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LIN28B (lin-28 homolog B (C. elegans))

Written2011-07Yung-Ming Jeng
Department of Biochemistry, Molecular Biology, College of Medicine, National Taiwan University, Taipei, Taiwan

(Note : for Links provided by Atlas : click)

Identity

Alias_nameslin-28 homolog B (C. elegans)
Alias_symbol (synonym)FLJ16517
CSDD2
Other aliasLin28.2
HGNC (Hugo) LIN28B
LocusID (NCBI) 389421
Atlas_Id 45723
Location 6q16.3  [Link to chromosome band 6q16]
Location_base_pair Starts at 104957048 and ends at 105083332 bp from pter ( according to hg19-Feb_2009)  [Mapping LIN28B.png]
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
LIN28B (6q16.3) / STX7 (6q23.2)
Note Size: 146,72 kb. Orientation: plus strand.

DNA/RNA

Description The gene spans over 125 kb on plus strand; 4 exons.
Transcription The gene is mainly expressed in fetal tissues and not expressed in adult tissue and reexpressed in cancer tissue.

Protein

Description Lin28B is an oncofetal RNA-binding protein. Lin-28B protein consists of two domains that contain RNA-binding motif: the N-terminal cold shock domain and a pair of retroviral-type CCHC zinc fingers. It inhibits biosynthesis of let-7 microRNA through binding to the 5'-GGAG-3' motif in the terminal loop of pre-let-7 and promoting terminal uridylation of let-7 precusor by TUTase4. Uridylated pre-let-7 miRNAs fail to be processed by Dicer and undergo degradation.
Expression Cytoplasm.
Function It inhibits biosynthesis of let-7 microRNA through promoting terminal uridylation of let-7 precusor by TUTase4.
Homology Lin28

Mutations

Note No somatic mutation of Lin28B was identified in cancer.

Implicated in

Note
  
Entity Hepatocellular carcinoma
Note Lin28B expression is more frequently noted in high-grade hepatocellular carcinoma with high alpha-fetoprotein levels. Knockdown of Lin28B by RNA interference in the HCC cell line suppressed proliferation in vitro and reduced in vivo tumor growth in NOD/SCID mice. In contrast, overexpression of Lin28B in the HCC cell line enhanced tumorigenicity. Overexpression of Lin28B also induced epithelial-mesenchymal transition in HA22T cells and hence, invasion capacity.
  
  
Entity Colorectal cancer
Note Lin28B is overexpressed in colorectal cancer. It promotes cell migration, invasion and transforms immortalized colonic epithelial cells. In addition, constitutive LIN28B expression increases expression of intestinal stem cell markers LGR5 and PROM1 in the presence of let-7 restoration.
  
  
Entity Ovarian cancer
Note Lin28B is overexpressed in high grade serous ovarian cancer. Pleomorphism in Lin28B promoter region is associated with susceptibility to epithelium ovarian cancer. Patients with high Lin28B ovarian cancer had shorter progression-free and overall survival than those with low Lin28B ovarian cancer.
  
  
Entity Age at menarche
Note A sequence variation in Lin28B is identified as the SNP most significant associated with age at menarche in one genome wide study. Besides, a meta-analysis of 32 genome-wide association studies in 87802 women found polymorphism of Lin28B is strongly associated with age at menarche. Knockout mice of Lin28B also show delay in puberty onset.
  
  
Entity Body height
Note A LIN28B SNP, rs314277, is associated with final body height.
  

Bibliography

Genome-wide association studies identify loci associated with age at menarche and age at natural menopause.
He C, Kraft P, Chen C, Buring JE, Pare G, Hankinson SE, Chanock SJ, Ridker PM, Hunter DJ, Chasman DI.
Nat Genet. 2009 Jun;41(6):724-8. Epub 2009 May 17.
PMID 19448621
 
Deregulation of MYCN, LIN28B and LET7 in a molecular subtype of aggressive high-grade serous ovarian cancers.
Helland A, Anglesio MS, George J, Cowin PA, Johnstone CN, House CM, Sheppard KE, Etemadmoghadam D, Melnyk N, Rustgi AK, Phillips WA, Johnsen H, Holm R, Kristensen GB, Birrer MJ; Australian Ovarian Cancer Study Group, Pearson RB, Borresen-Dale AL, Huntsman DG, deFazio A, Creighton CJ, Smyth GK, Bowtell DD.
PLoS One. 2011 Apr 13;6(4):e18064.
PMID 21533284
 
