PHOX2B (paired-like homeobox 2b)

2013-04-01   Tiziana Bachetti , Isabella Ceccherini 

UOC Medical Genetics, G Gaslini Institute, 16147 Genova, Italy

Identity

HGNC
LOCATION
4p13
IMAGE
Atlas Image
LEGEND
Cytogenetic location of PHOX2B on chromosome 4.
LOCUSID
ALIAS
CCHS,NBLST2,NBPhox,PMX2B

DNA/RNA

Note

Genomic: NCBI Reference Sequence: NG_008243.1.
Atlas Image
PHOX2B gene structure: untranslated regions (orange boxes), introns (black lines) and coding regions (blue boxes) are shown.

Description

The PHOX2B gene is 4888bp long; the coding region (CDS) is 945bp and is composed of 3 exons: exon 1 (241bp), exon 2 (188bp), exon 3 (516bp).
Other features: 5UTR: 361bp; 3UTR: 1725bp.

Transcription

mRNA: NCBI Reference Sequence NM_003924.3. The PHOX2B mRNA is 3218bp long; no alternative splice site is known.

Pseudogene

No pseudogene is reported.

Proteins

Note

NCBI Reference Sequence: NP_003915.2.
Atlas Image
Representation of the PHOX2B protein. The three exons (blue) are shown, with the number of aminoacids (aa) they code for, in addition to the homeodomain (red) and the polyalanine stretches (yellow). In the upper part of the figure, the first and last aminoacid positions for each of these crucial regions is indicated.

Description

PHOX2B protein is 314 aminoacids long. A homeodomain region spanning exons 1 and 2 (from residue 99 to residue 148) is responsible for the binding of this transcription factor to target DNA elements. In exon 3 there are two sequences characterized by stretches of 9 and 20 alanine residues, encoded by GC(N) triplets. Their functional role is still unknown.

Expression

PHOX2B is expressed during neural development in central autonomic circuits and peripheral neural crest derivatives, and particularly in the retrotrapezoid nucleus, noradrenergic centres and hindbrain (Pattyn et al., 1997; Dubreuil et al., 2002; Stornetta et al., 2006; Kang et al., 2007).
PHOX2B expression is transcriptionally regulated by the PHOX2B protein itself, through its direct binding to four promoter elements which give rise to a positive autoregulatory loop (Cargnin et al., 2005). In addition, PHOX2B expression is known to be regulated at specific sympathetic and enteric nervous system developmental stages by E2a and Hand2 (Hashimoto et al., 2011). Finally, SOX10 (Nagashimada et al., 2012), as well as PHOX2A and HASH1 (reviewed by Brunet and Pattyn, 2002) have shown a degree of cross-regulation with respect to PHOX2B. Hoxb1 and Hoxb2 have also shown to form a trimer with Pbx1 and Meis 1 to regulate PHOX2B transcription (Samad et al., 2004).

Localisation

PHOX2B is localized within the nuclear compartment.

Function

PHOX2B is a transcription factor essential for the development of autonomic neural crest derivatives (Pattyn et al., 1999). It controls the development of motoneurons (Pattyn et al., 2000) and drives a somatic-to-visceral switch in cranial sensory pathways (DAutréaux et al., 2011).
PHOX2B regulates the transcriptional expression of several genes: TH (Lo et al., 1999), DBH (Adachi et al., 2000), PHOX2A (Flora et al., 2011), PHOX2B itself (Cargnin et al., 2005), RET (Bachetti et al., 2005a), TLX-2 (Borghini et al., 2006), ALK (Bachetti et al., 2010), SOX10 (Nagashimada et al., 2012), Hand1 (Vincentz et al., 2012), SCG2 (Wen et al., 2007), MSX1 (Revet et al., 2008).
CREB-binding protein (CREBBP/CBP) interacts with PHOX2B and serves as its coactivator to mediate synergistic trans-activation (Wu et al., 2009). Using a yeast two-hybrid screening, TRIM11 was isolated as an additional PHOX2B interacting protein (Hong et al., 2008).

Homology

The amino acid sequence of the human PHOX2B is 100% identical to those of the chimpanzee, rat and mouse, suggesting that the function of PHOX2B is highly conserved in Mammals.

