Integrated Transcriptome and Metabolome Analysis of Photoperiod Effects on Testosterone Secretion in ChaHua Chicken No.2 Roosters
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Obesity is a multifactorial metabolic disease with profound changes in the biomolecular composition and function of multiple organs and tissues. Omics technologies allow for the comprehensive characterization of a near-complete complement of genes, proteins, and metabolites, and have been applied quite extensively for understanding the molecular pathogenesis of obesity and for identifying markers of weight gain and weight loss. This chapter concentrates on transcriptomics-, proteomics-, and metabolomics-based observations about obesity, seen through the lens of profiling studies, tissue-specific omics, omics in special populations (e.g., non-Caucasian ethnicities, maternal and childhood obesity), and omics-based inquiries into obesity interventions. Within each omics platform, some common themes emerge for obesity-associated changes, along with findings restricted to more specialized settings. Broadly, the weight of evidence implicates gene and protein-level changes in pathways related to lipid metabolism, inflammatory signaling, mitochondrial function, and extracellular matrix remodeling in obesity. Metabolomics studies attest to frequently observed changes in branched-chain amino acid and aromatic amino acids, phospholipids and lysophospholipids, and bile acids and tryptophan/kynurenine metabolism, among others. A survey of the literature also illuminates limitations of technology, study designs, and scope within each omics platform and highlights areas of obesity research in need of more data and areas amenable to more sophisticated investigations in the future.
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Molecular changes elicited by common bean (Phaseolus vulgaris L.) in response to Fusarium oxysproum f. sp. Phaseoli (FOP) remain elusive. We studied the changes in root metabolism during common bean–FOP interactions using a combined de novo transcriptome and metabolome approach. Our results demonstrated alterations of transcript levels and metabolite concentrations in common bean roots 24 h post infection as compared to control. The transcriptome and metabolome responses in common bean roots revealed significant changes in structural defense i.e., cell-wall loosening and weakening characterized by hyper accumulation of cell-wall loosening and degradation related transcripts. The levels of pathogenesis related genes were significantly higher upon FOP inoculation. Interestingly, we found the involvement of glycosylphosphatidylinositol- anchored proteins (GPI-APs) in signal transduction in response to FOP infection. Our results confirmed that hormones have strong role in signaling pathways i.e., salicylic acid, jasmonate, and ethylene pathways. FOP induced energy metabolism and nitrogen mobilization in infected common bean roots as compared to control. Importantly, the flavonoid biosynthesis pathway was the most significantly enriched pathway in response to FOP infection as revealed by the combined transcriptome and metabolome analysis. Overall, the observed modulations in the transcriptome and metabolome flux as outcome of several orchestrated molecular events are determinant of host’s role in common bean–FOP interactions.
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Liver homeostasis is ensured in part by time-of-day-dependent processes, many of them being paced by the molecular circadian clock. Liver functions are compromised in metabolic dysfunction-associated steatotic liver disease (MASLD) and metabolic dysfunction-associated steatohepatitis (MASH), and clock disruption increases susceptibility to MASLD progression in rodent models. We therefore investigated whether the time-of-day-dependent transcriptome and metabolome are significantly altered in human steatotic and MASH livers.Liver biopsies, collected within an 8 h-window from a carefully phenotyped cohort of 290 patients and histologically diagnosed to be either normal, steatotic or MASH hepatic tissues, were analyzed by RNA sequencing and unbiased metabolomic approaches. Time-of-day-dependent gene expression patterns and metabolomes were identified and compared between histologically normal, steatotic and MASH livers.Herein, we provide a first-of-its-kind report of a daytime-resolved human liver transcriptome-metabolome and associated alterations in MASLD. Transcriptomic analysis showed a robustness of core molecular clock components in steatotic and MASH livers. It also revealed stage-specific, time-of-day-dependent alterations of hundreds of transcripts involved in cell-to-cell communication, intracellular signaling and metabolism. Similarly, rhythmic amino acid and lipid metabolomes were affected in pathological livers. Both TNFα and PPARγ signaling were predicted as important contributors to altered rhythmicity.MASLD progression to MASH perturbs time-of-day-dependent processes in human livers, while the differential expression of core molecular clock components is maintained.This work characterizes the rhythmic patterns of the transcriptome and metabolome in the human liver. Using a cohort of well-phenotyped patients (n = 290) for whom the time-of-day at biopsy collection was known, we show that time-of-day variations observed in histologically normal livers are gradually perturbed in liver steatosis and metabolic dysfunction-associated steatohepatitis. Importantly, these observations, albeit obtained across a restricted time window, provide further support for preclinical studies demonstrating alterations of rhythmic patterns in diseased livers. On a practical note, this study indicates the importance of considering time-of-day as a critical biological variable which may significantly affect data interpretation in animal and human studies of liver diseases.
