Applications of Multi-omics Approaches for Food and Nutritional Security

Food systems are constantly changing to accommodate the advancement of societies. Increased challenges, including the World Wars, natural disasters, and the COVID-19 pandemic, have stimulated the improvement of the economics, quantity, and quality of food around the globe. Food security was introduced to alleviate and eradicate hunger and poverty with an aim to provide access to enough food and calories to everybody all the time. In society, this was translated to an increase in food rich in carbohydrates but not specifically all the nutrients and minerals required for healthy growth and development. Agriculturally, this has resulted in a rise in large-scale production of starch and filling food that can be used as staples worldwide. While hunger is not a problem in most countries, malnutrition is rampant on many levels. There are several cohorts of people suffering from metabolic disorders related to an imbalance in nutrients, including diabetes, obesity, and anemia, amongst others. The introduction of nutritional security is to ensure that everybody has access to nutrients from all food groups;this means proteins, carbohydrates, fibers, vitamins, and minerals. Rapid development in omics research has resulted in high-throughput techniques that can profile the makeup of crops, environmental samples, food, and human biofluids. Genomics, transcriptomics, proteomics, and metabolomics all explain how the different systems behave. Multi-omics is the assembly of all the complex data recorded to explain what is happening at a macroscale. This chapter provides an overview of the most up-to-date applications of multi-omics in food and nutrition security. © The Author(s), under exclusive license to Springer Nature Switzerland AG 2023.

Omics and systems view of innate immune pathways.

Multiomics approaches to studying systems biology are very powerful techniques that can elucidate changes in the genomic, transcriptomic, proteomic, and metabolomic levels within a cell type in response to an infection. These approaches are valuable for understanding the mechanisms behind disease pathogenesis and how the immune system responds to being challenged. With the emergence of the COVID-19 pandemic, the importance and utility of these tools have become evident in garnering a better understanding of the systems biology within the innate and adaptive immune response and for developing treatments and preventative measures for new and emerging pathogens that pose a threat to human health. In this review, we focus on state-of-the-art omics technologies within the scope of innate immunity.

Integrative multi-omics approach for identifying molecular signatures and pathways and deriving and validating molecular scores for COVID-19 severity and status.

BACKGROUND: There is still more to learn about the pathobiology of COVID-19. A multi-omic approach offers a holistic view to better understand the mechanisms of COVID-19. We used state-of-the-art statistical learning methods to integrate genomics, metabolomics, proteomics, and lipidomics data obtained from 123 patients experiencing COVID-19 or COVID-19-like symptoms for the purpose of identifying molecular signatures and corresponding pathways associated with the disease. RESULTS: We constructed and validated molecular scores and evaluated their utility beyond clinical factors known to impact disease status and severity. We identified inflammation- and immune response-related pathways, and other pathways, providing insights into possible consequences of the disease. CONCLUSIONS: The molecular scores we derived were strongly associated with disease status and severity and can be used to identify individuals at a higher risk for developing severe disease. These findings have the potential to provide further, and needed, insights into why certain individuals develop worse outcomes.

The promise and challenge of spatial omics in dissecting tumour microenvironment and the role of AI.

Growing evidence supports the critical role of tumour microenvironment (TME) in tumour progression, metastases, and treatment response. However, the in-situ interplay among various TME components, particularly between immune and tumour cells, are largely unknown, hindering our understanding of how tumour progresses and responds to treatment. While mainstream single-cell omics techniques allow deep, single-cell phenotyping, they lack crucial spatial information for in-situ cell-cell interaction analysis. On the other hand, tissue-based approaches such as hematoxylin and eosin and chromogenic immunohistochemistry staining can preserve the spatial information of TME components but are limited by their low-content staining. High-content spatial profiling technologies, termed spatial omics, have greatly advanced in the past decades to overcome these limitations. These technologies continue to emerge to include more molecular features (RNAs and/or proteins) and to enhance spatial resolution, opening new opportunities for discovering novel biological knowledge, biomarkers, and therapeutic targets. These advancements also spur the need for novel computational methods to mine useful TME insights from the increasing data complexity confounded by high molecular features and spatial resolution. In this review, we present state-of-the-art spatial omics technologies, their applications, major strengths, and limitations as well as the role of artificial intelligence (AI) in TME studies.

