Characterization of the hypothalamic transcriptome in response to food deprivation reveals global changes in long noncoding RNA, and cell cycle response genes

Experimental reporting of fish transcriptomic responses in environmental toxicology and ecotoxicology

Due to its increasing affordability and efforts to understand transcriptional responses of organisms to biotic and abiotic stimuli, transcriptomics has become an important tool with significant impact on toxicological investigations and hazard and risk assessments, especially during development and application of new approach methodologies (NAMs). Data generated using transcriptomic methodologies have directly informed adverse outcome pathway frameworks, chemical and biological read across, and aided in the identification of points of departure. Using data reporting frameworks for transcriptomics data offers improved transparency and reproducibility of research and an opportunity to identify barriers to adoption of these NAMs, especially in environmental toxicology and ecotoxicology with aquatic models. Improved reporting also allows for reexamination of existing data, limiting needs for experiment replication and further reducing animal experimentation. Here, we use a standardized form of data reporting for omics-based studies, the Organisation for Economic Co-operation and Development omics reporting framework, which specifically reports on a list of parameters that should be included in transcriptomics studies used in a regulatory context. We focused specifically on fish studies using RNA- Sequencing (Seq)/microarray technologies within a toxicology context. Inconsistencies in reporting and methodologies among the experimental designs (toxicology vs. molecular characterization) were observed in addition to foundational differences in reporting of sample concentration or preparation or quality assessments, which can affect reproducibility and read across, confidence in results, and contribute substantially to understanding molecular mechanisms of toxicants and toxins. Our findings present an opportunity for improved research reporting. We also provide several recommendations as logical steps to reduce barriers to adoption of transcriptomics within environmental toxicology and ecotoxicology.

Epigenetic regulation is involved in reversal of obesity

Epigenetic processes play a crucial role in mediating the impact of environmental energetic challenges, from overconsumption to starvation. Over-nutrition of energy-dense foods and sedentary lifestyles contribute to the development of obesity, characterized by excessive fat storage and impaired metabolic signaling, stemming from disrupted brain signaling. Conversely, dieting and physical activity facilitate body weight rebalancing and trigger adaptive neural responses. These adaptations involve the upregulation of neurogenesis, synaptic plasticity and optimized brain function and energy homeostasis, balanced hormone signaling, normal metabolism, and reduced inflammation. The transition of the brain from a maladaptive to an adaptive state is partially guided by epigenetic mechanisms. While epigenetic mechanisms underlying obesity-related brain changes have been described, their role in mediating the reversal of maladaptation/obesity through lifestyle interventions remains less explored. This review focuses on elucidating epigenetic mechanisms involved in hypothalamic adaptations induced by lifestyle interventions. Given that lifestyle interventions are widely prescribed and accessible approaches for weight loss and maintenance, it is our challenge to uncover epigenetic mechanisms moderating these hypothalamic-functional beneficial changes.

Molecular profile and response to energy deficit of leptin-receptor neurons in the lateral hypothalamus

Leptin exerts its effects on energy balance by inhibiting food intake and increasing energy expenditure via leptin receptors in the hypothalamus. While LepR neurons in the arcuate nucleus of the hypothalamus, the primary target of leptin, have been extensively studied, LepR neurons in other hypothalamic nuclei remain understudied. LepR neurons in the lateral hypothalamus contribute to leptin's effects on food intake and reward, but due to the low abundance of this population it has been difficult to study their molecular profile and responses to energy deficit. We here explore the transcriptome of LepR neurons in the LH and their response to energy deficit. Male LepR-Cre mice were injected in the LH with an AAV carrying Cre-dependent L10:GFP. Few weeks later the hypothalami from fed and food-restricted (24-h) mice were dissected and the TRAP protocol was performed, for the isolation of translating mRNAs from LepR cells in the LH, followed by RNA sequencing. After mapping and normalization, differential expression analysis was performed with DESeq2. We confirm that the isolated mRNA is enriched in LepR transcripts and other known neuropeptide markers of LepR^LH neurons, of which we investigate the localization patterns in the LH. We identified novel markers of LepR^LH neurons with association to energy balance and metabolic disease, such as Acvr1c, Npy1r, Itgb1, and genes that are differentially regulated by food deprivation, such as Fam46a and Rrad. Our dataset provides a reliable and extensive resource of the molecular makeup of LH LepR neurons and their response to food deprivation.

