An NT-3-releasing bioscaffold supports the formation of TrkC-modified neural stem cell-derived neural network tissue with efficacy in repairing spinal cord injury.

The mechanism underlying neurogenesis during embryonic spinal cord development involves a specific ligand/receptor interaction, which may be help guide neuroengineering to boost stem cell-based neural regeneration for the structural and functional repair of spinal cord injury. Herein, we hypothesized that supplying spinal cord defects with an exogenous neural network in the NT-3/fibroin-coated gelatin sponge (NF-GS) scaffold might improve tissue repair efficacy. To test this, we engineered tropomyosin receptor kinase C (TrkC)-modified neural stem cell (NSC)-derived neural network tissue with robust viability within an NF-GS scaffold. When NSCs were genetically modified to overexpress TrkC, the NT-3 receptor, a functional neuronal population dominated the neural network tissue. The pro-regenerative niche allowed the long-term survival and phenotypic maintenance of the donor neural network tissue for up to 8 weeks in the injured spinal cord. Additionally, host nerve fibers regenerated into the graft, making synaptic connections with the donor neurons. Accordingly, motor function recovery was significantly improved in rats with spinal cord injury (SCI) that received TrkC-modified NSC-derived neural network tissue transplantation. Together, the results suggested that transplantation of the neural network tissue formed in the 3D bioactive scaffold may represent a valuable approach to study and develop therapies for SCI.

Predicting mendelian disease-causing non-synonymous single nucleotide variants in exome sequencing studies.

Exome sequencing is becoming a standard tool for mapping Mendelian disease-causing (or pathogenic) non-synonymous single nucleotide variants (nsSNVs). Minor allele frequency (MAF) filtering approach and functional prediction methods are commonly used to identify candidate pathogenic mutations in these studies. Combining multiple functional prediction methods may increase accuracy in prediction. Here, we propose to use a logit model to combine multiple prediction methods and compute an unbiased probability of a rare variant being pathogenic. Also, for the first time we assess the predictive power of seven prediction methods (including SIFT, PolyPhen2, CONDEL, and logit) in predicting pathogenic nsSNVs from other rare variants, which reflects the situation after MAF filtering is done in exome-sequencing studies. We found that a logit model combining all or some original prediction methods outperforms other methods examined, but is unable to discriminate between autosomal dominant and autosomal recessive disease mutations. Finally, based on the predictions of the logit model, we estimate that an individual has around 5% of rare nsSNVs that are pathogenic and carries ~22 pathogenic derived alleles at least, which if made homozygous by consanguineous marriages may lead to recessive diseases.

GATES: a rapid and powerful gene-based association test using extended Simes procedure.

The gene has been proposed as an attractive unit of analysis for association studies, but a simple yet valid, powerful, and sufficiently fast method of evaluating the statistical significance of all genes in large, genome-wide datasets has been lacking. Here we propose the use of an extended Simes test that integrates functional information and association evidence to combine the p values of the single nucleotide polymorphisms within a gene to obtain an overall p value for the association of the entire gene. Our computer simulations demonstrate that this test is more powerful than the SNP-based test, offers effective control of the type 1 error rate regardless of gene size and linkage-disequilibrium pattern among markers, and does not need permutation or simulation to evaluate empirical significance. Its statistical power in simulated data is at least comparable, and often superior, to that of several alternative gene-based tests. When applied to real genome-wide association study (GWAS) datasets on Crohn disease, the test detected more significant genes than SNP-based tests and alternative gene-based tests. The proposed test, implemented in an open-source package, has the potential to identify additional novel disease-susceptibility genes for complex diseases from large GWAS datasets.

Identification of genes with allelic imbalance on 6p associated with nasopharyngeal carcinoma in southern Chinese.

