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LMO1 (LIM domain only 1 (rhombotin 1))

Written2011-08Norihisa Saeki, Hiroki Sasaki
Genetics Division, National Cancer Center Research Institute, Tokyo 104-0045, Japan

(Note : for Links provided by Atlas : click)

Identity

Alias_namesRBTN1
rhombotin 1
Alias_symbol (synonym)TTG1
RHOM1
Other alias
HGNC (Hugo) LMO1
LocusID (NCBI) 4004
Atlas_Id 33
Location 11p15.4  [Link to chromosome band 11p15]
Location_base_pair Starts at 8224304 and ends at 8268635 bp from pter ( according to hg19-Feb_2009)  [Mapping LMO1.png]
Local_order Telomeric to STK33 gene; centromeric to RIC3 gene.
 
  LMO1 gene is located between RIC3 and STK33 genes in Chromosome 11p15. The arrow indicates the orientation of the genes.
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
C2CD5 (12p12.1) / LMO1 (11p15.4)LMO1 (11p15.4) / SPACA6 (19q13.41)TRBV20OR9-2 (-) / LMO1 (11p15.4)

DNA/RNA

 
  Structure of LMO1 gene. The gene consists of 5 exons and several splicing variants were reported.
Description 4,4 kb (from the beginning of the 1st exon to the end of the 5th exon) consisting of 5 exons.
Transcription mRNA of approximately 700 - 1000 bp, depending on the splicing variants.
Pseudogene Not reported.

Protein

Description The protein contains two highly conserved, cysteine-rich motifs known as LIM domains, which interact with other proteins. As LMO1 has no DNA-binding domain, its DNA binding ability is dependent on the other proteins with which it interacts. The proteins known for binding to LMO1 include TAL1/SCL and LDB1, and the molecules have an oncogenic function in T cell acute leukemia with the chromosomal translocation t(11;14)(p15;q11).
Expression LMO1 expression is prominent in the central nervous system in both human and mouse. In mice it was observed by an in situ hybridization technique in the cerebral cortex, diencephalon, mesencephalon, cerebellum, myeloencephalon and spinal cord. Northern blot analysis revealed its expression in the thymus, kidney and placenta of adult mice.
Localisation Nucleus.
Function Transcription factor.

Mutations

Note Not reported.

Implicated in

Note
  
Entity Neuroblastoma
Disease Genome-wide association studies revealed a corelation between neuroblastoma and a single nucleotide polymorphism in LMO1 gene, rs110419 (A/G), of which the A allele was shown to promote LMO1 expression and to corelate the cases. The DNA copy number gain of the LMO1 locus due to duplication was also demonstrated to associate with the cases. These findings suggest that the gene has a role in the development and/or progression of neuroblastoma. It was also reported that LMO3 is a neuroblastoma oncogene.
  
  
Entity Apoptosis of the gastric epithelial cells
Note In some gastric-cancer derived cell lines, LMO1 is upregulated by TGFbeta signalling and induces their apoptosis through enhancing GSDMA expression. This TGFbeta-LMO1-GSDMA cascade is considered a mechanism for apoptosis induction in the gastric epithelial cells, and has a role in maintaining their homeostasis.
 
LMO1 induces apoptosis of the pit cells in TGFbeta signalling. This function is assumed to have a role in homeostasis of the gastric epithelium.
  
  
Entity T-cell acute lymphoblastic leukemia (T-ALL)
Disease Originally, the LMO1 gene was identified at a break point of the translocation t(11;14)(p15;q11), which was frequently observed in T-ALL. Using LMO1 as a probe, LMO2 and LMO3 were identified. LMO1 is expressed in inmature T cells but suppressed in the mature cells, and overexpression of the gene in thymocytes, hematopoeitic progeniter cells located in the thymus, resulted in developing T-ALL in mice. LMO1 acts cooperatively with SCL (Stem cell leukemia) as a transcriptional activator or represser, dependent on the genes and the cells, and enforced expression of LMO1 and SCL in the thymocytes inhibits T-cell differentiation and causes T-ALL. It is known that the LMO1-SCL complex regulates several genes, including suppression of NFKB1 (nuclear factor of kappa light polypeptide gene enhancer in B-cells 1) and PTCRA (pre T-cell antigen receptor alpha), activation of NKX3.1 (NK3 homeobox 1).
  

Bibliography

LMO3 interacts with neuronal transcription factor, HEN2, and acts as an oncogene in neuroblastoma.
Aoyama M, Ozaki T, Inuzuka H, Tomotsune D, Hirato J, Okamoto Y, Tokita H, Ohira M, Nakagawara A.
Cancer Res. 2005 Jun 1;65(11):4587-97.
PMID 15930276
 
The rhombotin family of cysteine-rich LIM-domain oncogenes: distinct members are involved in T-cell translocations to human chromosomes 11p15 and 11p13.
Boehm T, Foroni L, Kaneko Y, Perutz MF, Rabbitts TH.
Proc Natl Acad Sci U S A. 1991 May 15;88(10):4367-71.
PMID 2034676
 
