Omics Analysis Research Articles

Auxiliary diagnosis of primary bone tumors based on Machine learning model

ObjectiveResearch on auxiliary diagnosis of primary bone tumors can enhance diagnostic accuracy, facilitate early detection, and enable personalized treatment, thereby reducing misdiagnosis and missed cases, ultimately leading to improved patient prognosis and survival rates. In this study, we established a whole slide imaging (WSI) database comprising histopathological samples from all categories of bone tumors and integrated multiple neural network architectures for machine learning models. We then evaluated the accuracy of these models in diagnosing primary bone tumors. MethodsIn this paper, the machine learning model based on the deep convolutional neural network (DC-NN) method was combined with imaging omics analysis to analyze and discuss its clinical value in diagnosing primary bone tumors. In addition, this paper proposed a screening method for differentially expressed genes. Based on the paired T-test method, the process first estimated the tumor purity in the experimental data of each sample case, then assessed the actual gene expression value of the experimental data of each sample case, and finally calculated the optimized paired T-test statistics, and screened differentially expressed genes according to the threshold value. ResultsThe selected model demonstrated excellent diagnostic accuracy in distinguishing between normal and tumor images, with overall accuracy of (99.8 ± 0.4) % for five rounds of testing using the DCNN model and positive and negative predictive values of (100.0 ± 0.0) % and (99.6 ± 0.8) %, respectively. The mean area under each dataset’s curve (AUC) was (0.998 ± 0.004). Further, ten rounds of testing using the DCNN model showed an overall accuracy of (71.2 ± 1.6) % and a substantial positive predictive value of (91.9 ± 8.5) % in distinguishing benign from malignant bone tumors, with an average AUC of (0.62 ± 0.06) across datasets. ConclusionThe deep learning model accurately classifies bone tumor histopathology based on the degree of infiltration, achieving diagnostic performance comparable to that of senior pathologists. These findings affirm the feasibility and effectiveness of histopathological diagnosis in bone tumors, providing a theoretical foundation for the application and advancement of machine learning-assisted histopathological diagnosis in this field.

Combining transcriptome and metabolome analyses to reveal the response of maize roots to Pb stress

As a major food crop, maize (Zea mays L.) is facing a serious threat of lead (Pb) pollution. Research into its Pb tolerance is crucial for ensuring food security and human health, however, the molecular mechanism underlying the response to Pb remains incompletely understood. Here, we investigated the transcriptomic and metabolome of two maize lines (BY001, a Pb-resistant line; BY006, a Pb-sensitive line) under different concentrations of Pb stress (0, 500, 1000, 2000 and 3000 mg/L). The results showed that BY001 performed well, whereas the BY006 exhibited minimal development of lateral roots upon exposure to high concentration of Pb. The antioxidant enzyme activity of BY001 remained relatively stable, while that of BY006 declined significantly. Transcriptomic analysis revealed that under high concentration of Pb stress, BY001 produced 5057 differentially expressed genes, whereas BY006 produced 3374. Functional annotation showed that these genes were primarily involved in carbohydrate metabolism, root growth, and plant resistance to external Pb stress. Further untargeted metabolomics indicated that Pb stress triggered distinct alterations in the levels of 47 diverse metabolite types across 13 distinct classes, particularly amino acids, carbohydrates, and organic acids. A conjoint omics analysis suggested that the pathways of starch and sucrose metabolism, as well as cutin, suberin, and wax biosynthesis in BY001, play a key role in the Pb resistance. These findings elucidate the biological mechanisms employed by maize to counter the effects of Pb stress, and provide a basis for breeding of maize cultivars with low Pb accumulation or tolerance.

Bacteriocin Microcin J25's antibacterial infection effects and novel non-microbial regulatory mechanisms: differential regulation of dopaminergic receptors.

