Low RET mutation frequency and polymorphism analysis of the RET and EDNRB genes in patients with Hirschsprung disease in Taiwan

Negative Association Between lncRNA HOTTIP rs3807598 C>G and Hirschsprung Disease

Background

Hirschsprung disease (HSCR) is a congenital disease that arises from defective intestinal neural system. LncRNA HOTTIP is a critical gene in various diseases, including HSCR. No epidemiological studies have explored the correlation between lncRNA HOTTIP single nucleotide polymorphisms (SNPs) and HSCR risk. We here lead as a pioneer to explore whether SNPs in lncRNA HOTTIP impact the risk of HSCR and HSCR subtypes in an unrelated Chinese population.

Methods

We used the TaqMan method to genotype rs3807598 C>G of the lncRNA HOTTIP gene using 1470 HSCR cases and 1473 healthy controls. Of them, 1441 cases and 1434 controls were successfully genotyped. We adopted odds ratios (ORs) and 95% confidence intervals (CIs) to quantify the relationship.

Results

We got an unexpected outcome that lncRNA HOTTIP SNP rs3807598 C>G could not modify the risk of HSCR (CG vs. CC: adjusted OR=0.89, 95% CI=0.74–1.07; GG vs. CC: adjusted OR=1.10, 95% CI=0.89–1.37; GG/CG vs CC: adjusted OR=0.95, 95% CI=0.80–1.13; and GG vs. CC/CG: adjusted OR=1.19, 95% CI=0.99–1.43). What’s more, risk effect of lncRNA HOTTIP rs3807598 C>G is still not obvious in stratification analysis by HSCR subtype.

Conclusion

Our studies did not provide statistical evidence of a correlation between lncRNA HOTTIP SNP rs3807598 C>G and susceptibility of HSCR in the Chinese population that is being studied. Further validation study with a larger sample size covering multi-ethnic groups is warranted.

Downregulation of PRMT1 promotes the senescence and migration of a non-MYCN amplified neuroblastoma SK-N-SH cells

Protein arginine methyltransferase 1 (PRMT1) catalyzing the formation of asymmetric dimethylarginines has been implicated in cancer development, metastasis, and prognosis. In this study, we investigated the effects of low PRMT1 levels on a non-MYCN amplified neuroblastoma SK-N-SH cell line. Stable PRMT1-knockdown (PRMT1-KD) cells showed reduced growth rates and cell cycle arrest at G₂/M. They also exhibited senescent phenotypes and increased p53 expression. p21 and PAI-1, which are two p53 downstream targets critical for senescence, were significantly induced in SK-N-SH cells subjected to either PRMT1-KD or inhibitor treatment. The induction was suppressed by a p53 inhibitor and marginal in a p53-null SK-N-AS cell line, suggesting dependence on p53. In general, the DNA damage and ROS levels of the PRMT1-KD SK-N-SH cells were slightly increased. Their migration activity also increased with the induction of PAI-1. Thus, PRMT1 downregulation released the repression of cellular senescence and migration activity in SK-N-SH cells. These results might partially explain the poor prognostic outcome of low PRMT1 in a non-MYCN-amplified cohort and indicate the multifaceted complexity of PRMT1 as a biological regulator of neuroblastoma.

Potential association of VAMP5 polymorphisms with total colonic aganglionosis in Hirschsprung disease

BACKGROUND

Hirschsprung disease (HSCR) is a congenital bowel disease caused by the absence of nerve cells in portions of the intestine. Our recent genome-wide association study has identified a variant (rs1254900) of vesicle-associated membrane protein 5 (VAMP5) as a potential risk locus for total colonic aganglionosis (TCA) in HSCR. In addition, VAMP5 is a member of the VAMP/synaptobrevin protein complex, which participates in nerve signal transduction by regulating the vesicular fusion of the neurotransmitter in synaptic transmission.

METHODS

A total of 11 single nucleotide polymorphisms (SNPs), including those in the functionally important coding region, were selected on the basis of linkage disequilibrium and genotyped in 187 HSCR patients and 283 unaffected controls by using a TaqMan assay. Logistic analysis was conducted to investigate the possible association between VAMP5 SNPs and the risk of HSCR.

KEY RESULTS

Genetic variants of VAMP5 showed increased association signals in the TCA subgroup of HSCR patients (minimum p = 9.69 × 10(-5) , OR = 3.93 at rs10206961) compared to other subgroups, even after Bonferroni correction (pcorr = 0.002). In haplotype analysis, three haplotypes (BL1_ht1, BL2_ht1, and BL2_ht2) were associated with the risk of TCA (minimum pcorr = 0.005). In additional combined analysis after imputation based on our previous GWAS, five SNPs still retained significant associations with the TCA subtype (minimum pcorr = 0.006 at rs10206961).

