Omics Approaches Research Articles

Exploring Extracellular Vesicles: A Novel Approach in Nonalcoholic Fatty Liver Disease.

Nonalcoholic fatty liver disease (NAFLD) represents an increasing public health concern. The underlying pathophysiological mechanisms of NAFLD remains unclear, and as a result, there is currently no specific therapy for this condition. However, recent studies focus on extracellular vesicles (EVs) as a novelty in their role in cellular communication. An imbalance in the gut microbiota composition may contribute to the progression of NAFLD, making the gut-liver axis a promising target for therapeutic strategies. This review aims to provide a comprehensive overview of EVs in NAFLD. Additionally, exosome-like nanovesicles derived from plants (PELNs) and probiotics-derived extracellular vesicles (postbiotics) have demonstrated the potential to re-establish intestinal equilibrium and modulate gut microbiota, thus offering the potential to alleviate NAFLD via the gut-liver axis. Further research is needed using multiple omics approaches to comprehensively characterize the cargo including protein, metabolites, genetic material packaged, and biological activities of extracellular vesicles derived from diverse microbes and plants.

Lipidomic Expression Analysis In Carotid Atherosclerotic Disease: A Systematic Review.

Lipids are key molecules for atherosclerosis, with tight regulation mechanisms, making them potential biomarkers for disease-specific diagnostics and therapeutics. Therefore, we aim to perform a systematic literature review on lipidomic analysis in serum/plasma and plaque samples of patients with carotid atherosclerosis. We performed a systematic review following the PRISMA guidelines on the lipidomic profile in serum/plasma and carotid artery plaques from patients with significant carotid disease by degree of stenosis in preoperative imaging and clinical presentation (symptomatic, asymptomatic, radiation-induced carotid disease). Main outcome was the differential lipidomic expression of serum/plasma, and plaque lipids of patients with carotid artery atherosclerosis. Studies were screened using the Newcastle-Ottawa Scale to determine the quality of the design and content of the selected manuscripts. We included fourteen studies, from which ten included plaque analysis. The lipidomic analysis revealed that sterols and hydroxycholesterols were consistently found in both blood and plaque across studies. Triacylglycerols were present in both sample types, with specific forms linked to radiation-induced carotid artery disease. Symptomatic patients exhibited esterified hydroxyeicosatetraenoic acids and arachidonic acid precursors exclusively in plaque with an inflammatory profile of the disease. In contrast, docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA) were associated with plaque stability. Diabetics showed nonesterified fatty acids and specific phospholipids only in plaque, indicating localized lipid changes. Other pathways relevant to disease progression include the sphingolipids and ceramide pathways with inflammatory profiling. Lipidomic provides an innovative approach to stratify carotid atherosclerotic disease. Integrating lipidomic data with other -omics approaches may further enhance our understanding of disease mechanisms and aid in the development of precision medicine approaches, specifically in those patients at risk for early carotid atherosclerotic disease.

A Menu for Microbes: Unraveling Appetite Regulation and Weight Dynamics Through the Microbiota-Brain Connection Across the Lifespan.

Appetite, as the internal drive for food intake, is often dysregulated in a broad spectrum of conditions associated with over- and under-nutrition across the lifespan. Appetite regulation is a complex, integrative process comprising psychological and behavioral events, peripheral and metabolic inputs, and central neurotransmitter and metabolic interactions. The microbiota-gut-brain axis has emerged as a critical mediator of multiple physiological processes, including energy metabolism, brain function, and behavior. Therefore, the role of the microbiota-gut-brain axis in appetite and obesity is receiving increased attention. Omics approaches such as genomics, epigenomics, transcriptomics, proteomics, and metabolomics in appetite and weight regulation offer new opportunities for featuring obesity phenotypes. Furthermore, gut microbiota-targeted approaches such as pre- pro- post- and synbiotic, personalized nutrition, and fecal microbiota transplantation are novel avenues for precision treatments. The aim of this narrative review is (1) to provide an overview of the role of the microbiota-gut-brain-axis in appetite regulation across the lifespan and (2) to discuss the potential of omics and gut microbiota-targeted approaches to deepen understanding of appetite regulation and obesity.

Using Multi-Omics Methods to Understand Gouty Arthritis.

