Identification of lncRNAs Associated With Neuroblastoma in Cross-Sectional Databases: Potential Biomarkers.

Long non-coding RNAs (lncRNAs) have emerged as an important regulatory control in biological systems. Though the field of lncRNA has been progressing rapidly, a complete understanding of the role of lncRNAs in neuroblastoma pathogenesis is still lacking. To identify the abrogated lncRNAs in primary neuroblastoma and in the metastasized as well as the relapsed form of neuroblastoma, we analyzed an RNA-seq dataset on neuroblastoma that is available online to identify the lncRNAs that could potentially be contributing to the biology of neuroblastoma. The identified lncRNAs were further scrutinized using a publicly available epigenetic dataset of neuroblastoma and a cancer database. After this cross-sectional study, we were able to identify three significant lncRNAs, CASC15, PPP1R26-AS1, and USP3-AS1, which could serve as potential biomarkers in clinical studies of neuroblastoma pathogenesis.

Altered platelet monoamine oxidase-B activity in idiopathic Parkinson's disease.

A case-control study was undertaken to investigate the status of platelet monoamine oxidase-B (MAO-B) activity in Indian cases of idiopathic Parkinson's disease. A significant increase in the activity of platelet MAO-B was observed in Parkinson's cases (n = 26) as compared to controls (n = 26). No significant change in the activity of the enzyme was observed while the data was analysed with respect to age, sex and duration of disease. A trend of decrease in platelet MAO-B activity was observed in Parkinson's cases with respect to stage although the change was not significant. No correlation in platelet MAO-B activity was observed with respect to age and sex in the control subjects. Parkinson's cases treated with L-DOPA and MAO-B inhibitor exhibited decreased platelet MAO-B activity as compared to drug naive cases and those treated with L-DOPA alone. Interestingly, Parkinson's cases treated with L-DOPA and amantadine also had lower platelet MAO-B activity as compared to drug naive cases and those treated with L-DOPA alone. Activity of platelet MAO-B in Parkinson's patients was increased in naive cases and those treated with L-DOPA alone or in combination with other drugs compared to controls. The results of the present study indicate that phenotypic activity of platelet MAO-B is high in Indian Parkinson's cases. Further, action mechanism of drugs used in the treatment of Parkinson's disease could be understood by assay of platelet MAO-B activity. It is an interesting observation and may be looked further in large number of cases.

Differences in the expression and inducibility of cytochrome P450 2B isoenzymes in cultured rat brain neuronal and glial cells.

Studies initiated to investigate the distribution of cytochrome P450 2B (CYP2B) isoenzymes in rat brain cells revealed significant activity of CYP2B-dependent 7-pentoxyresorufin-O-dealkylase (PROD) in microsomes prepared from both, cultured rat brain neuronal and glial cells. Neuronal cells exhibited 2-fold higher activity of PROD than the glial cells. RT-PCR and immunocytochemical studies demonstrated significant constitutive mRNA and protein expression of CYP2B in cultured neuronal and glial cells. Induction studies with phenobarbital (PB), a known CYP2B inducer, revealed significant concentration dependent increase in the activity of PROD in cultured brain cells with glial cells exhibiting greater magnitude of induction than the neuronal cells. This difference in the increase in enzyme activity was also observed with RT-PCR and immunocytochemical studies indicating differences in the induction of CYP2B1 and 2B2 mRNA as well as protein expression in the cultured brain cells. Furthermore, a greater magnitude of induction was observed in CYP2B2 than CYP2B1 in the brain cells. Our data indicating differences in the expression and sensitivity of the CYP2B isoenzymes in cultured rat brain cells will help in identifying and distinguishing xenobiotic metabolizing capability of these cells and understanding the vulnerability of the specific cell types toward neurotoxins.

Cytochrome P450 1A isoenzymes in brain cells: Expression and inducibility in cultured rat brain neuronal and glial cells.