Systems genetics identifies miRNA-mediated regulation of host response in COVID-19.

BACKGROUND: Individuals infected with SARS-CoV-2 vary greatly in their disease severity, ranging from asymptomatic infection to severe disease. The regulation of gene expression is an important mechanism in the host immune response and can modulate the outcome of the disease. miRNAs play important roles in post-transcriptional regulation with consequences on downstream molecular and cellular host immune response processes. The nature and magnitude of miRNA perturbations associated with blood phenotypes and intensive care unit (ICU) admission in COVID-19 are poorly understood. RESULTS: We combined multi-omics profiling-genotyping, miRNA and RNA expression, measured at the time of hospital admission soon after the onset of COVID-19 symptoms-with phenotypes from electronic health records to understand how miRNA expression contributes to variation in disease severity in a diverse cohort of 259 unvaccinated patients in Abu Dhabi, United Arab Emirates. We analyzed 62 clinical variables and expression levels of 632 miRNAs measured at admission and identified 97 miRNAs associated with 8 blood phenotypes significantly associated with later ICU admission. Integrative miRNA-mRNA cross-correlation analysis identified multiple miRNA-mRNA-blood endophenotype associations and revealed the effect of miR-143-3p on neutrophil count mediated by the expression of its target gene BCL2. We report 168 significant cis-miRNA expression quantitative trait loci, 57 of which implicate miRNAs associated with either ICU admission or a blood endophenotype. CONCLUSIONS: This systems genetics study has given rise to a genomic picture of the architecture of whole blood miRNAs in unvaccinated COVID-19 patients and pinpoints post-transcriptional regulation as a potential mechanism that impacts blood traits underlying COVID-19 severity. The results also highlight the impact of host genetic regulatory control of miRNA expression in early stages of COVID-19 disease.

A machine learning analysis to evaluate the outcome measures in inflammatory myopathies.

OBJECTIVE: To assess the long-term outcome in patients with Idiopathic Inflammatory Myopathies (IIM), focusing on damage and activity disease indexes using artificial intelligence (AI). BACKGROUND: IIM are a group of rare diseases characterized by involvement of different organs in addition to the musculoskeletal. Machine Learning analyses large amounts of information, using different algorithms, decision-making processes and self-learning neural networks. METHODS: We evaluate the long-term outcome of 103 patients with IIM, diagnosed on 2017 EULAR/ACR criteria. We considered different parameters, including clinical manifestations and organ involvement, number and type of treatments, serum creatine kinase levels, muscle strength (MMT8 score), disease activity (MITAX score), disability (HAQ-DI score), disease damage (MDI score), and physician and patient global assessment (PGA). The data collected were analysed, applying, with R, supervised ML algorithms such as lasso, ridge, elastic net, classification, and regression trees (CART), random forest and support vector machines (SVM) to find the factors that best predict disease outcome. RESULTS AND CONCLUSION: Using artificial intelligence algorithms we identified the parameters that best correlate with the disease outcome in IIM. The best result was on MMT8 at follow-up, predicted by a CART regression tree algorithm. MITAX was predicted based on clinical features such as the presence of RP-ILD and skin involvement. A good predictive capacity was also demonstrated on damage scores: MDI and HAQ-DI. In the future Machine Learning will allow us to identify the strengths or weaknesses of the composite disease activity and damage scores, to validate new criteria or to implement classification criteria.

Systems analysis of human innate immunity in COVID-19.

