The Common miRNA Signatures Associated with Mitochondrial Dysfunction in Different Muscular Dystrophies.

Secondary mitochondrial damage in skeletal muscles is a common feature of different neuromuscular disorders, which fall outside the mitochondrial cytopathies. The common cause of mitochondrial dysfunction and structural changes in skeletal muscle tissue remains to be discovered. Although they are associated with different clinical, genetic, and pathologic backgrounds, the pathomechanisms underlying neuromuscular disorders might be attributed to the complex interaction and cross talk between mitochondria and the associated miRNAs. This study aimed to identify the common miRNA signatures that are associated with mitochondrial damage in different muscular dystrophies (MDs; Duchenne muscular dystrophy, megaconial congenital muscular dystrophy, Ullrich congenital muscular dystrophy, and α-dystroglycanopathy). The miRNome profiles of skeletal muscle biopsies acquired from four different MD groups and control individuals were analyzed by miRNA microarray. We identified 17 common up-regulated miRNAs in all of the tested MD groups. A specific bioinformatics approach identified 10 of these miRNAs to be specifically related to the mitochondrial pathways. Six miRNAs, miR-134-5p, miR-199a-5p, miR-382-5p, miR-409-3p, miR-497-5p, and miR-708-5p, were associated with the top four mitochondrial pathways and were thus selected as priority candidates for further validation by quantitative real-time PCR analysis. We demonstrate, for the first time, common up-regulated miRNAs that are associated with mitochondrial damage in different MD groups, therefore contributing to the pathophysiology. Our findings may open a new gate toward therapeutics.

The altered expression of perineuronal net elements during neural differentiation.

BACKGROUND: Perineuronal nets (PNNs), which are localized around neurons during development, are specialized forms of neural extracellular matrix with neuroprotective and plasticity-regulating roles. Hyaluronan and proteoglycan link protein 1 (HAPLN1), tenascin-R (TNR) and aggrecan (ACAN) are key elements of PNNs. In diseases characterized by neuritogenesis defects, the expression of these proteins is known to be downregulated, suggesting that PNNs may have a role in neural differentiation. METHODS: In this study, the mRNA and protein levels of HAPLN1, TNR and ACAN were determined and compared at specific time points of neural differentiation. We used PC12 cells as the in vitro model because they reflect this developmental process. RESULTS: On day 7, the HAPLN1 mRNA level showed a 2.9-fold increase compared to the non-differentiated state. However, the cellular HAPLN1 protein level showed a decrease, indicating that the protein may have roles in neural differentiation, and may be secreted during the early period of differentiation. By contrast, TNR mRNA and protein levels remained unchanged, and the amount of cellular ACAN protein showed a 3.7-fold increase at day 7. These results suggest that ACAN may be secreted after day 7, possibly due to its large amount of post-translational modifications. CONCLUSIONS: Our results provide preliminary data on the expression of PNN elements during neural differentiation. Further investigations will be performed on the role of these elements in neurological disease models.

Transcript levels of plastin 3 and neuritin 1 modifier genes in spinal muscular atrophy siblings.

BACKGROUND: In single gene disorders, patients with the same genotype may have variations in severity. One of the main factors affecting disease severity is modifier genes. Spinal muscular atrophy (SMA) is an autosomal recessive neuromuscular disorder caused by degeneration of alpha motor neurons. Plastin 3 (PLS3) is a phenotypic modifier of SMA, and neuritin 1 (NRN1) has also been suggested as a possible modifier gene. The aim of the present study was therefore to analyze PLS3 and NRN1 expression in SMA siblings in four families. METHODS: The study group consisted of four SMA families with seven with discordant phenotype and two affected siblings. Total RNA was isolated from whole blood. PLS3 and NRN1 expression was analyzed on quantitative real-time polymerase chain reaction. RESULTS: In family 1 only NRN1 expression was increased in the mildly affected sister. In family 2 only PLS3 had a modifier effect. Family 3, which had type III siblings with identical clinical phenotypes, had similar PLS3 expression between the siblings but no NRN1 expression. In family 4, neither PLS3 nor NRN1 had any correlation with severity. CONCLUSION: On analysis of the expression of NRN1 in SMA patients for the first time, NRN1 could be a potential modifier gene. PLS3 expression does not always modify SMA phenotype. In patients with no modifier effect of known genes, genome sequencing and transcriptome analysis are promising for the identification of novel modifiers and understanding of SMA pathophysiology.