Lin28 mediates the terminal uridylation of let-7 precursor MicroRNA.
Heo I, Joo C, Cho J, Ha M, Han J, Kim VN.
Mol Cell. 2008 Oct 24;32(2):276-84.
PMID 18951094
 
LIN28B promotes colon cancer progression and metastasis.
King CE, Cuatrecasas M, Castells A, Sepulveda AR, Lee JS, Rustgi AK.
Cancer Res. 2011 Jun 15;71(12):4260-8. Epub 2011 Apr 21.
PMID 21512136
 
LIN28B fosters colon cancer migration, invasion and transformation through let-7-dependent and -independent mechanisms.
King CE, Wang L, Winograd R, Madison BB, Mongroo PS, Johnstone CN, Rustgi AK.
Oncogene. 2011 May 30. [Epub ahead of print]
PMID 21625210
 
Pluripotent factor lin-28 and its homologue lin-28b in epithelial ovarian cancer and their associations with disease outcomes and expression of let-7a and IGF-II.
Lu L, Katsaros D, Shaverdashvili K, Qian B, Wu Y, de la Longrais IA, Preti M, Menato G, Yu H.
Eur J Cancer. 2009 Aug;45(12):2212-8. Epub 2009 May 26.
PMID 19477633
 
Lin28 promotes transformation and is associated with advanced human malignancies.
Viswanathan SR, Powers JT, Einhorn W, Hoshida Y, Ng TL, Toffanin S, O'Sullivan M, Lu J, Phillips LA, Lockhart VL, Shah SP, Tanwar PS, Mermel CH, Beroukhim R, Azam M, Teixeira J, Meyerson M, Hughes TP, Llovet JM, Radich J, Mullighan CG, Golub TR, Sorensen PH, Daley GQ.
Nat Genet. 2009 Jul;41(7):843-8. Epub 2009 May 31.
PMID 19483683
 

Citation

This paper should be referenced as such :
Jeng, YM. LIN28B (lin-28 homolog B (C
elegans))
Atlas Genet Cytogenet Oncol Haematol. 2012;16(1):20-21.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/LIN28BID45723ch6q16.html


