Browse GMDS

Summary
SymbolGMDS
NameGDP-mannose 4,6-dehydratase
Aliases GMD; SDR3E1; short chain dehydrogenase/reductase family 3E, member 1; GDP-D-mannose dehydratase; GDP-mannose ......
Chromosomal Location6p25
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
 
Subcellular Location -
Domain PF16363 GDP-mannose 4
Function

Catalyzes the conversion of GDP-D-mannose to GDP-4-dehydro-6-deoxy-D-mannose.

> Gene Ontology
 
Biological Process GO:0007219 Notch signaling pathway
GO:0009225 nucleotide-sugar metabolic process
GO:0009226 nucleotide-sugar biosynthetic process
GO:0019673 GDP-mannose metabolic process
GO:0042350 GDP-L-fucose biosynthetic process
GO:0042351 'de novo' GDP-L-fucose biosynthetic process
GO:0046368 GDP-L-fucose metabolic process
Molecular Function GO:0008446 GDP-mannose 4,6-dehydratase activity
GO:0016829 lyase activity
GO:0016835 carbon-oxygen lyase activity
GO:0016836 hydro-lyase activity
GO:0048037 cofactor binding
GO:0050661 NADP binding
GO:0050662 coenzyme binding
GO:0070401 NADP+ binding
Cellular Component -
> KEGG and Reactome Pathway
 
KEGG hsa00051 Fructose and mannose metabolism
hsa00520 Amino sugar and nucleotide sugar metabolism
hsa01100 Metabolic pathways
Reactome R-HSA-446203: Asparagine N-linked glycosylation
R-HSA-446193: Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein
R-HSA-6787639: GDP-fucose biosynthesis
R-HSA-392499: Metabolism of proteins
R-HSA-597592: Post-translational protein modification
R-HSA-446219: Synthesis of substrates in N-glycan biosythesis
Summary
SymbolGMDS
NameGDP-mannose 4,6-dehydratase
Aliases GMD; SDR3E1; short chain dehydrogenase/reductase family 3E, member 1; GDP-D-mannose dehydratase; GDP-mannose ......
Chromosomal Location6p25
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Literatures that report relations between GMDS 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
 
  Literatures describing the relation between GMDS and anti-tumor immunity in human cancer.
PMID Cancer type Relation to immunity Evidence sentences
19361506Colon carcinomaPromote immunity (NK cell function)When mock and GMDS-rescued cells were transplanted into athymic mice, tumor growth and metastasis of the GMDS-rescued cells were dramatically suppressed through NK cell-mediated tumor surveillance.
22027835Colon CarcinomaPromote immunityGDP-mannose-4,6-dehydratase (GMDS) deficiency renders colon cancer cells resistant to tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) receptor- and CD95-mediated apoptosis by inhibiting complex II formation. DR4, but not DR5, was found to be fucosylated; however, GMDS deficiency inhibited both DR4- and DR5-mediated apoptosis despite the absence of fucosylation on DR5. In addition, GMDS deficiency also inhibited CD95-mediated apoptosis but not the intrinsic apoptosis pathway induced by anti-cancer drugs. Binding of TRAIL and CD95 ligand to their cognate receptors primarily leads to formation of a complex comprising the receptor, FADD, and caspase-8, referred to as the death-inducing signaling complex (DISC). GMDS deficiency did not affect formation of the primary DISC or recruitment to and activation of caspase-8 on the DISC. However, formation of secondary FADD-dependent complex II, comprising caspase-8 and cFLIP, was significantly inhibited by GMDS deficiency.
Summary
SymbolGMDS
NameGDP-mannose 4,6-dehydratase
Aliases GMD; SDR3E1; short chain dehydrogenase/reductase family 3E, member 1; GDP-D-mannose dehydratase; GDP-mannose ......
Chromosomal Location6p25
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
  Statistical results of GMDS in screening data sets for detecting immune reponses.
PMID Screening System Cancer Type Cell Line Data Set Statistical Results Relation to immunity
29301958CRISPR-Cas9 melanomaB16F10Pmel-1 T cell NA/NSNA/NS
29301958CRISPR-Cas9 melanomaB16F10OT-1 T cell NA/NSNA/NS
28783722CRISPR-Cas9 melanomaMel6242CT-CRISPR NA/NSNA/NS
28723893CRISPR-Cas9 melanomaB16GVAX+Anti-PD1 NA/NSNA/NS
28723893CRISPR-Cas9 melanomaB16GVAX NA/NSNA/NS
25691366RNAiBreast cancerMCF7Luc-CTL assay NA/NSNA/NS
24476824shRNAmelanomaB16Primary screen NA/NSNA/NS
24476824shRNAmelanomaB16Secondary screen NA/NSNA/NS
Summary
SymbolGMDS
NameGDP-mannose 4,6-dehydratase
Aliases GMD; SDR3E1; short chain dehydrogenase/reductase family 3E, member 1; GDP-D-mannose dehydratase; GDP-mannose ......
Chromosomal Location6p25
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
 