Gouty arthritis is a common arthritic disease caused by the deposition of monosodium urate crystals in the joints and the tissues around it. The main pathogenesis of gout is the inflammation caused by the deposition of monosodium urate crystals. Omics studies help us evaluate global changes in gout during recent years, but most studies used only a single omics approach to illustrate the mechanisms of gout. In this review, we review the genomics, transcriptomics, epigenetics, proteomics, and metabolomics of gout, observing that different genes, DNA methylation, miRNAs, LncRNAs, circRNAs, proteins, and metabolites are found between hyperuricemia, acute gout arthritis, and chronic gout arthritis, and some of them are associated with disease activity, prognosis or treatment, which help us broaden our understanding of the pathogenesis and provide important clues for valuable biomarkers. To our knowledge, this is the first study that combines all omics studies from genomics to metabolomics and may serve as a reference for future studies to identify the key underlying pathways in gout.

Exploring the Frontiers of Nanopore Sequencing in Food Safety and Food Microbiology.

Foodborne illnesses are a significant global public health challenge, with an estimated 600 million cases annually. Conventional food microbiology methods tend to be laborious and time consuming, pose difficulties in real-time utilization, and can display subpar accuracy or typing capabilities. With the recent advancements in third-generation sequencing and microbial omics, nanopore sequencing technology and its long-read sequencing capabilities have emerged as a promising platform. In recent years, nanopore sequencing technology has been benchmarked for its amplicon sequencing, whole-genome and transcriptome analysis, meta-analysis, and other advanced omics approaches. This review comprehensively covers nanopore sequencing technology's current advances in food safety applications, including outbreak investigation, pathogen surveillance, and antimicrobial resistance profiling. Despite significant progress, ongoing research and development are crucial to overcoming challenges in sequencing chemistry, accuracy, bioinformatics, and real-time adaptive sampling to fully realize nanopore sequencing technology's potential in food safety and food microbiology.

Snake venom galactoside-binding lectin from Bothrops jararacussu: Special role in leukocytes activation and function.

Snake venom galactoside-binding lectins (SVgalLs) comprise a group of toxins with the ability to bind specifically, reversibly, and non-covalently to galactose-containing carbohydrates in a Ca2+-dependent manner. Several SVgalLs have been identified and isolated from Bothrops snake venoms, presenting highly similar structures and biological functions. BjcuL is a galactoside binding C-type lectin isolated from the venom of South America Bothrops jararacussu and consists of the most investigated lectin. Previous studies have deeply investigated the participation of BjcuL in physiopathological events, especially involving its participation in inflammation. The lectin has been demonstrated as a pro-inflammatory agent, capable of triggering inflammatory events related to local and systemic leukocyte function. This activity is mediated by its binding to galactose-containing glycans on the cell surface to trigger different intracellular signaling and promote functional activation as rolling, adhesion, and migration of leukocytes, production of inflammatory mediators, and a killing profile of phagocytes. Furthermore, this review highlights not only the current understanding of snake venom lectins in pathophysiology and inflammation research but also explores potential future advancements, including the application of emerging technologies such as structural bioinformatics, high-throughput screening, and advanced omics approaches to uncover novel therapeutic targets and biotechnological applications.

Omics Approaches to Study Perilipins and Their Significant Biological Role in Cardiometabolic Disorders.

Lipid droplets (LDs), highly dynamic cellular organelles specialized in lipid storage and maintenance of lipid homeostasis, contain several proteins on their surface, among which the perilipin (Plin) family stands out as the most abundant group of LD-binding proteins. They play a pivotal role in influencing the behavior and functionality of LDs, regulating lipase activity, and preserving a balance between lipid synthesis and degradation, which is crucial in the development of obesity and abnormal accumulation of fat in non-adipose tissues, causing negative adverse biological effects, such as insulin resistance, mitochondrial dysfunction, and inflammation. The expression levels of Plins are often associated with various diseases, such as hepatic steatosis and atherosclerotic plaque formation. Thus, it becomes of interest to investigate the Plin roles by using appropriate "omics" approaches that may provide additional insight into the mechanisms through which these proteins contribute to cellular and tissue homeostasis. This review is intended to give an overview of the most significant omics studies focused on the characterization of Plin proteins and the identification of their potential targets involved in the development and progression of cardiovascular and cardiometabolic complications, as well as their interactors that could be useful for more efficient therapeutic and preventive approaches for patients.