Recent developments in sequencing technologies, the computer and data sciences, as well as increasingly high-throughput immunological measurements have made it possible to derive holistic views on pathophysiological processes of disease and treatment effects directly in humans. We and others have illustrated that incredibly predictive data for immune cell function can be generated by single cell multi-omics (SCMO) technologies and that these technologies are perfectly suited to dissect pathophysiological processes in a new disease such as COVID-19, triggered by SARS-CoV-2 infection. Systems level interrogation not only revealed the different disease endotypes, highlighted the differential dynamics in context of disease severity, and pointed towards global immune deviation across the different arms of the immune system, but was already instrumental to better define long COVID phenotypes, suggest promising biomarkers for disease and therapy outcome predictions and explains treatment responses for the widely used corticosteroids. As we identified SCMO to be the most informative technologies in the vest to better understand COVID-19, we propose to routinely include such single cell level analysis in all future clinical trials and cohorts addressing diseases with an immunological component.

Multi-omic longitudinal study reveals immune correlates of clinical course among hospitalized COVID-19 patients.

The IMPACC cohort, composed of >1,000 hospitalized COVID-19 participants, contains five illness trajectory groups (TGs) during acute infection (first 28 days), ranging from milder (TG1-3) to more severe disease course (TG4) and death (TG5). Here, we report deep immunophenotyping, profiling of >15,000 longitudinal blood and nasal samples from 540 participants of the IMPACC cohort, using 14 distinct assays. These unbiased analyses identify cellular and molecular signatures present within 72 h of hospital admission that distinguish moderate from severe and fatal COVID-19 disease. Importantly, cellular and molecular states also distinguish participants with more severe disease that recover or stabilize within 28 days from those that progress to fatal outcomes (TG4 vs. TG5). Furthermore, our longitudinal design reveals that these biologic states display distinct temporal patterns associated with clinical outcomes. Characterizing host immune responses in relation to heterogeneity in disease course may inform clinical prognosis and opportunities for intervention.

Multi-Omics Profiling for Health.

The world has witnessed a steady rise in both non-infectious and infectious chronic diseases, prompting a cross-disciplinary approach to understand and treating disease. Current medical care focuses on treating people after they become patients rather than preventing illness, leading to high costs in treating chronic and late-stage diseases. Additionally, a "one-size-fits all" approach to health care does not take into account individual differences in genetics, environment, or lifestyle factors, decreasing the number of people benefiting from interventions. Rapid advances in omics technologies and progress in computational capabilities have led to the development of multi-omics deep phenotyping, which profiles the interaction of multiple levels of biology over time and empowers precision health approaches. This review highlights current and emerging multi-omics modalities for precision health and discusses applications in the following areas: genetic variation, cardio-metabolic diseases, cancer, infectious diseases, organ transplantation, pregnancy, and longevity/aging. We will briefly discuss the potential of multi-omics approaches in disentangling host-microbe and host-environmental interactions. We will touch on emerging areas of electronic health record and clinical imaging integration with muti-omics for precision health. Finally, we will briefly discuss the challenges in the clinical implementation of multi-omics and its future prospects.

Publicly available resources in COVID-19 research and their applications

In late December 2019, pneumonia of an unidentified cause was reported in Wuhan, China, and on March 11, 2020, the World Health Organization proclaimed a pandemic of coronavirus disease 2019 (COVID-19). Today, this disease is still infecting millions of people worldwide and is responsible for forcing billions of people to stay under lockdown. This virus posed novel challenges to the research community and had a huge impact on available bioinformatics tools. Hence, the aim of the present chapter is to briefly summarize the role of bioinformatics in COVID-19 research, focusing on publicly available resources such as specific genomic, proteomic, epigenetic, transcriptomic, and toxicogenomic databases and tools for analysis;in vivo and clinical trial databases for COVID-19 drugs;bioinformatics tools and databases for severe acute respiratory syndrome coronavirus 2 drug designing and vaccine developments, resources and tools for clinicians;and mobile apps for tracking the pandemic. © 2023 Elsevier Inc. All rights reserved.

