Clinical and molecular characterization of POU3F4 mutations in multiple DFNX2 Chinese families.

BACKGROUND: Many X-linked non-syndromic hearing loss (HL) cases are caused by various mutations in the POU domain class 3 transcription factor 4 (POU3F4) gene. This study aimed to identify allelic variants of this gene in two Chinese families displaying X-linked inheritance deafness-2 (DFNX2) and one sporadic case with indefinite inheritance pattern. METHODS: Direct DNA sequencing of the POU3F4 gene was performed in these families and in 100 Chinese individuals with normal hearing. RESULTS: There are characteristic imaging findings in DFNX2 Chinese families with POU3F4 mutations. The temporal bone computed tomography (CT) images of patients with DFNX2 are characterized by a thickened stapes footplate, hypoplasia of the cochlear base, absence of the bony modiolus, and dilated internal acoustic meatus (IAM) as well as by abnormally wide communication between the IAM and the basal turn of the cochlea. We identified three causative mutations in POU3F4 for three probands and their extended families. In family 1468, we observed a novel deletion mutation, c.973delT, which is predicted to result in a p.Trp325Gly amino acid frameshift. In family 2741, the mutation c.927delCTC was identified, which is predicted to result in the deletion of serine at position 310. In both families, the mutations were located in the POU homeodomain and are predicted to truncate the C-terminus of the POU domain. In the third family, a novel de novo transversion mutation (c.669 T > A) was identified in a 5-year-old boy that resulted in a nonsense mutation (p.Tyr223*). The mutation created a new stop codon and is predicted to result in a truncated POU3F4 protein. CONCLUSIONS: Based on characteristic radiological findings and clinical features, POU3F4 gene mutation analysis will increase the success rate of stapes operations and cochlear implantations, and improve molecular diagnosis, genetic counseling, and knowledge of the molecular epidemiology of HL among patients with DFNX2.

A novel pore-region mutation, c.887G > A (p.G296D) in KCNQ4, causing hearing loss in a Chinese family with autosomal dominant non-syndromic deafness 2.

BACKGROUND: Hereditary non-syndromic hearing loss is the most common inherited sensory defect in humans. The KCNQ4 channel belongs to a family of potassium ion channels that play crucial roles in physiology and disease. Mutations in KCNQ4 underlie deafness non-syndromic autosomal dominant 2, a subtype of autosomal dominant, progressive, high-frequency hearing loss. METHODS: A six-generation Chinese family from Hebei Province with autosomal dominantly inherited, sensorineural, postlingual, progressive hearing loss was enrolled in this study. Mutation screening of 129 genes associated with hearing loss was performed in five family members by next-generation sequencing (NGS). We also carried out variant analysis on DNA from 531 Chinese individuals with normal hearing as controls. RESULTS: This family exhibits postlingual, progressive, symmetrical, bilateral, non-syndromic sensorineural hearing loss. NGS, bioinformatic analysis, and Sanger sequencing confirmed the co-segregation of a novel mutation [c.887G > A (p.G296D)] in KCNQ4 with the disease phenotype in this family. This mutation leads to a glycine-to-aspartic acid substitution at position 296 in the pore region of the KCNQ4 channel. This mutation affects a highly conserved glutamic acid. NGS is a highly efficient tool for identifying gene mutations causing heritable disease. CONCLUSIONS: Progressive hearing loss is common in individuals with KCNQ4 mutations. NGS together with Sanger sequencing confirmed that the five affected members of this Chinese family inherited a missense mutation, c.887G > A (p.G296D), in exon 6 of KCNQ4. Our results increase the number of identified KCNQ4 mutations.

Phenotypic Heterogeneity in a DFNA20/26 family segregating a novel ACTG1 mutation.