Snord116 Post-transcriptionally Increases Nhlh2 mRNA Stability: Implications for Human Prader-Willi Syndrome

The smallest genomic region causing Prader-Willi Syndrome (PWS) deletes the non-coding RNA SNORD116 cluster; however, the function of SNORD116 remains a mystery. Previous work in the field revealed the tantalizing possibility that expression of NHLH2, a gene previously implicated in both obesity and hypogonadism, was downregulated in PWS patients and differentiated stem cells. In silico RNA: RNA modeling identified several potential interaction domains between SNORD116 and NHLH2 mRNA. One of these interaction domains was highly conserved in most vertebrate NHLH2 mRNAs examined. A construct containing the Nhlh2 mRNA, including its 3'-UTR, linked to a c-myc tag was transfected into a hypothalamic neuron cell line in the presence and absence of exogenously-expressed Snord116. Nhlh2 mRNA expression was upregulated in the presence of Snord116 dependent on the length and type of 3'UTR used on the construct. Furthermore, use of actinomycin D to stop new transcription in N29/2 cells demonstrated that the upregulation occurred through increased stability of the Nhlh2 mRNA in the 45 minutes immediately following transcription. In silico modeling also revealed that a single nucleotide variant (SNV) in the NHLH2 mRNA could reduce the predicted interaction strength of the NHLH2:SNORD116 diad. Indeed, use of an Nhlh2 mRNA construct containing this SNV significantly reduces the ability of Snord116 to increase Nhlh2 mRNA levels. For the first time, these data identify a motif and mechanism for SNORD116-mediated regulation of NHLH2, clarifying the mechanism by which deletion of the SNORD116 snoRNAs locus leads to PWS phenotypes.

Contribution of Growth Arrest-Specific 5/miR-674 to the Hypothalamus Pituitary Adrenal Axis Regulation Effect by Electroacupuncture following Trauma

BACKGROUND

Electroacupuncture (EA) can improve trauma-induced hypothalamus pituitary adrenal axis (HPA) hyperactivity. However, the mechanism underlying the EA effect has not been fully understood.

METHODS AND STUDY DESIGN

This study was undertaken to explore the role of hypothalamic growth arrest-specific 5 (Gas5) in the regulation of EA on HPA axis function post-surgery. Paraventricular nuclear Gas5 levels were upregulated in rats using an intracerebroventricular injection of pAAV-Gas5. Primary hypothalamic neurons and 293T cells were cultured for miRNA and siRNAs detection. Radioimmunoassay, PCR, Western blot, and immunohistochemistry were used for HPA axis function evaluation.

RESULTS

The overexpression of Gas5 abolished the effect of EA on the regulation of trauma-induced HPA axis hyperactivity. Using a bioinformatics analysis and dual luciferase assay, we determined that miRNA-674 was a target of Gas5. Additionally, miRNA-674 levels were found to have decreased in trauma rats, and this effect was reversed after EA intervention. TargetScan analysis showed that serum and glucocorticoid inducible kinase 1 (SGK1) were targets of miR-674. Moreover, we found that SGK1 protein levels increased in trauma rats and SGK1 expression inhibition alleviated HPA axis abnormality post-surgery. EA could improve the number of hypothalamus iba-1 positive cells and hypothalamic interleukin 1 beta protein expression.

CONCLUSIONS

Our study demonstrated the involvement of the hypothalamic Gas5/miRNA-674/SGK1 signaling pathway in EA regulation of HPA axis function after trauma.