Omics approaches in COVID-19: An overview

COVID-19 caused by the virus SARS-CoV2 exhibits its devastating consequences worldwide in terms of health and economic loss. SARS-CoV2 is a novel coronavirus whose mechanism of infection and development of symptoms in patients leading to mortalities are poorly understood. Although primarily a respiratory virus, people infected with SARS-CoV2 show a series of symptoms involving multiple human organs including cardiac abnormalities, neuronal dysfunction, etc. Developing effective drugs to control the pandemic is overwhelmingly important and urgent. Ongoing rigorous scientific research based on molecular biology, genetics, genomics, proteomics, and informatics are in progress to develop suitable therapy. Using the omics-based approach, the correlation of vast amount of COVID-19 patient-related experimental data with patient-specific medical information is necessary prerequisite to manage COVID-19 patients and develop successful therapy especially in rural and urban areas where access to proper healthcare is limited. Conclusive data of these coordinated approaches would immensely help to manage a large number of critically ill patients to improve the treatment outcome and reduce mortalities. © 2023 Elsevier Inc. All rights reserved.

Gene expression in organoids: an expanding horizon.

Recent development of human three-dimensional organoid cultures has opened new doors and opportunities ranging from modelling human development in vitro to personalised cancer therapies. These new in vitro systems are opening new horizons to the classic understanding of human development and disease. However, the complexity and heterogeneity of these models requires cutting-edge techniques to capture and trace global changes in gene expression to enable identification of key players and uncover the underlying molecular mechanisms. Rapid development of sequencing approaches made possible global transcriptome analyses and epigenetic profiling. Despite challenges in organoid culture and handling, these techniques are now being adapted to embrace organoids derived from a wide range of human tissues. Here, we review current state-of-the-art multi-omics technologies, such as single-cell transcriptomics and chromatin accessibility assays, employed to study organoids as a model for development and a platform for precision medicine.

Integrating AI/ML Models for Patient Stratification Leveraging Omics Dataset and Clinical Biomarkers from COVID-19 Patients: A Promising Approach to Personalized Medicine.

The COVID-19 pandemic has presented an unprecedented challenge to the healthcare system. Identifying the genomics and clinical biomarkers for effective patient stratification and management is critical to controlling the spread of the disease. Omics datasets provide a wealth of information that can aid in understanding the underlying molecular mechanisms of COVID-19 and identifying potential biomarkers for patient stratification. Artificial intelligence (AI) and machine learning (ML) algorithms have been increasingly used to analyze large-scale omics and clinical datasets for patient stratification. In this manuscript, we demonstrate the recent advances and predictive accuracies in AI- and ML-based patient stratification modeling linking omics and clinical biomarker datasets, focusing on COVID-19 patients. Our ML model not only demonstrates that clinical features are enough of an indicator of COVID-19 severity and survival, but also infers what clinical features are more impactful, which makes our approach a useful guide for clinicians for prioritization best-fit therapeutics for a given cohort of patients. Moreover, with weighted gene network analysis, we are able to provide insights into gene networks that have a significant association with COVID-19 severity and clinical features. Finally, we have demonstrated the importance of clinical biomarkers in identifying high-risk patients and predicting disease progression.

Harnessing Deep Learning for Omics in an Era of COVID-19.

Omics data are multidimensional, heterogeneous, and high throughput. Robust computational methods and machine learning (ML)-based models offer new prospects to accelerate the data-to-knowledge trajectory. Deep learning (DL) is a powerful subset of ML inspired by brain structure and has created unprecedented momentum in bioinformatics and computational biology research. This article provides an overview of the current DL models applied to multi-omics data for both the beginner and the expert user. Additionally, COVID-19 will continue to impact planetary health as a pandemic and an endemic disease, with genomic and multi-omic pathophysiology. DL offers, therefore, new ways of harnessing systems biology research on COVID-19 diagnostics and therapeutics. Herein, we discuss, first, the statistical ML algorithms and essential deep architectures. Then, we review DL applications in multi-omics data analysis and their intersection with COVID-19. Finally, challenges and several promising directions are highlighted going forward in the current era of COVID-19.

