical features. > Overall survival analysis > Cancer stage > Tumor grade

> Overall survival [ TOP ]

> Stage [ TOP ]

> Grade [ TOP ]

Summary
Symbol	SPTLC2
Name	serine palmitoyltransferase, long chain base subunit 2
Aliases	KIAA0526; LCB2; LCB2A; hLCB2a; HSN1C; NSAN1C; LCB 2; SPT 2; long chain base biosynthesis protein 2a; serine ......
Chromosomal Location	14q24.3
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Drugs targeting SPTLC2 collected from DrugBank database.

> Drugs from DrugBank database

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Details on drugs targeting SPTLC2.

ID	Name	Drug Type	Targets	#Targets
DB00114	Pyridoxal Phosphate	Small Molecule	AADAT, ABAT, AGXT, AGXT2, ALAS1, ALAS2, AZIN2, BCAT1, BCAT2, CBS, ......	54
DB00133	Serine	Small Molecule	AGXT, CBS, SARS, SDS, SPTLC1, SPTLC2, SRR	7

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