Browse KDM1A

Summary
SymbolKDM1A
Namelysine (K)-specific demethylase 1A
Aliases KIAA0601; BHC110; LSD1; AOF2; KDM1; amine oxidase (flavin containing) domain 2; lysine (K)-specific demethyl ......
Chromosomal Location1p36.12
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 Nucleus
Domain PF01593 Flavin containing amine oxidoreductase
PF04433 SWIRM domain
Function

Histone demethylase that demethylates both 'Lys-4' (H3K4me) and 'Lys-9' (H3K9me) of histone H3, thereby acting as a coactivator or a corepressor, depending on the context. Acts by oxidizing the substrate by FAD to generate the corresponding imine that is subsequently hydrolyzed. Acts as a corepressor by mediating demethylation of H3K4me, a specific tag for epigenetic transcriptional activation. Demethylates both mono- (H3K4me1) and di-methylated (H3K4me2) H3K4me. May play a role in the repression of neuronal genes. Alone, it is unable to demethylate H3K4me on nucleosomes and requires the presence of RCOR1/CoREST to achieve such activity. Also acts as a coactivator of androgen receptor (ANDR)-dependent transcription, by being recruited to ANDR target genes and mediating demethylation of H3K9me, a specific tag for epigenetic transcriptional repression. The presence of PRKCB in ANDR-containing complexes, which mediates phosphorylation of 'Thr-6' of histone H3 (H3T6ph), a specific tag that prevents demethylation H3K4me, prevents H3K4me demethylase activity of KDM1A. Demethylates di-methylated 'Lys-370' of p53/TP53 which prevents interaction of p53/TP53 with TP53BP1 and represses p53/TP53-mediated transcriptional activation. Demethylates and stabilizes the DNA methylase DNMT1. Required for gastrulation during embryogenesis. Component of a RCOR/GFI/KDM1A/HDAC complex that suppresses, via histone deacetylase (HDAC) recruitment, a number of genes implicated in multilineage blood cell development. Effector of SNAI1-mediated transcription repression of E-cadherin/CDH1, CDN7 and KRT8. Required for the maintenance of the silenced state of the SNAI1 target genes E-cadherin/CDH1 and CDN7.