Effects of flavonoid quercetin on survival of motor neuron gene expression.

Spinal muscular atrophy (SMA) is a progressive neurodegenerative disease that results in muscle weakness and atrophy. To attenuate disease severity, drug development studies have been applied mainly to target the Survival of Motor Neuron 2 (SMN2) gene, which is an important modifier of SMA. Although several compounds have been tested, there is still no cure for SMA. In this study, SMN2-inducing effects of quercetin, an abundant flavonoid polyphenol in human diet, was investigated in the fibroblast cell lines of two SMA type I patients. Gene expression studies showed that quercetin upregulates SMN2 mRNA up to fourfold, but not the SMN protein level.

Cystic fibrosis newborn screening: Five-year experience from a tertiary care center.

BACKGROUND: Newborn screening (NBS) for cystic fibrosis (CF) was implemented in our country on January 1, 2015, based on immunoreactive trypsinogen tests (IRT/IRT). Here, we aimed to evaluate the diagnoses of patients and follow-up process within the first 5 years of NBS from a tertiary care center. METHODS: This retrospective cohort study was conducted on patients who were admitted to our pediatric pulmonology department for sweat test (ST) via NBS. Patients with CF with negative NBS results and those with CF with positive NBS and joined our follow-up were also investigated. Clinical outcome measures were compared between patients with CF with positive and negative NBS. RESULTS: Six hundred sixty infants who were referred for ST via NBS were included. Across the entire study population (n = 683), 11.4% of patients had CF (14.1% of had negative NBS in this CF group). The sensitivity of NBS was found as 84.9% and the positive predictive value (PPV) was 9.4%. The median age at diagnosis was older (p < 0.001), reluctance for feeding and Pseudobartter syndrome (PBS) were significantly higher at presentation in the negative NBS group. There was no statistically significant difference between the groups regarding weight-for-age (p = 0.899) and height-for-age (p = 0.491) in the first 2 years' follow-ups. CONCLUSIONS: Our findings showed the low sensitivity and PPV of NBS; therefore, further studies based on all patients in our country are necessary for new cut-off values. PBS and reluctance for feeding should be alarm symptoms for CF even if the infants had negative NBS. Additionally, later diagnosis of patients who had negative NBS did not affect the nutritional outcomes; we need large-scale prospective studies to optimize nutritional benefits for all infants diagnosed via NBS.

Differentially expressed genes associated with disease severity in siblings with cystic fibrosis.

Cystic fibrosis (CF) is an autosomal recessive disease caused by CFTR gene mutations. Despite having the same mutation, CF patients may demonstrate clinical variability in severity and prognosis of the disease. In this study, we aimed to determine differentially expressed genes between mild and severe siblings with same genotype. We performed targeted real-time polymerase chain reaction based transcriptomic analysis of nasal epithelial cells obtained from two families with two siblings with Class II mutations (F508del/F508del) and (F508del/G85E), one family with three siblings with Class IV mutation (I1234V/I1234V). In severe siblings with Class II mutations, TNFRSF11A, KCNE1, STX1A, SLC9A3R2 were found to be up regulated. CXCL1, CFTR, CXCL2 were found to be down regulated. In the severe sibling with Class IV mutation; mainly genes responsible from complement and coagulation system were identified. Comparison of CF patients to non-CF control; showed that ICAM1 was up regulated whereas EZR, TNFRSF1A, HSPA1A were down regulated in patients. As a result of this study, differentially expressed genes responsible for clinical severity among affected siblings carrying the same mutation were identified. The results will provide an opportunity for the development of novel target molecules for treatment of disease.

The relationship between vitamin D receptor gene polymorphisms and bone density, osteocalcin level and growth in adolescents.