Molecular mechanism of Chinese alligator (Alligator sinensis) adapting to hibernation

Hibernation is a physiological state for Chinese alligators to cope with cold weather. In mammals, gene expression changes during hibernation and their regulatory mechanisms have been extensively studied, however, these studies in reptiles are still rare. Here, integrated analysis of messenger RNA (mRNA), microRNA (miRNA), and long noncoding RNA (lncRNA) reveals the molecular mechanisms of the hypothalamus, liver, and skeletal muscle in hibernating and active individuals. During hibernation, the number of genes increased in the hypothalamus, liver, and skeletal muscle was 585, 282, and 297, while the number of genes decreased was 215, 561, and 627, respectively, as compared with active individuals. Through Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis, the differential expressed genes were mainly enriched in DNA damage repair, biological rhythm, energy metabolism, myoprotein degradation, and other related items and pathways. Besides, 4740 miRNAs were identified in three tissues. Through the comprehensive analysis of miRNA and mRNA abundance profiles, 12,291, 6997, and 8232 miRNA-mRNA pairs all showed a negative correlation in the hypothalamus, liver, and skeletal muscle, respectively. Some miRNA target genes were related tobiological rhythm and energy metabolism, suggesting that miRNA may play an important role in the physiological metabolism of the hibernating adaptability of Chinese alligators. Moreover, 402, 230, and 130 differentially expressed lncRNAs were identified in the hypothalamus, liver, and skeletal muscle, respectively. The targeting relationship of four lncRNA-mRNA pairs were predicted, with the main function of target genes involved in the amino acid transportation. These results are helpful to further understand the molecular regulatory basis of the hibernation adaptation in Chinese alligators.

Transcriptomic responses of hypothalamus to acute exercise in type 2 diabetic Goto-Kakizaki rats

The hypothalamus has an integral role in energy homeostasis regulation, and its dysfunctions lead to the development of type 2 diabetes (T2D). Physical activity positively affects the prevention and treatment of T2D. However, there is not much information on the adaptive mechanisms of the hypothalamus. In this study, RNA sequencing was used to determine how acute exercise affects hypothalamic transcriptome from both type 2 diabetic Goto-Kakizaki (GK) and control Wistar rats with or without a single session of running (15 m/min for 60 min). Through pairwise comparisons, we identified 957 differentially expressed genes (DEGs), of which 726, 197, and 98 genes were found between GK and Wistar, exercised GK and GK, and exercised Wistar and Wistar, respectively. The results of Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment revealed that lipid metabolism-related terms and pathways were enriched in GK and exercised GK rats, and nervous system related terms and pathways were enriched in exercised GK and Wistar rats. Furthermore, 45 DEGs were associated with T2D and related phenotypes according to the annotations in the Rat Genome Database. Among these 45 DEGs, several genes (Plin2, Cd36, Lpl, Wfs1, Cck) related to lipid metabolism or the nervous system are associated with the exercise-induced benefits in the hypothalamus of GK rats. Our findings might assist in identifying potential therapeutic targets for T2D prevention and treatment.

The role of epigenetics in hypothalamic energy balance control: implications for obesity

Despite enormous social and scientific efforts, obesity rates continue to increase worldwide. While genetic factors contribute to obesity development, genetics alone cannot explain the current epidemic. Obesity is essentially the consequence of complex genetic-environmental interactions. Evidence suggests that contemporary lifestyles trigger epigenetic changes, which can dysregulate energy balance and thus contribute to obesity. The hypothalamus plays a pivotal role in the regulation of body weight, through a sophisticated network of neuronal systems. Alterations in the activity of these neuronal pathways have been implicated in the pathophysiology of obesity. Here, we review the current knowledge on the central control of energy balance with a focus on recent studies linking epigenetic mechanisms in the hypothalamus to the development of obesity and metabolic disorders.

Long Non-Coding RNAs in Metabolic Organs and Energy Homeostasis

Single cell organisms can surprisingly exceed the number of human protein-coding genes, which are thus not at the origin of the complexity of an organism. In contrast, the relative amount of non-protein-coding sequences increases consistently with organismal complexity. Moreover, the mammalian transcriptome predominantly comprises non-(protein)-coding RNAs (ncRNA), of which the long ncRNAs (lncRNAs) constitute the most abundant part. lncRNAs are highly species- and tissue-specific with very versatile modes of action in accordance with their binding to a large spectrum of molecules and their diverse localization. lncRNAs are transcriptional regulators adding an additional regulatory layer in biological processes and pathophysiological conditions. Here, we review lncRNAs affecting metabolic organs with a focus on the liver, pancreas, skeletal muscle, cardiac muscle, brain, and adipose organ. In addition, we will discuss the impact of lncRNAs on metabolic diseases such as obesity and diabetes. In contrast to the substantial number of lncRNA loci in the human genome, the functionally characterized lncRNAs are just the tip of the iceberg. So far, our knowledge concerning lncRNAs in energy homeostasis is still in its infancy, meaning that the rest of the iceberg is a treasure chest yet to be discovered.

