NUMB (numb homolog (Drosophila))

2011-03-01   Stefano Confalonieri , Salvatore Pece , Pier Paolo Di Fiore 

IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Via Adamello 16, 20139, Milan, Italy (SC, SP, PPDF); IEO, Istituto Europeo di Oncologia, Via Ripamonti 435, 20141, Milan, Italy (SC, SP, PPDF)

Identity

HGNC
LOCATION
14q24.2
LOCUSID
ALIAS
C14orf41,S171,c14_5527
FUSION GENES

DNA/RNA

Atlas Image
Figure 1: Structure of NUMB gene. Asterisks indicate exons that undergo alternative splicing during NUMB transcript maturation.

Description

The NUMB locus spans 183368 bp on the minus (-) strand of the long arm of chromosome 14 and is composed of 13 exons.

Transcription

As a result of three alternative splicing events the NUMB locus can generate six different transcripts of 3647 bp (isoform 1), 3503 bp (isoform 2), 3614 bp (isoform 3) and of 3470 bp (isoform 4); isoforms 5 and 6 are only partial and cover only the coding sequence and their representation* is putative.

Pseudogene

No known pseudogenes.

Proteins

Atlas Image
The modular structure of the longest human Numb isoform is shown.

Description

The human Numb gene is transcribed in 6 different splicing variants (see above), due to the alternate skipping of three exons. Arrowheads indicate the boundaries of the protein sequences encoded by the three alternative exons. The PTB (Phospho-Tyrosine Binding) domain and the NumbF domain (domain found in the Numb family of proteins adjacent to the PTB domain) are indicated. The position of the DPF (responsible for binding to alpha-adaptin) and NPF motifs (responsible for binding to the EH domain of endocytic proteins) are indicated as gray and red boxes respectively.

Expression

From an in-silico analysis Numb RNA messenger seems broadly expressed in human tissues. However in mouse and drosophila it has been demonstrated that isoforms 1 to 4 are expressed in a tissue-specific and developmental stage-specific manner.

Localisation

Mostly cytosolic partially associated to the plasma membrane and vesicles; may be found also in the nucleus.