Integrating Metabolomics and Genomics to Uncover the Impact of Fermented Total Mixed Ration on Heifer Growth Performance Through Host-Dependent Metabolic Pathways.

With the increasing demand for enhancing livestock production performance and optimizing feed efficiency, this study aimed to investigate the effects of fermented total mixed ration (FTMR) containing different proportions of rice straw and sheath and leaves of Zizania latifolia on systemic nutrient metabolism and oxidative metabolism under host genetic regulation and on growth performance of heifers. A total of 157 heifers aged 7-8 months were selected, and their hair was collected for whole-genome sequencing. They were randomly assigned into four groups of 18 to 21 cattle each and fed FTMR containing varying levels of rice straw (21% in LSF, 28% in MSF, 35% in HSF) or 31% sheath and leaves of Zizania latifolia (ZF) for a two-month period. At the end of trial, blood and urine samples were collected to measure biochemical indexes and metabolomics. The results showed that high rice straw content and ZF diets could increase blood glucose and non-protein nitrogen in heifers, that is, blood glucose and urea nitrogen levels in HSF and ZF groups were higher than those in LSF and MSF groups (p < 0.05). Meanwhile, the two diets could improve the antioxidant level of heifers. Urine metabolomics analysis between the groups identified three differential metabolic pathways, including 11 metabolites. Among them, l-homoserine and o-acetylserine had significant SNPs associated with them, which promoted glutathione metabolism. Although there was no significant effect of diet on heifers' average daily gain (ADG) in body weight (p > 0.05), there was substantial inter-individual variation in metabolites among all animals, as further correlation analyses illustrated. Twenty-eight metabolites were significantly associated with ADG (R > 0.3, p < 0.05). Four of them were identified as biomarkers, primarily regulating energy metabolism and oxidative balance. In conclusion, feeding HSF and ZF FTMR enhances glutathione metabolism and antioxidant capacity in heifers, positioning key metabolites as candidates for ADG markers. This integrative omics approach underscores the potential for enhancing livestock productivity and promoting sustainable agricultural practices.

The Interplay of Diet, Genome, Metabolome, and Gut Microbiome in Cardiovascular Disease: A Narrative Review.

The responsiveness to dietary interventions is influenced by complex, multifactorial interactions among genetics, diet, lifestyle, gut microbiome, environmental factors, and clinical characteristics, such as the metabolic phenotype. Detailed metabolic and microbial phenotyping using large human datasets is essential for better understanding the link between diet, the gut microbiome, and host metabolism in cardiovascular diseases (CVD). This review provides an overview of the interplay between diet, genome, metabolome, and gut microbiome in CVD. A literature review was conducted using PubMed and Scopus databases to identify pertinent cohort studies published between January 2022 and May 2024. This review focused on English articles that assessed the interplay of diet, genome, metabolome, and gut microbiome in relation to CVD in humans. This narrative review explored the role of single-omics technologies-genomics, metabolomics, and the gut microbiome-and multi-omics approaches to understand the molecular basis of the relationship between diet and CVD. Omics technologies enabled the identification of new genes, metabolites, and molecular mechanisms related to the association of diet and CVD. The integration of multiple omics approaches allows for more detailed phenotyping, offering a broader perspective on how dietary factors influence CVD. Omics approaches hold great potential for deciphering the intricate crosstalk between diet, genome, gut microbiome, and metabolome, as well as their roles in CVD. Although large-scale studies integrating multiple omics in CVD research are still limited, notable progress has been made in uncovering molecular mechanisms. These findings could guide the development of targeted dietary strategies and guidelines to prevent CVD.

Emergent properties of the lysine methylome reveal regulatory roles via protein interactions and histone mimicry.

