Multi-omics in food safety and authenticity in terms of food components

One of the main goals of food science is to ensure the high quality and safety of food. The inspection technology for known hazards has matured, and the identification of unknown and potential food safety hazards, as well as the identification of their composition and origin, is a challenge faced by food safety. Food safety and authenticity require multi-omics methods to support the implementation of qualitative discrimination to precise quantitative analysis, from targeted screening to non-target detection, and from multi component to full component analysis to address these challenges. The present review aims to provide characterizations, advantages, the latest progress, and prospects of using omics (including genomics, proteomics, and metabonomics) in food safety and authenticity. Multi omics strategies used to detect and verify different standard biomarkers of food will contribute to understanding the basic relationship between raw materials, processing, foods, nutrition, food safety, and human health.

Identification of Potential Genomic Alterations Using Pan-Cancer Cell-Free DNA Next-Generation Sequencing in Patients With Gastric Cancer

Background

Molecular cancer profiling may lead to appropriate trials for molecularly targeted therapies. Cell-free DNA (cfDNA) is a promising diagnostic and/or prognostic biomarker in gastric cancer (GC). We characterized somatic genomic alterations in cfDNA of patients with GC.

Methods

Medical records and cfDNA data of 81 patients diagnosed as having GC were reviewed. Forty-nine and 32 patients were tested using the Oncomine Pan-Cancer Cell-Free Assay on the Ion Torrent platform and AlphaLiquid 100 kit on the Illumina platform, respectively.

Results

Tier I or II alterations were detected in 64.2% (52/81) of patients. Biomarkers for potential targeted therapy were detected in 55.6% of patients (45/81), and clinical trials are underway. ERBB2 amplification is actionable and was detected in 4.9% of patients (4/81). Among biomarkers showing potential for possible targeted therapy, TP53 mutation (38.3%, 35 variants in 31 patients, 31/81) and FGFR2 amplification (6.2%, 5/81) were detected the most.

Conclusions

Next-generation sequencing of cfDNA is a promising technique for the molecular profiling of GC. Evidence suggests that cfDNA analysis can provide accurate and reliable information on somatic genomic alterations in patients with GC, potentially replacing tissue biopsy as a diagnostic and prognostic tool. Through cfDNA analysis for molecular profiling, it may be possible to translate the molecular classification into therapeutic targets and predictive biomarkers, leading to personalized treatment options for patients with GC in the future.

DNA methylation drives a new path in gastric cancer early detection: Current impact and prospects

Gastric cancer (GC) is one of the most common and deadly cancers worldwide. Early detection offers the best chance for curative treatment and reducing its mortality. However, the optimal population-based early screening for GC remains unmet. Aberrant DNA methylation occurs in the early stage of GC, exhibiting cancer-specific genetic and epigenetic changes, and can be detected in the media such as blood, gastric juice, and feces, constituting a valuable biomarker for cancer early detection. Furthermore, DNA methylation is a stable epigenetic alteration, and many innovative methods have been developed to quantify it rapidly and accurately. Nonetheless, large-scale clinical validation of DNA methylation serving as tumor biomarkers is still lacking, precluding their implementation in clinical practice. In conclusion, after a critical analysis of the recent existing literature, we summarized the evolving roles of DNA methylation during GC occurrence, expounded the newly discovered noninvasive DNA methylation biomarkers for early detection of GC, and discussed its challenges and prospects in clinical applications.

Thrombospondin-1 in drug activity and tumor response to therapies

Thrombospondins (TSPs) have numerous different roles in cancer, regulating the behavior of cancer cells and non-neoplastic cells, and defining the responses of tumor cells to environmental changes, thorough their ability to orchestrate cellular and molecular interactions in the tumor microenvironment (TME). As a result of these activities, TSPs can also control drug delivery and activity, tumor response and resistance to therapies, with different outcomes depending on the nature of TSP-interacting cell types, receptors, and ligands, in a highly context-dependent manner. This review, focusing primarily on TSP-1, discusses the effects of TSPs on tumor response to chemotherapy, antiangiogenic, low-dose metronomic chemotherapy, immunotherapy, and radiotherapy, by analyzing TSP activity on different cell compartments - tumor cells, vascular endothelial cells and immune cells. We review evidence of the value of TSPs, specifically TSP-1 and TSP-2, as biomarkers of prognosis and tumor response to therapy. Finally, we examine possible approaches to develop TSP-based compounds as therapeutic tools to potentiate the efficacy of anticancer therapy.

