Unraveling genotype-dependent metabolic and transcriptional differences between yellow and orange senescent leaves of Pistacia chinensis via multi-omics analysis

As one of the most common otologic diseases in the elderly, age-related hearing loss (ARHL) usually characterized by hearing loss and cognitive disorders, which have a significant impact on the elderly's physical and mental health and quality of life. However, as a typical disease of aging, it is unclear why aging causes widespread hearing impairment in the elderly. As molecular biological experiments have been conductedfor research recently, ARHL is gradually established at various levels with the application and development of integrated multi-omics analysis in the studies of ARHL. Here, the recent progress in the application of multi-omics analysis in the molecular mechanisms of ARHL development and therapeutic regimens, including the combined analysis of different omics, such as transcriptome, proteome, and metabolome, to screen for risk sites, risk genes, and differences in lipid metabolism, etc., is outlined and the integrated histological data further promote the profound understanding of the disease process as well as physiological mechanisms of ARHL. The advantages and disadvantages of multi-omics analysis in disease research are also discussed and the authors speculate on the future prospects and applications of this part-to-whole approach, which may provide more comprehensive guidance for ARHL and aging disease prevention and treatment.

Saccharomyces cerevisiae, a widespread yeast present both in the wild and in fermentative processes, like winemaking. During the colonization of these human-associated fermentative environments, certain strains of S. cerevisiae acquired differential adaptive traits that enhanced their physiological properties to cope with the challenges imposed by these new ecological niches. The advent of omics technologies allowed unveiling some details of the molecular bases responsible for the peculiar traits of S. cerevisiae wine strains. However, the metabolic diversity within yeasts remained poorly explored, in particular that existing between wine and wild strains of S. cerevisiae. For this purpose, we performed a dual transcriptomic and metabolomic comparative analysis between a wild and a wine S. cerevisiae strains during wine fermentations performed at high and low temperatures. By using this approach, we could correlate the differential expression of genes involved in metabolic pathways, such as sulfur, arginine and thiamine metabolisms, with differences in the amounts of key metabolites that can explain some important differences in the fermentation performance between the wine and wild strains.

In livestock production, deeply understanding the molecular mechanisms of growth and metabolic differences in different breeds of cattle is of great significance for optimizing breeding strategies, improving meat quality, and promoting sustainable development. This study aims to comprehensively reveal the molecular-level differences between Chinese domestic cattle and Simmental crossbred cattle through multi-omics analysis, and further provide a theoretical basis for the efficient development of the beef cattle industry. The domestic cattle in China are a unique genetic breed resource. They have characteristics like small size, strong adaptability, and distinctive meat quality. There are significant differences in the growth rate and meat production between these domestic cattle and Simmental hybrid cattle. However, the specific molecular-level differences between them are still unclear. This study conducted a comprehensive comparison between the domestic cattle in China and Simmental crossbred cattle, focusing on microbiology, short-chain fatty acids, blood metabolome, and transcriptome. The results revealed notable differences in the microbial Simpson index between the domestic and Simmental crossbred cattle. The differential strain Akkermansia was found to be highly negatively correlated with the differential short-chain fatty acid isocaproic acid, suggesting that Akkermansia may play a key role in the differences observed in isocaproic acid levels or phenotypes. Furthermore, the transcriptional metabolomics analysis indicated that the differentially expressed genes and metabolites were co-enriched in pathways related to insulin secretion, thyroid hormone synthesis, bile secretion, aldosterone synthesis and secretion, and Cyclic Adenosine Monophosphate (cAMP) signaling pathways. Key genes such as ADCY8 and 1-oleoyl-sn-glycero-3-phosphocholine emerged as crucial regulators of growth and metabolism in beef cattle.

Multi-omics analyses reveal mechanism for high resistant starch formation in an indica rice SSIIIa mutant

Bats have unique characteristics compared to other mammals, including increased longevity and higher resistance to cancer and infectious disease. While previous studies have analyzed the metabolic requirements for flight, it is still unclear how bat metabolism supports these unique features, and no study has integrated metabolomics, transcriptomics, and proteomics to characterize bat metabolism. In this work, we performed a multi-omics data analysis using a computational model of metabolic fluxes to identify fundamental differences in central metabolism between primary lung fibroblast cell lines from the black flying fox fruit bat (Pteropus alecto) and human. Bat cells showed higher expression levels of Complex I components of electron transport chain (ETC), but, remarkably, a lower rate of oxygen consumption. Computational modeling interpreted these results as indicating that Complex II activity may be low or reversed, similar to an ischemic state. An ischemic-like state of bats was also supported by decreased levels of central metabolites and increased ratios of succinate to fumarate in bat cells. Ischemic states tend to produce reactive oxygen species (ROS), which would be incompatible with the longevity of bats. However, bat cells had higher antioxidant reservoirs (higher total glutathione and higher ratio of NADPH to NADP) despite higher mitochondrial ROS levels. In addition, bat cells were more resistant to glucose deprivation and had increased resistance to ferroptosis, one of the characteristics of which is oxidative stress. Thus, our studies revealed distinct differences in the ETC regulation and metabolic stress responses between human and bat cells.