BACKGROUND/OBJECTIVE: The relationship between vitamin D receptor gene polymorphisms and bone density, osteocalcin and growth was investigated. SUBJECTS: Eighty eight adolescents aged between 8-15, with no history of illness influencing the level of bone parameters, were examined in our study. METHODS: Areal BMD for lumbar spine (L1-4) was assessed by dual energy X-ray absorptiometry (DEXA). Height and weight were measured on the day of the DEXA scans. Serum osteocalcin level was determined by using ELISA method. DNA was extracted from white blood cells, amplified by the polymerase chain reaction (PCR) and the polymorphic sites were analyzed by using ApaI, TaqI and FokI restriction enzymes. RESULTS: The most frequent genotypes were FF (% 54.6), Aa (% 53.4) and Tt (% 48.8). No significant relationship was found between VDR genotypes and areal BMD, osteocalcin level or growth in either sex. But there was a strong tendency for a higher BMD at the lumbar spine of TT and AA genotypes compared to tt and Aa genotypes. The children with TT genotype were taller and heavier than the children with tt genotype CONCLUSION: Our results suggest that VDR gene TaqI polymorphism may be associated with body weight and bone mass, but more studies with larger groups should be conducted.

Mutations of the CFTR gene and novel variants in Turkish patients with cystic fibrosis: 24-years experience.

BACKGROUND: Cystic fibrosis, the most prevalent autosomal recessive genetic disease, is caused by mutations in the CFTR gene. The spectrum and frequency of CFTR mutations in Turkish patients show heterogeneity. METHODS: We investigated CFTR gene mutations in samples from 604 cystic fibrosis patients diagnosed at Hacettepe University, the largest referral CF center in Turkey, by different techniques such as strip assay and direct sequencing. We also analyzed the effects of novel variants and predicted pathogenicity by integrating information from different insilico tools. RESULTS: We showed that mutation detection rate increased to 76.7% with direct sequencing of the coding region and exon/intron boundaries. Ten variants were described for the first time. All variants except T788R were reported as pathogenic. CONCLUSION: Characterization of patients with CFTR mutations that occur at very low frequencies is necessary for mutation-based treatments. Population specific genetic screening panels should be designed since none of them are suitable for Turkish patients due to heterogeneous mutation distribution. The preliminary data obtained from in silico results of novel variants will pave the way for functional analysis by using samples obtained from patients. These observations will facilitate the discovery and development of new targeted and personalized therapies.

Molecular modifications on carboxylic acid derivatives as potent histone deacetylase inhibitors: Activity and docking studies.

In the light of known HDAC inhibitors, 33 carboxylic acid derivatives were tested to understand the structural requirements for HDAC inhibition activity. Several modifications were applied to develop the structure-activity relationships of carboxylic acid HDAC inhibitors. HDAC inhibition activities were investigated in vitro by using HeLa nuclear extract in a fluorimetric assay. Molecular docking was also carried out for the human HDAC8 enzyme in order to predict inhibition activity and the 3D poses of inhibitor-enzyme complexes. Of these compounds, caffeic acid derivatives such as chlorogenic acid and curcumin were found to be highly potent compared to sodium butyrate, which is a well-known HDAC inhibitor.

A preliminary report on spinal muscular atrophy lymphoblastoid cell lines: are they an appropriate tool for drug screening?

INTRODUCTION: Spinal muscular atrophy (SMA) is a neurodegenerative disease of the motor neurons that results in progressive muscle weakness. It is also the leading hereditary cause of infant mortality. Homozygous loss of the survival motor neuron (SMN1) gene causes SMA, and the number of copies of the SMN2 gene modulates the severity of the disease. Increasing the expression of the SMN2 gene by pharmacological agents is one of the therapeutic approaches currently being implemented. METHODS: In this preliminary study, we investigated the effect of phenylbutyrate, a histone deacetylase (HDAC) inhibitor, on SMN2 expression in two SMA type III Epstein-Barr virus (EBV)-transformed lymphoblastoid cell lines to understand the suitability of lymphoblastoid cell lines in drug screening. These cell lines are regarded as a good source as they can easily be established from the peripheral leucocytes of patients. Quantitative analysis of SMN2 mRNA was performed on established cell lines treated with various concentrations of phenylbutyrate and for a range of incubation periods using real-time polymerase chain reaction. Western blot analysis was used to determine SMN protein levels. RESULTS: Real-time polymerase chain reaction and Western blot analysis demonstrated that the levels of SMN2 full-length (fl-SMN2) transcripts and protein were not increased in phenylbutyrate-treated cell lines compared to non-treated controls. CONCLUSION: These results suggest that EBV-transformed lymphoblastoid cell lines are not suitable for studying the effect of certain HDAC inhibitors on SMN2 gene expression.

