Relationship between serum vitamin D levels semen parameters and sperm DNA damage in men with unexplained infertility.

OBJECTIVE: The aim of the study was to investigate the relationship between serum level of vitamin D, semen analysis parameters and sperm DNA damage in men with unexplained subfertility. PATIENTS AND METHODS: Fifty-eight men diagnosed with unexplained infertility and 50 age and BMI matched fertile men were included in the study. A participant whose semen parameter is normal but pregnancy is not achieved was accepted as unexplained male infertility. Blood samples were taken from all participants following three-day abstinence for measurement of vitamin D. Sperm DNA damage was assessed by Aniline Blue staining of the collected samples. RESULTS: Compared with the fertile men, male patients with unexplained infertility had significantly lower vit D levels (27.00 ng/mL (12.63-39.30) vs. 23.66 ng/mL (7.50-55.00), p<0.004). While the number of patients with vitamin D levels lower than 20 ng/mL was 26 (44.8%) in the infertile group, it was recorded as 5 (10.0%) in the fertile group (p<0.001). DNA damage was found in 31.50% (9.0-71.0) of the infertile men and 26.00% (11.0-54.0) of the fertile men. DNA damage was found to be significantly higher in the unexplained infertile group (p<0.002). In men with unexplained male infertility, serum vit D levels were positively correlated with total sperm count (r = 0.527, p<0.001), total motility (r = 0.527, p<0.001) and sperm morphology (r = 0.416, p = 0.001). There was a negative and significant correlation between vit D levels and sperm DNA damage (r = -0.605, p<0.001). In the logistic regression analysis, serum vit D > 20 ng/mL led to an improvement in fertility outcome. CONCLUSIONS: Men with unexplained infertility exhibit decreased serum vit D levels and increased sperm DNA damage.

Do tumor localization, microsatellite instability and mismatch repair deficiency have an impact on the prognosis of colorectal cancer?

BACKGROUND: Recent reports have shown that left-and right-sided colon cancers display different clinical and biological features. Chromosomal instability, epigenetic alterations, and defects in the deoxyribonucleic acid (DNA) mismatch repair (MMR) system may lead to the development of colorectal cancer (CRC). Besides microsatellite instability (MSI) caused by DNA MMR activity degradation increases the risk for CRC. AIM: We aimed to show the differences between CRCs in different locations, to research the cause of these differences, to present whether there is a relation between MMR and MSI, and to evaluate their effects on prognosis. PATIENTS AND METHODS: 641 CRC cases were divided into three groups: Group 1 (right-sided), Group 2 (left-sided), and Group 3 (rectum). Demographics, cancer stages, location of the tumors, number of the lymph nodes removed, MMR deficiency or proficiency, MSI status, and survival were assessed by retrospective review of the patients. RESULTS: Among 641 patients, 64.9% were males. Group 1, 2, and 3 comprised 31.2%, 45.7%, and 23.1% of all the cases, respectively. There was a significant difference in terms of survival and location only in stage II tumors. Stage II left colon cancer (LCCs) had a statistically significant lower survival rate. There was no significant difference in survival between both MSI and MMR statuses. In addition, cases were also stratified by stages. According to this data, 10.1, 45.7, and 44.2% of the patients had stages I, II, and III disease, respectively. CONCLUSIONS: Although it was not statistically significant, tumors with MMR deficiency (dMMR) and high microsatellite instability (MSI-H) are more common in right-sided colon tumors.

Endoscopic resection for giant oesophageal fibrovascular polyp.

A fibrovascular polyp is a rare benign pseudotumour of the oesophagus and hypopharynx. Although patients usually present with dysphagia, aspiration related mortality may occur. If the tumour is too large and/or located in the proximal oesophagus, it may protrude from the mouth. The general approach to treatment is complete reconstruction with cervicotomy. We present our experience of a giant oesophageal fibrovascular polyp that was protruding from the mouth and treated with endoscopic resection. A 55-year-old man was admitted to our outpatient clinic complaining of a mass protruding from his mouth when he coughed. Endoscopy and bronchoscopy both revealed a 15-18cm long polypoid mass originating from the proximal oesophagus (at the level of the hypopharynx). Complete resection was performed via endoscopy.