The seasonal variations of biofilm communities in a municipal wastewater treatment plant were investigated using multi-omics techniques. The abundance of the main phyla of microorganisms varied with summer (July 2019) and winter (January 2019) samples considerably, the Bacteroidetes enriched in winter and Chloroflexi in summer. The results of metaproteomic and metagenomic showed that most of the functional microorganisms belonged to the Betaproteobacteria class, and the enrichment of Flavobacteria class in winter guaranteed the stability of denitrification performance to some extent. Seasonal variations affected the proteomic expression profiling, a total of 2835 differentially expressed proteins identified were significantly enriched in quorum sensing, two-component system, ribosome, benzoate degradation, butanoate metabolism, tricarboxylic acid cycle (TCA cycle), and cysteine and methionine metabolism pathways. With the expression of nitrogen metabolic proteins decreases in winter, the overall expression of denitrification-related enzymes in winter was much lower than that in summer, the nitrogen metabolism pathway varied significantly. Seasonal variations also induced the alteration of the biofilm metabolite profile; a total of 66 differential metabolites, 8 potential biomarkers, and 8 perturbed metabolic pathways such as TCA cycle were detected. It was found that most of the perturbed pathways are directly related to nitrogen metabolism, and several amino acids and organic acids associated with the TCA cycle were significantly perturbed, the accumulation of TCA cycle intermediates, ornithine, and L-histidine in winter might be conducive to resisting cold temperatures. Furthermore, the correlation between biofilm microbial communities and metabolites was identified by the combined analysis of metabolomic and metaproteomic. The differences of microbial community structure, function, and metabolism between winter and summer in a full-scale pre-denitrification biofilter were revealed for the first time, strengthening our understanding of the microbial ecology of biofilm communities.

Integrative multi-omics analysis reveals liver-gut axis adaptation in high-altitude goats.

Multi-Omics Integration Analysis Identifies Lipoproteins As Biomarkers for Glucocorticoid Response in Immune Thrombocytopenia

Multi-omics joint analysis of the effect of temperature on microbial communities, metabolism, and genetics in full-scale biogas reactors with food waste

Macrobrachium rosenbergii is an essential species for freshwater economic aquaculture in China, but in the larval process, their salinity requirement is high, which leads to salinity stress in the water. In order to elucidate the mechanisms regulating the response of M. rosenbergii to acute low-salinity exposure, we conducted a comprehensive study of the response of M. rosenbergii exposed to different salinities’ (0‰, 6‰, and 12‰) data for 120 h. The activities of catalase, superoxide dismutase, and glutathione peroxidase were found to be significantly inhibited in the hepatopancreas and muscle following low-salinity exposure, resulting in oxidative damage and immune deficits in M. rosenbergii. Differential gene enrichment in transcriptomics indicated that low-salinity stress induced metabolic differences and immune and inflammatory dysfunction in M. rosenbergii. The differential expressions of MIH, JHEH, and EcR genes indicated the inhibition of growth, development, and molting ability of M. rosenbergii. At the proteomic level, low salinity induced metabolic differences and affected biological and cellular regulation, as well as the immune response. Tyramine, trans-1,2-Cyclohexanediol, sorbitol, acetylcholine chloride, and chloroquine were screened by metabolomics as differential metabolic markers. In addition, combined multi-omics analysis revealed that metabolite chloroquine was highly correlated with low-salt stress.

Polyploidy plays a crucial role in plant evolution, as polyploid plants possess larger genomes compared to their diploid counterparts. This genomic expansion leads to changes in gene redundancy and interactions, which alter the physiological metabolism of polyploids. Carbohydrate metabolism is a crucial energy metabolism pathway in plants, significantly impacting plant growth and development. In this study, we employed multi-omics analysis to investigate the differences in carbohydrate metabolism between diploid and tetraploid flag leaves during both day and night periods at the grain-filling stage. Our results revealed significant differences in carbohydrate metabolism between diploid (GFD-2X) and autopolyploid (GFD-4X) rice during both day and night periods. Chromosome doubling resulted in GFD-4X exhibiting reduced sucrose catabolism during the daytime, while starch synthesis and catabolism were stronger in GFD-4X compared to GFD-2X during both daytime and nighttime. Additionally, the phosphorylation of monosaccharides was enhanced in GFD-4X, suggesting that changes in chromosome ploidy altered carbohydrate metabolism, thereby benefiting the regulation and redistribution of carbohydrates in tetraploid rice. Furthermore, analysis of respiration-related pathways indicated that tetraploid rice may have more vigorous respiratory activity. Specifically, GFD-4X exhibited enhanced glycolysis and TCA cycle activity at night, resulting in more efficient energy production, which in turn influenced growth and the developmental process. This study examined the regulatory networks of genes, proteins, and metabolites involved in carbohydrate metabolism in diploid and tetraploid rice during both day and night periods. Our findings offer insights into how chromosome ploidy affects carbohydrate metabolism and reveal the distinct growth and developmental mechanisms of tetraploid rice.