Lnc‑IL7R promotes the growth of fibroblast‑like synoviocytes through interaction with enhancer of zeste homolog 2 in rheumatoid arthritis

Rheumatoid arthritis (RA) is an inflammatory and autoimmune disease that affects ~1% of the world's population. Although the precise mechanism of RA has yet to be elucidated, accumulating evidence suggests that fibroblast‑like synoviocytes (FLSs) serve critical roles in the initiation and progression of RA. However, the underlying molecular mechanisms of FLS proliferation have yet to be elucidated. Long noncoding‑interleukin‑7 receptor (lnc‑IL7R) has been recently identified, which is activated by lipopolysaccharide (LPS) stimulation and diminishes the LPS‑induced inflammatory response. In the present study, gain‑ and loss‑of‑function assays were performed in order to investigate the role of lnc‑IL7R in FLS. It is demonstrated, to the best of the authors' knowledge for the first time, that lnc‑IL7R promotes cell proliferation, cell cycle progression and inhibits apoptosis in FLS. Further investigation identified that lnc‑IL7 interacts with enhancer of zeste homolog 2 (EZH2) and is required for polycomb repressive complex 2 (PRC2)‑mediated suppression, including cyclin‑dependent kinase inhibitor 1A and cyclin‑dependent kinase inhibitor 2A. Lnc‑IL7R may be a promising therapeutic target for the treatment of RA.

A molecular conundrum involving hypothalamic responses to and roles of long non-coding RNAs following food deprivation

Long non-coding RNAs (lncRNAs) are one of most poorly understood RNA classes in the mammalian transcriptome. However, they are emerging as important players in transcriptional regulation, especially within the complexity of the nervous system. This review summarizes the known information about lncRNAs, and their roles in endocrine processes, as well as the lesser-known information about lncRNAs in the brain, and in the neuroendocrine hypothalamus. A "call-to-action" is presented for researchers to use archival transcriptome data to characterize differentially expressed lncRNA species within the hypothalamus. In accordance, we analyze for differential-expression of lncRNA between normal mice and mice with a targeted deletion of the nescient helix-loop-helix 2 gene, and between C57Bl/6 and 129Sv/J mice. Finally, strategies and approaches for researchers to analyze their own datasets or those on the NCBI GEO datasets repository are provided, in hopes that future studies will reveal many new roles for lncRNAs in hypothalamic physiological responses, solving this so-called "molecular conundrum" once and for all.

Up-regulation of Long Non-coding RNA TUG1 in Hibernating Thirteen-lined Ground Squirrels

Mammalian hibernation is associated with multiple physiological, biochemical, and molecular changes that allow animals to endure colder temperatures. We hypothesize that long non-coding RNAs (lncRNAs), a group of non-coding transcripts with diverse functions, are differentially expressed during hibernation. In this study, expression levels of lncRNAsH19 and TUG1 were assessed via qRT-PCR in liver, heart, and skeletal muscle tissues of the hibernating thirteen-lined ground squirrels (Ictidomys tridecemlineatus). TUG1 transcript levels were significantly elevated 1.94-fold in skeletal muscle of hibernating animals when compared with euthermic animals. Furthermore, transcript levels of HSF2 also increased 2.44-fold in the skeletal muscle in hibernating animals. HSF2 encodes a transcription factor that can be negatively regulated by TUG1 levels and that influences heat shock protein expression. Thus, these observations support the differential expression of the TUG1–HSF2 axis during hibernation. To our knowledge, this study provides the first evidence for differential expression of lncRNAs in torpid ground squirrels, adding lncRNAs as another group of transcripts modulated in this mammalian species during hibernation.