Omics Sciences Research Articles

Mapping barriers and bottlenecks for personalized preventive approaches in health systems worldwide

Abstract Over the past decades, the growing prevalence of chronic disease globally raised the public health need to plan tailored personalized preventive approaches, mainly through big data and -omic sciences. However, a conspicuous body of literature highlighted the existence of many barriers and bottlenecks hindering their actual implementation in real-word settings. From here, this scoping review of reviews aims to map all known barriers and bottlenecks to the implementation of personalized preventive approaches in European health systems and beyond. PubMed, Web of Science, Scopus and gray literature sources were consulted from 2017 to January 2023, identified barriers and bottlenecks were analyzed against the Consolidated Framework for Implementation Research (CFIR). Out of 11,602 records, 220 were deemed eligible for full-text screening, and a final sample of 34 review studies were extracted. Studies were mainly performed in USA 15 (44%) and UK 3 (9%), followed by Canada 2 (6%), India 2 (6%) and Italy 2 (6%). From our results, the lack of evidence on clinical utility, guidelines, specialized professionals, citizen trust and cultural issues are the most frequently reported barriers to the implementation of personalized preventive approaches worldwide. These in turn affect country specific policies and the applicability of such innovations across different populations, raising the risk of increasing health inequalities and discrimination concerns. Findings confirmed that most translational challenges pertain to primary and secondary prevention levels across several chronic diseases, with particular concerns for non-European ancestry individuals. Key messages • The identification of bottlenecks are informative of future precision public health interventions. • Barriers reported in most of the studies suggest the need to establish a targeted agenda.

A BIOPIRATARIA NA ÉPOCA DAS CIÊNCIAS ÔMICAS

Other nations have appropriated Brazil’s natural resources since the arrival of the Portuguese on Brazilian soil. Throughout history, countless explorers have arrived here to appropriate Brazil’s riches, especially its biodiversity. With advances in genetic engineering and omics sciences, there has been a change in how biopiracy is practiced, moving from the trafficking of fauna and flora species to the appropriation of genetic information from species belonging to the natural genetic heritage with biotechnological potential. This change has important repercussions on the global patent registration system and poses new challenges to monitoring and protecting Brazil’s genetic heritage.

The ROSMAP project: aging and neurodegenerative diseases through omic sciences.

The Religious Order Study and Memory and Aging Project (ROSMAP) is an initiative that integrates two longitudinal cohort studies, which have been collecting clinicopathological and molecular data since the early 1990s. This extensive dataset includes a wide array of omic data, revealing the complex interactions between molecular levels in neurodegenerative diseases (ND) and aging. Neurodegenerative diseases (ND) are frequently associated with morbidity and cognitive decline in older adults. Omics research, in conjunction with clinical variables, is crucial for advancing our understanding of the diagnosis and treatment of neurodegenerative diseases. This summary reviews the extensive omics research-encompassing genomics, transcriptomics, proteomics, metabolomics, epigenomics, and multiomics-conducted through the ROSMAP study. It highlights the significant advancements in understanding the mechanisms underlying neurodegenerative diseases, with a particular focus on Alzheimer's disease.

First person – Daisy Pineda-Suazo

ABSTRACT First Person is a series of interviews with the first authors of a selection of papers published in Biology Open, helping researchers promote themselves alongside their papers. Daisy Pineda-Suazo is first author on ‘ Evaluation of Octopus maya enzyme activity of the digestive gland and gastric juice’, published in BiO. Daisy is a postdoc in the Applied Ecophysiology laboratory at Universidad Nacional Autónoma de México, Sisal, México, investigating bioinformatics, molecular biology, omics sciences, biochemistry.

Volatilomics: An emerging discipline within Omics Sciences - A systematic review

Introduction Volatilomics is an omics science that is characterized as being a specific subbranch of metabolomics, which studies the different types of volatile organic compounds that may be present in a certain biological matrix. It has had impacts on the identification of new natural compounds and food safety processes, since it allows the evaluation of emerging contaminants that are present on food matrices, through the identification of biomarkers generated in response to this type of xenobiotic compounds through xenovolatilomic studies. Objective In this way, this review seeks to understand the scientific advances reported towards volatilomic studies, for which different types of primary research are reported depending on the main instrumental techniques used for the characterization of different types of VOCs that have been reported in our country between 2012 and 2022. Methodology Using a qualitative methodology, a search was carried out in the Scopus database, from which the bibliometric information of the primary research reported during this time was obtained, to later analyze the different research concerning the use of volatilomic studies and the fields of action that are currently used, as well as the different techniques for obtaining these compounds and the data analysis methodologies established for the processing of this type of research. Conclusions Finally, it can be concluded that, from the present review, the applicability of volatilomic studies is shown. The incursion carried out by this type of science on the verification of food safety in different types of matrices, in addition to allowing the study of the volatile profile formed by the different volatile organic compounds expressed by said matrix and the respective ecological role expressed by these compounds with the environment in which they are found.