> Gene Ontology
 
Biological Process GO:0000018 regulation of DNA recombination
GO:0000375 RNA splicing, via transesterification reactions
GO:0000377 RNA splicing, via transesterification reactions with bulged adenosine as nucleophile
GO:0000380 alternative mRNA splicing, via spliceosome
GO:0000398 mRNA splicing, via spliceosome
GO:0000724 double-strand break repair via homologous recombination
GO:0000725 recombinational repair
GO:0001701 in utero embryonic development
GO:0002262 myeloid cell homeostasis
GO:0002521 leukocyte differentiation
GO:0002573 myeloid leukocyte differentiation
GO:0006144 purine nucleobase metabolic process
GO:0006282 regulation of DNA repair
GO:0006302 double-strand break repair
GO:0006310 DNA recombination
GO:0006397 mRNA processing
GO:0006476 protein deacetylation
GO:0006479 protein methylation
GO:0006482 protein demethylation
GO:0007596 blood coagulation
GO:0007599 hemostasis
GO:0008213 protein alkylation
GO:0008214 protein dealkylation
GO:0008361 regulation of cell size
GO:0008380 RNA splicing
GO:0008630 intrinsic apoptotic signaling pathway in response to DNA damage
GO:0009112 nucleobase metabolic process
GO:0009314 response to radiation
GO:0009411 response to UV
GO:0009416 response to light stimulus
GO:0009636 response to toxic substance
GO:0010212 response to ionizing radiation
GO:0010332 response to gamma radiation
GO:0010569 regulation of double-strand break repair via homologous recombination
GO:0010720 positive regulation of cell development
GO:0010725 regulation of primitive erythrocyte differentiation
GO:0010817 regulation of hormone levels
GO:0010975 regulation of neuron projection development
GO:0010976 positive regulation of neuron projection development
GO:0014074 response to purine-containing compound
GO:0016570 histone modification
GO:0016571 histone methylation
GO:0016574 histone ubiquitination
GO:0016575 histone deacetylation
GO:0016577 histone demethylation
GO:0018022 peptidyl-lysine methylation
GO:0018205 peptidyl-lysine modification
GO:0021536 diencephalon development
GO:0021537 telencephalon development
GO:0021543 pallium development
GO:0021700 developmental maturation
GO:0021983 pituitary gland development
GO:0021987 cerebral cortex development
GO:0030099 myeloid cell differentiation
GO:0030218 erythrocyte differentiation
GO:0030219 megakaryocyte differentiation
GO:0030330 DNA damage response, signal transduction by p53 class mediator
GO:0030851 granulocyte differentiation
GO:0030900 forebrain development
GO:0031056 regulation of histone modification
GO:0031057 negative regulation of histone modification
GO:0031058 positive regulation of histone modification
GO:0031060 regulation of histone methylation
GO:0031061 negative regulation of histone methylation
GO:0031346 positive regulation of cell projection organization
GO:0031396 regulation of protein ubiquitination
GO:0031398 positive regulation of protein ubiquitination
GO:0032091 negative regulation of protein binding
GO:0032259 methylation
GO:0032350 regulation of hormone metabolic process
GO:0032352 positive regulation of hormone metabolic process
GO:0032535 regulation of cellular component size
GO:0032844 regulation of homeostatic process
GO:0032846 positive regulation of homeostatic process
GO:0033169 histone H3-K9 demethylation
GO:0033182 regulation of histone ubiquitination
GO:0033184 positive regulation of histone ubiquitination
GO:0034101 erythrocyte homeostasis
GO:0034644 cellular response to UV
GO:0034720 histone H3-K4 demethylation
GO:0034968 histone lysine methylation
GO:0035162 embryonic hemopoiesis
GO:0035270 endocrine system development
GO:0035561 regulation of chromatin binding
GO:0035563 positive regulation of chromatin binding
GO:0035601 protein deacylation
GO:0042445 hormone metabolic process
GO:0042446 hormone biosynthetic process
GO:0042551 neuron maturation
GO:0042692 muscle cell differentiation
GO:0042770 signal transduction in response to DNA damage
GO:0042771 intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator
GO:0043392 negative regulation of DNA binding
GO:0043393 regulation of protein binding
GO:0043414 macromolecule methylation
GO:0043433 negative regulation of sequence-specific DNA binding transcription factor activity
GO:0043516 regulation of DNA damage response, signal transduction by p53 class mediator
GO:0043518 negative regulation of DNA damage response, signal transduction by p53 class mediator
GO:0045637 regulation of myeloid cell differentiation
GO:0045639 positive regulation of myeloid cell differentiation
GO:0045646 regulation of erythrocyte differentiation
GO:0045648 positive regulation of erythrocyte differentiation
GO:0045652 regulation of megakaryocyte differentiation
GO:0045654 positive regulation of megakaryocyte differentiation
GO:0045666 positive regulation of neuron differentiation
GO:0045793 positive regulation of cell size
GO:0045995 regulation of embryonic development
GO:0046098 guanine metabolic process
GO:0046683 response to organophosphorus
GO:0046885 regulation of hormone biosynthetic process
GO:0046886 positive regulation of hormone biosynthetic process
GO:0048469 cell maturation
GO:0048568 embryonic organ development
GO:0048732 gland development