Function

Numb plays a multifaceted role in cellular homeostasis and is implicated in a variety of biochemical pathways connected with signaling, endocytosis, determination of polarity and ubiquitination. The pleiotropic biochemical functions of Numb lie at the heart of its involvement in diverse physiological processes, including cell fate developmental decisions, maintenance of the homeostasis of stem cell compartments, regulation of cell polarity, adhesion and migration. Loss of Numb is implicated in different types of human cancers, underscoring its complex function as a tumor suppressor in normal tissue homeostasis. The role of Numb as an intrinsic molecular determinant of cell fate during developmental programs is inextricably intertwined with the execution of asymmetric mitotic divisions, that is the mechanism through which a mother cell generates two daughter cells with different fates. The unequal distribution of Numb between two daughter cells causes a biochemical asymmetry of pathways epistatically regulated by Numb, a condition epitomized by the differential regulation of the Notch circuitry in the two daughter cells derived from the asymmetric mitotic division of the sensory organ precursor (SOP) in drosophila neurogenesis. This mechanism appears to be conserved between flies and mammals. Numb is involved at different levels in the process of endocytosis and intracellular trafficking. It interacts with the EH domain of several endocytic proteins, such as Eps15 and Eps15R, and with the major clathrin adaptor AP-2, and is subcellularly localized in endocytic/recycling organelles. Numb is also required for the internalization and recycling of transmembrane proteins, such as Sanpodo in drosophila, and different types of integrins or other transmembrane molecules in mammals.The role of Numb in the regulation of cell polarity is exerted through its interaction with core components of the evolutionary conserved Par3/Par6/aPKC (PAR) complex, and through the regulation of adherens and tight junctions. At the biochemical level, Numb is endowed with pleiotropic signaling functions. In fact, besides intersecting the Notch pathway, Numb also modulates the Hedgehog and the p53 circuitry. In general terms, the role of Numb in the regulation of specific molecular pathways is a function of a number of liaisons between Numb itself and components of the ubiquitin/proteasomal machinery. For instance, the interaction of Numb with the E3-ubiquitin ligase Itch is required for the Itch-dependent ubiquitination and ensuing proteasomal degradation of Notch. Likewise, the Numb/Itch interaction is a prerequisite for targeting Itch to the transcription factor Gli1, which ultimately affects Gli1 stability and therefore suppresses Hedgehog signaling. Furthermore, the ability of Numb to bind and inhibit the E3-ligase Hdm2 (Mdm2 in mouse) protects p53 from Hdm2-mediated ubiquitination and consequent proteasomal degradation, thus resulting in a positive regulation of the cellular levels of p53 and of its tumor suppressor activity. The downregulatory function of Numb over Hdm2 occurs in the context of a Numb/p53/Hdm2 tricomplex. Loss of this regulatory circuitry results in impaired p53-mediated cellular responses, such as apoptosis, DNA-damage and cell cycle checkpoint activation response, and is relevant to the intrinsic resistance of Numb-defective breast cancers to genotoxic agents. The networking of Numb into ubiquitin-based circuitries appears also to be at the heart of the regulation of cellular Numb levels in homeostasis. E3-ubiquitin ligases, such as Siah1 and LNX, have been implicated in targeting Numb for ubiquitin-dependent degradation. Ubiquitin-based biochemical pathways that regulate Numb levels under physiological conditions are likely relevant to cancer as well since, both in breast and in lung Numb-defective tumors, loss of Numb is due to its exaggerated ubiquitination and degradation. Considering its pleiotropic functions in many critical cellular processes, subversion of Numb has been linked to important human pathologies, and in particular to cancer.

Homology

Numb appears in evolution roughly with bilateral animals. Mammalian Numb homologues evolved from a common ancestral gene, possibly owing to gene duplication followed by the divergence of two gene families, Numb and Numbl. In the tree, mammalian Numb and NumbL formed two distinct clusters. A gene duplication of the ancestral Numb gene may be occurred prior to the appearance and the divergence of the major vertebrate clades, since one Numb gene is present in the chordate Ciona intestinalis, and one of the two duplicated genes evolved into NumbL via the acquisition of two Numbl unique motifs. Two of the known cellular functions to which Numb participates, endocytosis and ubiquitination, have ancient origins. Endocytosis is widely held to represent one of the distinguishing features between eukaryotes and prokaryotes. There is evidence that endocytosis is present as far back as the last eukaryotic common ancestor. In actual fact, endocytosis might be even older than this, as recent evidence demonstrates that: i) bacteria of the phyla Planctomycetes and Verrucomicrobia display intracellular membranous compartmentalization, and have membrane coat-like proteins; ii) the planctomycete Gemmata obscuriglobus exhibits endocytic-like protein uptake. Similarly, while ubiquitination is certainly one of the distinctive, and highly conserved, features of eukaryotes, its ancestry can now be traced back to bacteria, both in terms of ubiquitin-like molecules and of enzymatic molecular machinery. By the time Numb appears in phylogenesis, endocytosis and ubiquitination are already cornerstones of the eukaryotic make-up that are deeply interconnected. It is unlikely, therefore, that Numb might have evolved in direct conjunction with these processes. At the same time, the appearance of Numb roughly coincides with the appearance of the PAR complex. While polarity is perhaps as old as cellular life, a clear existence of proteins of the PAR complex can be traced back in animals only until roughly 500 million years ago, probably with the emergence of ancestors of bilateral animals (e.g., nematodes, flies and mammals). It is possible therefore that Numb evolved (or co-evolved) together with the PAR complex. Regardless, Numb might represent (and might have evolved to be) a critical connector between polarization and endocytosis. Thus, Numb might have evolved with an original role in polarity, but because of its membrane location might have subsequently acquired additional roles in the connected endocytic/ubiquitin networks: acting as a go-between between these networks and the hardware of polarity, as well as participating in them in a polarity-independent fashion.
Atlas Image
Numb in evolution. The phylogenesis of Numb in bilateral animals is shown.