Points in the above scatter plot represent the expression difference of GMDS in various data sets.
No PMID Cancer type Group Drug # Res # NRes Log2 (Fold Change) P value Anno
126997480MelanomaallAnti-PD-1 (pembrolizumab and nivolumab)14120.1820.52
226997480MelanomaMAPKiAnti-PD-1 (pembrolizumab and nivolumab)65-0.1210.95
326997480Melanomanon-MAPKiAnti-PD-1 (pembrolizumab and nivolumab)870.3980.793
428552987Urothelial cancerallAnti-PD-L1 (atezolizumab) 9160.2410.505
528552987Urothelial cancersmokingAnti-PD-L1 (atezolizumab) 590.2590.864
628552987Urothelial cancernon-smokingAnti-PD-L1 (atezolizumab) 470.2210.91
729033130MelanomaallAnti-PD-1 (nivolumab) 26230.1320.69
829033130MelanomaNIV3-PROGAnti-PD-1 (nivolumab) 1511-0.0020.998
929033130MelanomaNIV3-NAIVEAnti-PD-1 (nivolumab) 11120.2030.883
1029301960Clear cell renal cell carcinoma (ccRCC)allAnti-PD-1 (nivolumab) 48-0.2690.843
1129301960Clear cell renal cell carcinoma (ccRCC)VEGFRiAnti-PD-1 (nivolumab) 2001
1229301960Clear cell renal cell carcinoma (ccRCC)non-VEGFRiAnti-PD-1 (nivolumab) 28-0.3530.858
1329443960Urothelial cancerallAnti-PD-L1 (atezolizumab) 682300.1180.134
> Mutation difference between responders and non-responders
 
Points in the above scatter plot represent the mutation difference of GMDS in various data sets.
No PMID Cancer type Group Drug # Res # NRes % Mut/Res % Mut/NRes % Diff (R vs NR) Pval Anno
125765070Non-small cell lung cancer (NSCLC)allAnti-PD-1 (pembrolizumab) 14170001
225765070Non-small cell lung cancer (NSCLC)smokingAnti-PD-1 (pembrolizumab) 1030001
325765070Non-small cell lung cancer (NSCLC)non-smokingAnti-PD-1 (pembrolizumab) 4140001
426359337MelanomaallAnti-CTLA-4 (ipilimumab) 277301.4-1.41
526359337MelanomaBRAFiAnti-CTLA-4 (ipilimumab) 0140001
626359337Melanomanon-BRAFiAnti-CTLA-4 (ipilimumab) 275901.7-1.71
726997480MelanomaallAnti-PD-1 (pembrolizumab and nivolumab)21179.509.50.492
826997480MelanomaMAPKiAnti-PD-1 (pembrolizumab and nivolumab)8612.5012.51
926997480Melanomanon-MAPKiAnti-PD-1 (pembrolizumab and nivolumab)13117.707.71
1028552987Urothelial cancerallAnti-PD-L1 (atezolizumab) 9160001
1128552987Urothelial cancersmokingAnti-PD-L1 (atezolizumab) 590001
1228552987Urothelial cancernon-smokingAnti-PD-L1 (atezolizumab) 470001
1329033130MelanomaallAnti-PD-1 (nivolumab) 38270001
1429033130MelanomaNIV3-PROGAnti-PD-1 (nivolumab) 22130001
1529033130MelanomaNIV3-NAIVEAnti-PD-1 (nivolumab) 16140001
1629301960Clear cell renal cell carcinoma (ccRCC)allAnti-PD-1 (nivolumab) 11130001
1729301960Clear cell renal cell carcinoma (ccRCC)VEGFRiAnti-PD-1 (nivolumab) 610001
1829301960Clear cell renal cell carcinoma (ccRCC)non-VEGFRiAnti-PD-1 (nivolumab) 5120001
Summary
SymbolGMDS
NameGDP-mannose 4,6-dehydratase
Aliases GMD; SDR3E1; short chain dehydrogenase/reductase family 3E, member 1; GDP-D-mannose dehydratase; GDP-mannose ......
Chromosomal Location6p25
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Relations between abundance of tumor-infiltrating lymphocytes (TILs) and expression, copy number, methylation, or mutation of GMDS. 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
 
