Evaluation of IRX Genes and Conserved Noncoding Elements in a Region on 5p13.3 Linked to Families with Familial Idiopathic Scoliosis and Kyphosis

Cytoskeletal Keratins Are Overexpressed in a Zebrafish Model of Idiopathic Scoliosis

Idiopathic scoliosis (IS) is a three-dimensional rotation of the spine >10 degrees with an unknown etiology. Our laboratory established a late-onset IS model in zebrafish (Danio rerio) containing a deletion in kif7. A total of 25% of kif7^co63/co63 zebrafish develop spinal curvatures and are otherwise developmentally normal, although the molecular mechanisms underlying the scoliosis are unknown. To define transcripts associated with scoliosis in this model, we performed bulk mRNA sequencing on 6 weeks past fertilization (wpf) kif7^co63/co63 zebrafish with and without scoliosis. Additionally, we sequenced kif7^co63/co63, kif7^co63/+, and AB zebrafish (n = 3 per genotype). Sequencing reads were aligned to the GRCz11 genome and FPKM values were calculated. Differences between groups were calculated for each transcript by the t-test. Principal component analysis showed that transcriptomes clustered by sample age and genotype. kif7 mRNA was mildly reduced in both homozygous and heterozygous zebrafish compared to AB. Sonic hedgehog target genes were upregulated in kif7^co63/co63 zebrafish over AB, but no difference was detected between scoliotic and non-scoliotic mutants. The top upregulated genes in scoliotic zebrafish were cytoskeletal keratins. Pankeratin staining of 6 wpf scoliotic and non-scoliotic kif7^co63/co63 zebrafish showed increased keratin levels within the zebrafish musculature and intervertebral disc (IVD). Keratins are major components of the embryonic notochord, and aberrant keratin expression has been associated with intervertebral disc degeneration (IVDD) in both zebrafish and humans. The role of increased keratin accumulation as a molecular mechanism associated with the onset of scoliosis warrants further study.

Investigating Role of IRX Family in Development of Female Adolescent Idiopathic Scoliosis: Which One Is Real Cause?

BACKGROUND

Previous studies showed that several variants located around the IRX family may have functional roles in the development of adolescent idiopathic scoliosis (AIS). However, there was lack of knowledge concerning the target gene of the region on 5p13.3 and the role of IRX genes in the etiology of AIS. This study aimed to validate the relationship between the IRX family and AIS in a large-scale general population and to further investigate the target gene of the region, which was associated with AIS.

METHODS

SNP rs12517904 and rs117273909 were genotyped in 1323 patients and 1670 age-matched healthy controls. Paraspinal muscle was collected from 70 AIS patients and 20 congenital scoliosis patients. Student's t-test was used to compare the IRX1 expression between AIS patients and controls. The 1-way analysis of variance test was used to compare the expression of the IRX genes among different genotypes.

RESULTS

For rs12517904, patients were found to have a significantly higher frequency of allele T than the controls (37.6% vs. 34.7%, P = 0.02). Allele T can significantly add to the risk of AIS with an odds ratio of 1.14. AIS patients were found to have significantly lower IRX1 expression than the controls. Patients with genotype TT were found to have significantly lower IRX1 expression than those with genotype GG.

CONCLUSIONS

Our large-scale case control study validated that the IRX1 gene could be the disease-associated gene of AIS. The variant rs12517904 of the IRX1 gene is functionally associated with the development of AIS in the Chinese population. The role of IRX1 in the onset of AIS is worthy of further investigation.

Evolutionary Loss of Genomic Proximity to Conserved Noncoding Elements Impacted the Gene Expression Dynamics During Mammalian Brain Development

Conserved noncoding elements (CNEs) have a significant regulatory influence on their neighboring genes. Loss of proximity to CNEs through genomic rearrangements can, therefore, impact the transcriptional states of the cognate genes. Yet, the evolutionary implications of such chromosomal alterations have not been studied. Through genome-wide analysis of CNEs and the cognate genes of representative species from five different mammalian orders, we observed a significant loss of genes' linear proximity to CNEs in the rat lineage. The CNEs and the genes losing proximity had a significant association with fetal, but not postnatal, brain development as assessed through ontology terms, developmental gene expression, chromatin marks, and genetic mutations. The loss of proximity to CNEs correlated with the independent evolutionary loss of fetus-specific upregulation of nearby genes in the rat brain. DNA breakpoints implicated in brain abnormalities of germline origin had significant representation between a CNE and the gene that exhibited loss of proximity, signifying the underlying developmental tolerance of genomic rearrangements that allowed the evolutionary splits of CNEs and the cognate genes in the rodent lineage. Our observations highlighted a nontrivial impact of chromosomal rearrangements in shaping the evolutionary dynamics of mammalian brain development and might explain the loss of brain traits, like cerebral folding of the cortex, in the rodent lineage.