The HLA-Cw12 Allele Is an Important Susceptibility Allele for Psoriasis and Is Associated with Resistant Psoriasis in the Turkish Population.

BACKGROUND: Psoriasis is a multifactorial immune-mediated inflammatory disease triggered by both genetic and environmental factors. The strong association between psoriasis and HLA-C⁎06 allele has been demonstrated in various races. The HLA-C⁎12 allele is closely related to the HLA-C⁎06 family of alleles and shares identical sequences. To the best of our knowledge, there is no information about the relationship between HLA-C⁎12 and psoriasis in the Turkish population. The present study aims to determine this relationship. METHODS: This case control study involved 150 patients with plaque-type psoriasis and 145 age- and gender-matched healthy individuals. Severity of psoriasis was measured using the PASI scores of all patients and joint involvement was investigated with CASPAR criteria. HLA-C alleles were determined with a Tepnel-Lifecodes system. RESULTS: HLA-C⁎06, HLA-C⁎12, and HLA-C⁎04 alleles were most commonly observed in psoriasis patients. HLA-C⁎06 and HLA-C⁎12 were significantly more frequent in the psoriasis group. HLA-C⁎06 was 4.11 times more common in psoriasis patients. An increase in PASI (Psoriasis Area Severity Index) scores was compatible with HLA-C⁎12 positivity. A need for systemic treatment was highly noticeable in patients with the HLA-C⁎12 allele. CONCLUSIONS: HLA-C⁎12 was found as the second most frequent allele with psoriasis in Turkish population and was associated with severe psoriasis. Our study is limited as we could not investigate other potentially related alleles other than HLA-C alleles and risk factors increasing severity of psoriasis.

Targeted Resequencing of Deafness Genes Reveals a Founder MYO15A Variant in Northeastern Brazil.

Identifying the genetic etiology in a person with hearing loss (HL) is challenging due to the extreme genetic heterogeneity in HL and the population-specific variability. In this study, after excluding GJB2 variants, targeted resequencing of 180 deafness-related genes revealed the causative variants in 11 of 19 (58%) Brazilian probands with autosomal recessive HL. Identified pathogenic variants were in MYO15A (10 families) and CLDN14 (one family). Remarkably, the MYO15A p.(Val1400Met) variant was identified in eight families from the city of Monte Santo in the northeast region of Brazil. Haplotype analysis of this variant was consistent with a single founder. No other cases with this variant were detected among 105 simplex cases from other cities of northeastern Brazil, suggesting that this variant is confined to a geographical region. This study suggests that it is feasible to develop population-specific screening for deafness variants once causative variants are identified in different geographical groups.

Variations in Multiple Syndromic Deafness Genes Mimic Non-syndromic Hearing Loss.

The genetics of both syndromic (SHL) and non-syndromic hearing loss (NSHL) is characterized by a high degree of genetic heterogeneity. We analyzed whole exome sequencing data of 102 unrelated probands with apparently NSHL without a causative variant in known NSHL genes. We detected five causative variants in different SHL genes (SOX10, MITF, PTPN11, CHD7, and KMT2D) in five (4.9%) probands. Clinical re-evaluation of these probands shows that some of them have subtle syndromic findings, while none of them meets clinical criteria for the diagnosis of the associated syndrome (Waardenburg (SOX10 and MITF), Kallmann (CHD7 and SOX10), Noonan/LEOPARD (PTPN11), CHARGE (CHD7), or Kabuki (KMT2D). This study demonstrates that individuals who are evaluated for NSHL can have pathogenic variants in SHL genes that are not usually considered for etiologic studies.