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Populus alba × Populus glandulosa (84K poplar) is model material with excellent genetic engineering resource and ornamental value. In our study, AmRosea1 ( Antirrhinum majus ) was overexpressed in 84K poplar, and the transgenic 84K (AM) poplar with high content of anthocyanin exhibited red pigmentation leaves. The transcriptome analysis between wild type (WT) and AM showed that 170 differentially expressed genes (DEGs) (86 up-regulated and 84 down-regulated) were found, and some DEGs were involved in flavone and flavonol biosynthesis, flavonoid biosynthesis and anthocyanin biosynthesis. The metabolome analysis showed that 13 anthocyanins-related differentially accumulated metabolites (DAMs) were detected in AM. The correlation analysis between DEGs and DAMs were performed, and the results revealed that 18 DEGs, including 11 MYB genes, two BZ1 genes, one FG2 gene, one ANS gene, and three IF7MAT genes, were negatively or positively correlated with 13 DAMs. The phylogenetic analysis demonstrated that there was high homology between AmRosea1 and PagMYB113 , and MYB113 co-expressed with BZ1, ANS and DFR directly. Our results elucidated the molecular mechanism of plant color change mediated by anthocyanin biosynthesis pathway, which laid the foundation for the development and utilization of colorful woody plant.
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Colored potatoes with red and purple skin or flesh possess significant nutritional value and health benefits due to their rich anthocyanin content. To investigate the genetic mechanisms underlying color formation, the high-anthocyanin-content purple-skinned and purple-fleshed potato line 15-12-16, and the white-skinned and white-fleshed Xiazhai 65 variety were used for ultra-performance liquid chromatography-electrospray ionization-tandem mass spectrometry (UPLC-ESI-MS/MS) analysis, which was conducted to identify and quantify anthocyanins. RNA sequencing was performed to analyze the transcriptome. The results indicated a significant upregulation of genes within the anthocyanidin biosynthesis pathway in the purple potato, while these genes were either downregulated or absent in the white potato. The bHLH, MYB, and WRKY gene families exhibited a greater number of regulatory members, suggesting their pivotal role in color formation. Integrated analysis of the transcriptional and metabolic revealed that 12 differentially expressed genes (DEGs) related to the anthocyanidin biosynthetic had a significant correlation with 18 anthocyanin metabolites. Notably, the key gene
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Characterization of molecular mechanisms underlying pregnancy development of sows is important for the genetic improvement of pig breeding traits, and also provides resources for biomedical research on human pregnancy diseases. However, the transcriptome and metabolome across multiple developmental stages of sow pregnancy were still lacking. In this study, we obtained 84 distinct RNA sequencing and 42 metabolome datasets of pig blood across six development stages from estrus to lactation. We confirmed the initial sequence and exonic structural features, stage-specific molecules, expression or accumulation pattern of molecules, the regulatory mechanism of transcriptome and metabolome, and important pregnancy-related metabolites both in pigs and humans. In conclusion, we proposed the key differences among the stages of sows from estrus to lactation in RNAs and metabolites and put forward key markers. These data results were expected to provide essential resources for pig breeding and biomedical research on human pregnancy disease.
