Identification and comparison of m6A modifications in glioblastoma non-coding RNAs with MeRIP-seq and Nanopore dRNA-seq

The most prominent RNA modification - N6-methyladenosine (m6A) - affects gene regulation and cancer progression. The extent and effect of m6A on long non-coding RNAs (lncRNAs) is, however, still not clear. The most established method for m6A detection is methylated RNA immunoprecipitation and sequencing (MeRIP-seq). However, Oxford Nanopore Technologies recently developed direct RNA-seq (dRNA-seq) method, allowing m6A identification at higher resolution and in its native form. We performed whole transcriptome sequencing of the glioblastoma cell line U87-MG with both MeRIP-seq and dRNA-seq. For MeRIP-seq, m6A peaks were identified using nf-core/chipseq, and for dRNA-seq - EpiNano pipeline. MeRIP-seq analysis revealed 5086 lncRNAs transcripts, while dRNA-seq identified 336 lncRNAs transcripts from which 556 and 198 were found to be m6A modified, respectively. While 24 lncRNAs with m6A overlapped between two methods. Gliovis database analysis revealed that the expression of the major part of identified overlapping lncRNAs was associated with glioma grade or patient survival prognosis. We found that the frequency of m6A occurrence in lncRNAs varied more than 9-fold throughout the provided list of 24 modified lncRNAs. The highest m6A frequency was detected in MIR1915HG, THAP9-AS1, MALAT1, NORAD1, and NEAT1 (49-88nt), while MIR99AHG, SNHG3, LOXL1-AS1, ILF3-DT showed the lowest m6A frequency (445-261nt). Taken together, (1) we provide a high accuracy list of 24 m6A modified lncRNAs of U87-MG cells; (2) we conclude that MeRIP-seq is more suitable for an initial m6A screening study, due to its higher lncRNA coverage, whereas dRNA-seq is most useful when more in-depth analysis of m6A quantity and precise location is of interest.Abbreviations: (dRNA-seq) direct RNA-seq, (GBM) glioblastoma, (LGG) low-grade glioma, (lncRNAs) long non-coding RNAs, (m6A) N6-methyladenosine, (MeRIP-seq) methylated RNA immunoprecipitation and sequencing, (ncRNA) non-coding RNA, (ONT) Oxford Nanopore Technologi; Lietuvos Mokslo Taryba.

Effect of Selenium on the Iron Homeostasis and Oxidative Damage in Brain and Liver of Mice

Selenium is an essential trace element that maintains normal brain function, mainly due its antioxidant properties. Although the amount of Se in the body is tightly regulated by the liver, both an excess of and deficiency in Se can modulate the cellular redox status and affect the homeostasis of other essential elements for both humans and animals. The aim of this study was to determine the effect of inorganic selenium excess on oxidative stress and iron homeostasis in brain and liver of laboratory BALB/c mice, which were supplemented with Na₂SeO₃ solution (0.2 mg and 0.4 mg Se/kg body weight) for 8 weeks. The content of the lipid peroxidation product malondialdehyde and antioxidant enzyme catalase activity/gene expression were used as markers of oxidative damage and were evaluated by spectrophotometric assays. Selenium and iron concentrations were determined by inductively coupled plasma mass spectrometry (ICP-MS). Catalase gene expression was analyzed by qRT-PCR and ΔΔCt methods. Our results showed that doses of 0.2 mg Se and 0.4 mg Se caused a relatively low accumulation of Se in the brain of mice; however, it induced a 10-fold increase in its accumulation in the liver and also increased iron accumulation in both tested organs. Both doses of Se increased the content of malondialdehyde as well as decreased catalase activity in the liver, while the 0.4 mg Se dose has also activated catalase gene expression. Brain of mice exposed to 0.2 mg Se showed reduced lipid peroxidation; however, the exposure to 0.4 mg of Se increased the catalase activity as well as gene expression. One may conclude that exposure to both doses of Se caused the accumulation of this micronutrient in mice brain and liver and have also provided a disrupting effect on the levels of iron. Both doses of Se have triggered oxidative liver damage. In the brain, the effect of Se was dose dependent, where −0.2 mg of Se provided antioxidant activity, which was observed through a decrease in lipid peroxidation. On the contrary, the 0.4 mg dose increased brain catalase activity as well as gene expression, which may have contributed to maintaining brain lipid peroxidation at the control level.