GO:0048872 homeostasis of number of cells
GO:0050769 positive regulation of neurogenesis
GO:0050817 coagulation
GO:0050878 regulation of body fluid levels
GO:0051052 regulation of DNA metabolic process
GO:0051090 regulation of sequence-specific DNA binding transcription factor activity
GO:0051091 positive regulation of sequence-specific DNA binding transcription factor activity
GO:0051098 regulation of binding
GO:0051099 positive regulation of binding
GO:0051100 negative regulation of binding
GO:0051101 regulation of DNA binding
GO:0051567 histone H3-K9 methylation
GO:0051568 histone H3-K4 methylation
GO:0051569 regulation of histone H3-K4 methylation
GO:0051570 regulation of histone H3-K9 methylation
GO:0051572 negative regulation of histone H3-K4 methylation
GO:0051573 negative regulation of histone H3-K9 methylation
GO:0051591 response to cAMP
GO:0051962 positive regulation of nervous system development
GO:0055001 muscle cell development
GO:0060215 primitive hemopoiesis
GO:0060319 primitive erythrocyte differentiation
GO:0060992 response to fungicide
GO:0061351 neural precursor cell proliferation
GO:0061647 histone H3-K9 modification
GO:0070076 histone lysine demethylation
GO:0070988 demethylation
GO:0071214 cellular response to abiotic stimulus
GO:0071320 cellular response to cAMP
GO:0071407 cellular response to organic cyclic compound
GO:0071417 cellular response to organonitrogen compound
GO:0071478 cellular response to radiation
GO:0071479 cellular response to ionizing radiation
GO:0071480 cellular response to gamma radiation
GO:0071482 cellular response to light stimulus
GO:0072089 stem cell proliferation
GO:0072091 regulation of stem cell proliferation
GO:0072331 signal transduction by p53 class mediator
GO:0072332 intrinsic apoptotic signaling pathway by p53 class mediator
GO:0090066 regulation of anatomical structure size
GO:0097193 intrinsic apoptotic signaling pathway
GO:0098732 macromolecule deacylation
GO:1901796 regulation of signal transduction by p53 class mediator
GO:1901797 negative regulation of signal transduction by p53 class mediator
GO:1902165 regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator
GO:1902166 negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator
GO:1902229 regulation of intrinsic apoptotic signaling pathway in response to DNA damage
GO:1902230 negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage
GO:1902253 regulation of intrinsic apoptotic signaling pathway by p53 class mediator
GO:1902254 negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator
GO:1902275 regulation of chromatin organization
GO:1902532 negative regulation of intracellular signal transduction
GO:1903320 regulation of protein modification by small protein conjugation or removal
GO:1903322 positive regulation of protein modification by small protein conjugation or removal
GO:1903706 regulation of hemopoiesis
GO:1903708 positive regulation of hemopoiesis
GO:1905268 negative regulation of chromatin organization
GO:1905269 positive regulation of chromatin organization
GO:2000177 regulation of neural precursor cell proliferation
GO:2000179 positive regulation of neural precursor cell proliferation
GO:2000648 positive regulation of stem cell proliferation
GO:2000779 regulation of double-strand break repair
GO:2001020 regulation of response to DNA damage stimulus
GO:2001021 negative regulation of response to DNA damage stimulus
GO:2001233 regulation of apoptotic signaling pathway
GO:2001234 negative regulation of apoptotic signaling pathway
GO:2001242 regulation of intrinsic apoptotic signaling pathway
GO:2001243 negative regulation of intrinsic apoptotic signaling pathway
Molecular Function GO:0001085 RNA polymerase II transcription factor binding
GO:0002039 p53 binding
GO:0003682 chromatin binding
GO:0003713 transcription coactivator activity
GO:0004407 histone deacetylase activity
GO:0008134 transcription factor binding
GO:0016810 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds
GO:0016811 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
GO:0019213 deacetylase activity
GO:0030374 ligand-dependent nuclear receptor transcription coactivator activity
GO:0032451 demethylase activity
GO:0032452 histone demethylase activity
GO:0032453 histone demethylase activity (H3-K4 specific)
GO:0032454 histone demethylase activity (H3-K9 specific)
GO:0033558 protein deacetylase activity
GO:0034648 histone demethylase activity (H3-dimethyl-K4 specific)
GO:0035257 nuclear hormone receptor binding
GO:0035258 steroid hormone receptor binding
GO:0042162 telomeric DNA binding
GO:0043425 bHLH transcription factor binding
GO:0043426 MRF binding
GO:0048037 cofactor binding
GO:0050660 flavin adenine dinucleotide binding
GO:0050662 coenzyme binding
GO:0050681 androgen receptor binding
GO:0051427 hormone receptor binding
GO:0061752 telomeric repeat-containing RNA binding
Cellular Component GO:0000781 chromosome, telomeric region
GO:0000784 nuclear chromosome, telomeric region
GO:0000785 chromatin
GO:0000790 nuclear chromatin
GO:0005667 transcription factor complex
GO:0044454 nuclear chromosome part
GO:0098687 chromosomal region
GO:1990391 DNA repair complex
> KEGG and Reactome Pathway
 