Developmentally regulated and tissue specific expression of mRNAs encoding the two alternative forms of the LIM domain oncogene rhombotin: evidence for thymus expression.
Boehm T, Spillantini MG, Sofroniew MV, Surani MA, Rabbitts TH.
Oncogene. 1991 May;6(5):695-703.
PMID 2052354
 
NFKB1 is a direct target of the TAL1 oncoprotein in human T leukemia cells.
Chang PY, Draheim K, Kelliher MA, Miyamoto S.
Cancer Res. 2006 Jun 15;66(12):6008-13.
PMID 16778171
 
SCL and LMO1 alter thymocyte differentiation: inhibition of E2A-HEB function and pre-T alpha chain expression.
Herblot S, Steff AM, Hugo P, Aplan PD, Hoang T.
Nat Immunol. 2000 Aug;1(2):138-44.
PMID 11248806
 
NKX3.1 is a direct TAL1 target gene that mediates proliferation of TAL1-expressing human T cell acute lymphoblastic leukemia.
Kusy S, Gerby B, Goardon N, Gault N, Ferri F, Gerard D, Armstrong F, Ballerini P, Cayuela JM, Baruchel A, Pflumio F, Romeo PH.
J Exp Med. 2010 Sep 27;207(10):2141-56. Epub 2010 Sep 20.
PMID 20855495
 
Thymic overexpression of Ttg-1 in transgenic mice results in T-cell acute lymphoblastic leukemia/lymphoma.
McGuire EA, Rintoul CE, Sclar GM, Korsmeyer SJ.
Mol Cell Biol. 1992 Sep;12(9):4186-96.
PMID 1508213
 
TAL1 and LIM-only proteins synergistically induce retinaldehyde dehydrogenase 2 expression in T-cell acute lymphoblastic leukemia by acting as cofactors for GATA3.
Ono Y, Fukuhara N, Yoshie O.
Mol Cell Biol. 1998 Dec;18(12):6939-50.
PMID 9819382
 
GASDERMIN, suppressed frequently in gastric cancer, is a target of LMO1 in TGF-beta-dependent apoptotic signalling.
Saeki N, Kim DH, Usui T, Aoyagi K, Tatsuta T, Aoki K, Yanagihara K, Tamura M, Mizushima H, Sakamoto H, Ogawa K, Ohki M, Shiroishi T, Yoshida T, Sasaki H.
Oncogene. 2007 Oct 4;26(45):6488-98. Epub 2007 Apr 30.
PMID 17471240
 
The LMO1 and LDB1 proteins interact in human T cell acute leukaemia with the chromosomal translocation t(11;14)(p15;q11).
Valge-Archer V, Forster A, Rabbitts TH.
Oncogene. 1998 Dec 17;17(24):3199-202.
PMID 9872335
 
Integrative genomics identifies LMO1 as a neuroblastoma oncogene.
Wang K, Diskin SJ, Zhang H, Attiyeh EF, Winter C, Hou C, Schnepp RW, Diamond M, Bosse K, Mayes PA, Glessner J, Kim C, Frackelton E, Garris M, Wang Q, Glaberson W, Chiavacci R, Nguyen L, Jagannathan J, Saeki N, Sasaki H, Grant SF, Iolascon A, Mosse YP, Cole KA, Li H, Devoto M, McGrady PW, London WB, Capasso M, Rahman N, Hakonarson H, Maris JM.
Nature. 2011 Jan 13;469(7329):216-20. Epub 2010 Dec 1.
PMID 21124317
 

Citation

This paper should be referenced as such :
Saeki, N ; Sasaki, H
LMO1 (LIM domain only 1 (rhombotin 1))
Atlas Genet Cytogenet Oncol Haematol. 2012;16(2):84-86.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/LMO1ID33ch11p15.html


Other Leukemias implicated (Data extracted from papers in the Atlas) [ 4 ]
  t(7;9)(q34;q32) TRB/TAL2
t(11;14)(p13;q11) TRD/LMO2::t(7;11)(q35;p13) TRB/LMO2
t(11;14)(p15;q11) TRD/LMO1
T-lineage acute lymphoblastic leukemia (T-ALL)