Transcriptome-wide analysis of glioma stem cell specific m6A modifications in long-non-coding RNAs

The interest in chemical RNA modifications is rapidly growing in the field of molecular biology. Dynamic and reversible alterations of N6-methyladenosine (m6A) RNA modification are responsible for a platter of structural and functional changes in healthy and cancerous cell states. Although many studies reported the link between tumor initiation/progression and m6A modulators, there are few studies exploring transcriptome-wide m6A profile of non-coding RNAs. The aim of current study was to identify glioma stem cell (GSC) specific m6A landscape of long non-coding RNAs (lncRNAs) applying MeRIP-seq approach. MeRIP-seq analysis assigned 77.9% of m6A peaks to mRNAs and 8.16% to lncRNAs. GSCs and differentiated cells showed 76.4% conservation of m6A peaks, while 19.4% were unique to GSCs. Seven novel GSC-specific m6A modified lncRNAs were identified: HRAT92, SLCO4A1-AS1, CEROX1, PVT1, AGAP2-AS1, MIAT, and novel lncRNA gene ENSG00000262223. Analysis disclosed a strong negative correlation between lncRNAs m6A modification rate and expression. MeRIP-seq analysis revealed m6A modifications on previously reported glioma-associated lncRNAs: LINC000461, HOTTIP, CRNDE, TUG1, and XIST. Moreover, current study disclosed that most highly m6A modified lncRNAs primarily contain m6A modifications close to 3' and 5' ends. Our results provide basis and insight for further studies of m6A modifications in non-coding transcriptome of GSCs.

Effect of fasting on body composition and proteolysis gene expression in skeletal muscles and liver of BEH+/+ and BEL mice

Fasting improves health, but can cause muscle weakness. We assessed body composition in 21-week old males of Berlin high (BEH+/+) and Berlin low (BEL) strains after two bouts of 48-h or 40-h of fasting with 5-day refeeding in between, respectively. BEH+/+ mice tended to loose less weight than BEL in bout 1 and 2 (16.0 ± 2.7 versus 23.5 ± 2.9%, p < 0.001 and 17.1 ± 3.4 versus 20.4 ± 3.4%, p = 0.17, respectively). In spite of greater serum IGF-1 and body fat levels, BEH+/+ mice showed more severe muscle atrophy, but less marked liver wasting and fat depletion than BEL mice. BEH+/+ mice also showed smaller increases in expression of p62, Atrogin-1, and Mstn genes in skeletal muscles. In summary, BEL mice show resistance to fasting-induced muscle wasting in spite of low serum IGF-1 levels and high expression of genes associated with muscle atrophy.

Endurance exercise plus overload induces fatigue resistance and similar hypertrophy in mice irrespective of muscle mass

NEW FINDINGS

What is the central question of this study? Does combining endurance and hypertrophic stimuli blunt the adaptations to both modalities and is this effect greater in muscles with larger baseline fibre cross sectional area? What is the main finding and its importance? Endurance exercise and hypertrophic stimuli can be combined to increase fatigue resistance and fibre size without blunting either adaptation regardless of baseline fibre size.

ABSTRACT

Previous studies have demonstrated that fibre cross-sectional area (FCSA) is inversely related to oxidative capacity, which is thought to be determined by diffusion limitations of oxygen, ADP and ATP. Consequently, it is hypothesised that (1) when endurance training is combined with a hypertrophic stimulus the response to each will be blunted, and (2) muscles with a smaller FCSA will show a larger hypertrophic response than those with a large FCSA. To investigate this, we combined overload with endurance exercise in 12-month-old male mice from three different strains with different FCSA: Berlin High (BEH) (large fibres), C57BL/6J (C57) (normal-sized fibres) and Berlin Low (BEL) (small fibres). The right plantaris muscle was subjected to overload through denervation of synergists with the left muscle acting as an internal control. Half the animals trained 30 min per day for 6 weeks. The overload-induced hypertrophy was not blunted by endurance exercise, and the exercise-induced increase in fatigue resistance was not impaired by overload. All strains demonstrated similar absolute increases in FCSA, although the BEH mice with more fibres than the C57 mice demonstrated the largest increase in muscle mass and BEL mice with fewer fibres the smallest increase in muscle mass. This study suggests that endurance exercise and hypertrophic stimuli can be combined without attenuating adaptations to either modality, and that increases in FCSA are independent of baseline fibre size.