KEGG -
Reactome R-HSA-5625886: Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3
R-HSA-3247509: Chromatin modifying enzymes
R-HSA-4839726: Chromatin organization
R-HSA-983231: Factors involved in megakaryocyte development and platelet production
R-HSA-3214815: HDACs deacetylate histones
R-HSA-3214842: HDMs demethylate histones
R-HSA-109582: Hemostasis
R-HSA-195258: RHO GTPase Effectors
R-HSA-5625740: RHO GTPases activate PKNs
R-HSA-162582: Signal Transduction
R-HSA-194315: Signaling by Rho GTPases
Summary
SymbolKDM1A
Namelysine (K)-specific demethylase 1A
Aliases KIAA0601; BHC110; LSD1; AOF2; KDM1; amine oxidase (flavin containing) domain 2; lysine (K)-specific demethyl ......
Chromosomal Location1p36.12
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Literatures that report relations between KDM1A 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
 

There is no record.
Summary
SymbolKDM1A
Namelysine (K)-specific demethylase 1A
Aliases KIAA0601; BHC110; LSD1; AOF2; KDM1; amine oxidase (flavin containing) domain 2; lysine (K)-specific demethyl ......
Chromosomal Location1p36.12
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 KDM1A 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 logFC: 1.20; FDR: 0.001910 Sensitive to T cell-mediated killing
29301958CRISPR-Cas9 melanomaB16F10OT-1 T cell NA/NS NA/NS
28783722CRISPR-Cas9 melanomaMel6242CT-CRISPR NA/NS NA/NS
28723893CRISPR-Cas9 melanomaB16GVAX+Anti-PD1 NA/NS NA/NS
28723893CRISPR-Cas9 melanomaB16GVAX NA/NS NA/NS
25691366RNAiBreast cancerMCF7Luc-CTL assay NA/NS NA/NS
24476824shRNAmelanomaB16Primary screen NA/NS NA/NS
24476824shRNAmelanomaB16Secondary screen NA/NS NA/NS
Summary
SymbolKDM1A
Namelysine (K)-specific demethylase 1A
Aliases KIAA0601; BHC110; LSD1; AOF2; KDM1; amine oxidase (flavin containing) domain 2; lysine (K)-specific demethyl ......
Chromosomal Location1p36.12
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 KDM1A in various data sets.
No PMID Cancer type Group Drug # Res # NRes Log2 (Fold Change) P value Anno
126997480MelanomaallAnti-PD-1 (pembrolizumab and nivolumab)1412-0.0870.679
226997480MelanomaMAPKiAnti-PD-1 (pembrolizumab and nivolumab)650.2550.909
326997480Melanomanon-MAPKiAnti-PD-1 (pembrolizumab and nivolumab)87-0.3380.839
428552987Urothelial cancerallAnti-PD-L1 (atezolizumab) 9160.1410.66
528552987Urothelial cancersmokingAnti-PD-L1 (atezolizumab) 590.0390.986
628552987Urothelial cancernon-smokingAnti-PD-L1 (atezolizumab) 470.2730.928
729033130MelanomaallAnti-PD-1 (nivolumab) 26230.2230.602
829033130MelanomaNIV3-PROGAnti-PD-1 (nivolumab) 15110.0070.997
929033130MelanomaNIV3-NAIVEAnti-PD-1 (nivolumab) 11120.4510.824
1029301960Clear cell renal cell carcinoma (ccRCC)allAnti-PD-1 (nivolumab) 480.3110.827
1129301960Clear cell renal cell carcinoma (ccRCC)VEGFRiAnti-PD-1 (nivolumab) 2001
1229301960Clear cell renal cell carcinoma (ccRCC)non-VEGFRiAnti-PD-1 (nivolumab) 280.9910.631
1329443960Urothelial cancerallAnti-PD-L1 (atezolizumab) 682300.2040.0089
> Mutation difference between responders and non-responders
 