External links

Nomenclature
HGNC (Hugo)LMO1   6641
LRG (Locus Reference Genomic)LRG_508
Cards
AtlasLMO1ID33ch11p15
Entrez_Gene (NCBI)LMO1  4004  LIM domain only 1
AliasesRBTN1; RHOM1; TTG1
GeneCards (Weizmann)LMO1
Ensembl hg19 (Hinxton)ENSG00000166407 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000166407 [Gene_View]  chr11:8224304-8268635 [Contig_View]  LMO1 [Vega]
ICGC DataPortalENSG00000166407
TCGA cBioPortalLMO1
AceView (NCBI)LMO1
Genatlas (Paris)LMO1
WikiGenes4004
SOURCE (Princeton)LMO1
Genetics Home Reference (NIH)LMO1
Genomic and cartography
GoldenPath hg38 (UCSC)LMO1  -     chr11:8224304-8268635 -  11p15.4   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)LMO1  -     11p15.4   [Description]    (hg19-Feb_2009)
EnsemblLMO1 - 11p15.4 [CytoView hg19]  LMO1 - 11p15.4 [CytoView hg38]
Mapping of homologs : NCBILMO1 [Mapview hg19]  LMO1 [Mapview hg38]
OMIM186921   
Gene and transcription
Genbank (Entrez)AW006226 BC039512 BC069673 BC069752 BC069793
RefSeq transcript (Entrez)NM_001270428 NM_002315
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)LMO1
Cluster EST : UnigeneHs.654426 [ NCBI ]
CGAP (NCI)Hs.654426
Alternative Splicing GalleryENSG00000166407
Gene ExpressionLMO1 [ NCBI-GEO ]   LMO1 [ EBI - ARRAY_EXPRESS ]   LMO1 [ SEEK ]   LMO1 [ MEM ]
Gene Expression Viewer (FireBrowse)LMO1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)4004
GTEX Portal (Tissue expression)LMO1
Human Protein AtlasENSG00000166407-LMO1 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP25800   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP25800  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP25800
Splice isoforms : SwissVarP25800
PhosPhoSitePlusP25800
Domaine pattern : Prosite (Expaxy)LIM_DOMAIN_1 (PS00478)    LIM_DOMAIN_2 (PS50023)   
Domains : Interpro (EBI)Znf_LIM   
Domain families : Pfam (Sanger)LIM (PF00412)   
Domain families : Pfam (NCBI)pfam00412   
Domain families : Smart (EMBL)LIM (SM00132)  
Conserved Domain (NCBI)LMO1
DMDM Disease mutations4004
Blocks (Seattle)LMO1
SuperfamilyP25800
Human Protein Atlas [tissue]ENSG00000166407-LMO1 [tissue]
Peptide AtlasP25800
HPRD01738
IPIIPI00396316   IPI01019052   IPI00607863   IPI00877062   IPI00979256   
Protein Interaction databases
DIP (DOE-UCLA)P25800
IntAct (EBI)P25800
FunCoupENSG00000166407
BioGRIDLMO1
STRING (EMBL)LMO1
ZODIACLMO1
Ontologies - Pathways
QuickGOP25800
Ontology : AmiGOnegative regulation of transcription from RNA polymerase II promoter  protein binding  nucleus  zinc ion binding  positive regulation of transcription from RNA polymerase II promoter  regulation of T cell homeostatic proliferation  
Ontology : EGO-EBInegative regulation of transcription from RNA polymerase II promoter  protein binding  nucleus  zinc ion binding  positive regulation of transcription from RNA polymerase II promoter  regulation of T cell homeostatic proliferation  
NDEx NetworkLMO1
Atlas of Cancer Signalling NetworkLMO1
Wikipedia pathwaysLMO1
Orthology - Evolution
OrthoDB4004
GeneTree (enSembl)ENSG00000166407
Phylogenetic Trees/Animal Genes : TreeFamLMO1
HOVERGENP25800
HOGENOMP25800
Homologs : HomoloGeneLMO1
Homology/Alignments : Family Browser (UCSC)LMO1
Gene fusions - Rearrangements
Fusion : MitelmanTRB/LMO1 [-/11p15.4]  [t(7;11)(q34;p15)]  
Fusion : MitelmanTRD/LMO1 [-/11p15.4]  [t(11;14)(p15;q11)]  
Tumor Fusion PortalLMO1
Fusion : TICdbTCR [LMO1]  -  11p15.4 []
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerLMO1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)LMO1
dbVarLMO1
ClinVarLMO1
1000_GenomesLMO1 
Exome Variant ServerLMO1
ExAC (Exome Aggregation Consortium)ENSG00000166407
GNOMAD BrowserENSG00000166407
Genetic variants : HAPMAP4004
Genomic Variants (DGV)LMO1 [DGVbeta]
DECIPHERLMO1 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisLMO1 
Mutations
ICGC Data PortalLMO1 
TCGA Data PortalLMO1 
Broad Tumor PortalLMO1
OASIS PortalLMO1 [ Somatic mutations - Copy number]
Cancer Gene: CensusLMO1 
Somatic Mutations in Cancer : COSMICLMO1  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDLMO1
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch LMO1
DgiDB (Drug Gene Interaction Database)LMO1
DoCM (Curated mutations)LMO1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)LMO1 (select a term)
intoGenLMO1
NCG5 (London)LMO1
Cancer3DLMO1(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM186921   
Orphanet548   
DisGeNETLMO1
MedgenLMO1
Genetic Testing Registry LMO1
NextProtP25800 [Medical]
TSGene4004
GENETestsLMO1
Target ValidationLMO1
Huge Navigator LMO1 [HugePedia]
snp3D : Map Gene to Disease4004
BioCentury BCIQLMO1
ClinGenLMO1
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD4004
Chemical/Pharm GKB GenePA30407
Clinical trialLMO1
Miscellaneous
canSAR (ICR)LMO1 (select the gene name)
Probes
Litterature
PubMed42 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineLMO1
EVEXLMO1
GoPubMedLMO1
iHOPLMO1
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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