Studies initiated to determine the expression of CYP1A1/1A2 isoenzymes in the primary cultures of rat brain neuronal and glial cells revealed significant activity of CYP1A-dependent 7-ethoxyresorufin-o-dealkylase (EROD) in microsomes prepared from both rat brain neuronal and glial cells. RT-PCR and immunocytochemical studies demonstrated constitutive mRNA and protein expression of CYP1A1 and 1A2 isoenzymes in cultured neuronal and glial cells. Cultured neurons exhibited relatively higher constitutive mRNA and protein expression of CYP1A1 and 1A2 isoenzymes, associated with higher activity of EROD than the glial cells. Induction studies with 3-methylchlorantherene (MC), a known CYP1A-inducer, resulted in significant concentration dependent increase in the activity of EROD in cultured rat brain cells with glial cells exhibiting a greater magnitude of induction than the neuronal cells. This difference in the increase in enzyme activity was also observed with RT-PCR and immunocytochemical studies, indicating relatively higher increase in CYP1A1 and 1A2 mRNA as well as protein expression in the cultured glial cells when compared to the neuronal cells. The greater magnitude of induction of CYP1A1 in glial cells is of significance, as these cells are components of the blood-brain barrier and it is suggested that they have a potential role in the toxication-detoxication mechanism. Our data indicating differences in the expression and sensitivity of CYP1A1 isoenzymes in cultured rat brain cells will not only help in identifying and distinguishing xenobiotic metabolizing capability of these cells but also in understanding the vulnerability of these specific cell types towards neurotoxicants.

Regional specificity in deltamethrin induced cytochrome P450 expression in rat brain.

Oral administration of deltamethrin (5 mg/kg x7 or 15 or 21 days) was found to produce a time-dependent increase in the mRNA expression of xenobiotic metabolizing cytochrome P450 1A1 (CYP1A1), 1A2 and CYP2B1, 2B2 isoenzymes in rat brain. RT-PCR studies further showed that increase in the mRNA expression of these CYP isoenzymes observed after 21 days of exposure was region specific. Hippocampus exhibited maximum increase in the mRNA expression of CYP1A1, which was followed by pons-medulla, cerebellum and hypothalamus. The mRNA expression of CYP2B1 also exhibited maximum increase in the hypothalamus and hippocampus followed by almost similar increase in midbrain and cerebellum. In contrast, mRNA expression of CYP1A2 and CYP2B2, the constitutive isoenzymes exhibited relatively higher increase in pons-medulla, cerebellum and frontal cortex. Immunoblotting studies carried out with polyclonal antibody raised against rat liver CYP1A1/1A2 or CYP2B1/2B2 isoenzymes also showed increase in immunoreactivity comigrating with CYP1A1/1A2 or 2B1/2B2 in the microsomal fractions isolated from hippocampus, hypothalamus and cerebellum of rat treated with deltamethrin. Though the exact relationship of the xenobiotic metabolizing CYPs with the physiological function of the brain is yet to be clearly understood, the increase in the mRNA expression of the CYPs in the brain regions that regulate specific brain functions affected by deltamethrin have further indicated that modulation of these CYPs could be associated with the various endogenous functions of the brain.

Evidence for cytochrome P450 3A expression and catalytic activity in rat blood lymphocytes.