Precision or Personalized Nutrition: A Bibliometric Analysis.

Food systems face the challenge of maintaining adequate nutrition for all populations. Inter-individual responses to the same diet have made precision or personalized nutrition (PN) an emerging and relevant topic. The aim of this study is to analyze the evolution of the PN field, identifying the principal actors and topics, and providing a comprehensive overview. Therefore, a bibliometric analysis of the scientific research available through the Web of Science (WOS) database was performed, revealing 2148 relevant papers up to June 2024. VOSviewer and the WOS platform were employed for the processing and analysis, and included an evaluation of diverse data such as country, author or most frequent keywords, among others. The analysis revealed a period of exponential growth from 2015 to 2023, with the USA, Spain, and England as the top contributors. The field of "Nutrition and Dietetics" is particularly significant, comprising nearly 33% of the total publications. The most highly cited institutions are the universities of Tufts, College Dublin, and Navarra. The relationship between nutrition, genetics, and omics sciences, along with dietary intervention studies, has been a defining factor in the evolution of PN. In conclusion, PN represents a promising field of research with significant potential for further advancement and growth.

Omics Science and Social Aspects in Detecting Biomarkers for Diagnosis, Risk Prediction, and Outcomes of Carotid Stenosis.

Carotid stenosis is characterized by the progressive narrowing of the carotid arteries due to the formation of atherosclerotic plaque, which can lead to stroke and death as major complications. Numerous biomarkers allow for its study and characterization, particularly those related to "omics" sciences. Through the most common research databases, we report representative studies about carotid stenosis biomarkers based on genomics, transcriptomics, proteomics, and metabolomics in a narrative review. To establish a priority among studies based on their internal validity, we used a quality assessment tool, the Scale for the Assessment of Narrative Review Articles (SANRA). Genes, transcriptomes, proteins, and metabolites can diagnose the disease, define plaque connotations, predict consequences after revascularization interventions, and associate carotid stenosis with other patient comorbidities. It also emerged that many aspects determining the patient's psychological and social sphere are implicated in carotid disease. In conclusion, when taking the multidisciplinary approach that combines human sciences with biological sciences, it is possible to comprehensively define a patient's health and thus improve their clinical management through precision medicine.

BioPipeline Creator—a user-friendly Java-based GUI for managing and customizing biological data pipelines

Bioinformatics tools are essential for performing analyses in the omics sciences. Given the numerous experimental opportunities arising from advances in the field of omics and easier access to high-throughput sequencing platforms, these tools play a fundamental role in research projects. Despite the considerable progress made possible by the development of bioinformatics tools, some tools are tailored to specific analytical goals, leading to challenges for non-bioinformaticians who need to integrate the results of these specific tools into a customized pipeline. To solve this problem, we have developed the BioPipeline Creator, a user-friendly Java-based GUI that allows different software tools to be integrated into the repertoire while ensuring easy user interaction via an accessible graphical interface. Consisting of client and server software components, BioPipeline Creator provides an intuitive graphical interface that simplifies the use of various bioinformatics tools for users without advanced computer skills. It can run on less sophisticated devices or workstations, allowing users to keep their operating system without having to switch to another compatible system. The server is responsible for the processing tasks and can perform the analysis in the user's local or remote network structure. Compatible with the most important operating systems, available at https://github.com/allanverasce/bpc.git.

Understanding the Conundrum of Pancreatic Cancer in the Omics Sciences Era.

Pancreatic cancer (PC) is an increasing cause of cancer-related death, with a dismal prognosis caused by its aggressive biology, the lack of clinical symptoms in the early phases of the disease, and the inefficacy of treatments. PC is characterized by a complex tumor microenvironment. The interaction of its cellular components plays a crucial role in tumor development and progression, contributing to the alteration of metabolism and cellular hyperproliferation, as well as to metastatic evolution and abnormal tumor-associated immunity. Furthermore, in response to intrinsic oncogenic alterations and the influence of the tumor microenvironment, cancer cells undergo a complex oncogene-directed metabolic reprogramming that includes changes in glucose utilization, lipid and amino acid metabolism, redox balance, and activation of recycling and scavenging pathways. The advent of omics sciences is revolutionizing the comprehension of the pathogenetic conundrum of pancreatic carcinogenesis. In particular, metabolomics and genomics has led to a more precise classification of PC into subtypes that show different biological behaviors and responses to treatments. The identification of molecular targets through the pharmacogenomic approach may help to personalize treatments. Novel specific biomarkers have been discovered using proteomics and metabolomics analyses. Radiomics allows for an earlier diagnosis through the computational analysis of imaging. However, the complexity, high expertise required, and costs of the omics approach are the main limitations for its use in clinical practice at present. In addition, the studies of extracellular vesicles (EVs), the use of organoids, the understanding of host-microbiota interactions, and more recently the advent of artificial intelligence are helping to make further steps towards precision and personalized medicine. This present review summarizes the main evidence for the application of omics sciences to the study of PC and the identification of future perspectives.