Nasopharyngeal carcinoma (NPC) is a malignancy of epithelial origin. The etiology of NPC is complex and includes multiple genetic and environmental factors. We employed case-control analysis to study the association of chromosome 6p regions with NPC. In total, 360 subjects and 360 healthy controls were included, and 233 single nucleotide polymorphisms (SNPs) on 6p were examined. Significant single-marker associations were found for SNPs rs2267633 (p = 4.49 × 10(-5)), rs2076483 (most significant, p = 3.36 × 10(-5)), and rs29230 (p=1.43 × 10(-4)). The highly associated genes were the gamma-amino butyric acid B receptor 1 (GABBR1), human leukocyte antigen (HLA-A), and HLA complex group 9 (HCG9). Haplotypic associations were found for haplotypes AAA (located within GABBR1, p-value  = 6.46 × 10(-5)) and TT (located within HLA-A, p = 0.0014). Further investigation of the homozygous genotype frequencies between cases and controls suggested that micro-deletion regions occur in GABBR1 and neural precursor cell expressed developmentally down-regulated 9 (NEDD9). Quantitative real-time polymerase chain reaction (qPCR) using 11 pairs of NPC biopsy samples confirmed the significant decline in GABBR1 and NEDD9 mRNA expression in the cancer tissues compared to the adjacent non-tumor tissue (p<0.05). Our study demonstrates that multiple chromosome 6p susceptibility loci contribute to the risk of NPC, possibly though GABBR1 and NEDD9 loss of function.

Potential effect of inter-genic action on peak bone mass (PBM) in Chinese females.

Peak bone mass (PBM) is a complex trait, determined by both genetic and environmental factors and also their interactions. Vitamin D receptor (VDR) estrogen receptor alpha (ERalpha), interleukin 6 (IL6), parathyroid hormone (PTH), collagen type I alpha 2 (COL1A2), bone Gla protein (BGP), alpha2-HS glycoprotein (AHSG) are among the important candidate genes of bone metabolism. The study aims to detect significant effect of potential inter-genic action underlying PBM in Chinese females. 361 unrelated healthy premenopausal Chinese females (aged 20 -44 years) with Han ethnicity were recruited from the Shanghai city in China. Bone mineral density (BMD) at the hip and the lumbar spine (L1-4) was measured using a Hologic QDR 2000 + dual-energy X-ray absorptiometry (DXA) scanner. Eight polymorphisms among the seven genes were genotyped, i. e. Apa I in VDR, Pvu II and Xba I in ERa (ERX and ERP, respectively), BsrB I in IL6, BstB I in PTH, Msp I in COL1A2, Hind III in BGP, and Sac I in AHSG, using PCR-RFLP (polymerase chain reaction-restriction fragment length polymorphism) methods. Two-way analysis of variance (ANOVA) showed significant effects of IL6 x ERP interaction on PBM at the total hip (P = 0.019), intertrochanter (P = 0.016), and femoral neck (P =0. 019). The BMD difference between GGPp carriers and GGpp subjects (at these two loci) amounted to 18.0%, 19.5%, and 14.8% at the hip,intertrochanter,and femoral neck,respectively. The potential interaction effect of AHSG x IL6 was observed on femoral neck PBM (P = 0.046). GGSS individuals (at these two loci) had, on average, 18.8% higher femoral neck BMD than those subjects with GGSs genotype. The population-level statistical analysis indicates that IL6 x ERP and AHSG x IL6 have significant inter-genic effect on the genetic determination of PBM in Chinese females.

Association and linkage analyses of interleukin-6 gene 634C/G polymorphism and bone phenotypes in Chinese.

In this study, we tested the interleukin-6 (IL-6) gene as an important candidate gene for its linkage and association with the variation of bone phenotypes (bone mineral density [BMD] and bone size) in young Chinese female subjects. We genotyped the IL-6 gene at the -634C/G restriction fragment length polymorphism (RFLP) site (ID, RS1800796) in 1263 individuals from 402 Chinese nuclear families, composed of both parents and at least one healthy daughter (mean age +/- SD, 31.4 +/- 5.8 years). Using the daughters' bone phenotypes, we tested total-family association, within-family association (via transmission disequilibrium test, [TDT]), and linkage, between the -634C/G marker and bone phenotypes at the spine and the hip. No significant association or linkage was found for bone size and BMD, although a trend was observed for linkage between the IL-6 gene -634C/G marker and L1-4 spinal BMD (adjusted for age, weight, and height). Our results, together with the findings from other studies, indicate that the IL-6 gene, although important for postmenopausal bone loss, may have a limited impact on peak bone mass variation in a Chinese population.