CONCLUSIONS & INFERENCES

Considering that differential genetic effects on the development of the enteric nervous system, our results suggest that VAMP5 may be associated with the TCA of HSCR. However, further replications and functional evaluations are required.

RET and EDNRB mutation screening in patients with Hirschsprung disease: Functional studies and its implications for genetic counseling

Hirschsprung disease (HSCR) is a major cause of chronic constipation in children. HSCR can be caused by germline mutations in RET and EDNRB. Defining causality of the mutations identified is difficult and almost exclusively based on in silico predictions. Therefore, the reported frequency of pathogenic mutations might be overestimated. We combined mutation analysis with functional assays to determine the frequencies of proven pathogenic RET and EDNRB mutations in HSCR. We sequenced RET and EDNRB in 57 HSCR patients. The identified RET-coding variants were introduced into RET constructs and these were transfected into HEK293 cells to determine RET phosphorylation and activation via ERK. An exon trap experiment was performed to check a possible splice-site mutation. We identified eight rare RET-coding variants, one possible splice-site variant, but no rare EDNRB variants. Western blotting showed that three coding variants p.(Pr270Leu), p.(Ala756Val) and p.(Tyr1062Cys) resulted in lower activation of RET. Moreover, only two RET variants (p.(Ala756Val) and p.(Tyr1062Cys)) resulted in reduced ERK activation. Splice-site assays on c.1880-11A>G could not confirm its pathogenicity. Our data suggest that indeed almost half of the identified rare variants are proven pathogenic and that, hence, functional studies are essential for proper genetic counseling.

Correlation between multiple RET mutations and severity of Hirschsprung's disease

PURPOSE

The enteric nervous system (ENS), comprising neurons and glial cells, organized as interconnected ganglia within the gut wall, controls peristalsis and the production of secretions. The RET receptor tyrosine kinase is expressed throughout enteric neurogenesis and is required for normal ENS development. Humans with mutations in the RET locus have Hirschsprung's disease (HSCR), and mice lacking RET exhibit total intestinal aganglionosis. Although a number of mutations with the potential for causing HSCR have been reported, their precise correlation with phenotype and symptom severity in HSCR is not clearly understood. Our study investigates the correlation between mutations in the RET locus and symptom severity in HSCR.

METHODS

We performed a comprehensive nucleotide analysis of the RET coding region in 18 HSCR patients and 87 controls, performed cellular biological analysis by Western blotting using the expression vector, and analyzed cell proliferation with anti-Ki67 antibody under immunofluorescence confocal microscopy (ICM).

RESULTS

We identified three novel mutations, D489N, L769L, and V778D in the RET coding region in our HSCR patients. In the allelic distribution of D489N and L769L, the difference between HSCR patients and controls reached statistical significance (p = 0.0373 and p = 0.0004, respectively), whereas no statistical difference was observed in the allelic distribution of V778D (p = 0.1073). One HSCR patient who died from total colonic aganglionosis had a combination of homozygous mutation of D489N, L769L, and heterozygous mutation of V778D. Western blotting of full mutant RET from this patient showed significantly increased 150kD-band, which corresponds to the immature form compared with wild-type and single mutant RET. ICM showed that overexpression of full mutant RET significantly reduced cellular proliferation in comparison with wild-type and single mutant RET.

CONCLUSION

A combination of mutations in the RET locus may correlate with symptom severity in HSCR as a consequence of reduced cellular proliferation secondary to altered maturation of RET.

Comprehensive analysis of RET common and rare variants in a series of Spanish Hirschsprung patients confirms a synergistic effect of both kinds of events

Background

RET is the major gene associated to Hirschsprung disease (HSCR) with differential contributions of its rare and common, coding and noncoding mutations to the multifactorial nature of this pathology. In the present study, we have performed a comprehensive study of our HSCR series evaluating the involvement of both RET rare variants (RVs) and common variants (CVs) in the context of the disease.

Methods

RET mutational screening was performed by dHPLC and direct sequencing for the identification of RVs. In addition Taqman technology was applied for the genotyping of 3 RET CVs previously associated to HSCR, including a variant lying in an enhancer domain within RET intron 1 (rs2435357). Statistical analyses were performed using the SPSS v.17.0 to analyze the distribution of the variants.