Genome-wide expression analysis in a Fabry disease human podocyte cell line

Fabry disease (FD) is an X-linked lysosomal disease caused by an enzyme deficiency of alpha-galactosidase A (α-gal A). This deficiency leads to the accumulation of glycosphingolipids in lysosomes, resulting in a range of clinical symptoms. The complex pathogenesis of FD involves lysosomal dysfunction, altered autophagy, and mitochondrial abnormalities. Omics sciences, particularly transcriptomic analysis, comprehensively understand molecular mechanisms underlying diseases. This study focuses on genome-wide expression analysis in an FD human podocyte model to gain insights into the underlying mechanisms of podocyte dysfunction. Human control and GLA-edited podocytes were used. Gene expression data was generated using RNA-seq analysis, and differentially expressed genes were identified using DESeq2. Principal component analysis and Spearman correlation have explored gene expression trends. Functional enrichment and Reporter metabolite analyses were conducted to identify significantly affected metabolites and metabolic pathways. Differential expression analysis revealed 247 genes with altered expression levels in GLA-edited podocytes compared to control podocytes. Among these genes, 136 were underexpressed, and 111 were overexpressed in GLA-edited cells. Functional analysis of differentially expressed genes showed their involvement in various pathways related to oxidative stress, inflammation, fatty acid metabolism, collagen and extracellular matrix homeostasis, kidney injury, apoptosis, autophagy, and cellular stress response. The study provides insights into molecular mechanisms underlying Fabry podocyte dysfunction. Integrating transcriptomics data with genome-scale metabolic modeling further unveiled metabolic alterations in GLA-edited podocytes. This comprehensive approach contributes to a better understanding of Fabry disease and may lead to identifying new biomarkers and therapeutic targets for this rare lysosomal disorder.

Surgical optomics: hyperspectral imaging and deep learning towards precision intraoperative automatic tissue recognition-results from the EX-MACHYNA trial.

Hyperspectral imaging (HSI), combined with machine learning, can help to identify characteristic tissue signatures enabling automatic tissue recognition during surgery. This study aims to develop the first HSI-based automatic abdominal tissue recognition with human data in a prospective bi-center setting. Data were collected from patients undergoing elective open abdominal surgery at two international tertiary referral hospitals from September 2020 to June 2021. HS images were captured at various time points throughout the surgical procedure. Resulting RGB images were annotated with 13 distinct organ labels. Convolutional Neural Networks (CNNs) were employed for the analysis, with both external and internal validation settings utilized. A total of 169 patients were included, 73 (43.2%) from Strasbourg and 96 (56.8%) from Verona. The internal validation within centers combined patients from both centers into a single cohort, randomly allocated to the training (127 patients, 75.1%, 585 images) and test sets (42 patients, 24.9%, 181 images). This validation setting showed the best performance. The highest true positive rate was achieved for the skin (100%) and the liver (97%). Misclassifications included tissues with a similar embryological origin (omentum and mesentery: 32%) or with overlaying boundaries (liver and hepatic ligament: 22%). The median DICE score for ten tissue classes exceeded 80%. To improve automatic surgical scene segmentation and to drive clinical translation, multicenter accurate HSI datasets are essential, but further work is needed to quantify the clinical value of HSI. HSI might be included in a new omics science, namely surgical optomics, which uses light to extract quantifiable tissue features during surgery.

The Third-Generation Sequencing Challenge: Novel Insights for the Omic Sciences.

The understanding of the human genome has been greatly improved by the advent of next-generation sequencing technologies (NGS). Despite the undeniable advantages responsible for their widespread diffusion, these methods have some constraints, mainly related to short read length and the need for PCR amplification. As a consequence, long-read sequencers, called third-generation sequencing (TGS), have been developed, promising to overcome NGS. Starting from the first prototype, TGS has progressively ameliorated its chemistries by improving both read length and base-calling accuracy, as well as simultaneously reducing the costs/base. Based on these premises, TGS is showing its potential in many fields, including the analysis of difficult-to-sequence genomic regions, structural variations detection, RNA expression profiling, DNA methylation study, and metagenomic analyses. Protocol standardization and the development of easy-to-use pipelines for data analysis will enhance TGS use, also opening the way for their routine applications in diagnostic contexts.