Mutations

Note

There is a clear correlation between types of PHOX2B mutations and clinical manifestations. Indeed, while the vast majority of PHOX2B mutations identified in isolated Congenital Central Hypoventilation Syndrome (CCHS) are PARMs (Polyalanine repeats mutation), those present in HSCR-NB (Hirschsprungs disease-neuroblastoma) associated CCHS are non-PARMs (NPARM), namely either missense mutations or nucleotide deletions/insertions causing frameshifts of the open reading frame. Moreover, inherited and de novo missense and frameshift mutations in exons 2 and 3 of the PHOX2B gene have been detected in both sporadic (NB) and syndromic (NB+CCHS) cases (Weese-Mayer et al., 2010; Bachetti et al., 2005b), thus suggesting that PHOX2B may play a role in isolated NB pathogenesis.
Atlas Image
Fig.4: Localization of mutations within the PHOX2B gene. In the figure some PARMS (yellow) and NPARMS (black) PHOX2B mutations are shown (see also Weese-Mayer et al., 2010).
Table 1: NPARMS and PARMS mutations of PHOX2B in human disease. Table 1 reports PHOX2B mutations detected so far, with detailed description of the nucleotide and aminoacid changes. Associated phenotypes are also annotated. Legend: NB neuroblastoma, TSNS tumor sympathetic nervous system, CCHS congenital central hypoventilation syndrome, LO-CHS late onset central hypoventialtion syndrome, NF1 neurofibromatosis type 1, (?) undetermined associations.

Germinal

Germline PHOX2B mutations are responsible for Congenital Central Hypoventilation Syndrome (CCHS). The vast majority of mutations is represented by in frame triplet duplications of a sequence stretch coding for 20 Alanine residues in exon 3, also known as polyalanine (polyAla) expansions or PARM (Polyalanine repeats mutation). The duplication length is variable, starting from 12 bp up to 39 bp, thus leading from +4 Ala up to +13 Ala expansions (Amiel et al., 2003; Sasaki et al., 2003; Weese-Mayer et al., 2003; Matera et al., 2004; Trochet et al., 2008a).
Ninety percent of constitutive (germinal) mutations detected in CCHS patients are represented by polyAla expansions. Among these, 75% have arisen de novo while 25% is inherited from one parent (Bachetti et al., 2011; Meguro et al., 2012).
In addition, germline PHOX2B missense, frameshift, nonsense non polyAla mutations (NPARMs) have been detected in a small fraction of mainly syndromic patients characterized by CCHS+other neurocristophaties such as neuroblastoma (NB) and/or Hirschsprungs disease (HSCR) (Trochet et al., 2005; Matera et al., 2004). A few specific missense PHOX2B mutations have been detected in isolated NB and/or HSCR, as reported in Table 1.
In frame deletions within the polyAla stretch have been identified in healthy subjects, but also in association with schizophenia (Toyota et al., 2004).

Somatic

No CCHS patient has ever been proven to be a somatic mosaic for PHOX2B mutation; however, somatic and therefore germline mosaicism has been demonstrated in a proportion of CCHS parents (Parodi et al., 2008; Bachetti et al., 2011; Bachetti et al., 2013).
Somatic PHOX2B mutations have been identified in NB cell lines and NB tumor samples as reported in the Table 1.

Implicated in

Entity name
PARMs (from +4 to +13 polyAla expansions)
Note
A correlation between the length of the expanded tract and the severity of the CCHS phenotype has already been reported (Matera et al., 2004; Weese-Mayer et al., 2010). Additional dysfunction of the autonomous nervous system, such as HSCR, NB, ocular defects, cardiac rythm alterations, etc., may be found in association with the especially largest polyAla expansions (Weese-Mayer et al., 2010).
Disease
Congenital Central Hypovention Syndrome (CCHS).
Prognosis
Congenital central hypoventilation syndrome (CCHS) is characterized by alveolar hypoventilation and autonomic dysregulation. It is a life-long, still untreatable disease.
Oncogenesis
Among PARMs, only subjects with the 20/29 and 20/33 genotypes have been identified to have tumors of neural crest origin (ganglioneuromas and ganglioneuroblastomas). No children with genotypes 20/24 to 20/28 have been identified with tumors of neural crest origin (Weese-Mayer et al., 2010).
Entity name
NPARMS: non polyAla repeat mutations, either germline or somatic (i.e. missense, nonsense, indels and loss of the stop codon mutations)
Note
These mutations, listed in Table 1, include missense, nonsense, loss of stop codon and small indels mutations.
Disease
Neuroblastoma and/or Hirschsprungs disease (either sporadic or in association with CCHS).
Entity name
Neuroblastoma
Note
In neuroblastoma cell lines and tumor samples, PHOX2B expression has turned out to be much higher than in normal tissues (Longo et al., 2008). Moreover, LOH in about 10% of the tumors and rare aberrant CpG dinucleotide methylation of 500bp of PHOX2B promoter region have been reported as NB associated molecular event (De Pontual et al., 2007).