Recent Advances in Diagnostic, Prognostic, and Disease-Monitoring Biomarkers in Multiple Sclerosis

Multiple sclerosis (MS) is a highly heterogeneous disease. Currently, a combination of clinical features, MRI, and cerebrospinal fluid markers are used in clinical practice for diagnosis and treatment decisions. In recent years, there has been considerable effort to develop novel biomarkers that better reflect the pathologic substrates of the disease to aid in diagnosis and early prognosis, evaluation of ongoing inflammatory activity, detection and monitoring of disease progression, prediction of treatment response, and monitoring of disease-modifying treatment safety. In this review, the authors provide an overview of promising recent developments in diagnostic, prognostic, and disease-monitoring/treatment-response biomarkers in MS.

Gardenia extract protects against intrahepatic cholestasis by regulating bile acid enterohepatic circulation

ETHNOPHARMACOLOGICAL RELEVANCE

Cholestasis is the main manifestation of cholestatic liver disease, which has a risk of progression to end-stage liver disease. Gardeniae Fructus is the dried fruit of Gardeniae jasminoides Ellis, a plant of the Rubiaceae family. Gardeniae Fructus has shown therapeutic potential in cholestasis-related liver diseases and it is generally believed that Gardeniae Fructus ameliorates cholestasis, which could be related to its influence on bile acids (BAs) metabolism. However, the specific targets of Gardeniae Fructus and its impact on enterohepatic circulation of BAs have not yet been fully elucidated.

AIM OF THE STUDY

To systematically elucidate the mechanism by which Gardenia extract (GE, total iridoids in Gardeniae Fructus, which contains the predominant and characteristic phytoconstituents of Gardeniae Fructus) ameliorates alpha-naphthylisothiocyanate (ANIT)-induced cholestatic liver injury.

MATERIALS AND METHODS

Sprague-Dawley rats were orally administered water, obeticholic acid (OCA, 2 mg/kg), or GE (21 and 42 mg/kg) once daily for five days. On the third day, the model was established by administration of a single dose of ANIT (40 mg/kg) by oral gavage. Biochemical and pathological analyses, BA metabolomics, transcriptomics, and qRT-PCR were performed.

RESULTS

The profile of BAs in serum and liver confirmed that GE attenuated ANIT-induced acute cholestasis by affecting BA metabolism in a dose-dependent manner. Liver transcriptomic analysis indicated that GE mainly influenced the primary bile acid (PBA) biosynthesis and bile secretion pathways. GE mainly affected PBA biosynthesis in liver by upregulating Cyp8b1 gene expression, thereby significantly reducing the level of total bile acids (TBA). GE mainly promoted PBA excretion from liver into duodenum by upregulating Fxr and Oatp1 gene expression, thereby increasing the excretion of PBA in feces, and inhibiting PBA in liver entering the blood by alternative routes to reduce TBA levels in serum and urine and improve the enterohepatic circulation of BAs.

CONCLUSION

GE attenuated ANIT-induced hepatotoxicity and cholestasis in rats by upregulating Cyp8b1 expression to inhibit BA synthesis in the liver, while also promoting BA excretion via the intestinal-fecal route, and improving enterohepatic circulation of BAs.

