Expression patterns of the ADAMs in early developing chicken cochlea

Age-related transcriptome changes in Sox2+ supporting cells in the mouse cochlea

Background

Inner ear supporting cells (SCs) in the neonatal mouse cochlea are a potential source for hair cell (HC) regeneration, but several studies have shown that the regeneration ability of SCs decreases dramatically as mice age and that lost HCs cannot be regenerated in adult mice. To better understand how SCs might be better used to regenerate HCs, it is important to understand how the gene expression profile changes in SCs at different ages.

Methods

Here, we used Sox2^GFP/+ mice to isolate the Sox2+ SCs at postnatal day (P)3, P7, P14, and P30 via flow cytometry. Next, we used RNA-seq to determine the transcriptome expression profiles of P3, P7, P14, and P30 SCs. To further analyze the relationships between these age-related and differentially expressed genes in Sox2+ SCs, we performed gene ontology (GO) analysis.

Results

Consistent with previous reports, we also found that the proliferation and HC regeneration ability of isolated Sox2+ SCs significantly decreased as mice aged. We identified numerous genes that are enriched and differentially expressed in Sox2+ SCs at four different postnatal ages, including cell cycle genes, signaling pathway genes, and transcription factors that might be involved in regulating the proliferation and HC differentiation ability of SCs. We thus present a set of genes that might regulate the proliferation and HC regeneration ability of SCs, and these might serve as potential new therapeutic targets for HC regeneration.

Conclusions

In our research, we found several genes that might play an important role in regulating the proliferation and HC regeneration ability of SCs. These datasets are expected to serve as a resource to provide potential new therapeutic targets for regulating the ability of SCs to regenerate HCs in postnatal mammals.

Low levels of ADAM23 expression in epithelial ovarian cancer are associated with poor survival

BACKGROUND

ADAM23, a member of the disintegrin and metalloprotease (ADAM) family, has been reported to be expressed in several types of tumours. Nevertheless, the exact role of ADAM23 in epithelial ovarian cancer (EOC) remains unclear. The aim of this study was to investigate ADAM23 expression in EOC and evaluate its clinicopathological and prognostic significance.

METHODS

Immunohistochemistry (IHC), western blot and real-time PCR (RT-PCR) were used to analyse ADAM23 expression in 133 EOC, 42 benign ovarian tumour and 35 healthy control samples. Moreover, we evaluated the expression of ADAM23 in both public database (Oncomine and Kaplan-Meier plotter). The association between ADAM23 expression and various clinicopathological parameters was analysed.

RESULTS

The levels of ADAM23 mRNA and protein expression were significantly lower in EOC tissues than in corresponding control tissues and benign ovarian tumours, verifying results from the Oncomine databases. The loss of ADAM23 expression was significantly correlated with an advanced International Federation of Gynecology and Obstetrics (FIGO) stage and lymph node metastasis. The IHC data in the EOC samples correlated with the RT-PCR data. Furthermore, patients with low ADAM23 expression had shorter progression-free survival (PFS) and overall survival (OS) than patients with high ADAM23 expression. The multivariate analysis indicated that ADAM23 was an independent predictor in patients with EOC.

CONCLUSIONS

Our results demonstrate that ADAM23 expression is likely involved in the progression of EOC and may provide potential diagnostic and prognostic information regarding EOC.

Nonlinear Network Reconstruction from Gene Expression Data Using Marginal Dependencies Measured by DCOL

Reconstruction of networks from high-throughput expression data is an important tool to identify new regulatory relations. Given that nonlinear and complex relations exist between biological units, methods that can utilize nonlinear dependencies may yield insights that are not provided by methods using linear associations alone. We have previously developed a distance to measure predictive nonlinear relations, the Distance based on Conditional Ordered List (DCOL), which is sensitive and computationally efficient on large matrices. In this study, we explore the utility of DCOL in the reconstruction of networks, by combining it with local false discovery rate (lfdr)–based inference. We demonstrate in simulations that the new method named nlnet is effective in recovering hidden nonlinear modules. We also demonstrate its utility using a single cell RNA seq dataset. The method is available as an R package at https://cran.r-project.org/web/packages/nlnet.

Novel ADAM9 homozygous mutation in a consanguineous Egyptian family with severe cone-rod dystrophy and cataract

OBJECTIVE

To genetically and phenotypically describe a new ADAM9 homozygous mutation in a consanguineous family from Egypt with autosomal recessive cone-rod dystrophy (arCRD), anterior polar and posterior subcapsular cataract.

DESIGN, SETTING AND PARTICIPANTS

The parents and their six children were included. They underwent a complete ophthalmic examination with fundus photography and optical coherence tomography (OCT).

INTERVENTION

DNA was extracted from peripheral blood from all family members. Screening for mutations in genes known to be implicated in retinal disorders was done with the IROme, an in-solution enrichment array, followed by high-throughput sequencing. Validation of the results was done by bidirectional Sanger sequencing of ADAM9 exon 14, including exon-intron junctions. Screening of normal controls was done by denaturing high-performance liquid chromatography.

RESULTS

arCRD was diagnosed in the mother and two of her children. Bilateral anterior polar and posterior subcapsular cataract was observed in the mother and bilateral dot cataract was diagnosed in three of the four children not affected with arCRD, one of whom also had glaucoma. The characteristics of the arCRD were childhood-onset visual impairment, reorganisation of the retinal pigment epithelium with mid-periphery greyish-white discolouration, attenuated retinal vasculatur and optic disc pallor. A coloboma-like macular lesion was observed in one of the arCRD-affected children. IROme analysis identified a c.1396-2A>G homozygous mutation in the splice acceptor site of intron 13 of ADAM9. This mutation was homozygous in the two children affected by arCRD and in their affected mother. This mutation was heterozygous in the unaffected father and the four unaffected children.

CONCLUSIONS AND RELEVANCE

We identified a novel autosomal recessive ADAM9 mutation causing arCRD in a consanguineous Egyptian family. The percentage of arCRD cases caused by mutation in ADAM9 remains to be determined. Few families are reported in the literature to date; hence extensive clinical descriptions of families with ADAM9 mutations are of significant importance.