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The prevalence of non-alcoholic fatty liver diseases (NAFLD) has reached epidemic levels during recent years and a major driver of NAFLD are diets high in fat and fructose. A common practice in the treatment of NAFLD are life-style interventions including for example increased physical activity. The transcriptional coactivator peroxisome proliferator-activated receptor gamma coactivator 1α (PGC-1α) has been shown to be central in mediating the beneficial effects of exercise training by regulating the expression of key metabolic genes. However, the significance of hepatic PGC-1α for high fat high fructose (HFFD) induced changes in gene expression and metabolites associated with NAFLD has not been elucidated. Therefore the aim of the present study was to investigate the effect of hepatic PGC-1α on HFFD and exercise-induced changes in the hepatic transcriptome and metabolome in mice. Using gene-arrays and 1H NMR spectroscopy, the liver transcriptome and metabolome of liver-specific PGC-1α knock-out mice receiving either standard chow, HFFD or HFFD + exercise (HFFD + Ex) were determined. In total 122 genes were identified as differently expressed in mice receiving HFFD for 13 weeks compared to chow, while the loss of hepatic PGC-1α only had very minor effects on the transcriptome. The same was observed for the liver metabolome. The effect of 4 weeks exercise training in combination with 13 weeks of HFFD, had small effects on the transcriptome and metabolome compared to HFFD alone. Together our results highlight a minor regulatory effect of hepatic PGC-1α on the liver transcriptome during high fat high fructose diet and exercise training.
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This study utilized Beauveria bassiana to infect Leguminivora glycinivorella, analyzed the effects on the transcriptome and metabolome, and further investigated the antibacterial function of L. glycinivorella. We performed transcriptome and metabolome sequencing on the L. glycinivorella infected with B. bassiana and its control groups, and performed a joint analysis of transcriptome and metabolome results. Upon screening, 4560 differentially expressed genes were obtained in the transcriptome and 71 differentially expressed metabolites were obtained in the metabolome. On this basis, further integration of the use of transcriptomics and metabonomics combined an analysis of common enrichments of pathways of which there were three. They were glutathione S-transferase (GSTs) genes, heat shock protein (HSP) genes, and cytochrome P450 (CYP450) genes. These three pathways regulate the transport proteins, such as ppars, and thus affect the digestion and absorption of sugars and fats, thus regulating the development of pests. The above conclusion indicates that B. bassiana can affect the sugar metabolism, lipid metabolism, and amino acid metabolism pathways of L. glycinivorella, and can consume the necessary energy, protein, and lipids of L. glycinivorella. The research on the immune response mechanism of pests against pathogens can provide an important scientific basis and target for the development of immunosuppressants. This study laid an information foundation for the application of entomogenous fungi to control soybean borer at the molecular level.
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Information regarding transcriptome and metabolome has significantly contributed to identifying potential therapeutic targets for the management of a variety of cancers. Obesity has profound effects on both cancer cell transcriptome and metabolome that can affect the outcome of cancer therapy. The information regarding the potential effects of obesity on breast cancer (BC) transcriptome, metabolome and its integration to identify novel pathways related to disease progression are still elusive. We assessed the whole blood transcriptome and serum metabolome, as circulating metabolites, of obese BC patients compared them with non-obese BC patients. In these patients' samples, 186 significant differentially expressed genes (DEGs) were identified, comprising 156 upregulated and 30 downregulated. The expressions of these gene were confirmed by qRT-PCR. Furthermore, 96 deregulated metabolites were identified as untargeted metabolomics in the same group of patients. These detected DEGs and deregulated metabolites enriched in many cellular pathways. Further investigation, by integration analysis between transcriptomics and metabolomics data at the pathway levels, revealed seven unique enriched pathways in obese BC patients when compared with non-obese BC patients, which may provide resistance for BC cells to dodge the circulating immune cells in the blood. In conclusion, this study provides information on the unique pathways altered at transcriptome and metabolome levels in obese BC patients that could provide an important tool for researchers and contribute further to knowledge on the molecular interaction between obesity and BC. Further studies are needed to confirm this and to elucidate the exact underlying mechanism for the effects of obesity on the BC initiation or/and progression.
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