Colorectal cancer: Genetic alterations, novel biomarkers, current therapeutic strategies and clinical trials

Colorectal cancer (CRC) is the third most commonly detected cancer with a serious global health issue. The rates for incidence and mortality for CRC are alarming, especially since the prognosis is abysmal when the CRC is diagnosed at an advanced or metastatic stage. Both type of (modifiable/ non-modifiable) types of risk factors are established for CRC. Despite the advances in recent technology and sophisticated research, the survival rate is still meager due to delays in diagnosis. Therefore, there is urgently required to identify critical biomarkers aiming at early diagnosis and improving effective therapeutic strategies. Additionally, a complete understanding of the dysregulated pathways like PI3K/Akt, Notch, and Wnt associated with CRC progression and metastasis is very beneficial in designing a therapeutic regimen. This review article focused on the dysregulated signaling pathways, genetics and epigenetics alterations, and crucial biomarkers of CRC. This review also provided the list of clinical trials targeting signaling cascades and therapies involving small molecules. This review discusses up-to-date information on novel diagnostic and therapeutic strategies alongside specific clinical trials.

Advancements in Mid-Infrared spectroscopy of extracellular vesicles

Extracellular vesicles (EVs) are lipid vesicles secreted by all cells into the extracellular space and act as nanosized biological messengers among cells. They carry a specific molecular cargo, composed of lipids, proteins, nucleic acids, and carbohydrates, which reflects the state of their parent cells. Due to their remarkable structural and compositional heterogeneity, characterizing EVs, particularly from a biochemical perspective, presents complex challenges. In this context, mid-infrared (IR) spectroscopy is emerging as a valuable tool, providing researchers with a comprehensive and label-free spectral fingerprint of EVs in terms of their specific molecular content. This review aims to provide an up-to-date critical overview of the major advancements in mid-IR spectroscopy of extracellular vesicles, encompassing both fundamental and applied research achievements. We also systematically emphasize the new possibilities offered by the integration of emerging cutting-edge IR technologies, such as tip-enhanced and surface-enhanced spectroscopy approaches, along with the growing use of machine learning for data analysis and spectral interpretation. Additionally, to assist researchers in navigating this intricate subject, our manuscript includes a wide and detailed collection of the spectral peaks that have been assigned to EV molecular constituents up to now in the literature.

Do zebrafish become blind or is it too much red dye in water? Distinguishing the embryo-larval development and physiology effects of DR 60, 73, and 78

Some dyes currently used by the textile, pharmaceutical, food, cosmetic, and photographic industries have been shown to be toxic and/or mutagenic to aquatic life. Most of these dyes resist degradation processes available for treating wastewater, and these processes might generate even more toxic by-products. Despite the large number of available dyes and the large quantity of dyes released into the environment, studies on their toxicity are still scarce. We evaluated and compared the effects in the animal model Danio rerio (zebrafish) of environmentally relevant concentrations of Disperse Red 60 (DR 60), 73 (DR 73), and 78 (DR 78) using the fish embryo acute toxicity (FET) test, morphometric analysis, immunofluorescence imaging, and behavioral parameters. DR 60 caused ocular modifications, while the DR 73 caused non-inflation of the swim bladder (NISB), pericardial edema (PE), scoliosis (S) and abnormal yolk sac (AYS) from at 0.125 mg/L. In behavioral tests, all the dyes induced changes in velocity and time spent swimming of exposed larvae. However, these alterations in behavior seem to be caused by different factors dependent on the dye and its concentration. Nevertheless, behavior seems to add valuable information concerning the hazards analysis of dyes, since it reveals to be the most sensitive group of parameters tested in the current study. In conclusion, of the behavioral and developmental alterations caused by these dyes should be interpreted as an alert for greater attention when registering new dyes and releasing them into the environment. In the particular case of DR 60 the possibility that directly affects the eye of larvae is of great environmental concern, but also from the human health perspective.

TCF4 and RBFOX1 as peripheral biomarkers for the differential diagnosis and treatment of major depressive disorder

BACKGROUND

Recent genome-wide association studies on major depressive disorder (MDD) have indicated the involvement of LRFN5 and OLFM4; however, the expression levels and roles of these molecules in MDD remain unclear. The present study aimed to determine the serum levels of TCF4 and RBFOX1 in patients with MDD and to investigate whether these molecules could be used as biomarkers for MDD diagnosis.

