Integration of multi-omics in investigations on the mechanisms of action of Chinese herbal medicine interventions in metabolic diseases

The rapid development of bioinformatics has provided novel approaches and methods for exploring the mechanisms of disease treatment via Chinese herbal medicines.Compound Chinese herbal medicines formulas have complex compositions and are characterized by their multiple constituents and diverse array of biological targets.Therefore,the mechanisms of action of most compound Chinese herbal medicines formulas cannot be adequately explained using a single pathway.Omics technologies describe high-throughput-based analytical and detection techniques,which include transcriptomics,proteomics,and metabolomics and provide multilayer parameter information that can be integrated to characterize the overall relationships involved in the therapeutic effects of Chinese herbal medicines formulas.Through their combination with network biology and drug effect networks,omics technologies also enable investigations into the mechanisms of disease treatment in traditional Chinese medicine.The integration of multiple omics technologies is in line with the concept of holism in traditional Chinese medicine and provides an approach for combining modern science and technology with traditional Chinese medicine theories.In recent years,omics technologies have been widely used to elucidate the mechanisms of action of Chinese herbal medicines.The latest studies employing multi-omics integration for investigating the mechanisms of action of Chinese herbal medicines interventions in metabolic diseases have devoted greater attention to in-depth explorations of disease pathogenesis.This paper provides a review of the following multi-omics technologies,which are used in research on the treatment of common metabolic diseases(e.g.,type-2 diabetes mellitus,nonalcoholic fatty liver disease):network pharmacology combined with metabolomics,16S rRNA sequencing combined with transcriptomics,16S rRNA sequencing combined with metabolomics,and 16S rRNA sequencing combined with network pharmacology and metabolomics.

Application of omics technologies for a deeper insight into quali-quantitative production traits in broiler chickens:A review

The poultry industry is continuously facing substantial and different challenges such as the increasing cost of feed ingredients, the European Union’s ban of antibiotic as growth promoters, the antimicrobial resistance and the high incidence of muscle myopathies and breast meat abnormalities. In the last decade, there has been an extraordinary development of many genomic techniques able to describe global variation of genes, proteins and metabolites expression level. Proper application of these cutting-edge omics technologies(mainly transcriptomics, proteomics and metabolomics) paves the possibility to understand much useful information about the biological processes and pathways behind different complex traits of chickens. The current review aimed to highlight some important knowledge achieved through the application of omics technologies and proteo-genomics data in the field of feed efficiency, nutrition, meat quality and disease resistance in broiler chickens.

Advances in Genomic,Transcriptomic,and Metabolomic Analyses of Fruit Quality in Fruit Crops

Fruit quality is the main factor determining market competitiveness;it represents the combination of fruit flavor,color,size,and the contents of aromatic and bioactive substances.Research on the genetic basis of fruit quality can provide new information about fruit biology,promote genomic-assisted breeding,and provide technological support for the regulation of fruit quality via habitat selection and/or the control of environmental conditions.High-throughput sequencing is a powerful research method for studying fruit quality traits,and reference genome sequences for many important fruit crops have provided vast amounts of genomic data.To study fruit quality,it is important to select appropriate omics strategies and to analyze omics data meaningfully.Here,we summarize genomic mechanisms of fruit quality formation:gene duplication,transposable element insertion,structural variations and genome methylation in functional genes.We review the genomic,transcriptomic,and metabolomic strategies that have been used to study the genetic basis of fruit quality traits.We also describe some of the genes associated with fruit traits;these genes are a valuable resource for genomics-assisted breeding and are useful models for deciphering the mechanisms of agronomic traits,such as fruit color,size,hardness,aroma components,sugar and acid content.Finally,to maximize the application of omics information,we propose some further directions for research using omics strategies.