Spectrum of DNA variants for non-syndromic deafness in a large cohort from multiple continents.

Hearing loss is the most common sensory deficit in humans with causative variants in over 140 genes. With few exceptions, however, the population-specific distribution for many of the identified variants/genes is unclear. Until recently, the extensive genetic and clinical heterogeneity of deafness precluded comprehensive genetic analysis. Here, using a custom capture panel (MiamiOtoGenes), we undertook a targeted sequencing of 180 genes in a multi-ethnic cohort of 342 GJB2 mutation-negative deaf probands from South Africa, Nigeria, Tunisia, Turkey, Iran, India, Guatemala, and the United States (South Florida). We detected causative DNA variants in 25 % of multiplex and 7 % of simplex families. The detection rate varied between 0 and 57 % based on ethnicity, with Guatemala and Iran at the lower and higher end of the spectrum, respectively. We detected causative variants within 27 genes without predominant recurring pathogenic variants. The most commonly implicated genes include MYO15A, SLC26A4, USH2A, MYO7A, MYO6, and TRIOBP. Overall, our study highlights the importance of family history and generation of databases for multiple ethnically discrete populations to improve our ability to detect and accurately interpret genetic variants for pathogenicity.

ROR1 is essential for proper innervation of auditory hair cells and hearing in humans and mice.

Hair cells of the inner ear, the mechanosensory receptors, convert sound waves into neural signals that are passed to the brain via the auditory nerve. Little is known about the molecular mechanisms that govern the development of hair cell-neuronal connections. We ascertained a family with autosomal recessive deafness associated with a common cavity inner ear malformation and auditory neuropathy. Via whole-exome sequencing, we identified a variant (c.2207G>C, p.R736T) in ROR1 (receptor tyrosine kinase-like orphan receptor 1), cosegregating with deafness in the family and absent in ethnicity-matched controls. ROR1 is a tyrosine kinase-like receptor localized at the plasma membrane. At the cellular level, the mutation prevents the protein from reaching the cellular membrane. In the presence of WNT5A, a known ROR1 ligand, the mutated ROR1 fails to activate NF-κB. Ror1 is expressed in the inner ear during development at embryonic and postnatal stages. We demonstrate that Ror1 mutant mice are severely deaf, with preserved otoacoustic emissions. Anatomically, mutant mice display malformed cochleae. Axons of spiral ganglion neurons show fasciculation defects. Type I neurons show impaired synapses with inner hair cells, and type II neurons display aberrant projections through the cochlear sensory epithelium. We conclude that Ror1 is crucial for spiral ganglion neurons to innervate auditory hair cells. Impairment of ROR1 function largely affects development of the inner ear and hearing in humans and mice.

Comprehensive analysis via exome sequencing uncovers genetic etiology in autosomal recessive nonsyndromic deafness in a large multiethnic cohort.

PURPOSE: Autosomal recessive nonsyndromic deafness (ARNSD) is characterized by a high degree of genetic heterogeneity, with reported mutations in 58 different genes. This study was designed to detect deafness-causing variants in a multiethnic cohort with ARNSD by using whole-exome sequencing (WES). METHODS: After excluding mutations in the most common gene, GJB2, we performed WES in 160 multiplex families with ARNSD from Turkey, Iran, Mexico, Ecuador, and Puerto Rico to screen for mutations in all known ARNSD genes. RESULTS: We detected ARNSD-causing variants in 90 (56%) families, 54% of which had not been previously reported. Identified mutations were located in 31 known ARNSD genes. The most common genes with mutations were MYO15A (13%), MYO7A (11%), SLC26A4 (10%), TMPRSS3 (9%), TMC1 (8%), ILDR1 (6%), and CDH23 (4%). Nine mutations were detected in multiple families with shared haplotypes, suggesting founder effects. CONCLUSION: We report on a large multiethnic cohort with ARNSD in which comprehensive analysis of all known ARNSD genes identifies causative DNA variants in 56% of the families. In the remaining families, WES allows us to search for causative variants in novel genes, thus improving our ability to explain the underlying etiology in more families.Genet Med 18 4, 364-371.