METHODS

The study included 99 drug-naïve MDD patients, 90 drug-treated MDD patients, and 81 healthy controls (HCs). Serum TCF4 and RBFOX1 levels were measured by ELISA. Pearson's correlation analysis was conducted to determine the association between TCF4/RBFOX1 and clinical variables. Linear support vector machine classifier was used to evaluate the diagnostic capabilities of TCF4 and RBFOX1.

RESULTS

Serum TCF4 and RBFOX1 levels were substantially higher in MDD patients than in HCs and significantly lower in drug-treated MDD patients than in drug-naïve MDD patients. Moreover, serum TCF4 and RBFOX1 levels were associated with the Hamilton Depression Scale score, duration of illness, serum lipids levels, and hepatic function. Thus, both these molecules showed potential as biomarkers for MDD. TCF4 and RBFOX1 combination exhibited a higher diagnostic performance, with the mean area under the curve values of 0.9861 and 0.9936 in the training and testing sets, respectively.

LIMITATIONS

Small sample size and investigation of only the peripheral nervous system.

CONCLUSIONS

TCF4 and RBFOX1 may be involved in the pathogenesis of MDD, and their combination may serve as a diagnostic biomarker panel for MDD.

Composition and sources of sediment organic matter in a western Iberian salt marsh: Developing a novel prediction model of the bromine sedimentary pool

Salt marshes are sensitive highly productive habitats crucial for carbon cycling. This study presents a comprehensive analysis of organic geochemical indicators and geochronology in the Mira salt marsh (SW Portugal) over eight centuries. The closely intertwined carbon and bromine (Br) biogeochemical cycles in these environments can influence the fluxes of volatile compounds such as ozone-depleting methyl bromide, emphasizing the importance of understanding sediment organic matter (OM) origin, budget, and composition in salt marshes. To characterize the strong Br-OM relationship, we used n-alkane signatures, bulk elemental data (total carbon, total nitrogen, Corg/Nat ratio), and stable isotopes (δ15N, δ13C) from a sediment core. Findings revealed a mixed composition of terrestrial and marine OM, posing challenges in distinguishing ex situ higher plant sources from in situ production by marsh vegetation. n-Alkanes (C15 to C31) were found in all the sediment samples, predominantly C25-C29. Changes in their presence were linked to marsh succession, evolving from a vegetation-free tidal flat to a C3 halophyte-dominated high marsh ecosystem. Despite the area's low industrial and population impact, regulation of water flow through the dam affected the balance between continental and marine waters. This study aimed to create a cost-effective predictive model for total Br, enhancing paleoclimatic studies using sedimentary samples. The n-alkane model had limited resolution, but an alternative infrared (IR) spectroscopy-based model, requiring less time and smaller sample sizes, was developed. Combining FT-IR spectra with statistical analysis enabled the creation of a reliable total Br concentration prediction model (mean absolute error = 14.39). These findings have implications for controlling Br enrichment in marsh environments and can be applied in various coastal wetlands with different mineralogical and organic characteristics.

Proteomics approach reveals urinary markers for early pregnancy diagnosis in buffaloes