Rare variant of HSPG2 is not involved in the development of adolescent idiopathic scoliosis: evidence from a large-scale replication study

BACKGROUND

Rare variants of HSPG2 have recently been reported to function as a potential contributor to the susceptibility of adolescent idiopathic scoliosis (AIS) in the Caucasians. A replication study in the different population is warranted to validate the role of HSPG2 in AIS. The aim of this study was to determine the association between HSPG2 and AIS in the Chinese patients and to further investigate its influence on the phenotype of the patients.

METHODS

SNVs p.Asn786Ser of HSPG2 was genotyped in 1752 patients and 1584 normal controls using multiple ligase detection reactions. The mRNA expression of HSPG2 in the paraspinal muscles was quantified for 90 patients and 26 controls. The The Student's t test was used to analyze the inter-group comparison of the HSPG2 expression. The relationship between the HSPG2 expression and the curve magnitude of the patients was analyzed by the Pearson correlation analysis.

RESULTS

No case of mutation in the reported SNV p.Asn786Ser of HSPG2 was found in our cohort. The mRNA expression of HSPG2 in patients was comparable with that in the controls (0.0016 ± 0.0013 vs. 0.0019 ± 0.0012, p = 0.29). 42 patients with curve magnitude > 60 degrees were assigned to the severe curve group. The other 58 patients were assigned to the moderate curve group. These two groups were found to have comparable HSPG2 expression (0.0015 ± 0.0011 vs. 0.0017 ± 0.0014, p = 0.57). And there was no remarkable correlation between the expression level of HSPG2 and the curve severity (r = 0.131, p = 0.71).

CONCLUSIONS

HSPG2 gene was not associated with the susceptibility or the phenotypes of AIS in the Chinese population. The whole HSPG2 gene can be sequenced in more AIS patients to identify potentially causative mutations.

An N-Ethyl-N-Nitrosourea (ENU) Mutagenized Mouse Model for Autosomal Dominant Nonsyndromic Kyphoscoliosis Due to Vertebral Fusion

Kyphosis and scoliosis are common spinal disorders that occur as part of complex syndromes or as nonsyndromic, idiopathic diseases. Familial and twin studies implicate genetic involvement, although the causative genes for idiopathic kyphoscoliosis remain to be identified. To facilitate these studies, we investigated progeny of mice treated with the chemical mutagen N-ethyl-N-nitrosourea (ENU) and assessed them for morphological and radiographic abnormalities. This identified a mouse with kyphoscoliosis due to fused lumbar vertebrae, which was inherited as an autosomal dominant trait; the phenotype was designated as hereditary vertebral fusion (HVF) and the locus as Hvf. Micro-computed tomography (μCT) analysis confirmed the occurrence of nonsyndromic kyphoscoliosis due to fusion of lumbar vertebrae in HVF mice, consistent with a pattern of blocked vertebrae due to failure of segmentation. μCT scans also showed the lumbar vertebral column of HVF mice to have generalized disc narrowing, displacement with compression of the neural spine, and distorted transverse processes. Histology of lumbar vertebrae revealed HVF mice to have irregularly shaped vertebral bodies and displacement of intervertebral discs and ossification centers. Genetic mapping using a panel of single nucleotide polymorphic (SNP) loci arranged in chromosome sets and DNA samples from 23 HVF (eight males and 15 females) mice, localized Hvf to chromosome 4A3 and within a 5-megabase (Mb) region containing nine protein coding genes, two processed transcripts, three microRNAs, five small nuclear RNAs, three large intergenic noncoding RNAs, and 24 pseudogenes. However, genome sequence analysis in this interval did not identify any abnormalities in the coding exons, or exon-intron boundaries of any of these genes. Thus, our studies have established a mouse model for a monogenic form of nonsyndromic kyphoscoliosis due to fusion of lumbar vertebrae, and further identification of the underlying genetic defect will help elucidate the molecular mechanisms involved in kyphoscoliosis. © 2018 The Authors. JBMR Plus is published by Wiley Periodicals, Inc. on behalf of the American Society for Bone and Mineral Research.