FAM65B is a membrane-associated protein of hair cell stereocilia required for hearing.

In a large consanguineous Turkish kindred with recessive nonsyndromic, prelingual, profound hearing loss, we identified in the gene FAM65B (MIM611410) a splice site mutation (c.102-1G>A) that perfectly cosegregates with the phenotype in the family. The mutation leads to exon skipping and deletion of 52-amino acid residues of a PX membrane localization domain. FAM65B is known to be involved in myotube formation and in regulation of cell adhesion, polarization, and migration. We show that wild-type Fam65b is expressed during embryonic and postnatal development stages in murine cochlea, and that the protein localizes to the plasma membranes of the stereocilia of inner and outer hair cells of the inner ear. The wild-type protein targets the plasma membrane, whereas the mutant protein accumulates in cytoplasmic inclusion bodies and does not reach the membrane. In zebrafish, knockdown of fam65b leads to significant reduction of numbers of saccular hair cells and neuromasts and to hearing loss. We conclude that FAM65B is a plasma membrane-associated protein of hair cell stereocilia that is essential for hearing.

Branchio-oculo-facial syndrome in a newborn caused by a novel TFAP2A mutation.

We present an 18-day old boy with bilateral cervical cutaneous defect in the retroauricular region, low-set and posteriorly rotated ears, bilateral microphtalmia and bilateral pseudocleft of the upper lip. Histopathological evaluation of cervical cutaneous defect showed ulceration on the surface and ectopic thymus tissue in the deep dermis with cortex, medulla and Hassal's corpuscles. Clinical findings led to the diagnosis of Branchio-oculo-facial syndrome, characterized by branchial defects (erythematous cutaneous defects in cervical region), ocular anomalies (microphthalmia, anophthalmia, lacrimal duct obstruction, coloboma, cataract, ptosis) and facial defects (cleft lip and/or palate, pseudocleft or abnormal philtrum). DNA sequencing showed a novel heterozygous mutation, c.731T>C (p.L244P), in TFAP2A gene confirming the diagnosis of this rare autosomal dominant developmental disorder with variable clinical findings.

Single-port laparoscopic cholecystectomy versus the classical four port laparoscopic cholecystectomy: a randomized prospective clinical trial.

AIM: The objectives of this prospective study were to compare the advantages of single-port laparoscopic cholecystectomy (SPLC) versus the classical four-port laparoscopic cholecystectomy (CLC) and to discuss these advantages in the light of current literature. METHODS: Forty eligible patients were randomized to receive SPLC (Group A, N.=20) and CLC (Group B, N.=20), and investigated with regard to age, sex, BMI (body mass index), ASA (American Society of Anesthesiologists) score, type of surgery, operative time, per-operative complication, indication for conversion to open surgery, indication for additional trocar placement in SPLC technique, post-operative pain score, additional narcotic analgesic requirement, nausea and vomiting, post-operative complication and length of hospital stay. Visual analogue scale (VAS) was used for pain scoring in all cases. RESULTS: No significant difference was found among patients in Group A and Group B in terms of age, sex, weight/BMI, ASA score, VAS scores, additional analgesic requirement and length of hospital stay (P>0.05). On the other hand, mean operative time in Group A was significantly (P<0.005) greater than that in Group B. Mean operative time in Group A was observed to be reduced after the first 10 operations. Conversion to open surgery was not required in any of the patients; however, additional trocar placement was required in two patients in Group A due to body habitus and adhesions, and operations were completed laparoscopically. CONCLUSION: We conclude that SPLC is equally effective as CLC. Patient comfort is increased and pain is decreased as the surgeon gets experienced with the technique.

Comparison of different scoring systems in patients undergoing colorectal cancer surgery for predicting mortality and morbidity.