Metabolomics-based analysis of the diatom Cheatoceros tenuissimus combining NMR and GC–MS techniques

Metabolomics, a recent addition to omics sciences, studies small molecules across plants, animals, humans, and marine organisms. Nuclear magnetic resonance (NMR) and gas chromatography-mass spectrometry (GC–MS) are widely used in those studies, including microalgae metabolomics. NMR is non-destructive and highly reproducible but has limited sensitivity, which could be supplemented by joining GC–MS analysis. Extracting metabolites from macromolecules requires optimization for trustworthy results. Different extraction methods yield distinct profiles, emphasizing the need for optimization. The results indicated that the optimized extraction procedure successfully identified NMR and GC–MS-based metabolites in MeOH, CHCl3, and H2O extraction solvents. The findings represented the spectral information related to carbohydrates, organic molecules, and amino acids from the water-soluble metabolites fraction and a series of fatty acid chains, lipids, and sterols from the lipid fraction. Our study underscores the benefit of combining NMR and GC–MS techniques to comprehensively understand microalgae metabolomes, including high and low metabolite concentrations and abundances.•In this study, we focused on optimizing the extraction procedure and combining NMR and GC–MS techniques to overcome the low NMR sensitivity and the different detected range limits of NMR and GC–MS.•We explored metabolome diversity in a tropical strain of the small cells’ diatom Cheatoceros tenuissimus.

Immunotherapy and Cancer: The Multi-Omics Perspective.

Immunotherapies have revolutionized cancer treatment approaches. Because not all patients respond positively to immune therapeutic agents, it represents a challenge for scientists who strive to understand the mechanisms behind such resistance. In-depth exploration of tumor biology, using novel technologies such as omics science, can help decode the role of the tumor immune microenvironment (TIME) in producing a response to the immune blockade strategies. It can also help to identify biomarkers for patient stratification and personalized treatment. This review aims to explore these new models and highlight their possible pivotal role in changing clinical practice.

Neurolaw: Revisiting Huberty v. McDonald’s through the Lens of Nutritional Criminology and Food Crime

Recent studies have illuminated the potential harms associated with ultra-processed foods, including poor mental health, aggression, and antisocial behavior. At the same time, the human gut microbiome has emerged as an important contributor to cognition and behavior, disrupting concepts of the biopsychosocial ‘self’ and raising questions related to free will. Since the microbiome is undeniably connected to dietary patterns and components, the topics of nutrition and microbes are of heightened interest to neuroscience and psychiatry. Research spanning epidemiology, mechanistic bench science, and human intervention trials has brought legitimacy to nutritional criminology and the idea that nutrition is of relevance to the criminal justice system. The individual and community-level relationships between nutrition and behavior are also salient to torts and the relatively new field of food crime—that which examines the vast harms, including grand-scale non-communicable diseases and behavioral outcomes, caused by the manufacturers, distributors, and marketers of ultra-processed food products. Here in this essay, we will synthesize various strands of research, reflecting this emergent science, using a notable case that straddled both neurolaw and food crime, Huberty v. McDonald’s (1987). It is our contention that the legalome—microbiome and omics science applied in neurolaw and forensics—will play an increasing role in 21st-century courtroom discourse, policy, and decision-making.

Sustainability implications and relevance of using omics sciences to investigate cheeses with protected designation of origin.

Cheese, a fundamental component of the human diet and a cornerstone of the global food economy, has a significance beyond its role as a commodity, playing a crucial part in the cultural identity of various communities. The intricate natural aging process known as maturation involves a series of reactions that induce changes in the cheese's physical, biochemical, microbiological, and particularly sensory characteristics, making it a complex aspect of cheese production. Recently, the adoption of omics sciences (e.g., metagenomics, metabolomics, proteomics) has emerged as a new trend in studies related to protected designation of origin (PDO) cheese. This mini-summary aims to outline the relationship between omics studies in these food matrices and all the sustainability facets of the production chain in general, and to discuss and recognize that the importance of these studies goes beyond comprehending the cheese biome and extends to fostering and ensuring the sustainability of the production chain. In this context, numerous studies in recent years have linked the identification of intrinsic characteristics of PDO cheeses through omics sciences to crucial sustainability themes such as territoriality, biodiversity, and the preservation of product authenticity. The trajectory suggests that, increasingly, multidisciplinary studies spanning various omics sciences will not only contribute to the characterization of these products but will also address sustainability aspects directly related to the production chain (e.g., authenticity, microbial biodiversity, functionality). This expansion underscores the multidisciplinary nature of these studies, broadening their social impact beyond the academic realm. Consequently, these pivotal studies play a crucial role in advancing discussions on PDO products and sustainability. © 2024 Society of Chemical Industry.