Summary
SymbolGMDS
NameGDP-mannose 4,6-dehydratase
Aliases GMD; SDR3E1; short chain dehydrogenase/reductase family 3E, member 1; GDP-D-mannose dehydratase; GDP-mannose ......
Chromosomal Location6p25
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Relations between three kinds of immunomodulators and expression, copy number, methylation, or mutation of GMDS. These immunomo-dulators were collected from Charoentong's study. In this tab, users can examine which immunomodulators might be regulated by GMDS.
> Immunoinhibitor
> Immunostimulator
> MHC molecule
> Immunoinhibitor
 
> Immunostimulator
 
> MHC molecule
 
Summary
SymbolGMDS
NameGDP-mannose 4,6-dehydratase
Aliases GMD; SDR3E1; short chain dehydrogenase/reductase family 3E, member 1; GDP-D-mannose dehydratase; GDP-mannose ......
Chromosomal Location6p25
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Relations between chemokines (or receptors) and expression, copy number, methylation, or mutation of GMDS. In this tab, users can examine which chemokines (or receptors) might be regulated by the current gene.
> Chemokine
> Receptor
> Chemokine
 
> Receptor
 
Summary
SymbolGMDS
NameGDP-mannose 4,6-dehydratase
Aliases GMD; SDR3E1; short chain dehydrogenase/reductase family 3E, member 1; GDP-D-mannose dehydratase; GDP-mannose ......
Chromosomal Location6p25
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Distribution of GMDS expression across immune and molecular subtypes.
> Immune subtype
> Molecular subtype
> Immune subtype
 
> Molecular subtype
 
Summary
SymbolGMDS
NameGDP-mannose 4,6-dehydratase
Aliases GMD; SDR3E1; short chain dehydrogenase/reductase family 3E, member 1; GDP-D-mannose dehydratase; GDP-mannose ......
Chromosomal Location6p25
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Associations between GMDS and clinical features.
> Overall survival analysis
> Cancer stage
> Tumor grade
> Overall survival
 
> Stage
 
> Grade
 
Summary
SymbolGMDS
NameGDP-mannose 4,6-dehydratase
Aliases GMD; SDR3E1; short chain dehydrogenase/reductase family 3E, member 1; GDP-D-mannose dehydratase; GDP-mannose ......
Chromosomal Location6p25
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Drugs targeting GMDS collected from DrugBank database.
> Drugs from DrugBank database
 

  Details on drugs targeting GMDS.
ID Name Drug Type Targets #Targets
DB02547Guanosine-5'-Diphosphate-RhamnoseSmall MoleculeGMDS1
DB04315Guanosine-5'-DiphosphateSmall MoleculeADSSL1, ARF1, ARF4, ARF6, ARL1, ARL3, ARL5A, ARL5B, CDC42, EEF1A1, ......36