BACKGROUND: Preoperative risk estimation evaluating mortality and morbidity might help surgical decision. AIMS: The aim of this study was to compare the sensitivities of physiologic and operative severity score for the enumeration of mortality and morbidity (POSSUM), portsmouth-POSSUM (P-POSSUM), colorectal-POSSUM (CR-POSSUM), the Association of Coloproctology of Great Britain and Ireland colorectal cancer model (ACPGBI CRC) and revised ACPGBI CRC scoring systems that are used for evaluating mortality and morbidity in colorectal surgery performed in third-level healthcare centers. SETTINGS AND DESIGN: A retrospective analysis has been performed on 335 consecutive patients undergoing colorectal cancer surgery between 2002 and 2012. MATERIALS AND METHODS: Mortality and morbidity risks of 335 patients who underwent colorectal cancer were evaluated using these scoring systems and the results were compared with actual mortality and morbidity within postoperative 30-day that extend the duration of hospital stay. STATISTICAL ANALYSIS USED: The receiver operating characteristic (ROC) curves were designed to identify the score values. RESULTS: Results of POSSUM and P-POSSUM systems showed statistical differences compared with those of CR-POSSUM, ACPGBI CRC and revised ACPGBI CRC systems (P < 0.05). P-POSSUM was found to be the best scoring system for predicting mortality risk, although all scoring systems seem to be appropriate for this parameter. On the other hand POSSUM, which can predict morbidity, was found to have moderate differentiation ability due to the magnitude of the area under the ROC curve. CONCLUSIONS: Despite altering patient demographics and surgical conditions, POSSUM seems to lead as the best scoring system for predicting mortality and morbidity among others including those most-recently proposed.

SLITRK6 mutations cause myopia and deafness in humans and mice.

Myopia is by far the most common human eye disorder that is known to have a clear, albeit poorly defined, heritable component. In this study, we describe an autosomal-recessive syndrome characterized by high myopia and sensorineural deafness. Our molecular investigation in 3 families led to the identification of 3 homozygous nonsense mutations (p.R181X, p.S297X, and p.Q414X) in SLIT and NTRK-like family, member 6 (SLITRK6), a leucine-rich repeat domain transmembrane protein. All 3 mutant SLITRK6 proteins displayed defective cell surface localization. High-resolution MRI of WT and Slitrk6-deficient mouse eyes revealed axial length increase in the mutant (the endophenotype of myopia). Additionally, mutant mice exhibited auditory function deficits that mirrored the human phenotype. Histological investigation of WT and Slitrk6-deficient mouse retinas in postnatal development indicated a delay in synaptogenesis in Slitrk6-deficient animals. Taken together, our results showed that SLITRK6 plays a crucial role in the development of normal hearing as well as vision in humans and in mice and that its disruption leads to a syndrome characterized by severe myopia and deafness.

Screening of 38 genes identifies mutations in 62% of families with nonsyndromic deafness in Turkey.

More than 60% of prelingual deafness is genetic in origin, and of these up to 95% are monogenic autosomal recessive traits. Causal mutations have been identified in 1 of 38 different genes in a subset of patients with nonsyndromic autosomal recessive deafness. In this study, we screened 49 unrelated Turkish families with at least three affected children born to consanguineous parents. Probands from all families were negative for mutations in the GJB2 gene, two large deletions in the GJB6 gene, and the 1555A>G substitution in the mitochondrial DNA MTRNR1 gene. Each family was subsequently screened via autozygosity mapping with genomewide single-nucleotide polymorphism arrays. If the phenotype cosegregated with a haplotype flanking one of the 38 genes, mutation analysis of the gene was performed. We identified 22 different autozygous mutations in 11 genes, other than GJB2, in 26 of 49 families, which overall explains deafness in 62% of families. Relative frequencies of genes following GJB2 were MYO15A (9.9%), TMIE (6.6%), TMC1 (6.6%), OTOF (5.0%), CDH23 (3.3%), MYO7A (3.3%), SLC26A4 (1.7%), PCDH15 (1.7%), LRTOMT (1.7%), SERPINB6 (1.7%), and TMPRSS3 (1.7%). Nineteen of 22 mutations are reported for the first time in this study. Unknown rare genes for deafness appear to be present in the remaining 23 families.