Vitamin D receptor gene polymorphisms in Turkish children with vitamin D deficient rickets.

Vitamin D deficient rickets is prevalent in Turkey and a considerable number of children are at risk of growth retardation, impaired bone formation and fracture. In order to check whether vitamin D receptor (VDR) gene polymorphism relates to the vitamin D deficient rickets, we analyzed VDR gene FokI, TaqI and ApaI polymorphisms in 24 Turkish vitamin D deficient rickets patients and 100 healthy controls. We found that "A" (ApaI) allele is more abundant in patients than controls (83 vs 57%, p = 0.002) but there were no significant differences for FokI (p = 0.693) and TaqI (p = 0.804) allele frequencies between patients and controls. We also showed that the frequency of Tt and Aa genotypes was significantly decreased in patients. Our results indicated that VDR gene polymorphisms might be an important factor for genetic susceptibility to vitamin D deficient rickets in the Turkish population.

Do Perineuronal Net Elements Contribute to Pathophysiology of Spinal Muscular Atrophy? In Vitro and Transcriptomics Insights.

Spinal muscular atrophy (SMA) is one of the most common childhood onset neurodegenerative disorders in global health whereby novel biomarkers and therapeutic targets are sorely needed. SMA is an autosomal recessive genetic disorder resulting in degeneration of α-motor neurons in the brain stem and spinal cord that leads to mortality in infants worldwide. In majority of the patients, SMA is caused by homozygous deletion of the SMN1 gene. The clinical spectrum of the SMA displays, however, large person-to-person variations where the underlying mechanisms are poorly understood. We report in this study transcriptomics insights gleaned from patients with the severe type I (GM03813 and GM09677) and the mild type III. Pathway enrichment and functional analysis showed that especially extracellular matrix (ECM), synapse organization, and ECM receptor interaction pathways were affected. Among the neural ECM components, hyaluronan and proteoglycan link protein (HAPLN1), which is a key triggering molecule of the perineuronal net (PNN), was significantly downregulated in type I fibroblasts compared to type III. PNN is a specialized form of neural ECM around the neuronal cell bodies and dendrites in the central nervous system. In addition, we evaluated the PNN expression in vitro in a model established by SMN silencing in the PC12 rat pheochromocytoma cell line which can be differentiated into neurons with nerve growth factor treatment. In this neuronal in vitro model, we found that HAPLN1 showed a significant 50% decrease. Our results describe the association between PNN elements, especially HAPLN1, and SMA pathophysiology for the first time. These observations collectively inform future translational research on SMA for discovery of novel molecular targets for diagnostics and precision medicine innovation.

Establishment of primary myoblast cell cultures from cryopreserved skeletal muscle biopsies to serve as a tool in related research & development studies.

BACKGROUND: Primary myoblast cell cultures display the phenotypic characteristics and genetic defects of the donor tissue and represent an in vitro model system reflecting the disease pathology. They have been generated only from freshly harvested tissue biopsies. Here, we describe a novel technique to establish myoblast cell cultures from cryopreserved skeletal muscle biopsy tissues that are useful for diagnostic and research purposes. METHODS AND RESULTS: This protocol was performed on seven gradually frozen muscle biopsy specimens from various neuromuscular disorders that were stored in dimethylsulfoxide (DMSO)-supplemented freezing media at -80 °C for up to one year. After storage for varying periods of time, primary myoblast cultures were successfully established from all cryopreserved biopsy tissues without any chromosomal abnormality. Desmin immunoreactivity confirmed that the cell cultures contained >90% pure myoblasts. The myoblasts differentiated into multinucleated myotubes successfully. Furthermore, there were no statistically significant differences in cell viability, metabolic activity, population doubling time, and myocyte enhancer factor 2 (MEF2C) expression between cell cultures established from freshly harvested and one year-stored frozen tissue specimens. CONCLUSIONS: This protocol opens up new horizons for basic research and the pre-clinical studies of novel therapies by using cryopreserved skeletal muscle biopsies stored under suitable conditions in tissue banks.