This study aimed to compare urine proteomics from non- and pregnant buffaloes in order to identify potential biomarkers of early pregnancy. Forty-four females underwent hormonal ovulation synchronization and were randomly divided into two experimental groups: inseminated (n = 30) and non-inseminated (n = 14). The pregnant females were further divided into two groups: pregnant at Day 12 (P12; n = 8) and at Day 18 (P18; n = 8) post-ovulation. The non-pregnant group was also subdivided into two groups: non-pregnant at Day 12 (NP12; n = 7) and at Day 18 (NP18; n = 7). Urine was collected from all females on Days 12 or 18. The samples were processed for proteomics. A total of 798 proteins were reported in the urine considering all groups. The differential proteins play essential roles during pregnancy, acting in cellular transport and metabolism, endometrial remodeling, embryonic protection, and degradation of defective proteins. We suggest that some proteins from our study can be considered biomarkers for early pregnancy diagnosis, since they were increased in pregnant buffaloes. SIGNIFICANCE: Macromolecules have been studied for early pregnancy diagnosis, aiming to increase reproductive efficiency in cattle and buffaloes. Direct methods such as rectal palpation and ultrasonography have been considered late. Thus, this study aimed to compare urine proteomics from non- and pregnant buffaloes to identify potential biomarkers of early pregnancy. The differential proteins found in our study play essential roles during pregnancy, acting in cellular transport and metabolism, endometrial remodeling, embryonic protection, and degradation of defective proteins. We suggest that these proteins can be considered possible biomarkers for early pregnancy diagnosis since they were increased in the pregnant buffaloes.

Oxysterols as Biomarkers of Aging and Disease

Oxysterols derive from either enzymatic or non-enzymatic oxidation of cholesterol. Even though they are produced as intermediates of bile acid synthesis pathway, they are recognised as bioactive compounds in cellular processes. Therefore, their absence or accumulation have been shown to be associated with disease phenotypes. This chapter discusses the contribution of oxysterol to ageing, age-related diseases such as neurodegeneration and various disorders such as cancer, cardiovascular disease, diabetes, metabolic and ocular disorders. It is clear that oxysterols play a significant role in development and progression of these diseases. As a result, oxysterols are being investigated as suitable markers for disease diagnosis purposes and some drug targets are in development targeting oxysterol pathways. However, further research will be needed to confirm the suitability of these potentials.

Precise prediction of metabolites patterns using machine learning approaches in distinguishing honey and sugar diets fed to mice

As a natural sweetener produced by honey bees, honey was recognized as being healthier for consumption than table sugar. Our previous study also indicated thatmetaboliteprofiles in mice fed honey and mixedsugardiets aredifferent. However, it is still noteworthy about the batch-to-batch consistency of the metabolic differences between two diet types. Here, the machine learning (ML) algorithms were applied to complement and calibrate HPLC-QTOF/MS-based untargeted metabolomics data. Data were generated from three batches of mice that had the same treatment, which can further mine the metabolite biomarkers. Random Forest and Extra-Trees models could better discriminate between honey and mixed sugar dietary patterns under five-fold cross-validation. Finally, SHapley Additive exPlanations tool identified phosphatidylethanolamine and phosphatidylcholine as reliable metabolic biomarkers to discriminate the honey diet from the mixed sugar diet. This study provides us new ideas for metabolomic analysis of larger data sets.

Changes of the salivary and serum proteome in canine hypothyroidism

In this study, changes in salivary and serum proteome of dogs with hypothyroidism were studied using tandem mass tags (TMT) labelling and liquid chromatography-mass spectrometry (LC-MS/MS). Saliva and serum proteome from 10 dogs with hypothyroidism were compared with 10 healthy dogs. In saliva, a total of seven proteins showed significant changes between the two groups, being six downregulated and one upregulated, meanwhile, in serum, a total of six proteins showed significant changes, being five downregulated and one upregulated. The altered proteins reflected metabolic and immunologic changes, as well as, skin and coagulation alterations, and these proteins were not affected by gender. One of the proteins that were downregulated in saliva, lactate dehydrognease (LDH), was measured by a spectrophotometric assay in saliva samples from 42 dogs with hypothyroidism, 42 dogs with non-thyroid diseases and 46 healthy dogs. The activity of LDH was lower in the saliva of hypothyroid dogs when compared to non-thyroid diseased dogs and healthy controls. This study indicates that canine hypothyroidism can produce changes in the proteome of saliva and serum. These two sample types showed different variations in their proteins reflecting physiopathological changes that occur in this disease, mainly related to the immune system, metabolism, skin and coagulation. In addition, some of the proteins identified in this study, specially LDH in saliva, should be further explored as potential biomarkers of canine hypothyroidism.