Teaching mass spectrometry: A compilation of approaches to teaching theory and practice of mass spectrometry.

The areas of mass spectrometry applications seem to be much larger than those of any other analytical techniques. They extend from the determination of molecular mass in organic chemistry, through the analytical applications in forensic, environmental and omics sciences, the application in extra-terrestrial exploration and many others. Mass spectrometry, usually coupled with chromatographic techniques, has also found wide application in the pharmaceutical industry, forensic laboratories, laboratories of sanitary inspection or environmental inspection, etc. The growing areas of applications give rise to the demand for the comprehensive mass spectrometry education of undergraduates. This overview covers the body of literature describing various interesting ideas that can be successfully used for teaching mass spectrometry. Since mass spectrometry is a multidisciplinary field, old but dynamically developing, teaching mass spectrometry may be more problematic in comparison to teaching other analytical techniques, for example, there is the problem of position of mass spectrometry in the chemistry curriculum. On the other hand, it is obvious that the mass spectrometry community, besides difficult scientific work, does great and admirable teaching work, in order to perfectly educate undergraduates in the field of mass spectrometry and to make learning mass spectrometry as attractive as possible.

Artificial Intelligence Techniques and Pedigree Charts in Oncogenetics: Towards an Experimental Multioutput Software System for Digitization and Risk Prediction

Pedigree charts remain essential in oncological genetic counseling for identifying individuals with an increased risk of developing hereditary tumors. However, this valuable data source often remains confined to paper files, going unused. We propose a computer-aided detection/diagnosis system, based on machine learning and deep learning techniques, capable of the following: (1) assisting genetic oncologists in digitizing paper-based pedigree charts, and in generating new digital ones, and (2) automatically predicting the genetic predisposition risk directly from these digital pedigree charts. To the best of our knowledge, there are no similar studies in the current literature, and consequently, no utilization of software based on artificial intelligence on pedigree charts has been made public yet. By incorporating medical images and other data from omics sciences, there is also a fertile ground for training additional artificial intelligence systems, broadening the software predictive capabilities. We plan to bridge the gap between scientific advancements and practical implementation by modernizing and enhancing existing oncological genetic counseling services. This would mark the pioneering development of an AI-based application designed to enhance various aspects of genetic counseling, leading to improved patient care and advancements in the field of oncogenetics.

Advances in metabolomics profiling of pediatric kidney diseases: A review.

Pediatric renal diseases encompass a diverse array of pathological conditions, often engendering enduring ramifications. Metabolomics, an emergent branch of omics sciences, endeavors to holistically delineate alterations in metabolite compositions through the amalgamation of sophisticated analytical chemistry techniques and robust statistical methodologies. Recent advancements in metabolomics research within the realm of pediatric nephrology have been substantial, offering promising avenues for the identification of robust biomarkers, the elaboration of novel therapeutic targets, and the intricate elucidation of molecular mechanisms. The present discourse aims to critically review the progress in metabolomics profiling pertinent to pediatric renal disorders over the previous 12 years.

A Look into Ocular Diseases: The Pivotal Role of Omics Sciences in Ophthalmology Research.

Precision medicine is a new medical approach which considers both population characteristics and individual variability to provide customized healthcare. The transition from traditional reactive medicine to personalized medicine is based on a biomarker-driven process and a deep knowledge of biological mechanisms according to which the development of diseases occurs. In this context, the advancements in high-throughput omics technologies represent a unique opportunity to discover novel biomarkers and to provide an unbiased picture of the biological system. One of the medical fields in which omics science has started to be recently applied is that of ophthalmology. Ocular diseases are very common, and some of them could be highly disabling, thus leading to vision loss and blindness. The pathogenic mechanism of most ocular diseases may be dependent on various genetic and environmental factors, whose effect has not been yet completely understood. In this context, large-scale omics approaches are fundamental to have a comprehensive evaluation of the whole system and represent an essential tool for the development of novel therapies. This Review summarizes the recent advancements in omics science applied to ophthalmology in the last ten years, in particular by focusing on proteomics, metabolomics and lipidomics applications from an analytical perspective. The role of high-efficiency separation techniques coupled to (high-resolution) mass spectrometry ((HR)MS) is also discussed, as well as the impact of sampling, sample preparation and data analysis as integrating parts of the analytical workflow.