Metallomics: An Essential Tool for the Study of Potential Antiparasitic Metallodrugs

Metallomics is an emerging area of omics approaches that has grown enormously in the past few years. It integrates research related to metals in biological systems, in symbiosis with genomics and proteomics. These omics approaches can provide in-depth insights into the mechanisms of action of potential metallodrugs, including their physiological metabolism and their molecular targets. Herein, we review the most significant advances concerning cellular uptake and subcellular distribution assays of different potential metallodrugs with activity against Trypanosma cruzi, the protozoan parasite that causes Chagas disease, a pressing health problem in high-poverty areas of Latin America. Furthermore, the first multiomics approaches including metallomics, proteomics, and transcriptomics for the comprehensive study of potential metallodrugs with anti-Trypanosoma cruzi activity are described.

Metallophenolomics: A Novel Integrated Approach to Study Complexation of Plant Phenolics with Metal/Metalloid Ions

Plant adaptive strategies have been shaped during evolutionary development in the constant interaction with a plethora of environmental factors, including the presence of metals/metalloids in the environment. Among adaptive reactions against either the excess of trace elements or toxic doses of non-essential elements, their complexation with molecular endogenous ligands, including phenolics, has received increasing attention. Currently, the complexation of phenolics with metal(loid)s is a topic of intensive studies in different scientific fields. In spite of the numerous studies on their chelating capacity, the systemic analysis of phenolics as plant ligands has not been performed yet. Such a systematizing can be performed based on the modern approach of metallomics as an integral biometal science, which in turn has been differentiated into subgroups according to the nature of the bioligands. In this regard, the present review summarizes phenolics–metal(loid)s’ interactions using the metallomic approach. Experimental results on the chelating activity of representative compounds from different phenolic subgroups in vitro and in vivo are systematized. General properties of phenolic ligands and specific properties of anthocyanins are revealed. The novel concept of metallophenolomics is proposed, as a ligand-oriented subgroup of metallomics, which is an integrated approach to study phenolics–metal(loid)s’ complexations. The research subjects of metallophenolomics are outlined according to the methodology of metallomic studies, including mission-oriented biometal sciences (environmental sciences, food sciences and nutrition, medicine, cosmetology, coloration technologies, chemical sciences, material sciences, solar cell sciences). Metallophenolomics opens new prospects to unite multidisciplinary investigations of phenolic–metal(loid) interactions.

Recent and ancient evolutionary events shaped plant elemental composition of edaphic endemics: a phylogeny-wide analysis of Iberian gypsum plants

The analysis of plant elemental composition and the underlying factors affecting its variation are a current hot topic in ecology. Ecological adaptation to atypical soils may shift plant elemental composition. However, no previous studies have evaluated its relevance against other factors such as phylogeny, climate or individual soil conditions. We evaluated the effect of the phylogeny, environment (climate, soil), and affinity to gypsum soils on the elemental composition of 83 taxa typical of Iberian gypsum ecosystems. We used a new statistical procedure (multiple phylogenetic variance decomposition, MPVD) to decompose total explained variance by different factors across all nodes in the phylogenetic tree of target species (covering 120 million years of Angiosperm evolution). Our results highlight the relevance of phylogeny on the elemental composition of plants both at early (with the development of key preadaptive traits) and recent divergence times (diversification of the Iberian gypsum flora concurrent with Iberian gypsum deposit accumulation). Despite the predominant phylogenetic effect, plant adaptation to gypsum soils had a strong impact on the elemental composition of plants, particularly on sulphur concentrations, while climate and soil effects were smaller. Accordingly, we detected a convergent evolution of gypsum specialists from different lineages on increased sulphur and magnesium foliar concentrations.

Simultaneous quantification of 70 elements in biofluids within 5 min using inductively coupled plasma mass spectrometry to reveal elementomic phenotypes of healthy Chinese adults

High-throughput quantification of the composition of all chemical elements (elementome) in biological samples is essential for understanding their diverse functions in large cohort studies. We, here, established an ICP-MS method to simultaneously quantify 70 elements in 50 μL biofluids within 5 min. This validated method had excellent quantification linearity (R² > 0.998), sensitivity (with LOD as low as 1.0 ng/L), precision (CV<15%), accuracy (|RE|<20% except Hg), recovery (80-120%), throughput and coverage with minute samples. The method also showed good applicability to multiple biofluids including human serum, plasma, urine and goat serum samples. By using this method, we furture measured 70 elements in blood plasma samples from 758 Chinese adult participants and established the first reference intervals for the concentration of these elements from 127 healthy adults in this population. This offers a high-throughput quantitative elementomics method to define population elementomic phenotypes and for investigating the diverse biological functions of many elements in multiple biological matrices.