Neglected scrub typhus:An updated review with a focus on omics technologies

Scrub typhus is a neglected disease and one of the most serious health problems in the Asia-Pacific region.The disease is caused by an obligate intracellular bacteria Orientia tsutsugamushi,which is transmitted by chigger bites or larval mite bites.Scrub typhus is a threat to billions of people worldwide causing different health complications and acute encephalitis in infants and growing children.The disease causes multiple organ failure and mortality rates may reach up to 70%due to a lack of appropriate healthcare.Currently available genome and proteome databases,and bioinformatics methods are valuable tools to develop novel therapeutics to curb the pathogen.This review discusses the state-of-the-art of information about Orientia tsutsugamushi-mediated scrub typhus and delineates the role of omics technologies to develop drugs against the pathogen.The role of proteome-wide in silico approaches for the identification of therapeutic targets is also highlighted.

Advances and applications in spatial transcriptomics

Spatial transcriptomics is an organizational study done on tissue sections that preserves the spatial information of the sample.Spatial transcriptomics aims to combine spatial information with gene expression data to quantify the mRNA expression of a large number of genes in the spatial context of tissues and cells.As a paradigm shift in biological research,spatial transcriptomics can provide both spatial location information and transcriptome-level cellular gene expression data,elucidating the interactions between cells and the microenvironment.From the understanding of the entire functional life cycle of RNA to the characterization of molecular mechanisms to the mapping of gene expression in various tissue regions,by choosing the appropriate spatial transcriptome technology,researchers can achieve a deeper exploration of biological developmental processes,disease pathogenesis,etc.In recent years,the field of spatial transcriptomics has ushered in several challenges along with its rapid development,such as the dependence on sample types,the resolution of visualized genes,the difficulty of commercialization,and the ability to obtain detailed single-cell information.In this paper,we summarize and review the four major categories of spatial transcriptome technologies and compare and analyze the technical advantages and major challenges of multiple research strategies to assist current experimental design and research analysis.Finally,the importance of spatial transcriptomics in the integration of multi-omics analysis and disease modeling as well as the future development prospects are summarized and outlined.

Novel Time-dependent Multi-omics Integration in Sepsis-associated Liver Dysfunction

The recently developed technologies that allow the analysis of each single omics have provided an unbiased insight into ongoing disease processes.However,it remains challenging to specify the study design for the subsequent integration strategies that can associate sepsis pathophysiology and clinical outcomes.Here,we conducted a time-dependent multi-omics integration(TDMI)in a sepsis-associated liver dysfunction(SALD)model.We successfully deduced the relation of the Toll-like receptor 4(TLR4)pathway with SALD.Although TLR4 is a critical factor in sepsis progression,it is not specified in single-omics analyses but only in the TDMI analysis.This finding indicates that the TDMI-based approach is more advantageous than single-omics analyses in terms of exploring the underlying pathophysiological mechanism of SALD.Furthermore,TDMI-based approach can be an ideal paradigm for insightful biological interpretations of multi-omics datasets that will potentially reveal novel insights into basic biology,health,and diseases,thus allowing the identification of promising candidates for therapeutic strategies.

Metabolic engineering based on systems biology for chemicals production

Microorganisms have been the main sources for the production of chemicals.Production of chemicals requires the development of low-cost and higher-yield processes.Towards this goal,microbial strains with higher levels of production should be first considered.Metabolic engineering has been used extensively over the past two to three decades to increase production of these chemicals.Advances in omics technology and computational simulation are allowing us to perform metabolic engineering at the systems level.By combining the results of omics analyses and computational simulation,systems biology allows us to understand cellular physiology and characteristics,which can subsequently be used for designing strategies.Here,we review the current status of metabolic engineering based on systems biology for chemical production and discuss future prospects.

Strategies for Revitalization of Traditional Medicine

Traditional medicine (TM) plays an inevitable role in drug discovery and development. Most of the therapeutically useful molecules used in the present day are inspired from TM. Herbal drugs are the oldest forms of medicines used for the treatment of various ailments and the TM of every country has a long history of their usage. To develop more data on their quality, safety, and efficacy, so also to improve the consumer’s need of modern days several thrust areas of research are to be focused on the development of TM. Based on the above concept, a paradigm shift is required for the revitalization of TM. These facts along with the modern scientific approaches, molecular tools, and strategies make it necessary for TM to be revitalized. Confluencing several strategies with the technological and scientific developments including pharmacogenomics, nutrigenomics, system biology, and related approaches, the scientific potential of TM can be explored further with international coordination and collaborations.