Mutations

Germinal

None found.

Somatic

Two mutations are reported in the COSMIC database, both of them are silent mutations:
- c.1452G>T (Substitution), p.G484G (Substitution - coding silent) in one out of 447 glioma samples screened
- c.354C>T (Substitution), p.A118A (Substitution - coding silent) in one out of 6 malignant melanoma samples screened.

Implicated in

Entity name
Breast cancer
Prognosis
Loss of Numb in breast cancer correlates with poor prognosis and with clinico/pathological parameters of biological aggressiveness, such as a poorly differentiated tumor phenotype (high grade), high proliferative index (Ki67 expression), a basal-like phenotype and expression of cancer stem cell markers.
Oncogenesis
Numb is a tumor suppressor in the human mammary gland and its expression is frequently lost in breast cancer. Numb-defective breast tumors are addicted to loss of Numb, as witnessed by the loss of their proliferative advantage caused by re-expression of Numb. In these tumors, loss of Numb results in overactivation of oncogenic Notch signaling and impaired tumor suppression function of p53, two molecular events that are causal for transformation. Loss of Numb expression in breast cancer is due to its exaggerated ubiquitination and ensuing proteasomal degradation.
Entity name
Lung cancer
Oncogenesis
The expression of Numb is frequently lost in non-small cell lung cancer (NSCLC). In NSCLC, loss of Numb results in enhanced activation of the Notch pathway, and addiction of these tumors to deregulated Notch activity. Likewise breast cancer, loss of Numb in NSCLCs is due to enhanced destruction of this protein through the proteasomal machinery.
Entity name
Salivary gland cancer
Prognosis
Reduced Numb levels correlate with poor prognosis and with clinico/pathological parameters of biological aggressiveness (high grade and proliferative index) in salivary gland carcinomas. The molecular mechanism underlying loss of Numb in these tumors are not yet defined.
Oncogenesis
In a mouse model of chronic myelogenous leukemia (CML), Ito et al. found that reduced Numb expression is necessary for the establishment of blast crisis. A molecular mechanism different from enhanced proteasomal degradation appears to be involved in reduced Numb expression during CML progression, which is represented by the high levels of Musashi2, a repressor of Numb translation. An upregulation of Musashi2 expression was found in human CML patients during disease progression towards blast crisis, concomitant to downregulation of numb expression.