Epigenomics has significantly advanced through the incorporation of Systems Biology approaches. This study aims to investigate the human lysine methylome as a system, using a data-science approach to reveal its emergent properties, particularly focusing on histone mimicry and the broader implications of lysine methylation across the proteome. We employed a data-science-driven OMICS approach, leveraging high-dimensional proteomic data to study the lysine methylome. The analysis focused on identifying sequence-based recognition motifs of lysine methyltransferases and evaluating the prevalence and distribution of lysine methylation across the human proteome. Our analysis revealed that lysine methylation impacts 15% of the known proteome, with a notable bias toward mono-methylation. We identified sequence-based recognition motifs of 13 lysine methyltransferases, highlighting candidates for histone mimicry. These findings suggest that the selective inhibition of individual lysine methyltransferases could have systemic effects rather than merely targeting histone methylation. The lysine methylome has significant mechanistic value and should be considered in the design and testing of therapeutic strategies, particularly in precision oncology. The study underscores the importance of considering non-histone proteins involved in DNA damage and repair, cell signaling, metabolism, and cell cycle pathways when targeting lysine methyltransferases.

Omics approaches: Role in acute myeloid leukemia biomarker discovery and therapy.

Acute myeloid leukemia (AML) is the most common acute leukemia in adults and has the highest fatality rate. Patients aged 65 and above exhibit the poorest prognosis, with a mere 30 % survival rate within one year. One important issue in optimizing outcomes for AML patients is their limited ability to predict responses to specific therapies, response duration, and likelihood of relapse. Despite rigorous therapeutic interventions, a significant proportion of patients experience relapse. Consequently, there is a pressing need to introduce new targets for therapy. Sequencing and biotechnology have come a long way in the last ten years. This has made it easier for many omics technologies, like genomics, transcriptomics, proteomics, and metabolomics, to study molecular mechanisms of AML. An integrative approach is necessary to understand a complex biological process fully and offers an important opportunity to understand the information underlying diseases. In this review, we studied papers published between 2010 and 2024 employing omics approaches encompassing diagnosis, prognosis, and risk stratification of AML. Finally, we discuss prospects and challenges in applying -omics technologies to the discovery of novel biomarkers and therapy targets. Our review may be helpful for omics researchers who want to study AML from different molecular aspects.

A Proteogenomic Approach for the Identification of Virulence Factors in Leishmania Parasites.

Identifying new genes involved in virulence and drug resistance may hold the key to a better understanding of parasitic diseases. The proteogenomic profiling of various Leishmania species, the causative agents of leishmaniasis, has identified several novel genes, N- and C-terminal extensions of proteins, and corrections of existing gene models. Various virulence factors (VFs) responsible for leishmaniasis have been previously annotated through a proteogenomic approach, including the C-terminal extension of heat shock protein 70 (HSP70). Furthermore, the diversity of VFs across Leishmania donovani, L. infantum, L. major, and L. mexicana was determined using phylogenetic analysis. Moreover, protein-protein interaction networks (PPINs) of VFs with HSPs aid in making significant biological interpretations. Overall, an integrated omics approach involving proteogenomics was used to identify and study the relationship among VFs with other interacting proteins, including HSPs. This chapter provides a step-by-step guide to the identification of new genes in Leishmania using a proteogenomic approach and their functional assignment using a bioinformatics-based approach.

Advanced omics approach and sustainable strategies for heavy metal microbial remediation in contaminated environments

Advanced omics approach and sustainable strategies for heavy metal microbial remediation in contaminated environments

Proteomics and transcriptomic analyses provide new insights into the pectin polysaccharide biosynthesis in Premna puberula Pamp

Premna puberula Pamp. is a plant with similarities to both food and medicine, which has attracted the attention of researchers because of the rich pectin in its leaves. However, the mechanism of efficient pectin accumulation remains unclear. Through transcriptomic and proteomic analyses, this study investigated the differentially expressed genes and proteins associated with pectin during various developmental stages of P. puberula. The combined omics approach revealed that the majority of differential genes are mainly involved in the anabolic metabolism of primary and secondary metabolites. Notable differential pathways include starch and sucrose metabolism, amino acid sugar metabolism, and nucleotide sugar metabolism. The SWEET gene family was identified and analyzed, leading to the cloning of PpSWEET15 and subcellular localization. Overexpression of PpSWEET15 resulted in a significant decrease in sucrose content in leaves from 134.44 μg·g−1 to <10 μg·g−1. Glucose content decreased from 407.75 μg·g−1 to 318.38 μg·g−1, while fructose levels showed no significant difference between the two groups of leaves. This comprehensive transcriptomic and proteomic analysis provides valuable insights into the molecular mechanisms underlying the efficient accumulation of pectin in P. puberula.