BACKGROUND: Genetic factors play an important role in hearing loss, contributing to approximately 60% of cases of congenital hearing loss. Autosomal dominant deafness accounts for approximately 20% of cases of hereditary hearing loss. Diseases with autosomal dominant inheritance often show pleiotropy, different degrees of penetrance, and variable expressivity. METHODS: A three-generation Chinese family with autosomal dominant nonsyndromic hearing impairment (ADNSHI) was enrolled in this study. Audiometric data and blood samples were collected from the family. In total, 129 known human deafness genes were sequenced using next-generation sequencing (NGS) to identify the responsible gene mutation in the family. Whole Exome Sequencing (WES) was performed to exclude any other variant that cosegregated with the phenotype. RESULTS: The age of onset of the affected family members was the second decade of life. The condition began with high-frequency hearing impairment in all family members excluding III:2. The novel ACTG1 c.638A > G (p.K213R) mutation was found in all affected family members and was not found in the unaffected family members. A heterozygous c.638A > G mutation in ACTG1 and homozygous c.109G > A (p.V37I) mutation in GJB2 were found in III:2, who was born with hearing loss. The WES result concurred with that of targeted sequencing of known deafness genes. CONCLUSIONS: The novel mutation p.K213R in ACTG1 was found to be co-segregated with hearing loss and the genetic cause of ADNSHI in this family. A homozygous mutation associated with recessive inheritance only rarely co-acts with a dominant mutation to result in hearing loss in a dominant family. In such cases, the mutations in the two genes, as in ACTG1 and GJB2 in the present study, may result in a more severe phenotype. Targeted sequencing of known deafness genes is one of the best choices to identify the genetic cause in hereditary hearing loss families.

A sub-pathway-based approach for identifying drug response principal network.

MOTIVATION: The high redundancy of and high degree of cross-talk between biological pathways hint that a sub-pathway may respond more effectively or sensitively than the whole pathway. However, few current pathway enrichment analysis methods account for the sub-pathways or structures of the tested pathways. We present a sub-pathway-based enrichment approach for identifying a drug response principal network, which takes into consideration the quantitative structures of the pathways. RESULT: We validated this new approach on a microarray experiment that captures the transcriptional profile of dexamethasone (DEX)-treated human prostate cancer PC3 cells. Compared with GeneTrail and DAVID, our approach is more sensitive to the DEX response pathways. Specifically, not only pathways but also the principal components of sub-pathways and networks related to prostate cancer and DEX response could be identified and verified by literature retrieval.

lncRNA LEF1-AS1 Acts as a Novel Biomarker and Promotes Hypopharyngeal Squamous Cell Carcinoma Progression and Metastasis by Targeting the miR-221-5p/GJA1 Axis.

Hypopharyngeal squamous cell carcinoma (HSCC) is highly malignant and extremely aggressive, making it one of the worst prognoses among all kinds of head and neck squamous cell carcinoma (HNSCC); therefore, gaining insight into molecular mechanisms of HSCC is of profound significance. In the current manuscript, we revealed the elevated expression of long noncoding RNA (lncRNA) LEF1-AS1 in HNSCC which was associated with the poor prognosis by bioinformatic analysis. Moreover, we noticed that LEF1-AS1 dramatically accelerated the proliferation, migration, invasion, and epithelial-mesenchymal transition (EMT) process in HSCC cell line FaDu. Most importantly, we illustrated that LEF1-AS1 played as a competitive endogenous RNA (ceRNA) via sponging miR-221-5p and thereby positively regulated gap junction protein alpha 1 (GJA1) expression, thus aggravated tumor progression and EMT. In conclusion, for the first time, we demonstrated lncRNA LEF1-AS1 as a novel biomarker for HNSCC and suggested LEF1-AS1/miR-221-5p/GJA1 axis as promising diagnostic and therapeutic target for HSCC treatment.

Pharmacokinetics of luteolin and tetra-acetyl-luteolin assayed by HPLC in rats after oral administration.

Accurate and reproducible HPLC methods were developed and validated for the determination of concentrations of luteolin (LT) and tetra-acetyl-luteolin (TALT) in rat plasma. HPLC analyses were performed on an Agilent TC-C(18) column protected by a guard Agilent Zorbax Eclipse Plus. The mobile phase for LT was a binary mixture of acetonitrile-water (40:60, v/v) containing 0.5% phosphoric acid at a flow rate of 1.0 mL/min, and that for TALT was a binary mixture of methanol-water (70 : 30, v/v) containing 0.5% glacial acetic acid at the same flow rate. The UV detection wavelength for both analytes was set at 350 nm. The calibration curve was linear over the range of 40-1800 ng/mL, the lower limit of quantitation was 40 ng/mL and the lower limit of detection was 20 ng/mL for both LT and TALT. The intra- and inter-day precision (RSD) values for all samples were within 7.9%. The concentration-time curves of LT and TALT after oral administration (30 mg/kg) were both fitted to a two-compartment model. The pharmacokinetic characteristics of TALT were better than that of LT in the maximum plasma concentration (C(max)) and the area under the concentration-time curve (AUC).

Genetic mutations in non-syndromic deafness patients in Hainan Province have a different mutational spectrum compared to patients from Mainland China.