Polymorphisms of vitamin D receptor gene in Turkish familial psoriasis patients.

Psoriasis is characterized by hyperproliferation and abnormal differentiation of keratinocytes, and inflammation. 1,25-Dihydroxyvitamin D3, which is used for the treatment of psoriasis, binds to vitamin D receptor (VDR) and modulates gene transcription. We analyzed VDR gene FokI, ApaI and TaqI polymorphisms in 51 Turkish familial psoriasis patients (psoriasis vulgaris and psoriatic arthritis) and 100 healthy subjects, and evaluated the correlation between VDR genotypes and calcipotriol response. We found that the TT genotype was significantly more frequent in the patients than in the controls (51 vs. 35%: P < or = 0.05). The frequency of the T allele in patients was also significantly higher than that in the controls (73.5 vs. 59.5%: P < or = 0.025). In psoriatic arthritis patients, T allele frequency was even higher (91.7%: P < or = 0.05). With regard to response to calcipotriol treatment, in nonresponsive patients TT genotype and T allele frequencies were higher than they were in the controls (63.6 vs. 35%: P < or = 0.025, 81.8 vs. 59.5%: P < or = 0.01, respectively). In conclusion, we show that VDR gene TaqI polymorphism is associated with familial psoriasis in the Turkish population. We also demonstrate that VDR gene polymorphisms may play a role in partial resistance to calcipotriol therapy.

Effects of Exercise on Low Density Lipoprotein Receptor Related Protein 5 Gene Expression in Patients With Postmenopausal Osteoporosis.

OBJECTIVES: This study aims to investigate the effects of aerobic exercise on low density lipoprotein receptor related protein 5 (LRP5) gene messenger ribonucleic acid expression and evaluate the relationship between the clinical parameters and gene expression in patients with postmenopausal osteoporosis (OP). PATIENTS AND METHODS: Seven patients with postmenopausal OP (mean age 60.0±5.3 years; range 51 to 66 years) were included in the study. An exercise protocol/program consisting of treadmill exercising for 30 minutes three days a week for six weeks was performed at a moderate intensity. LRP5 gene expression levels were evaluated before the onset of the exercise program and then four hours after the end of the first session and 12th (fourth week) and 18th (sixth week) sessions of exercise. RESULTS: Our results demonstrated variable changes in the LRP5 gene expression after the aerobic exercise sessions. Excluding one patient, the LRP5 gene expression levels showed a slight tendency to increase. In spite of this tendency, gene expression differences during the exercise sessions were not significant. CONCLUSION: Our results suggest that interindividual variations of LRP5 gene expression exist after moderate intensity aerobic exercises in patients with postmenopausal OP. Despite of this variability, LRP5 gene expression levels increased slightly, except in peripheral blood in one patient. Future studies with larger sample sizes and different sampling time/tissues are required to shed more light on the impact of exercise at molecular level in OP.

Carboxylic acid derivatives of histone deacetylase inhibitors induce full length SMN2 transcripts: a promising target for spinal muscular atrophy therapeutics.