External links

Nomenclature
HGNC (Hugo)LIN28B   32207
Cards
AtlasLIN28BID45723ch6q16
Entrez_Gene (NCBI)LIN28B  389421  lin-28 homolog B
AliasesCSDD2
GeneCards (Weizmann)LIN28B
Ensembl hg19 (Hinxton)ENSG00000187772 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000187772 [Gene_View]  chr6:104957048-105083332 [Contig_View]  LIN28B [Vega]
ICGC DataPortalENSG00000187772
TCGA cBioPortalLIN28B
AceView (NCBI)LIN28B
Genatlas (Paris)LIN28B
WikiGenes389421
SOURCE (Princeton)LIN28B
Genetics Home Reference (NIH)LIN28B
Genomic and cartography
GoldenPath hg38 (UCSC)LIN28B  -     chr6:104957048-105083332 +  6q16.3-q21   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)LIN28B  -     6q16.3-q21   [Description]    (hg19-Feb_2009)
EnsemblLIN28B - 6q16.3-q21 [CytoView hg19]  LIN28B - 6q16.3-q21 [CytoView hg38]
Mapping of homologs : NCBILIN28B [Mapview hg19]  LIN28B [Mapview hg38]
OMIM611044   
Gene and transcription
Genbank (Entrez)AK131411 AW674597 BC127712 BC127713 BC137526
RefSeq transcript (Entrez)NM_001004317
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)LIN28B
Cluster EST : UnigeneHs.23616 [ NCBI ]
CGAP (NCI)Hs.23616
Alternative Splicing GalleryENSG00000187772
Gene ExpressionLIN28B [ NCBI-GEO ]   LIN28B [ EBI - ARRAY_EXPRESS ]   LIN28B [ SEEK ]   LIN28B [ MEM ]
Gene Expression Viewer (FireBrowse)LIN28B [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)389421
GTEX Portal (Tissue expression)LIN28B
Human Protein AtlasENSG00000187772-LIN28B [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ6ZN17   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ6ZN17  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ6ZN17
Splice isoforms : SwissVarQ6ZN17
PhosPhoSitePlusQ6ZN17
Domaine pattern : Prosite (Expaxy)ZF_CCHC (PS50158)   
Domains : Interpro (EBI)CSD    CSP_DNA-bd    NA-bd_OB-fold    Znf_CCHC   
Domain families : Pfam (Sanger)CSD (PF00313)    zf-CCHC (PF00098)   
Domain families : Pfam (NCBI)pfam00313    pfam00098   
Domain families : Smart (EMBL)CSP (SM00357)  ZnF_C2HC (SM00343)  
Conserved Domain (NCBI)LIN28B
DMDM Disease mutations389421
Blocks (Seattle)LIN28B
PDB (SRS)4A4I   
PDB (PDBSum)4A4I   
PDB (IMB)4A4I   
PDB (RSDB)4A4I   
Structural Biology KnowledgeBase4A4I   
SCOP (Structural Classification of Proteins)4A4I   
CATH (Classification of proteins structures)4A4I   
SuperfamilyQ6ZN17
Human Protein Atlas [tissue]ENSG00000187772-LIN28B [tissue]
Peptide AtlasQ6ZN17
HPRD13366
IPIIPI00398131   IPI00854717   
Protein Interaction databases
DIP (DOE-UCLA)Q6ZN17
IntAct (EBI)Q6ZN17
FunCoupENSG00000187772
BioGRIDLIN28B
STRING (EMBL)LIN28B
ZODIACLIN28B
Ontologies - Pathways
QuickGOQ6ZN17
Ontology : AmiGODNA binding  RNA binding  protein binding  nucleus  nucleolus  cytosol  regulation of transcription, DNA-templated  zinc ion binding  miRNA catabolic process  pre-miRNA processing  RNA 3'-end processing  
Ontology : EGO-EBIDNA binding  RNA binding  protein binding  nucleus  nucleolus  cytosol  regulation of transcription, DNA-templated  zinc ion binding  miRNA catabolic process  pre-miRNA processing  RNA 3'-end processing  
NDEx NetworkLIN28B
Atlas of Cancer Signalling NetworkLIN28B
Wikipedia pathwaysLIN28B
Orthology - Evolution
OrthoDB389421
GeneTree (enSembl)ENSG00000187772
Phylogenetic Trees/Animal Genes : TreeFamLIN28B
HOVERGENQ6ZN17
HOGENOMQ6ZN17
Homologs : HomoloGeneLIN28B
Homology/Alignments : Family Browser (UCSC)LIN28B
Gene fusions - Rearrangements
Fusion : MitelmanLIN28B/STX7 [6q16.3/6q23.2]  
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerLIN28B [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)LIN28B
dbVarLIN28B
ClinVarLIN28B
1000_GenomesLIN28B 
Exome Variant ServerLIN28B
ExAC (Exome Aggregation Consortium)ENSG00000187772
GNOMAD BrowserENSG00000187772
Genetic variants : HAPMAP389421
Genomic Variants (DGV)LIN28B [DGVbeta]
DECIPHERLIN28B [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisLIN28B 
Mutations
ICGC Data PortalLIN28B 
TCGA Data PortalLIN28B 
Broad Tumor PortalLIN28B
OASIS PortalLIN28B [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICLIN28B  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDLIN28B
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch LIN28B
DgiDB (Drug Gene Interaction Database)LIN28B
DoCM (Curated mutations)LIN28B (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)LIN28B (select a term)
intoGenLIN28B
NCG5 (London)LIN28B
Cancer3DLIN28B(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM611044   
Orphanet548   
MedgenLIN28B
Genetic Testing Registry LIN28B
NextProtQ6ZN17 [Medical]
TSGene389421
GENETestsLIN28B
Target ValidationLIN28B
Huge Navigator LIN28B [HugePedia]
snp3D : Map Gene to Disease389421
BioCentury BCIQLIN28B
ClinGenLIN28B
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD389421
Chemical/Pharm GKB GenePA142671543
Clinical trialLIN28B
Miscellaneous
canSAR (ICR)LIN28B (select the gene name)
Probes
Litterature
PubMed92 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineLIN28B
EVEXLIN28B
GoPubMedLIN28B
iHOPLIN28B
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Thu Oct 12 16:26:00 CEST 2017

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