Freshly isolated peripheral blood lymphocytes from control rats were found to catalyze the N-demethylation of erythromycin, known to be mediated by cytochrome P450 3A (CYP3A) isoenzymes in rat liver. Pretreatment of rats with dexamethasone (100 mg/kgx3 days, i.p.), a CYP3A inducer, resulted in 3-4-fold increase in the activity of erythromycin demethylase (EMD) in freshly isolated peripheral blood lymphocytes. This increase in the enzyme activity was found to be associated with an increase in the rate of the reaction and affinity of the substrate towards the enzyme. Significant inhibition of the EMD activity on in vitro addition of ketoconazole, a specific CYP3A inhibitor in liver and polyclonal antibody raised against rat liver CYP3A have suggested that EMD activity in blood lymphocytes is catalyzed primarily by CYP3A isoenzymes. Further, immunoblot analysis with polyclonal antibody raised against rat liver CYP3A revealed significant immunoreactivity, co-migrating with the liver isoenzyme, indicating constitutive expression of CYP3A in blood lymphocytes. Pretreatment with dexamethasone was found to significantly increase the expression of CYP3A protein in freshly isolated rat blood lymphocytes, as observed with liver. Likewise, significant CYP3A mRNA detected in control rat blood lymphocytes has further demonstrated constitutive expression of CYP3A isoenzymes in blood lymphocytes. Furthermore, several fold increase in CYP3A mRNA expression following pretreatment with dexamethasone showed similarities in the regulation of CYP3A isoenzymes in rat blood lymphocytes with the liver enzyme. The data suggest that the blood lymphocytes can be used to monitor tissue expression of CYP3A isoenzymes and validate the suitability of lymphocytes as surrogates of CYP status in less accessible target tissues.

Differences in sensitivity of cultured rat brain neuronal and glial cytochrome P450 2E1 to ethanol.

The expression of the cytochrome P450s (CYPs) may vary in the different brain cells depending on their specialization and the presence of different endogenous factors. The present study was initiated to investigate the expression and catalytic activity of the constitutive and inducible forms of CYP2E1, the major ethanol inducible CYP, in cultured rat brain neuronal and glial cells. These cells exhibited relatively two-fold higher activity of N-nitrosodimethylamine demethylase (NDMA-d) when compared with the liver enzyme. Pretreatment with ethanol revealed a significant time and concentration dependent induction in NDMA-d activity in both cell types. Western blot, immunocytochemistry and RT-PCR also indicated significant induction of CYP2E1 in the cultured brain cells. Interestingly, the neuronal cells exhibited greater magnitude of induction than the glial cells. The relatively higher degree of induction in cultures of neurons has indicated enhanced sensitivity of neurons to the inductive effects of ethanol. This enhanced induction of CYP2E1 in neuronal cells has indicated that like regional specificity, cell specificity also exists in the induction of CYP2E1 and other CYPs.

Expression of constitutive and inducible cytochrome P450 2E1 in rat brain.

Studies initiated to investigate the expression of cytochrome P450 2E1 (CYP2E1) in rat brain demonstrated low but detectable protein and mRNA expression in control rat brain. Though mRNA and protein expression of CYP2E1 in brain was several fold lower as compared to liver, relatively high activity of N-nitrosodimethylamine demethylase (NDMA-d) was observed in control rat brain microsomes. Like liver, pretreatment with CYP2E1 inducers such as ethanol or pyrazole or acetone significantly increased the activity of brain microsomal NDMA-d. Kinetic studies also showed an increase in the Vmax and affinity (Km) of the substrate towards the brain enzyme due to increased expression of CYP2E1 in microsomes of brain isolated from ethanol pretreated rats. In vitro studies using organic inhibitors, specific for CYP2E1 and anti-CYP2E1 significantly inhibited the brain NDMA-d activity indicating that like liver, NDMA-d activity in rat brain is catalyzed by CYP2E1. Olfactory lobes exhibited the highest CYP2E1 expression and catalytic activity in control rats. Furthermore, several fold increase in the mRNA expression and activity of CYP2E1 in cerebellum and hippocampus while a relatively small increase in the olfactory lobes and no significant change in other brain regions following ethanol pretreatment have indicated that CYP2E1 induction maybe involved in selective sensitivity of these brain areas to ethanol induced free radical damage and neuronal degeneration.

Cytochrome P4503A: evidence for mRNA expression and catalytic activity in rat brain.

