Browse APOBEC3B

Summary
SymbolAPOBEC3B
Nameapolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3B
Aliases PHRBNL; FLJ21201; phorbolin 3; ARCD3; DJ742C19.2; bK150C2.2; apolipoprotein B mRNA editing enzyme catalytic ......
Chromosomal Location22q13.1-q13.2
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 PF08210 APOBEC-like N-terminal domain
Function

DNA deaminase (cytidine deaminase) which acts as an inhibitor of retrovirus replication and retrotransposon mobility via deaminase-dependent and -independent mechanisms. After the penetration of retroviral nucleocapsids into target cells of infection and the initiation of reverse transcription, it can induce the conversion of cytosine to uracil in the minus-sense single-strand viral DNA, leading to G-to-A hypermutations in the subsequent plus-strand viral DNA. The resultant detrimental levels of mutations in the proviral genome, along with a deamination-independent mechanism that works prior to the proviral integration, together exert efficient antiretroviral effects in infected target cells. Selectively targets single-stranded DNA and does not deaminate double-stranded DNA or single-or double-stranded RNA. Exhibits antiviral activity against simian immunodeficiency virus (SIV), hepatitis B virus (HBV) and human T-cell leukemia virus type 1 (HTLV-1) and may inhibit the mobility of LTR and non-LTR retrotransposons.

> Gene Ontology
 
Biological Process GO:0009615 response to virus
GO:0010528 regulation of transposition
GO:0010529 negative regulation of transposition
GO:0032196 transposition
GO:0051607 defense response to virus
GO:0098542 defense response to other organism
Molecular Function GO:0016810 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds
GO:0016814 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines
GO:0019239 deaminase activity
GO:0047844 deoxycytidine deaminase activity
Cellular Component -
> KEGG and Reactome Pathway
 
KEGG -
Reactome R-HSA-75094: Formation of the Editosome
R-HSA-74160: Gene Expression
R-HSA-75072: mRNA Editing
R-HSA-72200: mRNA Editing
Summary
SymbolAPOBEC3B
Nameapolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3B
Aliases PHRBNL; FLJ21201; phorbolin 3; ARCD3; DJ742C19.2; bK150C2.2; apolipoprotein B mRNA editing enzyme catalytic ......
Chromosomal Location22q13.1-q13.2
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Literatures that report relations between APOBEC3B 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 APOBEC3B and anti-tumor immunity in human cancer.
PMID Cancer type Relation to immunity Evidence sentences
27233495Breast CarcinomaInhibit immunityAnalysis of breast cancers from METABRIC revealed breast cancers from APOBEC3B deletion carriers to have significantly higher abundance of tumour-infiltrating immune cells.
Summary
SymbolAPOBEC3B
Nameapolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3B
Aliases PHRBNL; FLJ21201; phorbolin 3; ARCD3; DJ742C19.2; bK150C2.2; apolipoprotein B mRNA editing enzyme catalytic ......
Chromosomal Location22q13.1-q13.2
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 APOBEC3B 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
SymbolAPOBEC3B
Nameapolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3B
Aliases PHRBNL; FLJ21201; phorbolin 3; ARCD3; DJ742C19.2; bK150C2.2; apolipoprotein B mRNA editing enzyme catalytic ......
Chromosomal Location22q13.1-q13.2
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 APOBEC3B in various data sets.
No PMID Cancer type Group Drug # Res # NRes Log2 (Fold Change) P value Anno
126997480MelanomaallAnti-PD-1 (pembrolizumab and nivolumab)1412-0.5490.0924
226997480MelanomaMAPKiAnti-PD-1 (pembrolizumab and nivolumab)65-1.0920.375
326997480Melanomanon-MAPKiAnti-PD-1 (pembrolizumab and nivolumab)87-0.1570.876
428552987Urothelial cancerallAnti-PD-L1 (atezolizumab) 916-0.2830.524
528552987Urothelial cancersmokingAnti-PD-L1 (atezolizumab) 59-0.3680.817
628552987Urothelial cancernon-smokingAnti-PD-L1 (atezolizumab) 47-0.1740.932
729033130MelanomaallAnti-PD-1 (nivolumab) 26230.2260.525
829033130MelanomaNIV3-PROGAnti-PD-1 (nivolumab) 15110.2220.809
929033130MelanomaNIV3-NAIVEAnti-PD-1 (nivolumab) 11120.3310.714
1029301960Clear cell renal cell carcinoma (ccRCC)allAnti-PD-1 (nivolumab) 480.0120.99
1129301960Clear cell renal cell carcinoma (ccRCC)VEGFRiAnti-PD-1 (nivolumab) 2001
1229301960Clear cell renal cell carcinoma (ccRCC)non-VEGFRiAnti-PD-1 (nivolumab) 28-0.3230.834
1329443960Urothelial cancerallAnti-PD-L1 (atezolizumab) 682300.60.00749
> Mutation difference between responders and non-responders
 