Speciomics as a concept involving chemical speciation and omics

The study of chemical speciation and the refinement and expansion of omics-based methods are both consolidated and highly active research fields. Although well established, such fields are extremely dynamic and are driven by the emergence of new strategies and improvements in instrumentation. In the case of omics-based studies, subareas including lipidomics, proteomics, metallomics, metabolomics and foodomics have emerged. Here, speciomics is being proposed as an "umbrella" term, that incorporates all of these subareas, to capture studies where the evaluation of chemical species is carried out using omics approaches. This paper contextualizes both speciomics and the speciome, and reviews omics applications used for species identification through examination of proteins, metalloproteins, metabolites, and nucleic acids. In addition, some implications from such studies and a perspective for future development of this area are provided. SIGNIFICANCE: The synergic effect between chemical speciation and omics is highlighted in this work, demonstrating an emerging area of research with a multitude of possibilities in terms of applications and further developments. This work not only defines and contextualizes speciomics and individual speciomes, but also demonstrates with some examples the great potential of this new interdisciplinary area of research.

Nuclease-resistant signaling nanostructures made entirely of DNA oligonucleotides

Nucleic acid probes have the advantages of excellent biocompatibility, biodegradability, versatile functionalities and remarkable programmability. However, the low biostability of nucleic acid probes under complex physiological conditions limits their in vivo application. Despite impressive progress in the development of inorganic material-mediated biostable nucleic acid nanostructures, uncertain systemic toxicity of composite nanocarriers has hindered their application in living organisms. In the field of biomedicine, as a promising alternative capable of avoiding potential cytotoxicity, biologically stable nanostructures composed entirely of DNA oligonucleotides have been rapidly developed in recent years, offering an exciting in vivo tool for cancer diagnosis and clinical treatment. In this review, we summarize the recent advances in the development of nuclease-resistant DNA nanostructures with different geometrical shapes, such as tetrahedron, octahedron, DNA triangular prism (DTP), DNA nanotubes and DNA origami, introduce innovative assembly strategies, and discuss unique structural advantages and especially biological applications in cellular imaging and targeted drug delivery in an organism. Finally, we conclude with the challenges in the clinical development of DNA nanostructures and present an outlook of the future of this rapidly expanding field.

Comparative nanometallomics as a new tool for nanosafety evaluation

Nanosafety evaluation is paramount since it is necessary not only for human health protection and environmental integrity but also as a cornerstone for industrial and regulatory bodies. The current nanometallomics did not cover non-metallic nanomaterials, which is an important part of nanomaterials. In this critical review, the concept of nanometallomics was expanded to incorporate all nanomaterials. The impacts on metal(loid) and metallo-biomolecular homeostasis by nanomaterials will be focused upon in nanometallomics study. Besides, the impacts on elemental and biomolecular homeostasis by metallo-nanomaterials are also considered as the research subjects of nanometallomics. Based on the new concept of nanometallomics, comparative nanometallomics was proposed as a new tool for nanosafety evaluation, which is high throughput and will be precise considering the nature of machine learning techniques. The perspectives of nanometallomics like metallo-wide association study and non-target nanometallomics were put forward.

Fluorescent probes for bioimaging of potential biomarkers in Parkinson's disease

This review comprehensively summarizes various types of fluorescent probes for PD and their applications for detection of various PD biomarkers.

Anaplasma pathogen infection alters chemical composition of the exoskeleton of hard ticks (Acari: Ixodidae)

Ticks are arthropod ectoparasites and vectors of pathogens affecting human and animal health worldwide. The exoskeleton is a structure that protect arthropods from natural threats such as predators and diseases. Both structural proteins and chemical elements are components of the exoskeleton. However, the chemical composition and effect of pathogen infection on tick exoskeleton properties has not been characterized. In this study, we characterized the chemical composition of tick exoskeleton and the effect of Anaplasma pathogen infection on the chemical elements of the exoskeleton and selected structural proteins. The chemical composition was characterized ventral, dorsal upper and dorsal lower regions of tick exoskeleton by scanning electron microscopy and energy dispersive spectroscopy and compared between infected and uninfected ticks. The levels of selected structural proteins were analyzed in infected and uninfected I. scapularis salivary glands by immunofluorescence analysis. The results showed that tick exoskeleton contains chemical elements also found in other arthropods. Some of the identified elements such as Mg and Al may be involved in tick exoskeleton stabilization through biomineralization of structural proteins that may be overrepresented in response to pathogen infection. These results suggested that pathogen infection alters the chemical composition of tick exoskeleton by mechanisms still to be characterized and with tick species and exoskeleton region-specific differences.

Metabolomic and metallomic profile differences between Veterans and Civilians with Pulmonary Sarcoidosis

Sarcoidosis is a disorder characterized by granulomatous inflammation of unclear etiology. In this study we evaluated whether veterans with sarcoidosis exhibited different plasma metabolomic and metallomic profiles compared with civilians with sarcoidosis. A case control study was performed on veteran and civilian patients with confirmed sarcoidosis. Proton nuclear magnetic resonance spectroscopy (1H NMR), hydrophilic interaction liquid chromatography mass spectrometry (HILIC-MS) and inductively coupled plasma mass spectrometry (ICP-MS) were applied to quantify metabolites and metal elements in plasma samples. Our results revealed that the veterans with sarcoidosis significantly differed from civilians, according to metabolic and metallomics profiles. Moreover, the results showed that veterans with sarcoidosis and veterans with COPD were similar to each other in metabolomics and metallomics profiles. This study suggests the important role of environmental risk factors in the development of different molecular phenotypic responses of sarcoidosis. In addition, this study suggests that sarcoidosis in veterans may be an occupational disease.