Bibliography

Pubmed IDLast YearTitleAuthors
172536252007A switch in numb isoforms is a critical step in cortical development.Bani-Yaghoub M et al
121948532002The endocytic protein alpha-Adaptin is required for numb-mediated asymmetric cell division in Drosophila.Berdnik D et al
161392152005Localization-dependent and -independent roles of numb contribute to cell-fate specification in Drosophila.Bhalerao S et al
211791882010Zebrafish numb and numblike are involved in primitive erythrocyte differentiation.Bresciani E et al
181724992008NUMB controls p53 tumour suppressor activity.Colaluca IN et al
105518801999Characterization of four mammalian numb protein isoforms. Identification of cytoplasmic and membrane-associated variants of the phosphotyrosine binding domain.Dho SE et al
171150282006Numb is a suppressor of Hedgehog signalling and targets Gli1 for Itch-dependent ubiquitination.Di Marcotullio L et al
199446842010The multiple functions of Numb.Gulino A et al
87554761996Control of daughter cell fates during asymmetric division: interaction of Numb and Notch.Guo M et al
155989812005Targeted deletion of numb and numblike in sensory neurons reveals their essential functions in axon arborization.Huang EJ et al
206398632010Regulation of myeloid leukaemia by the cell-fate determinant Musashi.Ito T et al
197850072009Numb promotes an increase in skeletal muscle progenitor cells in the embryonic somite.Jory A et al
96327821998The Mdm2 oncoprotein interacts with the cell fate regulator Numb.Juven-Gershon T et al
200385782010Stress-induced switch in Numb isoforms enhances Notch-dependent expression of subtype-specific transient receptor potential channel.Kyriazis GA et al
146875462003Inactivation of Numb and Numblike in embryonic dorsal forebrain impairs neurogenesis and disrupts cortical morphogenesis.Li HS et al
181797512007Prognostic implications of NUMB immunoreactivity in salivary gland carcinomas.Maiorano E et al
126820592003Mammalian numb proteins promote Notch1 receptor ubiquitination and degradation of the Notch1 intracellular domain.McGill MA et al
117824292002LNX functions as a RING type E3 ubiquitin ligase that targets the cell fate determinant Numb for ubiquitin-dependent degradation.Nie J et al
184930602008Caenorhabditis elegans num-1 negatively regulates endocytic recycling.Nilsson L et al
176091072007Numb controls integrin endocytosis for directional cell migration with aPKC and PAR-3.Nishimura T et al
129196752003Numb inhibits membrane localization of Sanpodo, a four-pass transmembrane protein, to promote asymmetric divisions in Drosophila.O'Connor-Giles KM et al
97391211998Mesodermal cell fate decisions in Drosophila are under the control of the lineage genes numb, Notch, and sanpodo.Park M et al
209400302011NUMB-ing down cancer by more than just a NOTCH.Pece S et al
154920442004Loss of negative regulation by Numb over Notch is relevant to human breast carcinogenesis.Pece S et al
197952052010Numb protein expression correlates with a basal-like phenotype and cancer stem cell markers in primary breast cancer.Rennstam K et al
83134691994Asymmetric distribution of numb protein during division of the sensory organ precursor cell confers distinct fates to daughter cells.Rhyu MS et al
94284221997Segregation of myogenic lineages in Drosophila requires numb.Ruiz Gómez M et al
93035391997Binding specificity and in vivo targets of the EH domain, a novel protein-protein interaction module.Salcini AE et al
111214472000Numb is an endocytic protein.Santolini E et al
123619752002Asymmetric Numb distribution is critical for asymmetric cell division of mouse cerebral cortical stem cells and neuroblasts.Shen Q et al
186570692008AAK1 regulates Numb function at an early step in clathrin-mediated endocytosis.Sorensen EB et al
87554751996Numb antagonizes Notch signaling to specify sibling neuron cell fates.Spana EP et al
85822631995Asymmetric localization of numb autonomously determines sibling neuron identity in the Drosophila CNS.Spana EP et al
117524542001Siah-1 binds and regulates the function of Numb.Susini L et al
165083112006Distinct functions of human numb isoforms revealed by misexpression in the neural stem cell lineage in the Drosophila larval brain.Toriya M et al
27524271989numb, a gene required in determination of cell fate during sensory organ formation in Drosophila embryos.Uemura T et al
114258792001Nucleocytoplasmic shuttling of endocytic proteins.Vecchi M et al
104686331999Distinct human NUMB isoforms regulate differentiation vs. proliferation in the neuronal lineage.Verdi JM et al
88053721996Mammalian NUMB is an evolutionarily conserved signaling adapter protein that specifies cell fate.Verdi JM et al
104021941999NUMB localizes in the basal cortex of mitotic avian neuroepithelial cells and modulates neuronal differentiation by binding to NOTCH-1.Wakamatsu Y et al
178052972007Polo inhibits progenitor self-renewal and regulates Numb asymmetry by phosphorylating Pon.Wang H et al
200077752009Alterations of the Notch pathway in lung cancer.Westhoff B et al
126462522003Mammalian Numb is a target protein of Mdm2, ubiquitin ligase.Yogosawa S et al
146413292003Distinct expression patterns of splicing isoforms of mNumb in the endocrine lineage of developing pancreas.Yoshida T et al
108415802000Mouse numb is an essential gene involved in cortical neurogenesis.Zhong W et al