Results

Our results confirm the strongest association to HSCR for the "enhancer" variant, and demonstrate a significantly higher impact of it in male versus female patients. Integration of the RET RVs and CVs analysis showed that in 91.66% of cases with both kinds of mutational events, the enhancer allele is in trans with the allele bearing the RET RV.

Conclusions

A gender effect exists on both the transmission and distribution of rare coding and common HSCR causing mutations. In addition, these RET CVs and RVs seem to act in a synergistic way leading to HSCR phenotype.

Correlating of GSTM1, GSTT1, and GSTP1 genetic polymorphisms with the risk and expressions in children with isolated Hirschsprung disease

PURPOSE

The present study aimed to examine an association between the glutathione S-transferases (GSTs) polymorphisms (GSTM1, GSTT1, and GSTP1) genetic polymorphisms with the risk and expression in children with isolated Hirschsprung disease (HD).

METHODS

GSTM1, GSTT1, and GSTP1 genetic polymorphisms were detected by polymerase chain reaction-restriction fragment length polymorphism analysis in 80 HD and 180 normal children (controls). The genic expressions were detected by semi-quantitative reverse transcription polymerase chain reaction (RT-PCR) and real-time quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR). The protein expressions were detected by Western blot.

RESULTS

The GSTM1 null genotype especially is associated with a greater risk of HD (X(2) = 1.129, P = 0.288, OR = 0.851, 95% CI = 0.632-1.146). The GSTT1 null genotype especially is associated with a greater risk of HD (X(2) = 6.165, P = 0.013, OR = 1.472, 95% CI = 1.084-1.999). The GSTP1 null genotype especially is associated with a greater risk of HD (X(2) = 4.748, P = 0.029, OR = 0.701, 95% CI = 0.509-0.964). GSTP1 and GSTP1 expressions were higher than GSTM1 in HD patients. Positive expressive rate of the GSTT1 and GSTP1 were 40.56% and 56.67% in HD. The mRNA and protein expressions level of GSTT1 and GSTP1 genes were significantly higher in HD than controls (P < 0.05). Positive expressive rate of the GSTM1 was 10.56% in HD. The GSTM1 was low expressed between in HD and controls (P > 0.05).

CONCLUSIONS

The GSTP1 genetic polymorphisms correlate to HD. We postulate that inherited gene deletion of GSTT1 and GSTP1 may produce increased genotoxic susceptibility for HD respectively, following exposure to xenobiotics that are substrates for these enzymes.

In silico functional profiling of human disease-associated and polymorphic amino acid substitutions

An important challenge in translational bioinformatics is to understand how genetic variation gives rise to molecular changes at the protein level that can precipitate both monogenic and complex disease. To this end, we compiled datasets of human disease-associated amino acid substitutions (AAS) in the contexts of inherited monogenic disease, complex disease, functional polymorphisms with no known disease association, and somatic mutations in cancer, and compared them with respect to predicted functional sites in proteins. Using the sequence homology-based tool SIFT to estimate the proportion of deleterious AAS in each dataset, only complex disease AAS were found to be indistinguishable from neutral polymorphic AAS. Investigation of monogenic disease AAS predicted to be nondeleterious by SIFT were characterized by a significant enrichment for inherited AAS within solvent accessible residues, regions of intrinsic protein disorder, and an association with the loss or gain of various posttranslational modifications. Sites of structural and/or functional interest were therefore surmised to constitute useful additional features with which to identify the molecular disruptions caused by deleterious AAS. A range of bioinformatic tools, designed to predict structural and functional sites in protein sequences, were then employed to demonstrate that intrinsic biases exist in terms of the distribution of different types of human AAS with respect to specific structural, functional and pathological features. Our Web tool, designed to potentiate the functional profiling of novel AAS, has been made available at http://profile.mutdb.org/.

Analyses of PRMT1 proteins in human colon tissues from Hirschsprung disease patients

BACKGROUND

Protein arginine methyltransferase 1 (PRMT1) catalyzes the majority of arginine methylation in cells and plays important roles in the differentiation and development of neurons. It is also implicated in the regulation of nitric oxide synthetase (NOS). Hirschsprung disease (HSCR) is characterized by the absence of intramural ganglion cells in the nerve plexuses of the distal gut.

METHODS

Western blot analyses revealed reduced PRMT1 protein levels in the aganglionosis segments of HSCR patients. Immunohistochemistry detected PRMT1 expression in the colonic mucosa, the enteric nervous system (ENS) and endothelial cells. Specific and strong PRMT1 expression in neuron cell bodies of the plexus was demonstrated by immunofluorescent double-labeling with neuron-specific marker HuC/D.