Elemental metabolomics

Elemental metabolomics is quantification and characterization of total concentration of chemical elements in biological samples and monitoring of their changes. Recent advances in inductively coupled plasma mass spectrometry have enabled simultaneous measurement of concentrations of > 70 elements in biological samples. In living organisms, elements interact and compete with each other for absorption and molecular interactions. They also interact with proteins and nucleotide sequences. These interactions modulate enzymatic activities and are critical for many molecular and cellular functions. Testing for concentration of > 40 elements in blood, other bodily fluids and tissues is now in routine use in advanced medical laboratories. In this article, we define the basic concepts of elemental metabolomics, summarize standards and workflows, and propose minimum information for reporting the results of an elemental metabolomics experiment. Major statistical and informatics tools for elemental metabolomics are reviewed, and examples of applications are discussed. Elemental metabolomics is emerging as an important new technology with applications in medical diagnostics, nutrition, agriculture, food science, environmental science and multiplicity of other areas.

Metallomics: The Science of Biometals and Biometalloids

Metallomics, a discipline integrating sciences that address the biometals and biometalloids, provides new opportunities for discoveries. As part of a systems biology approach, it draws attention to the importance of many chemical elements in biochemistry. Traditionally, biochemistry has treated life as organic chemistry, separating it from inorganic chemistry, considered a field reserved for investigating the inanimate world. However, inorganic chemistry is part of the chemistry of life, and metallomics contributes by showing the importance of a neglected fifth branch of building blocks in biochemistry. Metallomics adds chemical elements/metals to the four building blocks of biomolecules and the fields of their studies: carbohydrates (glycome), lipids (lipidome), proteins (proteome), and nucleotides (genome). The realization that non-essential elements are present in organisms in addition to essential elements represents a certain paradigm shift in our thinking, as it stipulates inquiries into the functional implications of virtually all the natural elements. This article discusses opportunities arising from metallomics for a better understanding of human biology and health. It looks at a biological periodic system of the elements as a sum of metallomes and focuses on the major roles of metals in about 30-40% of all proteins, the metalloproteomes. It emphasizes the importance of zinc and iron biology and discusses why it is important to investigate non-essential metal ions, what bioinformatics approaches can contribute to understanding metalloproteins, and why metallomics has a bright future in the many dimensions it covers.

A Comprehensive Diverse '-omics' Approach to Better Understanding the Molecular Pathomechanisms of Down Syndrome

Diverse ‘-omics’ technologies permit the comprehensive quantitative profiling of a variety of biological molecules. Comparative ‘-omics’ analyses, such as transcriptomics and proteomics, are powerful and useful tools for unraveling the molecular pathomechanisms of various diseases. As enhanced oxidative stress has been demonstrated in humans and mice with Down syndrome (DS), a redox proteomic analysis is useful for understanding how enhanced oxidative stress aggravates the state of individuals with oxidative stress-related disorders. In this review, ‘-omics’ analyses in humans with DS and mouse models of DS are summarized, and the molecular dissection of this syndrome is discussed.

Effects of chronic chromium(vi) exposure on blood element homeostasis: an epidemiological study

One hundred chromate production workers chronically exposed to low-level of hexavalent chromium [Cr(vi)] and eighty healthy individuals free from Cr exposure were recruited to the study. Personal sampling of airborne Cr was conducted and Cr content was quantified by Flame Atomic Absorption Spectrometry (FAAS). At the end of the sampling shift, blood samples were collected and element concentrations were measured by inductively coupled plasma mass spectrometry (ICP-MS) for Cr, Cd, Cu, Mo and Se and inductively coupled plasma atomic emission spectrometry (ICP-AES) for Ca, Fe, Mg and Zn. According to our results, 90% of the chromate production workers were exposed to airborne Cr in a concentration lower than 50 μg m(-3), which is the threshold limit value recommended by the American Conference of Governmental Industrial Hygienists and Chinese Ministry of Health. After Cr(vi) exposure, a significant increase in blood Cr, Cd, Fe, Mg, Mo, Se and Zn concentrations was observed, as well as a significant decrease in Ca concentration. A decrease in blood Cu was only observed among female workers. Blood Cr concentrations of the exposed workers (median = 15.68 ng mL(-1)) was four times higher than that of the controls (median = 3.03 ng mL(-1)), and significantly correlated with airborne Cr (r = 0.568, P<0.001). In addition, the inter-element correlations exhibited significant differences between the two groups. Our findings of the related health effects suggested that the underlying mechanisms of chronic Cr(vi) exposure on blood element homeostasis might be partly explained by oxidative stress in the body, dysfunction of Fe metabolism and renal injury.