Common Variant of POC5 Is Associated With the Susceptibility of Adolescent Idiopathic Scoliosis

STUDY DESIGN

A case-control study.

OBJECTIVE

To validate the relationship between POC5 and adolescent idiopathic scoliosis (AIS) in the Chinese patients and to further investigate the functional role of POC5.

SUMMARY OF BACKGROUND DATA

Three rare functional variants in the POC5 were recently reported to be strongly associated with the disease in a large family with multiple members affected with idiopathic scoliosis. To our knowledge, the association between the mutations of POC5 and AIS remains undetermined in the Chinese population.

METHODS

Single nucleotide variants c.1336G>A, c.1286C>T, and c.1363G>C of POC5 were genotyped in 2432 patients with AIS and 2292 healthy controls using multiple ligase detection reactions. Common variants covering POC5 gene were genotyped in 1446 patients and 2080 controls. The mRNA expression of POC5 was determined in the paraspinal muscles collected from 98 patients and 28 controls. The Student t test was used to compare mRNA expression level between the patients and the controls. In addition, the POC5 expression was compared among different genotypes of the remarkably associated single nucleotide polymorphism (SNP) with analysis of variance test.

RESULTS

There was no case of mutation for the three reported variants of POC5. SNP rs6892146 was observed to have significantly different distribution of minor allele frequency in the two group (0.485 vs. 0.446, P = 0.004). The mRNA expression of POC5 was 1.5-fold higher in patients than in the controls (0.00012 ± 0.00009 vs. 0.00008 ± 0.00006, P = 0.02). Patients with genotype GG have a significantly increased expression of POC5 than those with CC (0.00014 ± 0.00007 vs. 0.00009 ± 0.00007, P = 0.03).

CONCLUSION

Common variant rs6892146 of POC5 is associated with the development of AIS in the Chinese population. Targeted regional sequencing of POC5 may help identify novel mutations associated with AIS.

LEVEL OF EVIDENCE

4.

Conserved non-coding elements: developmental gene regulation meets genome organization

Comparative genomics has revealed a class of non-protein-coding genomic sequences that display an extraordinary degree of conservation between two or more organisms, regularly exceeding that found within protein-coding exons. These elements, collectively referred to as conserved non-coding elements (CNEs), are non-randomly distributed across chromosomes and tend to cluster in the vicinity of genes with regulatory roles in multicellular development and differentiation. CNEs are organized into functional ensembles called genomic regulatory blocks–dense clusters of elements that collectively coordinate the expression of shared target genes, and whose span in many cases coincides with topologically associated domains. CNEs display sequence properties that set them apart from other sequences under constraint, and have recently been proposed as useful markers for the reconstruction of the evolutionary history of organisms. Disruption of several of these elements is known to contribute to diseases linked with development, and cancer. The emergence, evolutionary dynamics and functions of CNEs still remain poorly understood, and new approaches are required to enable comprehensive CNE identification and characterization. Here, we review current knowledge and identify challenges that need to be tackled to resolve the impasse in understanding extreme non-coding conservation.

Chondrocyte-Specific Knockout of TSC-1 Leads to Congenital Spinal Deformity in Mice

Congenital spinal deformity is the most severe clinical orthopedic issue worldwide. Among all the pathological processes of congenital spinal deformity, the imbalance of endochondral ossification is considered to be the most important developmental cause of spinal dysplasia. We established chondrocyte-specific TSC-1 knockout (KO) mice to overactivate the energy metabolic component, mammalian target of rapamycin complex 1 (mTORC1), and measured the spinal development by general, imaging, histological, and Western-blot assessments. In addition to skeletal dysplasia, the KO mice displayed severe congenital spinal deformity and significant intervertebral disc changes. This study suggests that, in the process of endochondral ossification, excessive activation of mTORC1 signaling in chondrocytes induces obvious spinal deformity, and the chondrocytes may be the cell type responsible for congenital spinal deformity.