Interaction effects between estrogen receptor alpha and vitamin D receptor genes on age at menarche in Chinese women.

AIM: To evaluate whether estrogen receptor alpha (ER-alpha) and vitamin D receptor (VDR) genes are associated with the age at menarche in Chinese women. METHODS: A total of 390 pre-menopausal Chinese women were genotyped at the ER-alpha PvuII, XbaI, and VDR ApaI loci using polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP). RESULTS: Neither the ER-alpha gene nor the VDR gene individually had significant effects on the age at menarche in our subjects (P>0.10). However, evidence of interaction effects between the two genes were observed: with the aa genotype at the VDR ApaI locus, subjects with haplotype PX at the ER-alpha gene had, on average, 6 months later onset of menarche than the non-carriers (P=0.01). CONCLUSION: We found that neither the ER-alpha gene or the VDR gene had a significant association with the age at menarche individually. However, potential interaction effects between the two genes were observed in Chinese women.

The (CA)n polymorphism of the TNFR2 gene is associated with peak bone density in Chinese nuclear families.

Low peak bone density (PBD) in adulthood is an important determinant of osteoporotic fracture (OF) in the elderly. The tumor necrosis factor receptor 2 (TNFR2) gene has been considered as an important candidate gene for PBD due to its important role in bone turnover. In this study, we recruited a total of 1,263 subjects from 402 Chinese nuclear families composed of both parents and at least one daughter, and tested the association of the (CA)(n) polymorphism in intron 4 of the TNFR2 gene with PBD using a more contemporary quantitative transmission disequilibrium test (QTDT). Significant within-family association was detected between the CA16 allele and bone mineral density (BMD) at the lumbar spine with the P-value of 0.005 after permutations, which is still significant after correction for multiple testing. Some evidence of total-family association between the CA16 allele and lumbar spine BMD was found (P=0.021), although the significant level did not reach the empirical threshold (P< or =0.007). About 3.14% of lumbar spine BMD variation can be explained by the CA16 allele. In summary, our results suggest that the TNFR2 gene may play an important role in determining lumbar spine BMD variation in Chinese women.

Estrogen receptor alpha gene polymorphisms and peak bone density in Chinese nuclear families.

PBD is an important determinant of osteoporotic fractures. Few studies were performed to search for genes underlying PBD variation in Chinese populations. We tested linkage and/or association of the estrogen receptor alpha gene polymorphism with PBD in 401 Chinese nuclear families. This study suggests the ER-alpha gene may have some minor effects on PBM variation in the Chinese population. Low peak bone density (PBD) in adulthood is an important determinant of osteoporotic fractures in the elderly. PBD variation is mainly regulated by genetic factors. Extensive molecular genetics studies have been performed to search for genes underlying PBD variation, largely in whites. Few studies were performed in Chinese populations. In this study, we simultaneously test linkage and/or association of the estrogen receptor alpha (ER-alpha) gene polymorphism with PBD in 401 Chinese nuclear families (both parents plus their female children) of 1260 subjects, with the 458 children generally between 20 and 40 years of age. All the subjects were genotyped by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) at polymorphic PvuII and XbaI sites inside the ER-alpha gene. Bone mineral density was measured at the lumbar spine (L1-L4) and hip (femoral neck, trochanter, and intertrochanteric region). Raw bone mineral density values were adjusted by age, height, and weight as covariates. We detected marginally significant results for within-family association (transmission disequilibrium; p = 0.054) between the spine bone mineral density variation and the ER-alpha XbaI genotypes. For the hip bone mineral density variation, significant (p < 0.05) linkage results were generally found for the two intragenic markers. Analyses of the haplotypes defined by the two markers confer further evidence for linkage of the ER-alpha with the hip PBD variation. In conclusion, this study suggests that the ER-alpha gene may have minor effects on PBD variation in our Chinese population.