INTRODUCTION: Proximal spinal muscular atrophy (SMA) is a common autosomal recessively inherited neuromuscular disorder. It is caused by homozygous absence of the survival motor neuron 1 (SMN1) gene. SMN2, which modulates the severity of the disease, represents a major target for therapy. The aim of this study was to investigate whether SMN2 expression can be increased by caffeic acid, chlorogenic acid and curcumin, which are designed by modifications of the carboxylic acid class of histone deacetylase (HDAC) inhibitors. MATERIAL AND METHODS: Using quantitative real-time PCR, we analysed the levels of full-length SMN2 and Δ7SMN2 mRNA. We performed LDH cytotoxicity assay to analyse whether SMN2 activating concentrations of caffeic acid, chlorogenic acid and curcumin were cytotoxic to fibroblasts. RESULTS: We found that caffeic acid and curcumin were more efficient than chlorogenic acid and increased full-length SMN2 mRNA levels 1.5 and 1.7-fold, respectively. Δ7SMN2 mRNA levels were measured to investigate alternative splicing of exon 7. We also found that cytotoxicity was not observed at SMN2 activating concentrations. CONCLUSIONS: Our data suggest that carboxylic acid derivatives including phenolic structure and symmetry could be a good candidate for SMA treatment.

Evaluation of the effects of vitamin D receptor and estrogen receptor 1 gene polymorphisms on bone mineral density in postmenopausal women.

The aim of this study is to evaluate the effects of estrogen receptor 1 (ESR1) and vitamin D receptor (VDR) gene polymorphisms on bone mineral density (BMD) in a group of previously untreated osteoporotic women. Effects of demographic, environmental, and hormonal factors were also evaluated in this context. Fifty women who did not have a prior diagnosis or treatment of osteoporosis were compared with 50 nonosteoporotic postmenopausal women. Demographic and morphometric characteristics, medical history, dietary habits, exercise history, and sunlight exposure were recorded. The diagnosis of osteoporosis was made with regard to BMD measurements with DEXA. Blood samples were obtained for serum biochemistry, bone turnover markers, and VDR and ESR1 gene polymorphism analysis. Polymorphic sites of VDR and ESR1 genes were amplified by polymerase chain reaction and examined using restriction fragment length polymorphism. Bb genotype was significantly higher in the osteoporotic group when compared to controls (p=0.022). Each 1 U decrease in the body mass index (BMI) increased the risk of osteoporosis by 8% independent of the genotype. We could not observe a significant effect of ESR1 polymorphism on BMD or osteoporosis risk. The interaction of ApaI and BsmI genotypes were found to be significant (p=0.041) and the AaBb genotype, when corrected for BMI, was shown to increase the risk of osteoporosis five times (p=0.005). However, the results demonstrated insignificant p values when correction for multiple testing was performed with the Bonferroni method in the logistic regression model. A predominance of Bb genotype of the VDR gene was evident in this group of postmenopausal Turkish women. Moreover, the combined genotype AaBb conferred a five times increased risk for osteoporosis when corrected for clinical variables.

Histone deacetylase inhibition activity and molecular docking of (e )-resveratrol: its therapeutic potential in spinal muscular atrophy.

Spinal muscular atrophy is an autosomal recessive motor neuron disease that is caused by mutation of the survival motor neuron gene (SMN1) but all patients retain a nearly identical copy, SMN2. The disease severity correlates inversely with increased SMN2 copy. Currently, the most promising therapeutic strategy for spinal muscular atrophy is induction of SMN2 gene expression by histone deacetylase inhibitors. Polyphenols are known for protection against oxidative stress and degenerative diseases. Among our candidate prodrug library, we found that (E )-resveratrol, which is one of the polyphenolic compounds, inhibited histone deacetylase activity in a concentration-dependent manner and half-maximum inhibition was observed at 650 microM. Molecular docking studies showed that (E )-resveratrol had more favorable free energy of binding (-9.09 kcal/mol) and inhibition constant values (0.219 microM) than known inhibitors. To evaluate the effect of (E )-resveratrol on SMN2 expression, spinal muscular atrophy type I fibroblast cell lines was treated with (E )-resveratrol. The level of full-length SMN2 mRNA and protein showed 1.2- to 1.3-fold increase after treatment with 100 microM (E )-resveratrol in only one cell line. These results indicate that response to (E )-resveratrol treatment is variable among cell lines. This data demonstrate a novel activity of (E )-resveratrol and that it could be a promising candidate for the treatment of spinal muscular atrophy.