OBJECTIVES: To provide appropriate genetic testing and counseling for non-syndromic hearing impairment patients in Hainan Province, an island in the South China Sea. METHODS: 299 unrelated students with non-syndromic hearing loss who attended a special education school in Hainan Province were enrolled in this study. Three prominent deafness-related genes (GJB2, SLC26A4, and mtDNA 12S rRNA) were analyzed using Sanger sequencing. RESULTS: GJB2 mutations were detected in 32.78% (98/299) of the entire cohort; however, only 5.69% (17/299) had two confirmed pathogenic mutations. The most common mutation observed in this population was c.109G > A in the GJB2 gene, with an allelic frequency of 15.05% (90/598), which is significantly higher than that reported in previous cohorts. A total of 16 patients had two confirmed pathogenic SLC26A4 gene mutations, and 16 patients had one. The IVS7-2A > G mutation was the most commonly observed, with an allelic frequency of 3.51% (21/598). Three patients had a m.1555A > G mutation in the mtDNA 12S rRNA gene. CONCLUSIONS: These results reveal that genetic etiology occurred in 11.71% (35/299) of patients, suggesting that Hainan province have a different mutational spectrum compare to Mainland China in non-syndromic deafness patients, which provide useful information to genetic counseling in Hainan province.

A survey on hearing acuity of centenarians in Hainan Province.

OBJECTIVE: This study aimed to investigate hearing acuity of centenarians in Hainan Province and provide basis for interventional considerations. METHOD: Door-to-door follow-up was conducted to investigate hearing acuity of centenarians (aged 100 years or above) in Hainan Province. Physical examination, pure tone audiometry and acoustic impedance test were performed, and the results were analyzed. RESULT: A total of 460 centenarians (920 ears) were tested by pure tone audiometry. The rate of normal hearing was 0.2%, the rate of mild hearing loss was 1.5%, 12% for moderate hearing loss, 33.9% for moderate to severe hearing loss, 37.4% for severe hearing loss is and 15% for profound hearing loss. Acoustic impedance test was performed in 340 centenarians (668 ears). Tympanogram was type A in 41.2% of the ears, type As in 34.1% ears, type Ad in 6.4%, type B in 11.8%, and type C in 4.9% of the ears, while no response was elicited in 1.5% of the ears. CONCLUSION: Age related sensorineural hearing loss is prevalent among centenarians in Hainan Province. A probably beneficial intervention may be the use of hearing aids for effective communication.

Cyanobacterial bloom significantly boosts hypolimnelic anammox bacterial abundance in a subtropical stratified reservoir.

The degradation of freshwater quality induced by cyanobacterial blooms is a major global environmental concern. Microbially driven nitrogen removal could alleviate eutrophication to some degree in freshwater ecosystems. However, the response of anaerobic ammonium oxidizing (anammox) bacterial communities to cyanobacterial blooms remains poorly understood, especially in reservoir ecosystems. Here we compared the dynamics of anammox bacterial communities during and after a cyanobacterial bloom in a subtropical reservoir. Our data showed that a cyanobacterial bloom triggered a significant increase in bottom anammox bacterial abundance. During the bloom period, anammox bacterial abundance in bottom waters was 9-fold and 52-fold higher compared with non-bloom stratification and mixing periods, respectively. The community composition of anammox bacteria in surface waters changed substantially accompanied by the disappearance of the cyanobacterial bloom, and a shift of dominance from unidentified anammox genera to Ca. Brocadia was observed. Although Ca. Brocadia was always predominant in both middle and bottom waters, the non-bloom period had more unique taxa than the bloom period. Cyanobacterial bloom-related changes in environmental conditions (e.g. NH4-N and total organic carbon) and water stratification together influenced the distribution and dynamics of anammox bacteria. Altogether, our study lays the basis for a better understanding of the breakdown of cyanobacterial blooms in a stratified reservoir.

The relationship between the GJB3 c.538C>T variant and hearing phenotype in the Chinese population.