Response to Three Weeks of Sprint Interval Training Cannot Be Explained by the Exertional Level

Background and Objectives: The all-out mode of sprint interval training (SIT) has been shown to be an efficient method for improving sports performance, exercise capacity, and aerobic fitness. Although the benefits of SIT are well described, the mechanisms underlying the different degrees of response remain largely unexplored. We aimed to assess the effects of exertion on the responsiveness to SIT. Materials and Methods: The participants were 28 young untrained men (mean ± SD age 25.7 ± 6.03 years) who exhibited either a large or small increase in Wingate test average power in response to nine SIT sessions performed over three weeks. Each training session comprised four-six bouts of 30 s all-out cycling interspaced with 4 min of rest. Individual responses were assessed using heart rate (HR) during exercise for all nine sessions, as well as blood lactate concentration up to 1 h, and the decrement in maximal voluntary knee extension torque (MVC) up to 24 h after the first and last training sessions. Peak oxygen uptake (VO₂peak) and maximum HR were measured before and after training during an incremental cycling test to exhaustion. Results: Although all participants showed benefits of SIT such as increased VO₂peak, the increase in anaerobic cycling power varied between participants. We identified 17 high responders and nine low responders, whose average power outputs were 0.80 ± 0.22 and 0.22 ± 0.19 W/kg, respectively. The HR achieved during any of the training sessions did not differ between high and low responders. The lactate kinetics did not differ between groups before and after the intervention. Training resulted in a more rapid recovery of MVC without any discernible differences between the high and low responders. Conclusion: The differences in the responses to SIT are not dependent on the exertion level during training.

Acute effects of very low-volume high-intensity interval training on muscular fatigue and serum testosterone level vary according to age and training status

PURPOSE

To compare the acute physiological responses of three different very low-volume cycling sessions (6 × 5 s, 3 × 30 s, and 3 × 60 s) and their dependence on age and training status.

METHODS

Subjects were untrained young men (mean ± SD; age 22.3 ± 4.6 years, VO₂peak 42.4 ± 5.5 ml/kg/min, n = 10), older untrained men (69.9 ± 6.3 years, 26.5 ± 7.6 ml/kg/min, n = 11), and endurance-trained cyclists (26.4 ± 9.4 years, 55.4 ± 6.6 ml/kg/min, n = 10). Maximal voluntary contraction (MVC) and electrically stimulated knee extension torque, and low-frequency fatigue, as ratio of stimulation torques at 20-100 Hz (P20/100), were measured only 24 h after exercise. Serum testosterone (Te) and blood lactate concentrations were measured only 1 h after exercise.

RESULTS

All protocols increased the blood lactate concentration and decreased MVC and P20/100 in young men, but especially young untrained men. In old untrained men, 6 × 5 s decreased P20/100 but not MVC. Te increased after 3 × 30 s and 3 × 60 s in young untrained men and after 3 × 60 s in older untrained men. The increase in Te correlated with responses of blood lactate concentration, MVC, and P20/100 only in old untrained men.

CONCLUSIONS

As little as 6 × 5 s all-out cycling induced fatigue in young and old untrained and endurance-trained cyclists. Slightly higher-volume sessions with longer intervals, however, suppressed contractile function more markedly and also transiently increased serum testosterone concentration in untrained men.

Very Low Volume High-Intensity Interval Exercise Is More Effective in Young Than Old Women

We investigated the acute neuromuscular and stress responses to three different high-intensity interval training sessions in young (age 19.5 ± 1.3 years) and older (age 65.7 ± 2.8 years) women. Cycling exercise comprised either 6 × 5 s or 3 × 30 s all-out, or 3 × 60 s submaximal, efforts each performed 5 weeks apart in randomized order. Peak and average power was higher in young than in older women and was largest during the 6 × 5 s strategy in both groups (p < 0.05). The decrease in the ratio of torques evoked by 20 and 100 Hz electrical stimulation, representing low-frequency fatigue, was more evident after the 3 × 30 and 3 × 60 s than the 6 × 5 s bout in both groups and was larger in young than in older women (p < 0.05). Both groups preferred 6 × 5 s cycling for further training. In conclusion, in young women, very low volume (6 × 5 s) all-out exercise induces significant physiological stress and seems to be an effective means of training. For older women, longer exercise sessions (3 × 60 s) are more stressful than shorter ones but are still tolerable psychologically.