Antifouling modification for high-performance isolation of circulating tumor cells

Circulating tumor cells (CTCs), which shed from solid tumor tissue into blood circulatory system, have attracted wide attention as a biomarker in the early diagnosis and prognosis of cancer. Given their potential significance in clinics, many platforms have been developed to separate CTCs. However, the high-performance isolation of CTCs remains significant challenges including achieving the sensitivity and specificity necessary due to their extreme rarity and severe biofouling in blood, such as billions of background cells and various proteins. With the advancement of CTCs detection technologies in recent years, the highly efficient and highly specific detection platforms for CTCs have gradually been developed, resulting in improving CTC capture efficiency, purity and sensitivity. In this review, we systematically describe the current strategies with surface modifications by utilizing the antifouling property of polymer, peptide, protein and cell membrane for high-performance enrichment of CTCs. To wrap up, we discuss the substantial challenges facing by current technologies and the potential directions for future research and development.

Hydroxy fatty acids in the surface Earth system

Lipids are ubiquitous and highly abundant in a wide range of organisms and have been found in various types of environmental media. These molecules play a crucial role as organic tracers by providing a chemical perspective on viewing the material world, as well as offering a wealth of information on metabolic activities. Among the diverse lipid compounds, hydroxy fatty acids (HFAs) with one to multiple hydroxyl groups attached to the carbon chain stand out as important biomarkers for different sources of organic matter. HFAs are widespread in nature and are involved in biotransformation and oxidation processes in living organisms. The unique chemical and physical properties attributed to the hydroxyl group make HFAs ideal biomarkers in biomedicine and environmental toxicology, as well as organic geochemistry. The molecular distribution patterns of HFAs can be unique and diagnostic for a given class of organisms, including animals, plants, and microorganisms. Thus, HFAs can act as a valuable proxy for understanding the ecological relationships between different organisms and their environment. Furthermore, HFAs have numerous industrial applications due to their higher reactivity, viscosity, and solvent miscibility. This review paper integrates the latest research on the sources and chemical analyses of HFAs, as well as their applications in industrial/medicinal production and as biomarkers in environmental studies. This review article also provides insights into the biogeochemical cycles of HFAs in the surface Earth system, highlighting the importance of these compounds in understanding the complex interactions between living organisms and the environment.

Body mass index and implications for pediatric kidney health: a cross-sectional study with urinary biomarkers

BACKGROUND

Extremes of unhealthy body weight, particularly obesity, are known to increase the risk of chronic kidney diseases. However, the current knowledge of kidney health outcomes associated with unhealthy body weight remains incomprehensive, especially in pediatrics. Therefore, the present study aimed to evaluate body mass index (BMI) and its potential associations with kidney health in a selected subset of school students in Sri Lanka.

METHODS

This cross-sectional study was conducted among students of both sexes in the range of 11-18 years of age (N = 1078) in education zones with no reported cases of chronic kidney disease of uncertain etiology. Based on sex- and age-specific BMI percentiles (LMS method), the participants were classified into five BMI groups (severely thin, thin, healthy, overweight, and obese) for measurement of urinary biomarkers of kidney injury: kidney injury molecule (KIM-1), neutrophil gelatinase-associated lipocalin (NGAL), and albumin creatinine ratio (ACR).

RESULTS

The median urinary levels of NGAL, ACR, and particularly KIM-1, which is a more sensitive indicator of kidney injury, showed no significant differences across the BMI strata. Importantly, moderate correlations of BMI with KIM-1 and NGAL were identified in severely thin girls.

CONCLUSIONS

According to the present study, these findings do not produce plausibly strong evidence to establish a potential association of BMI with altered kidney function in the studied pediatric communities. Particularly, a likelihood of abnormal kidney health outcomes associated with undernutrition is apparent in severely thin girls. However, in-depth studies are warranted to develop a comprehensive understanding of the associations of nutritional status with pediatric kidney health in Sri Lanka. A higher resolution version of the Graphical abstract is available as Supplementary information.