BACKGROUND: Mutations in GJB3 were originally shown to underlie an autosomal dominant form of non-syndromic deafness in Chinese patients and the c.538C>T (p.R180*) variants caused high-frequency hearing loss. But after that, few reports have reported this mutation. This study investigated the relationship between the GJB3 c.538C>T variant and hearing phenotype in Chinese to assist with risk assessment and genetic counseling for hearing loss patients and their families. METHOD: The study enrolled 5700 patients with hearing loss and 4600 normal subjects. Deafness gene mutations were distinguished using a gene chip. The GJB3 c.538C>T variant rate was calculated from the results. RESULT: Of the 5700 patients, 23 (0.40%) carried a GJB3 c.538C>T heterozygous variant; of these, 11 patients had other gene (GJB2/SLC26A4) mutations simultaneously. Most patients had moderate to profound hearing loss. All 23 patients were sporadic cases and had no family history of deafness. Of the 4600 normal individuals, 11 (0.24%) had GJB3 c.538C>T heterozygous variant. There was no statistical difference in incidence between the two groups. CONCLUSIONS: Our results showed that the GJB3 c.538C>T variant has a very low incidence in the Chinese population, and there was no clear evidence to support a role of the GJB3 c.538C>T variant in the autosomal dominant form of non-syndromic deafness. Our findings suggested that GJB3 c.538C>T does not contribute to hearing loss, and this conclusion will assist with genetic counseling and risk prediction for deafness related to the GJB3 c.538C>T variant.

A novel mutation in POU3F4 in a Chinese family with X-linked non-syndromic hearing loss.

OBJECTIVE: Based on the clinical manifestations of a hearing loss patient, the POU3F4 gene was tested for diagnosis of etiology. METHODS: A comprehensive physical examination was performed on the proband to exclude abnormalities of other organs, and detailed audiological testing and temporal bone CT scan were also performed. Genomic DNA was extracted using the proband's peripheral blood leukocytes. Polymerase chain reactions (PCR) were performed in the coding sequence of the POU3F4 gene. Direct DNA sequencing was subsequently applied to screen the entire coding region of the POU3F4 gene. RESULTS: The proband had severe sensorineural hearing loss. Temporal CT showed bilateral cochlear incomplete partition, vestibule dysplasia, internal auditory canal fundus expansion, and cochlear interlink with the internal auditory canal fundus. A novel mutation (c.530C > A (p.S177X)) in the POU3F4 gene was found in this patient, creating an new stop codon and was predicted to result in a truncated protein lacking normal POU3F4 transcription factor function. CONCLUSION: Through analysis of the POU3F4 gene and clinical manifestations in the patient, we conclude that a novel mutation may have resulted in a premature stop codon, contributing to the mutation of POU3F4 gene.

The Relationship between the p.V37I Mutation in GJB2 and Hearing Phenotypes in Chinese Individuals.

The most common cause of nonsyndromic autosomal recessive hearing loss is mutations in GJB2. The mutation spectrum and prevalence of mutations vary significantly among ethnic groups, and the relationship between p.V37I mutation in GJB2 and the hearing phenotype is controversial. Among the 3,864 patients in this study, 106 (2.74%) had a homozygous p.V37I variation or a compound p.V37I plus other GJB2 pathogenic mutation, a frequency that was significantly higher than that in the control group (600 individuals, 0%). The hearing loss phenotype ranged from mild to profound in all patients with the homozygous p.V37I variation or compound p.V37I plus other GJB2 pathogenic mutation. There was no difference in the distribution of the hearing level in the group with the homozygous p.V37I variation and the group with the compound p.V37I variation plus pathogenic mutation. Most patients (66.04%) with the V37I-homozygous variation or p.V37I plus other pathogenic mutation had a mild or moderate hearing level. This study found a definite relationship between p.V37I and deafness, and most patients who carried the pathogenic combination with p.V37I mutation had mild or moderate hearing loss. Therefore, otolaryngologists should consider that the milder phenotype might be caused by the GJB2 p.V37I mutation.

[The study of GJB2 dominant mutaion distribution in Chinese deafness patient and the analysis of phenotype].

OBJECTIVE: Mutations in the GJB2 are the most common cause of nonsyndromic autosomal recessive sensorineural hearing loss. A few mutations in GJB2 have also been reported to cause dominant nonsyndromic or syndromic hearing loss. This study analysised the GJB2 dominant mutation in Chinese deafness. METHOD: 1641 patients as GJB2-related hearing loss were enrolled, summarized the type of dominant mutaion, analyzed the hearing level and other systerm lesion. RESULT: Nine probands with severe-profound hearing loss were diagnosed as GJB2 domiant mutation (R75W,G130V, R143Q,p. R184Q). And one patient with R75W mutation was diagosed as hearing loss and palmoplantar keratoderma. CONCLUSION: GJB2 dominant mutation can cause severe-to-profound bilateral sensorineural hearing impairment and not common with syndromic hearing loss in Chinese deafness.

KCNJ10 may not be a contributor to nonsyndromic enlargement of vestibular aqueduct (NSEVA) in Chinese subjects.