Points in the above scatter plot represent the mutation difference of KDM1A 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) 27737.41.460.177
526359337MelanomaBRAFiAnti-CTLA-4 (ipilimumab) 0140001
626359337Melanomanon-BRAFiAnti-CTLA-4 (ipilimumab) 27597.41.75.70.231
726997480MelanomaallAnti-PD-1 (pembrolizumab and nivolumab)21174.804.81
826997480MelanomaMAPKiAnti-PD-1 (pembrolizumab and nivolumab)860001
926997480Melanomanon-MAPKiAnti-PD-1 (pembrolizumab and nivolumab)13117.707.71
1028552987Urothelial cancerallAnti-PD-L1 (atezolizumab) 91606.2-6.21
1128552987Urothelial cancersmokingAnti-PD-L1 (atezolizumab) 59011.1-11.11
1228552987Urothelial cancernon-smokingAnti-PD-L1 (atezolizumab) 470001
1329033130MelanomaallAnti-PD-1 (nivolumab) 38277.907.90.26
1429033130MelanomaNIV3-PROGAnti-PD-1 (nivolumab) 221313.6013.60.279
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
SymbolKDM1A
Namelysine (K)-specific demethylase 1A
Aliases KIAA0601; BHC110; LSD1; AOF2; KDM1; amine oxidase (flavin containing) domain 2; lysine (K)-specific demethyl ......
Chromosomal Location1p36.12
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Relations between abundance of tumor-infiltrating lymphocytes (TILs) and expression, copy number, methylation, or mutation of KDM1A. 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
SymbolKDM1A
Namelysine (K)-specific demethylase 1A
Aliases KIAA0601; BHC110; LSD1; AOF2; KDM1; amine oxidase (flavin containing) domain 2; lysine (K)-specific demethyl ......
Chromosomal Location1p36.12
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Relations between three kinds of immunomodulators and expression, copy number, methylation, or mutation of KDM1A. These immunomo-dulators were collected from Charoentong's study. In this tab, users can examine which immunomodulators might be regulated by KDM1A.
> Immunoinhibitor
> Immunostimulator
> MHC molecule
> Immunoinhibitor
 
> Immunostimulator
 
> MHC molecule
 
Summary
SymbolKDM1A
Namelysine (K)-specific demethylase 1A
Aliases KIAA0601; BHC110; LSD1; AOF2; KDM1; amine oxidase (flavin containing) domain 2; lysine (K)-specific demethyl ......
Chromosomal Location1p36.12
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Relations between chemokines (or receptors) and expression, copy number, methylation, or mutation of KDM1A. In this tab, users can examine which chemokines (or receptors) might be regulated by the current gene.
> Chemokine
> Receptor
> Chemokine
 
> Receptor
 
Summary
SymbolKDM1A
Namelysine (K)-specific demethylase 1A
Aliases KIAA0601; BHC110; LSD1; AOF2; KDM1; amine oxidase (flavin containing) domain 2; lysine (K)-specific demethyl ......
Chromosomal Location1p36.12
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Distribution of KDM1A expression across immune and molecular subtypes.
> Immune subtype
> Molecular subtype
> Immune subtype
 
> Molecular subtype
 
Summary
SymbolKDM1A
Namelysine (K)-specific demethylase 1A
Aliases KIAA0601; BHC110; LSD1; AOF2; KDM1; amine oxidase (flavin containing) domain 2; lysine (K)-specific demethyl ......
Chromosomal Location1p36.12
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Associations between KDM1A and clinical features.
> Overall survival analysis
> Cancer stage
> Tumor grade
> Overall survival
 
> Stage
 
> Grade
 
Summary
SymbolKDM1A
Namelysine (K)-specific demethylase 1A
Aliases KIAA0601; BHC110; LSD1; AOF2; KDM1; amine oxidase (flavin containing) domain 2; lysine (K)-specific demethyl ......
Chromosomal Location1p36.12
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Drugs targeting KDM1A collected from DrugBank database.
> Drugs from DrugBank database
 

There is no record.