The Role of Natural Products as Sources of Therapeutic Agents for Innovative Drug Discovery

Emerging threats to human health require a concerted effort in search of both preventive and treatment strategies, placing natural products at the center of efforts to obtain new therapies and reduce disease spread and associated mortality. The therapeutic value of compounds found in plants has been known for ages, resulting in their utilization in homes and in clinics for the treatment of many ailments ranging from common headache to serious conditions such as wounds. Despite the advancement observed in the world, plant based medicines are still being used to treat many pathological conditions or are used as alternatives to modern medicines. In most cases, these natural products or plant-based medicines are used in an un-purified state as extracts. A lot of research is underway to identify and purify the active compounds responsible for the healing process. Some of the current drugs used in clinics have their origins as natural products or came from plant extracts. In addition, several synthetic analogues are natural product-based or plant-based. With the emergence of novel infectious agents such as the SARS-CoV-2 in addition to already burdensome diseases such as diabetes, cancer, tuberculosis and HIV/AIDS, there is need to come up with new drugs that can cure these conditions. Natural products offer an opportunity to discover new compounds that can be converted into drugs given their chemical structure diversity. Advances in analytical processes make drug discovery a multi-dimensional process involving computational designing and testing and eventual laboratory screening of potential drug candidates. Lead compounds will then be evaluated for safety, pharmacokinetics and efficacy. New technologies including Artificial Intelligence, better organ and tissue models such as organoids allow virtual screening, automation and high-throughput screening to be part of drug discovery. The use of bioinformatics and computation means that drug discovery can be a fast and efficient process and enable the use of natural products structures to obtain novel drugs. The removal of potential bottlenecks resulting in minimal false positive leads in drug development has enabled an efficient system of drug discovery. This review describes the biosynthesis and screening of natural products during drug discovery as well as methods used in studying natural products. © 2022 Elsevier Inc. All rights reserved

A Perspective on Emerging Inter-Disciplinary Solutions for the Sustainable Management of Food Waste

Since food waste is a contemporary and complicated issue that is widely debated across many societal areas, the world community has designated the reduction of food waste as a crucial aspect of establishing a sustainable economy. However, waste management has numerous challenges, such as inadequate funding, poor waste treatment infrastructure, technological limitations, limited public awareness of proper sanitary practices, and inadequate legal and regulatory frameworks. A variety of microorganisms participate in the process of anaerobic digestion, which can be used to convert organic waste into biogas (e.g., methane) and nutrient-rich digestate. In this study, we propose a synergy among multiple disciplines such as nanotechnology, omics, artificial intelligence, and bioengineering that leverage anaerobic digestion processes to optimize the use of current scientific and technological knowledge in addressing global food waste challenges. The integration of these fields carries with it a vast amount of potential for improved waste management. In addition, we highlighted the relevance, importance, and applicability of numerous biogas-generating technologies accessible in each discipline, as well as assessing the impact of the COVID-19 epidemic on waste production and management systems. We identify diverse solutions that acknowledge the necessity for integration aimed at drawing expertise from broad interdisciplinary research to address food waste management challenges. © 2022 by the authors.

Perspective: Multiomics and Machine Learning Help Unleash the Alternative Food Potential of Microalgae.

Food security has become a pressing issue in the modern world. The ever-increasing world population, ongoing COVID-19 pandemic, and political conflicts together with climate change issues make the problem very challenging. Therefore, fundamental changes to the current food system and new sources of alternative food are required. Recently, the exploration of alternative food sources has been supported by numerous governmental and research organizations, as well as by small and large commercial ventures. Microalgae are gaining momentum as an effective source of alternative laboratory-based nutritional proteins as they are easy to grow under variable environmental conditions, with the added advantage of absorbing carbon dioxide. Despite their attractiveness, the utilization of microalgae faces several practical limitations. Here, we discuss both the potential and challenges of microalgae in food sustainability and their possible long-term contribution to the circular economy of converting food waste into feed via modern methods. We also argue that systems biology and artificial intelligence can play a role in overcoming some of the challenges and limitations; through data-guided metabolic flux optimization, and by systematically increasing the growth of the microalgae strains without negative outcomes, such as toxicity. This requires microalgae databases rich in omics data and further developments on its mining and analytics methods.