Subcutaneous adipose tissues (SAT) are critical determinants of duck meat flavor and texture. Investigating metabolic differences in SAT deposition facilitates targeted breeding strategies for superior flavor profiles and feed formulation optimization. This study employed flavoromics and lipidomics to systematically compare the flavoromics and lipidomics profiles of SAT from Wuqin-10 duck (WQ) and Cherry valley duck (CV). Flavoromics analysis identified hexadecanal as the sole significantly upregulated differential flavor compounds in WQ ducks (P-value < 0.05), predominantly enriched in fatty acid degradation pathways. Lipidomics revealed 182 differential lipids (87 upregulated, 95 downregulated) between breeds, with Carnitine C4:1-2OH exhibiting 256-fold higher relative abundance in WQ ducks. Compositional analysis demonstrated elevated levels of long-chain triglycerides (TAGs), lysophosphatidylcholines (LPCs), and lysophosphatidylethanolamines (LPEs) in WQ ducks, whereas CV ducks showed higher abundance of phosphatidylserine (PS), phosphatidylethanolamine (PE), and phosphatidylcholine (PC). These differential lipids were significantly enriched in glycerophospholipid metabolism, GPI-anchor biosynthesis, and polyunsaturated fatty acid metabolic pathways. Integrated multi-omics analysis further identified significant positive correlations between flavor compounds (n-hexadecanoic acid and hexadecanal) and glycerolipids (TG/DG). Collectively, this work systematically elucidates substantial compositional divergences in flavor compounds and lipids between CV and WQ ducks, while flavor compound-lipid correlations reveal potential regulatory nodes within lipid metabolic networks, providing crucial molecular insights into breed-specific lipid metabolic characteristics.

Using VIS-NIR spectroscopy and multi-omics analysis to compare mango anthracnose under natural and inoculated conditions.

Despite improvements in cancer patient outcomes seen in the past decade, tumor resistance to therapy remains a major impediment to achieving durable clinical responses. Intratumoral heterogeneity related to genetic, epigenetic, transcriptomic, proteomic, and metabolic differences between individual cancer cells has emerged as a driver of therapeutic resistance. This cell to cell heterogeneity can be assessed using single cell profiling technologies that enable the identification of tumor cell clones that exhibit similar defining features like specific mutations or patterns of DNA methylation. Single cell profiling of tumors before and after treatment can generate new insights into the cancer cell characteristics that confer therapeutic resistance by identifying intrinsically resistant sub-populations that survive treatment and by describing new cellular features that emerge post-treatment due to tumor cell evolution. Integrative, single cell analytical approaches have already proven advantageous in studies characterizing treatment-resistant clones in cancers where pre- and post-treatment patient samples are readily available, such as leukemia. In contrast, little is known about other cancer subtypes like pediatric high grade glioma, a class of heterogeneous, malignant brain tumors in children that rapidly develop resistance to multiple therapeutic modalities, including chemotherapy, immunotherapy, and radiation. Leveraging single cell multi-omic technologies to analyze naïve and therapy-resistant glioma may lead to the discovery of novel strategies to overcome treatment resistance in brain tumors with dismal clinical outcomes. In this review, we explore the potential for single cell multi-omic analyses to reveal mechanisms of glioma resistance to therapy and discuss opportunities to apply these approaches to improve long-term therapeutic response in pediatric high grade glioma and other brain tumors with limited treatment options.

Critically ill patients with acute respiratory distress syndrome (ARDS) and sepsis exhibit distinct inflammatory phenotypes with divergent clinical outcomes and apparent heterogeneity of treatment effects, but the underlying molecular mechanisms remain poorly understood. These phenotypes, derived from clinical data and protein biomarkers, were associated with metabolic differences in a prior pilot study. This study investigated the metabolomic and transcriptomic differences between Hyperinflammatory and Hypoinflammatory phenotypes through integrative multi-omics analysis of blood samples from ARDS patients in the ROSE trial. Multi-omics integration revealed three molecular signatures strongly associated with the Hyperinflammatory phenotype and with mortality: enhanced innate immune activation coupled with increased glycolysis, hepatic dysfunction and immune dysfunction paired with impaired fatty acid beta-oxidation, and interferon program suppression coupled with altered mitochondrial respiration. A fourth molecular signature, not associated with inflammatory phenotype, identified redox impairment and cell proliferation pathways associated with mortality. Integrated multi-omics analysis within each inflammatory phenotype revealed distinct pathways associated with mortality. All mortality-associated molecular signatures including those within phenotypes were validated in an independent cohort of critically ill patients with sepsis (EARLI). These findings reveal distinct molecular mechanisms underlying ARDS/sepsis phenotypes and suggest potential therapeutic targets for precise treatment strategies in critical illness.