Points in the above scatter plot represent the mutation difference of APOBEC3B 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) 14177.107.10.452
225765070Non-small cell lung cancer (NSCLC)smokingAnti-PD-1 (pembrolizumab) 103100101
325765070Non-small cell lung cancer (NSCLC)non-smokingAnti-PD-1 (pembrolizumab) 4140001
426359337MelanomaallAnti-CTLA-4 (ipilimumab) 277302.7-2.71
526359337MelanomaBRAFiAnti-CTLA-4 (ipilimumab) 0140001
626359337Melanomanon-BRAFiAnti-CTLA-4 (ipilimumab) 275903.4-3.41
726997480MelanomaallAnti-PD-1 (pembrolizumab and nivolumab)21170001
826997480MelanomaMAPKiAnti-PD-1 (pembrolizumab and nivolumab)860001
926997480Melanomanon-MAPKiAnti-PD-1 (pembrolizumab and nivolumab)13110001
1028552987Urothelial cancerallAnti-PD-L1 (atezolizumab) 91611.1011.10.36
1128552987Urothelial cancersmokingAnti-PD-L1 (atezolizumab) 59200200.357
1228552987Urothelial cancernon-smokingAnti-PD-L1 (atezolizumab) 470001
1329033130MelanomaallAnti-PD-1 (nivolumab) 38272.63.7-1.11
1429033130MelanomaNIV3-PROGAnti-PD-1 (nivolumab) 221307.7-7.70.371
1529033130MelanomaNIV3-NAIVEAnti-PD-1 (nivolumab) 16146.206.21
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
SymbolAPOBEC3B
Nameapolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3B
Aliases PHRBNL; FLJ21201; phorbolin 3; ARCD3; DJ742C19.2; bK150C2.2; apolipoprotein B mRNA editing enzyme catalytic ......
Chromosomal Location22q13.1-q13.2
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Relations between abundance of tumor-infiltrating lymphocytes (TILs) and expression, copy number, methylation, or mutation of APOBEC3B. 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
SymbolAPOBEC3B
Nameapolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3B
Aliases PHRBNL; FLJ21201; phorbolin 3; ARCD3; DJ742C19.2; bK150C2.2; apolipoprotein B mRNA editing enzyme catalytic ......
Chromosomal Location22q13.1-q13.2
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Relations between three kinds of immunomodulators and expression, copy number, methylation, or mutation of APOBEC3B. These immunomo-dulators were collected from Charoentong's study. In this tab, users can examine which immunomodulators might be regulated by APOBEC3B.
> Immunoinhibitor
> Immunostimulator
> MHC molecule
> Immunoinhibitor
 
> Immunostimulator
 
> MHC molecule
 
Summary
SymbolAPOBEC3B
Nameapolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3B
Aliases PHRBNL; FLJ21201; phorbolin 3; ARCD3; DJ742C19.2; bK150C2.2; apolipoprotein B mRNA editing enzyme catalytic ......
Chromosomal Location22q13.1-q13.2
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Relations between chemokines (or receptors) and expression, copy number, methylation, or mutation of APOBEC3B. In this tab, users can examine which chemokines (or receptors) might be regulated by the current gene.
> Chemokine
> Receptor
> Chemokine
 
> Receptor
 
Summary
SymbolAPOBEC3B
Nameapolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3B
Aliases PHRBNL; FLJ21201; phorbolin 3; ARCD3; DJ742C19.2; bK150C2.2; apolipoprotein B mRNA editing enzyme catalytic ......
Chromosomal Location22q13.1-q13.2
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Distribution of APOBEC3B expression across immune and molecular subtypes.
> Immune subtype
> Molecular subtype
> Immune subtype
 
> Molecular subtype
 
Summary
SymbolAPOBEC3B
Nameapolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3B
Aliases PHRBNL; FLJ21201; phorbolin 3; ARCD3; DJ742C19.2; bK150C2.2; apolipoprotein B mRNA editing enzyme catalytic ......
Chromosomal Location22q13.1-q13.2
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Associations between APOBEC3B and clinical features.
> Overall survival analysis
> Cancer stage
> Tumor grade
> Overall survival
 
> Stage
 
> Grade
 
Summary
SymbolAPOBEC3B
Nameapolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3B
Aliases PHRBNL; FLJ21201; phorbolin 3; ARCD3; DJ742C19.2; bK150C2.2; apolipoprotein B mRNA editing enzyme catalytic ......
Chromosomal Location22q13.1-q13.2
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Drugs targeting APOBEC3B collected from DrugBank database.
> Drugs from DrugBank database
 

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