Insights into toxicological mechanisms of per-/polyfluoroalkyl substances by using omics-centered approaches.

The extensive presence of per-/polyfluoroalkyl substances (PFASs) in the environment and their adverse effects on organisms have garnered increasing concern. With the shift of industrial development from legacy to emerging PFASs, expanding the understanding of molecular responses to legacy and emerging PFASs is essential to accurately assess their risks to organisms. Compared with traditional toxicological approaches, omics technologies including transcriptomics, proteomics, metabolomics/lipidomics, and microbiomics allow comprehensive analysis of the molecular changes that occur in organisms after PFAS exposure. This paper comprehensively reviews the insights of omics approaches, especially the multi-omics approach, on the toxic mechanisms of both legacy and emerging PFASs in recent five years, focusing on hepatotoxicity, developmental toxicity, immunotoxicity, reproductive toxicity, neurotoxicity, and the endocrine-disrupting effect. PFASs exert various toxic effects via lipid and amino acid metabolism disruption, perturbations in several cell signal pathways, and binding to nuclear receptors. Notably, integrating multi-omics offers a thorough insight into the mechanisms of toxicity associated with PFASs. The gut microbiota plays an essential regulatory role in the toxic mechanisms of PFAS-induced hepatotoxicity. Finally, further research directions for PFAS toxicology based on omics technologies are prospected.

The Use of Omics in Untangling the Effect of Lifestyle Factors in Pregnancy and Gestational Diabetes: A Systematic Review.

To synthesise the evidence from clinical trials and observational studies using omics techniques to investigate the impact of diet and lifestyle factors on metabolite profile in pregnancy, and in the prevention and management of gestational diabetes mellitus (GDM). A systematic literature search was performed using PubMed, Ovid, CINAHL, and Web of Science databases in October 2023 and updated in September 2024. Inclusion criteria were randomised controlled trials (RCT) or non-RCTs in pregnant women with or without GDM, that measured diet and lifestyle factors, and which applied post-transcriptional omics approaches. Risk of bias was assessed using the ROBINS-I for non-RCTs and ROB-2 tool for RCTs. The results of all studies are narratively synthesised. Of 6293 studies identified, eight observational studies and three RCTs comprising 2639 pregnant women were included. Three studies reported on changes in diet-related metabolic phenotypes during pregnancy; however, the impact of certain foods on the metabolome and risk for GDM was less clear. Compared with women without GDM, women with GDM had a worse deterioration in metabolites, including saturated fatty acids, branched chain amino acids and purine degradation metabolites. There is limited evidence that conventional dietary treatment for GDM may modify the metabolome in women with GDM. Metabolome profiles in pregnancy may be altered by certain dietary choices; however, it is inconclusive whether improved diet related metabolite profiles have a beneficial impact in the prevention or management of GDM. High quality studies with larger sample sizes are needed to better understand the role that maternal nutrition plays in modulating the maternal metabolome, not only for a healthy pregnancy but also for the prevention and management of GDM.

Unveiling the mechanism of micro-and-nano plastic phytotoxicity on terrestrial plants: A comprehensive review of omics approaches.

Micro-and-nano plastics (MNPs) are pervasive in terrestrial ecosystems and represent an increasing threat to plant health; however, the mechanisms underlying their phytotoxicity remain inadequately understood. MNPs can infiltrate plants through roots or leaves, causing a range of toxic effects, including inhibiting water and nutrient uptake, reducing seed germination rates, and impeding photosynthesis, resulting in oxidative damage within the plant system. The effects of MNPs are complex and influenced by various factors including size, shape, functional groups, and concentration. Recent advancements in omics technologies such as proteomics, metabolomics, transcriptomics, and microbiomics, coupled with emerging technologies like 4D omics, phenomics, spatial transcriptomics, and single-cell omics, offer unprecedented insight into the physiological, molecular, and cellular responses of terrestrial plants to MNPs exposure. This literature review synthesizes current findings regarding MNPs-induced phytotoxicity, emphasizing alterations in gene expression, protein synthesis, metabolic pathways, and physiological disruptions as revealed through omics analyses. We summarize how MNPs interact with plant cellular structures, disrupt metabolic processes, and induce oxidative stress, ultimately affecting plant growth and productivity. Furthermore, we have identified critical knowledge gaps and proposed future research directions, highlighting the necessity for integrative omics studies to elucidate the complex pathways of MNPs toxicity in terrestrial plants. In conclusion, this review underscores the potential of omics approaches to elucidate the mechanisms of MNPs-phytotoxicity and to develop strategies for mitigating the environmental impact of MNPs on plant health.