Other Information

Locus ID:

NCBI: 8650
MIM: 603728
HGNC: 8060
Ensembl: ENSG00000133961

Variants:

dbSNP: 8650
ClinVar: 8650
TCGA: ENSG00000133961
COSMIC: NUMB

RNA/Proteins

Gene IDTranscript IDUniprot
ENSG00000133961ENST00000355058P49757
ENSG00000133961ENST00000355058A0A024R6F4
ENSG00000133961ENST00000356296A0A024R681
ENSG00000133961ENST00000359560A0A024R6C4
ENSG00000133961ENST00000535282A0A024R681
ENSG00000133961ENST00000554394G3V3R1
ENSG00000133961ENST00000554546A0A024R684
ENSG00000133961ENST00000554818G3V4S6
ENSG00000133961ENST00000555238P49757
ENSG00000133961ENST00000555238A0A024R6F4
ENSG00000133961ENST00000555307G3V3R1
ENSG00000133961ENST00000555394A0A024R681
ENSG00000133961ENST00000555859G3V3M5
ENSG00000133961ENST00000555987G3V433
ENSG00000133961ENST00000556772G3V3Z8
ENSG00000133961ENST00000557597A0A024R6C4

Expression (GTEx)

0
10
20
30
40
50
60

Pathways

PathwaySourceExternal ID
Notch signaling pathwayKEGGko04330
Notch signaling pathwayKEGGhsa04330
Signal TransductionREACTOMER-HSA-162582
Signaling by NOTCHREACTOMER-HSA-157118
Signaling by NOTCH1REACTOMER-HSA-1980143
Activated NOTCH1 Transmits Signal to the NucleusREACTOMER-HSA-2122948
Signaling by HedgehogREACTOMER-HSA-5358351
Hedgehog 'off' stateREACTOMER-HSA-5610787
Degradation of GLI1 by the proteasomeREACTOMER-HSA-5610780
Hedgehog 'on' stateREACTOMER-HSA-5632684
Developmental BiologyREACTOMER-HSA-1266738
Axon guidanceREACTOMER-HSA-422475
L1CAM interactionsREACTOMER-HSA-373760
Recycling pathway of L1REACTOMER-HSA-437239

Protein levels (Protein atlas)

Not detected
Low
Medium
High

References

Pubmed IDYearTitleCitations
154920442004Loss of negative regulation by Numb over Notch is relevant to human breast carcinogenesis.172
176091072007Numb controls integrin endocytosis for directional cell migration with aPKC and PAR-3.157
181724992008NUMB controls p53 tumour suppressor activity.154
171150282006Numb is a suppressor of Hedgehog signalling and targets Gli1 for Itch-dependent ubiquitination.116
243321782013RBM5, 6, and 10 differentially regulate NUMB alternative splicing to control cancer cell proliferation.98
217756252011Numb controls E-cadherin endocytosis through p120 catenin with aPKC.49
163941002006Role of numb in dendritic spine development with a Cdc42 GEF intersectin and EphB2.46
208184362011Numb activates the E3 ligase Itch to control Gli1 function through a novel degradation signal.46
237068212013Dynamic methylation of Numb by Set8 regulates its binding to p53 and apoptosis.32
243029912013miR-146a enhances the oncogenicity of oral carcinoma by concomitant targeting of the IRAK1, TRAF6 and NUMB genes.32

Citation

Stefano Confalonieri ; Salvatore Pece ; Pier Paolo Di Fiore

NUMB (numb homolog (Drosophila))

Atlas Genet Cytogenet Oncol Haematol. 2011-03-01

Online version: http://atlasgeneticsoncology.org/gene/43702/numb