BACKGROUND: Nonsyndromic enlargement of vestibular aqueduct (NSEVA) is an autosomal recessive hearing loss disorder that is associated with mutations in SLC26A4. However, not all patients with NSEVA carry biallelic mutations in SLC26A4. A recent study proposed that single mutations in both SLC26A4 and KCNJ10 lead to digenic NSEVA. We examined whether KCNJ10 excert a role in the pathogenesis of NSEVA in Chinese patients. METHODS: SLC26A4 was sequenced in 1056 Chinese patients with NSEVA. KCNJ10 was screened in 131 patients who lacked mutations in either one or both alleles of SLC26A4. Additionally, KCNJ10 was screened in 840 controls, including 563 patients diagnosed with NSEVA who carried biallelic SLC26A4 mutations, 48 patients with nonsyndromic hearing loss due to inner ear malformations that did not involve enlargement of the vestibular aqueduct (EVA), 96 patients with conductive hearing loss due to various causes, and 133 normal-hearing individuals with no family history of hereditary hearing loss. RESULTS: 925 NSEVA patients were found carrying two-allele pathogenic SLC26A4 mutations. The most frequently detected KCNJ10 mutation was c.812G>A (p.R271H). Compared with the normal-hearing control subjects, the occurrence rate of c.812G>A in NSEVA patients with lacking mutations in one or both alleles of SLC26A4 had no significant difference(1.53% vs. 5.30%, χ(2) = 2.798, p = 0.172), which suggested that it is probably a nonpathogenic benign variant. KCNJ10 c.1042C>T (p.R348C), the reported EVA-related mutation, was not found in patients with NSEVA who lacked mutations in either one or both alleles of SLC26A4. Furthermore, the normal-hearing parents of patients with NSEVA having two SLC26A4 mutations carried the KCNJ10 c.1042C>T or c.812G>A mutation and a SLC26A4 pathogenic mutation. CONCLUSION: SLC26A4 is the major genetic cause in Chinese NSEVA patients, accounting for 87.59%. KCNJ10 may not be a contributor to NSEVA in Chinese population. Other genetic or environmental factors are possibly play a role in the etiology of Chinese EVA patients with zero or monoallelic SLC26A4 mutation.

[Assessment of the curative effective of cochlear implantation in childer with GJB2-associated NSSNHL].

OBJECTIVE: To analyze the curative effect of CI in children with GJB2-associated NSSNHL. METHOD: The evaluations of curative effect with CI include auditory threshold, IT-MAIS/MAIS, CAP, SIR. MESP. The outcomes of 40 cases with GJB2-associated NSSNHI, were compared 80 patients with negative results of screening of gene mutation (control group). RESULT: In comparison with control group the auditory threshold in children with GJB2-associated NSSNIL is better, however had no significant difference in other tests (P > 0.05). CONCLUSION: CI could he performed on children with GJB2-associated NSSNHL. Postoperative outcomes of hearing and speech were satisfied.

Baiji genomes reveal low genetic variability and new insights into secondary aquatic adaptations.

The baiji, or Yangtze River dolphin (Lipotes vexillifer), is a flagship species for the conservation of aquatic animals and ecosystems in the Yangtze River of China; however, this species has now been recognized as functionally extinct. Here we report a high-quality draft genome and three re-sequenced genomes of L. vexillifer using Illumina short-read sequencing technology. Comparative genomic analyses reveal that cetaceans have a slow molecular clock and molecular adaptations to their aquatic lifestyle. We also find a significantly lower number of heterozygous single nucleotide polymorphisms in the baiji compared to all other mammalian genomes reported thus far. A reconstruction of the demographic history of the baiji indicates that a bottleneck occurred near the end of the last deglaciation, a time coinciding with a rapid decrease in temperature and the rise of eustatic sea level.

The genome of Prunus mume.

Prunus mume (mei), which was domesticated in China more than 3,000 years ago as ornamental plant and fruit, is one of the first genomes among Prunus subfamilies of Rosaceae been sequenced. Here, we assemble a 280M genome by combining 101-fold next-generation sequencing and optical mapping data. We further anchor 83.9% of scaffolds to eight chromosomes with genetic map constructed by restriction-site-associated DNA sequencing. Combining P. mume genome with available data, we succeed in reconstructing nine ancestral chromosomes of Rosaceae family, as well as depicting chromosome fusion, fission and duplication history in three major subfamilies. We sequence the transcriptome of various tissues and perform genome-wide analysis to reveal the characteristics of P. mume, including its regulation of early blooming in endodormancy, immune response against bacterial infection and biosynthesis of flower scent. The P. mume genome sequence adds to our understanding of Rosaceae evolution and provides important data for improvement of fruit trees.