KEY RESULTS

In the mucosa, PRMT1 was detected at all crypt cells. Intensive PRMT1 staining was detected in the submucosal and the myenteric plexuses in normal or oligoganglionosis segments. Aganglionosis segments from HSCR patients contain no plexuses, and thus not labeled with PRMT1. The phenomenon is specific to the megacolon of HSCR as strong PRMT1 staining was observed in plexuses of the rectal ectasia segments (dilated rectum and distal sigmoid not related with aganglionosis) from anorectal malformation patients. Furthermore, PRMT1 was also present in the same neuronal cells expressing neuronal NOS in the plexuses.

CONCLUSIONS & INFERENCES

We suggest that PRMT1 can be a useful marker for HSCR. This study is the first illustration of PRMT1 protein expression in human tissues from non-cancerous disease and set up the base for further investigations of PRMT1 function in ENS development and intestinal motility.

Polymorphisms of the RET gene in hirschsprung disease, anorectal malformation and intestinal pseudo-obstruction in Taiwan

BACKGROUND/PURPOSE

Mutations in the receptor tyrosine kinase RET gene are associated with Hirschsprung disease (HD), which is also known as congenital intestinal aganglionosis. We found an association with specific alleles in five single nucleotide polymorphism (SNP) sites of the RET gene in our HD patients.

METHODS

We compared the association of specific RET SNP alleles in patients with severe GI disorders such as anorectal malformation (ARM) or pediatric intestinal pseudo-obstruction (IPO) to that in HD patients. Sixty-four HD, 23 ARM and 35 IPO patients were included. Genomic DNA extracted from blood samples was analyzed by polymerase chain reaction and DNA sequencing analysis.

RESULTS

The allele distributions of all five RET SNPs in the HD patients deviated from those in the normal population (p < 0.05), whereas those of the ARM patients did not. The allele distributions of these RET SNPs in the IPO patients were all significantly different from those in the HD patients. Allele distributions of exon 2 and 13 in the IPO patients were also significantly different from those of the normal population. The frequencies of all the HD-predominant alleles were lower in the HD patients than the normal population, and were even lower in the IPO patients.

CONCLUSION

This study strengthens the association of specific RET SNP alleles with typical HD in Taiwan.

Analysis of the RET gene in subjects with sporadic Hirschsprung's disease

BACKGROUND

Hirschsprung's disease (HSCR), or aganglionic megacolon, is a hereditable disease of the enteric nervous system. It is an embryonic developmental disorder characterized by the absence of ganglion cells in the lower enteric plexus. Gut motility is compromised in HSCR, with consequent risk of intestinal obstruction.

METHODS

We sequenced the RET gene and characterized the clinical manifestations in 15 unrelated Chinese patients (9 males, 6 females; age range, 2-21 years) with sporadic HSCR. Genomic DNA extraction, PCR and DNA sequence analysis were performed according to standard procedures.

RESULTS

We identified heterozygous RET gene mutations in 2 patients. The mutations included a missense mutation in exon 2 (CGC --> CAC) resulting in a substitution of arginine by histidine at codon 67 (patient 1), and a missense mutation in exon 3 (TAC --> AAC) resulting in a substitution of tyrosine by asparagine at codon 146 (patient 2). The pathological findings disclosed short-segment HSCR in patient 1 and long-segment HSCR in patient 2, respectively.

CONCLUSION

We identified RET gene mutations in 2 of 15 patients with HSCR in Taiwan. The Y146N mutation we identified was novel.

Mutation analysis of endothelin-B receptor gene in patients with Hirschsprung disease in Taiwan

BACKGROUND

Endothelin-B receptor (EDNRB) signaling pathway is associated for Hirschsprung disease (HSCR). The aim of this study was to investigate the EDNRB gene mutation in patients with HSCR in Taiwan and correlate the genotype and phenotype.

PATIENTS AND METHODS

Using polymerase chain reaction amplification and direct sequencing, we screened for mutations in the coding regions and intron/exon boundaries of the EDNRB gene in 39 isolated HSCR cases and compared them with those in 400 control chromosomes.

RESULTS

In 3 cases, heterozygous variations in exon 1 and 2 of the EDNRB gene predicted missense mutations of the first cytosolic (M132I), second transmembrane (I157V), second exoplasmic (M173T), and third transmembrane (V185M) domains of the EDNRB protein. Three of the 4 mutations in our study have not been reported previously. For total 39 unrelated cases, the mutation rates were estimated to be 10% (3 of 30) for short-segment HSCR and 7.7% (3 of 39) for all HSCR cases.