Breakpoints

Note

Interestingly, other cytogenetic interstitial deletions, spanning from 0.29 to 2.6 Mb across the PHOX2B locus, have been detected in patients affected with atypical disorders, apparently sharing a loss of function/haploinsufficiency pathogenic mechanism, namely apparent-life threatening event including, Hirschsprung disease, transient neonatal hypoventilation and dysmorphic features. Neuroblastoma did not develop in any of these cases (Jennings et al., 2012).

Bibliography

Pubmed IDLast YearTitleAuthors
110345472000Paired-like homeodomain proteins Phox2a/Arix and Phox2b/NBPhox have similar genetic organization and independently regulate dopamine beta-hydroxylase gene transcription.Adachi M et al
126404532003Polyalanine expansion and frameshift mutations of the paired-like homeobox gene PHOX2B in congenital central hypoventilation syndrome.Amiel J et al
234605452014Recurrence of CCHS associated PHOX2B poly-alanine expansion mutation due to maternal mosaicism.Bachetti T et al
129191342003PMX2B, a new candidate gene for Hirschsprung's disease.Benailly HK et al
164029142006The TLX2 homeobox gene is a transcriptional target of PHOX2B in neural-crest-derived cells.Borghini S et al
121008892002Phox2 genes - from patterning to connectivity.Brunet JF et al
161448302005PHOX2B regulates its own expression by a transcriptional auto-regulatory mechanism.Cargnin F et al
221283342011Homeoprotein Phox2b commands a somatic-to-visceral switch in cranial sensory pathways.D'Autréaux F et al
123993152002The role of Phox2b in synchronizing pan-neuronal and type-specific aspects of neurogenesis.Dubreuil V et al
233420682013Contributions of PHOX2B in the pathogenesis of Hirschsprung disease.Fernández RM et al
115497132001Sp proteins and Phox2b regulate the expression of the human Phox2a gene.Flora A et al
214536802011Interaction of Hand2 and E2a is important for transcription of Phox2b in sympathetic nervous system neuron differentiation.Hashimoto Y et al
182758502008Trim11 increases expression of dopamine beta-hydroxylase gene by interacting with Phox2b.Hong SJ et al
218303192012Variable human phenotype associated with novel deletions of the PHOX2B gene.Jennings LJ et al
175590942007Central nervous system distribution of the transcription factor Phox2b in the adult rat.Kang BJ et al
102307901999Specification of neurotransmitter identity by Phox2 proteins in neural crest stem cells.Lo L et al
189493612008PHOX2A and PHOX2B genes are highly co-expressed in human neuroblastoma.Longo L et al
151217772004PHOX2B mutations and polyalanine expansions correlate with the severity of the respiratory phenotype and associated symptoms in both congenital and late onset Central Hypoventilation syndrome.Matera I et al
166915922006PHOX2B analysis in non-syndromic neuroblastoma cases shows novel mutations and genotype-phenotype associations.McConville C et al
224372072012Inheritance of polyalanine expansion mutation of PHOX2B in congenital central hypoventilation syndrome.Meguro T et al
153384622004Germline PHOX2B mutation in hereditary neuroblastoma.Mosse YP et al
229222602012Autonomic neurocristopathy-associated mutations in PHOX2B dysregulate Sox10 expression.Nagashimada M et al
181578322008Parental origin and somatic mosaicism of PHOX2B mutations in Congenital Central Hypoventilation Syndrome.Parodi S et al
107043822000Control of hindbrain motor neuron differentiation by the homeobox gene Phox2b.Pattyn A et al
103605751999The homeobox gene Phox2b is essential for the development of autonomic neural crest derivatives.Pattyn A et al
176377452008Prevalence and functional consequence of PHOX2B mutations in neuroblastoma.Raabe EH et al
182016992008The MSX1 homeobox transcription factor is a downstream target of PHOX2B and activates the Delta-Notch pathway in neuroblastoma.Revet I et al
152894352004Integration of anteroposterior and dorsoventral regulation of Phox2b transcription in cranial motoneuron progenitors by homeodomain proteins.Samad OA et al
145665592003Molecular analysis of congenital central hypoventilation syndrome.Sasaki A et al
170211862006Expression of Phox2b by brainstem neurons involved in chemosensory integration in the adult rat.Stornetta RL et al
147095962004Association between schizophrenia with ocular misalignment and polyalanine length variation in PMX2B.Toyota T et al
190582262009In Vitro studies of non poly alanine PHOX2B mutations argue against a loss-of-function mechanism for congenital central hypoventilation.Trochet D et al
156578732005PHOX2B genotype allows for prediction of tumor risk in congenital central hypoventilation syndrome.Trochet D et al
180794952008PHOX2B germline and somatic mutations in late-onset central hypoventilation syndrome.Trochet D et al
223237232012A Phox2- and Hand2-dependent Hand1 cis-regulatory element reveals a unique gene dosage requirement for Hand2 during sympathetic neurogenesis.Vincentz JW et al
202080422010An official ATS clinical policy statement: Congenital central hypoventilation syndrome: genetic basis, diagnosis, and management.Weese-Mayer DE et al
175847652007An ancestral variant of Secretogranin II confers regulation by PHOX2 transcription factors and association with hypertension.Wen G et al
191913212009Interaction between PHOX2B and CREBBP mediates synergistic activation: mechanistic implications of PHOX2B mutants.Wu HT et al
177655332007Methylation-associated PHOX2B gene silencing is a rare event in human neuroblastoma.de Pontual L et al
155169802004The Phox2B homeobox gene is mutated in sporadic neuroblastomas.van Limpt V et al