Studies initiated to investigate the presence of cytochrome P4503A (CYP3A) isoenzymes in brain revealed constitutive mRNA and protein expression of CYP3A1 in rat brain. Western blotting studies showed that pretreatment with CYP3A inducer such as pregnenolone-16alpha -carbonitrile (PCN) significantly increased the cross reactivity comigrating with hepatic CYP3A1 and CYP3A2 in rat brain microsomes. RT-PCR studies have also shown increase in mRNA expression of CYP3A1 following pretreatment of rats with PCN. The ability of rat brain microsomes to catalyze the demethylation of erythromycin, known to be mediated by CYP3A isoenzymes in liver and significant increase in the activity of erythromycin demethylase (EMD) following pretreatment with dexamethasone or PCN have indicated that CYP3A isoenzymes expressed in brain are functionally active. Kinetic studies revealed that increase in the enzyme activity following pretreatment with PCN resulted in increase in the apparent affinity (Km) and Vmax of the reaction. Similarities in the inhibition of the constitutive and inducible brain and liver EMD activity following in vitro addition of ketoconazole, a inhibitor specific for CYP3A catalysed reactions and anti-CYP3A have further indicated that like in liver, CYP3A isoenzymes catalyse the activity of EMD in rat brain. Data also revealed regional differences in the activity of EMD in the brain. Relatively higher constitutive as well as inducible mRNA expression of CYP3A1 in hypothalamus and hippocampus, the brain regions responsive to steroid hormones have suggested that CYP3A isoenzymes may not only be involved in the process of detoxication mechanism but also in the metabolism of endogenous substrates in brain.

Decreased platelet membrane fluidity in retinal periphlebitis in Eales' disease.

PURPOSE: Oxidative damage to cellular membranes plays an important role in the pathobiology of tissue injury. Free radical-induced peroxidation of membrane lipid and protein is associated with alterations in cellular, morphological, biochemical, and physical dynamics, which are related to the mobility of lipid molecules. Retinal photoreceptors and platelets have been shown to be an easy target of oxidants because of their high proportion of polyunsaturated fatty acids. This study was undertaken, for the first time, to investigate membrane fluidity in the platelets of patients with Eales' disease. METHODS: Assays of malonaldialdehyde levels and the enzymes superoxide dismutase and catalase and fluorescence polarization, for estimating membrane fluidity, were carried out on platelets from 20 patients with Eales' disease (stage 1 characterized by periphlebitis of small (1a) and large (1b) caliber vessels with superficial retinal hemorrhages) and 15 healthy controls. RESULTS: A significant increase was observed in the malonaldialdehyde levels. A significant decrease in the activity of superoxide dismutase and catalase was also observed. Platelet fluorescence polarization was significantly higher in the patients, indicating decreased membrane fluidity compared to controls (p<0.01). CONCLUSION: A decrease in platelet membrane fluidity occurs as a result of oxidative stress in retinal periphlebitis in Eales' disease. The decreased membrane fluidity suggests alterations in the physiological events, which may result in alterations in the functioning of retinal photoreceptors.

DNA damage in lymphocytes of Indian rickshaw pullers as measured by the alkaline Comet assay.

Rickshaw pullers (RPs) engage in strenuous physical activity and are exposed to the air pollutants found in urban environments. Air pollutants and the reactive oxygen species generated by the physical activity both potentially can damage DNA. In the present study, the Comet assay, a sensitive tool for measuring DNA damage in single cells, was used to study genomic DNA damage in lymphocytes of Indian RPs. The study evaluated DNA damage in 118 healthy male volunteers, including 63 RPs whose work demanded high levels of physical activity for 7-9 hr/day, and 55 controls matched for age, habits, socio-economic status, and exposure to air pollution. A significant increase was found for the mean Olive tail moment (arbitrary units) among the RPs (4.13 +/- 0.11; P < 0.001) in comparison with the controls (3.21 +/- 0.10). Likewise, comet tail length (microm) (RPs: 58.98 +/- 1.01 vs. controls: 52.38 +/- 1.24) and tail DNA (%) (RPs: 13.52 +/- 0.31 vs. controls: 10.04 +/- 0.24) were also significantly higher for RPs compared with those of their matched controls (both, P < 0.001). To our knowledge, this is the first demonstration that physical activity due to occupation can produce DNA damage in peripheral lymphocytes.