Quantitative Live Imaging Reveals Phase Dependency of PDAC Patient-Derived Organoids on ERK and AMPK Activity.

Patient-derived organoids represent a novel platform to recapitulate the cancer cells in the patient tissue. While cancer heterogeneity has been extensively studied by a number of omics approaches, little is known about the spatiotemporal kinase activity dynamics. Here we applied a live imaging approach to organoids derived from 10 pancreatic ductal adenocarcinoma (PDAC) patients to comprehensively understand their heterogeneous growth potential and drug responses. By automated wide-area image acquisitions and analyses, the PDAC cells were non-selectively observed to evaluate their heterogeneous growth patterns. We monitored single-cell ERK and AMPK activities to relate cellular dynamics to molecular dynamics. Furthermore, we evaluated two anti-cancer drugs, a MEK inhibitor, PD0325901, and an autophagy inhibitor, hydroxychloroquine (HCQ), by our analysis platform. Our analyses revealed a phase-dependent regulation of PDAC organoid growth, where ERK activity is necessary for the early phase and AMPK activity is necessary for the late stage of organoid growth. Consistently, we found PD0325901 and HCQ target distinct organoid populations, revealing their combination is widely effective to the heterogeneous cancer cell population in a range of PDAC patient-derived organoid lines. Together, our live imaging quantitatively characterized the growth and drug sensitivity of human PDAC organoids at multiple levels: in single cells, single organoids, and individual patients. This study will pave the way for understanding the cancer heterogeneity and promote the development of new drugs that eradicate intractable cancer.

Emerging technologies in polyphenol analysis: from traditional methods to -omics approaches

Recent advancements in analytical technologies have revolutionized our ability to characterize, identify, and quantify polyphenolic compounds in complex biological matrices. This comprehensive review examines the transformative journey from traditional analytical methods to cutting-edge -omics approaches in polyphenol analysis. We critically evaluate the evolution from conventional spectrophotometric and chromatographic techniques to sophisticated high-throughput platforms integrating mass spectrometry, metabolomics, and artificial intelligence. Particular attention is given to emerging technologies such as miniaturized systems, real-time monitoring platforms, and advanced bioinformatics tools that are reshaping the landscape of polyphenol research. The review also addresses current challenges in method standardization, data integration, and validation while highlighting opportunities for future technological developments. By synthesizing recent progress in analytical methodologies, this review provides valuable insights for researchers in food science, nutrition, natural products chemistry, and related fields, emphasizing how these technological advances contribute to our understanding of polyphenol composition, bioactivity, and potential health benefits.

Foodomics as a Tool for Evaluating Food Authenticity and Safety from Field to Table: A Review

The globalization of the food industry chain and the increasing complexity of the food supply chain present significant challenges for food authenticity and raw material processing. Food authenticity identification now extends beyond mere adulteration recognition to include quality evaluation, label compliance, traceability determination, and other quality-related aspects. Consequently, the development of high-throughput, accurate, and rapid analytical techniques is essential to meet these diversified needs. Foodomics, an innovative technology emerging from advancements in food science, enables both a qualitative judgment and a quantitative analysis of food authenticity and safety. This review also addresses crucial aspects of fully processing food, such as verifying the origin, processing techniques, label authenticity, and detecting adulterants, by summarizing the omics technologies of proteomics, lipidomics, flavoromics, metabolomics, genomics, and their analytical methodologies, recent developments, and limitations. Additionally, we analyze the advantages and application prospects of multi-omics strategies. This review offers a comprehensive perspective on the food chain, food safety, and food processing from field to table through omics approaches, thereby promoting the stable and sustained development of the food industry.