Other Information

Locus ID:

NCBI: 8929
MIM: 603851
HGNC: 9143
Ensembl: ENSG00000109132

Variants:

dbSNP: 8929
ClinVar: 8929
TCGA: ENSG00000109132
COSMIC: PHOX2B

RNA/Proteins

Gene IDTranscript IDUniprot
ENSG00000109132ENST00000226382Q99453

Expression (GTEx)

0
1
2
3
4
5

Protein levels (Protein atlas)

Not detected
Low
Medium
High

References

Pubmed IDYearTitleCitations
126404532003Polyalanine expansion and frameshift mutations of the paired-like homeobox gene PHOX2B in congenital central hypoventilation syndrome.157
181982762008A human mutation in Phox2b causes lack of CO2 chemosensitivity, fatal central apnea, and specific loss of parafacial neurons.106
150246932004Germline mutations of the paired-like homeobox 2B (PHOX2B) gene in neuroblastoma.73
199401792009Defective respiratory rhythmogenesis and loss of central chemosensitivity in Phox2b mutants targeting retrotrapezoid nucleus neurons.62
185808842008Confirmation of association of IRGM and NCF4 with ileal Crohn's disease in a population-based cohort.54
156578732005PHOX2B genotype allows for prediction of tumor risk in congenital central hypoventilation syndrome.41
156578732005PHOX2B genotype allows for prediction of tumor risk in congenital central hypoventilation syndrome.41
176377452008Prevalence and functional consequence of PHOX2B mutations in neuroblastoma.39
168882902006Congenital central hypoventilation syndrome: PHOX2B mutations and phenotype.34
201012092010Molecular pathogenesis of peripheral neuroblastic tumors.34

Citation

Tiziana Bachetti ; Isabella Ceccherini

PHOX2B (paired-like homeobox 2b)

Atlas Genet Cytogenet Oncol Haematol. 2013-04-01

Online version: http://atlasgeneticsoncology.org/gene/126/phox2b