Role of noncoding RNA ANRIL in genesis of plexiform neurofibromas in neurofibromatosis type 1.
BACKGROUND
Neurofibromatosis type 1 (NF1) is a tumor predisposition syndrome with a worldwide birth incidence of one in 2500. Genetic factors unrelated to the NF1 locus are thought to influence the number of plexiform neurofibromas (PNFs) in patients with NF1, but no factors have been identified to date.


METHODS
We used high-resolution array comparative genomic hybridization of tissue from 22 PNFs obtained from 18 NF1 patients to identify modifier genes involved in PNF development. We used a family-based association test for five previously identified cancer-susceptibility tag single-nucleotide polymorphisms (rs1063192, rs2151280, rs2218220, rs10757257, and rs7023329) located in chromosomal region 9p21.3 in 1105 subjects (740 NF1 patients and 365 non-affected relatives) from 306 families. To confirm the functional role of rs2151280, we used real-time quantitative reverse transcription-polymerase chain reaction to analyze the expression of cyclin-dependent kinase inhibitor 2A (CDKN2A), CDKN2B, alternate reading frame (ARF), and antisense noncoding RNA in the INK4 locus (ANRIL) in the peripheral blood of 124 NF1 patients. Relationships between CDKN2A, CDKN2B, ARF, and ANRIL expression and the rs2151280 genotype were tested by the Kruskal-Wallis test. All statistical tests were two-sided.


RESULTS
In NF1-associated PNFs, 9p21.3 deletions (including the CDKN2A/B-ANRIL locus) were found as the only recurrent somatic alterations. Single-nucleotide polymorphism rs2151280 (located in ANRIL) was statistically significantly associated with the number of PNFs (P < .001) in NF1 patients. In addition, allele T of rs2151280 was statistically significantly associated with reduced ANRIL transcript levels (P < .001), suggesting that modulation of ANRIL expression mediates PNF susceptibility.


CONCLUSIONS
Identification of ANRIL as a modifier gene in NF1 may offer clues to the molecular pathogenesis of PNFs, particularly neurofibroma formation, and emphasizes the unanticipated role of large noncoding RNA in activation of critical regulators of tumor development.
UMR745 INSERM, Université Paris Descartes, Sorbonne Paris Cité, Faculté des Sciences Pharmaceutiques et Biologiques, 4 avenue de l'Observatoire, Paris, France. eric.pasmant@gmail.com
Eric
E
Pasmant
Audrey
A
Sabbagh
Julien
J
Masliah-Planchon
Nicolas
N
Ortonne
Ingrid
I
Laurendeau
Lucie
L
Melin
Salah
S
Ferkal
Lucie
L
Hernandez
Karen
K
Leroy
Laurence
L
Valeyrie-Allanore
Béatrice
B
Parfait
Dominique
D
Vidaud
Ivan
I
Bièche
Laurent
L
Lantieri
Pierre
P
Wolkenstein
Michel
M
Vidaud
D000328:Adult; D000368:Aged; D002872:Chromosome Deletion; D002899:Chromosomes, Human, Pair 9; D015331:Cohort Studies; D055028:Comparative Genomic Hybridization; D050762:Cyclin-Dependent Kinase Inhibitor p15 / Q000235:genetics*; D019941:Cyclin-Dependent Kinase Inhibitor p16 / Q000235:genetics*; D005260:Female; D005602:France; D017353:Gene Deletion; D015972:Gene Expression Regulation, Neoplastic; D005787:Gene Frequency; D020022:Genetic Predisposition to Disease; D055106:Genome-Wide Association Study; D005838:Genotype; D006801:Humans; D015810:Linkage Disequilibrium; D008297:Male; D008875:Middle Aged; D018318:Neurofibroma, Plexiform / Q000235:genetics*; D009456:Neurofibromatosis 1 / Q000235:genetics*; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D062085:RNA, Long Noncoding; D012333:RNA, Messenger / Q000378:metabolism; D022661:RNA, Untranslated / Q000235:genetics / Q000378:metabolism*; D020133:Reverse Transcriptase Polymerase Chain Reaction
C561518:CDKN2B antisense RNA, human; C493966:CDKN2B protein, human; D050762:Cyclin-Dependent Kinase Inhibitor p15; D019941:Cyclin-Dependent Kinase Inhibitor p16; D062085:RNA, Long Noncoding; D012333:RNA, Messenger; D022661:RNA, Untranslated