DNA damage in lymphocytes of rural Indian women exposed to biomass fuel smoke as assessed by the Comet assay.

The Comet assay has found wide acceptance in monitoring human genotoxicity caused by lifestyle and occupational and environmental factors. In the present study, we have used the Comet assay to measure the DNA damage in a population of rural Indian women cooking with biomass fuels (BMFs; fire wood and cow dung cakes). Out of 144 volunteers, 70 used BMFs for domestic cooking, while the remaining 74 used liquefied petroleum gas (LPG) and served as a reference population. All the individuals had comparable socioeconomic backgrounds and were between 20 and 55 years of age. Significantly higher levels of DNA damage were observed for BMF users than for LPG users. For BMF users in comparison with the reference population, Olive tail moment was 3.83 +/- 0.15 (arbitrary units) vs. 2.77 +/- 0.07 (P < 0.001); % tail DNA was 11.19 +/- 0.35 vs. 8.29 +/- 0.20 (P < 0.001); and comet tail length (microm) was 51.15 +/- 1.37 vs. 40.26 +/- 0.88 (P < 0.001). Similar significant differences were found when the groups were stratified by age and length of exposure. This study suggests that exposure to BMF smoke leads to greater levels of DNA damage than exposure to LPG combustion products.

Comet assay responses in human lymphocytes are not influenced by the menstrual cycle: a study in healthy Indian females.

The single-cell gel electrophoresis or Comet assay measures qualitative and quantitative DNA damage in single cells. Its simplicity and non-invasive nature has made it widely accepted for the monitoring of human genotoxicity, employing peripheral blood lymphocytes. Factors, such as gender, age, and dietary and smoking habits are known to affect the Comet assay responses in lymphocytes. However, there is no information regarding the influence of the menstrual cycle on the results of the assay in lymphocytes of females. A study was therefore undertaken among 18 healthy Indian female volunteers to assess the effect of the menstrual cycle on Comet assay responses. During a complete menstrual cycle, only minor changes were observed in the basal levels of DNA damage in the lymphocytes as evident by Comet parameters, such as tail length (microm), tail DNA (%) and Olive tail moment (arbitrary units). To assess the effect of the estrogen 17beta-estradiol (at physiological concentrations of 0.5, 1.0 and 2.0 nM) on the Comet assay responses, an in vitro study was conducted in the human lymphocyte cell line JM-1 and the breast cancer cell line MCF-7. As was evident from the Comet parameters, a significant (p < 0.01) concentration-dependent increase in the level of DNA damage was observed in the MCF-7 cells while no significant change was found in the JM-1 cells. The results indicate that the menstrual cycle does not influence the Comet assay responses in lymphocytes; hence, these can serve as a model for monitoring genotoxicity in females.

Gender-related differences in basal DNA damage in lymphocytes of a healthy Indian population using the alkaline Comet assay.

The Comet assay, a sensitive, rapid and non-invasive technique, measures DNA damage in individual cells and has found wide acceptance in epidemiological and biomonitoring studies to determine the DNA damage resulting from lifestyle, occupational and environmental exposure. The present study was undertaken to measure the basal level of DNA damage in a normal, healthy Indian male and female population. Out of the 230 volunteers included in this study, 124 were male and 106 were female. All the individuals belonged to a comparable socio-economic background and aged between 20 and 30 years. They were also matched for their smoking and dietary habits. The period of sample collection was also matched. The results revealed a statistically significant higher level of DNA damage in males when compared to females as evident by an increase in the Olive tail moment [3.76+/-1.21 (arbitrary units) for males as compared to 3.37+/-1.47 for females (P<0.05)], tail DNA (%) [10.2+/-2.96 for males as compared to 9.40+/-2.83 for females (P<0.05)] and tail length (microm) [59.65+/-9.23 for males and 49.57+/-14.68 for females (P<0.001)]. To our knowledge, this report has, for the first time demonstrated significant differences in the basal level of DNA damage between males and females in a normal healthy Indian population.