Recurrent and private MYO15A mutations are associated with deafness in the Turkish population.

The identities and frequencies of MYO15A mutations associated with hearing loss in different populations remained largely unknown. We screened the MYO15A gene for mutations in 104 unrelated multiplex and consanguineous Turkish families with autosomal recessive nonsyndromic sensorineural hearing loss using autozygosity mapping. The screening of MYO15A in 10 families mapped to the DFNB3 locus revealed five previously unreported mutations: p.Y289X (1 family), p.V1400M (1 family), p.S1481P (1 family), p.R1937TfsX10 (3 families), and p.S3335AfsX121 (2 families). Recurrent mutations were associated with conserved haplotypes suggesting the presence of founder effects. Severe to profound sensorineural hearing loss was observed in all subjects with homozygous mutations except for two members of a family who were homozygous for the p.Y289X mutation in the N-terminal extension domain and had considerable residual hearing. We estimate the prevalence of homozygous MYO15A mutations in autosomal recessive nonsyndromic deafness in Turkey as 0.062 (95% confidence interval is 0.020-0.105).

A truncating mutation in SERPINB6 is associated with autosomal-recessive nonsyndromic sensorineural hearing loss.

More than 270 million people worldwide have hearing loss that affects normal communication. Although astonishing progress has been made in the identification of more than 50 genes for deafness during the past decade, the majority of deafness genes are yet to be identified. In this study, we mapped a previously unknown autosomal-recessive nonsyndromic sensorineural hearing loss locus (DFNB91) to chromosome 6p25 in a consanguineous Turkish family. The degree of hearing loss was moderate to severe in affected individuals. We subsequently identified a nonsense mutation (p.E245X) in SERPINB6, which is located within the linkage interval for DFNB91 and encodes for an intracellular protease inhibitor. The p.E245X mutation cosegregated in the family as a completely penetrant autosomal-recessive trait and was absent in 300 Turkish controls. The mRNA expression of SERPINB6 was reduced and production of protein was absent in the peripheral leukocytes of homozygotes, suggesting that the hearing loss is due to loss of function of SERPINB6. We also demonstrated that SERPINB6 was expressed primarily in the inner ear hair cells. We propose that SERPINB6 plays an important role in the inner ear in the protection against leakage of lysosomal content during stress and that loss of this protection results in cell death and sensorineural hearing loss.

Numerical prediction of steady-state detonation properties of condensed-phase explosives.

Within the scope of this study, a computer code named BARUT-X has been developed to calculate the detonation properties of C-H-N-O based condensed-phase explosives using the Chapman-Jouguet (C-J) theory. Determination of the detonation properties is performed in chemical equilibrium and steady-state conditions. Unlike other codes in the literature which use steepest descent optimization method, BARUT-X uses a nonlinear optimization code based on Generalized Reduced Gradient algorithm to compute the equilibrium composition of the detonation products. This optimization code provides a higher level of robustness of the solutions and global optimum determination efficiency. The Becker-Kistiakowsky-Wilson's (BKW) equation of state (EOS) is applied to the high-density gaseous detonation products at high pressures. BARUT-X uses RDX, TNT, BKWR, and BKWN set of constants in the BKW EOS. In addition, the Cowan-Fickett's EOS is applied for the compressible solid carbon in the detonation products. The calculated detonation properties for several condensed-phase explosives by BARUT-X have been compared with those computed by EXPLO5 and FORTRAN BKW codes as well as the experimental data in terms of detonation velocity and detonation pressure. Satisfactory agreement is obtained from these comparisons.