CONCLUSIONS

We did not detect a significant genotype-phenotype correlation. In conclusion, this study identified 4 mutations within the EDNRB gene associated with HSCR. Because HSCR is a multifactorial and multigene disorder, the higher mutation rate of 10% for short-segment HSCR suggests the important role that the EDNRB gene plays in the pathogenesis of short-segment HSCR in Taiwan.

Neurotrophic factor receptor RET: structure, cell biology, and inherited diseases

RET (REarranged during Transfection) is a transmembrane receptor tyrosine kinase that is activated by a complex consisting of a soluble glial cell line-derived neurotrophic factor (GDNF) family ligand (GFL) and a glycosyl phosphatidylinositol-anchored co-receptor, GDNF family receptors alpha (GFRalpha). RET signalling is crucial for the development of the enteric nervous system. RET also regulates the development of sympathetic, parasympathetic, motor, and sensory neurons, and is necessary for the postnatal maintenance of dopaminergic neurons. The effect of GFLs on sensory, motor, and dopaminergic neurons has raised clinical interest towards these ligands. Outside the nervous system, RET is crucial for development of the kidney and plays a key role in spermatogenesis. Inactivating mutations in RET cause the Hirschsprung's disease characterized by megacolon aganglionosis. In contrast, activating mutations give rise to different types of cancer, multiple endocrine neoplasia type 2A and type 2B, familial medullary thyroid carcinoma, and papillary thyroid carcinoma. The multiple disease phenotypes correlate with differences in the molecular and cell biological functions of different oncogenic RET proteins. In this review we summarize how the different domains of the RET protein contribute to its normal function and how mutations in these domains affect the function of the receptor.

A complex additive model of inheritance for Hirschsprung disease is supported by both RET mutations and predisposing RET haplotypes

PURPOSE

The RET proto-oncogene is considered to be the major susceptibility gene involved in Hirschsprung disease. Traditional RET germline mutations account for a small subset of Hirschsprung disease patients, but several studies have shown that there is a specific haplotype of RET associated with the sporadic forms of Hirschsprung disease. We have investigated for RET germline mutations and analyzed the RET haplotypic distribution in carriers versus noncarriers of RET germline mutations.

METHODS

We have screened the coding region of RET in 106 Spanish Hirschsprung disease patients using dHPLC technology. Statistical comparisons of the distribution of RET haplotypes between sporadic patients with and without a RET germline mutation were performed.

RESULTS

Nine novel germline mutations and one previously described were identified. A significant over-transmission of the "Hirschsprung disease haplotype" was detected when comparing transmitted versus nontransmitted alleles in the group of Hirschsprung disease triads without mutation. However, no distortion of the transmission of alleles was found in the group of mutated families.

CONCLUSIONS

These results would be concordant with a complex additive model of inheritance. The whole findings seem to suggest that low-penetrance mutations would be necessary but not sufficient and the additional presence of the "Hirschsprung disease haplotype" could contribute to the manifestation of the disease.

Mutations and polymorphisms of Hirschsprung disease candidate genes in Thai patients

Mutation and polymorphism data for Hirschsprung disease (HSCR) varies among ethnic groups. Single nucleotide polymorphisms (SNP) of RET proto-oncogene (RET) were recently shown to be associated with the disease, and with disease severity, in different populations. In this study, comprehensive analysis of RET, GDNF, EDNRB, ET-3, and SOX-10 genes among sporadic HSCR in Thailand was conducted by standard PCR-SSCP, RFLP, and sequencing methods. Of 41 patients, 30 cases had rectosigmoid disease (RSD) and 11 cases were assigned to the long-segment disease (LSD) group. Four missense mutations of RET, S100M, R231H, T278N, and G533S, were identified in three patients. One novel missense mutation, V111Q, was detected in EDNRB. For ET-3, two novel missense mutations, D166E and C173R, occurred concomitantly in a patient. The incidence of missense mutation was significantly higher in our female HSCR patient than in the male counterpart. Statistical analysis of the SNPs revealed a significant difference between allele distribution of RET L769L in patients in the LSD and RSD groups. The predominant genotype construct of RET A45A/L769L in our HSCR was GG/GG, which is obviously different from results from all previous studies. The GG/GG genotype construct was associated with RSD and with males. The study also detected a variant allele of RET S836S which has never been reported in Asian cohorts.