The antibacterial and immunomodulatory activities of bacteriocins make them attractive targets for development as anti-infective drugs. Although the importance of the enteric nervous system (ENS) in the struggle against infections of the intestine has been demonstrated, whether it is involved in bacteriocins anti-infective mechanisms is poorly defined. Here, we demonstrated that the bacteriocin Microcin J25 (J25) significantly alleviated diarrhea and intestinal inflammation in piglets caused by enterotoxigenic Escherichia coli (ETEC) infection. Mechanistically, macrophage levels were significantly downregulated after J25 treatment, and this was replicated in a mouse model. Omics analysis and validation screening revealed that J25 treatment induced significant changes in the dopaminergic neuron pathway, but little change in microbial structure. The alleviation of inflammation may occur by down-regulating dopamine receptor (DR) D1 and the downstream DAG-PKC pathway, thus inhibiting arachidonic acid decomposition, and the inhibition of macrophages may occur through the up-regulation of DRD5 and the downstream cAMP-PKA pathway, thus inhibiting NF-κB. Our studies' findings provide insight into the changes and possible roles of the ENS in J25 treatment of ETEC infection, providing a more sophisticated foundational understanding for developing the application potential of J25.

Effects of L-arginine on gut microbiota and muscle metabolism in fattening pigs based on omics analysis

IntroductionL-arginine is an α-amino acid and a semi-essential nutrient of significant biological interest. It plays a role in influencing various aspects of animal meat traits, gut microbiota composition, and physiological metabolism.MethodsThis study aimed to investigate the combined effects of L-arginine supplementation on gut microbiota composition and the metabolism of the longissimus dorsi muscle in fattening pigs. Eighteen Yorkshire commercial pigs were divided into two groups: a control group that received no supplements and a treatment group that was given 1% L-arginine for 52 days. The diversity and composition of microorganisms in the feces of the control (NC) and L-arginine (Arg) groups were analyzed by sequencing the 16S rRNA V3 -V4 region of the bacterial genome.ResultsThe findings indicated that L-arginine supplementation increased both the abundance and diversity of gut microbiota, particularly affecting the Firmicutes and Bacteroidetes phyla. KEGG enrichment analysis revealed significant changes in several metabolism-related pathways, including amino acid, carbohydrate, and lipid metabolism. Metabolomic analysis identified 85 differential metabolites between the arginine and control groups, with phospholipids ranking among the top 20. Additionally, functional predictions indicated an increased abundance in the glycerophospholipid metabolism pathway. Correlation analysis linked changes in gut microbiota to phospholipid levels, which subsequently influenced post-slaughter meat color and drip loss.DiscussionThese results suggest that L-arginine supplementation positively impacts gut microbiota composition and the metabolic profile of the longissimus dorsi muscle in fattening pigs, with potential implications for meat quality.

Mitochondrial elongation impairs breast cancer metastasis.

Mitochondrial dynamics orchestrate many essential cellular functions, including metabolism, which is instrumental in promoting cancer growth and metastatic progression. However, how mitochondrial dynamics influences metastatic progression remains poorly understood. Here, we show that breast cancer cells with low metastatic potential exhibit a more fused mitochondrial network compared to highly metastatic cells. To study the impact of mitochondrial dynamics on metastasis, we promoted mitochondrial elongation in metastatic breast cancer cells by individual genetic deletion of three key regulators of mitochondrial fission (Drp1, Fis1, Mff) or by pharmacological intervention with leflunomide. Omics analyses revealed that mitochondrial elongation causes substantial alterations in metabolic pathways and processes related to cell adhesion. In vivo, enhanced mitochondrial elongation by loss of mitochondrial fission mediators or treatment with leflunomide notably reduced metastasis formation. Furthermore, the transcriptomic signature associated with elongated mitochondria correlated with improved clinical outcome in patients with breast cancer. Overall, our findings highlight mitochondrial dynamics as a potential therapeutic target in breast cancer.

Analysis of Different Strains Fermented Douchi by GC×GC-TOFMS and UPLC-Q-TOFMS Omics Analysis.

Douchi is a kind of soybean-fermented food in China. To explore the common and differential compounds in different Douchi, Douchi was fermented by Aspergillus niger, Rhizopus arrhizus, and Bacillus circulans, respectively, and co-fermented by the three strains in this study. The common and characteristic flavor compounds and common and characteristic non-volatile components of different strains of fermented Douchi were explored through GC×GC-TOFMS and UPLC-Q-TOFMS omics analysis. The result suggested that Pyrazines, ketones, and alkenes such as tetramethyl-pyrazine, 2,5-dimethyl pyrazine, furaneol, 2,3-butanedione, gamma-terpinene might contribute to the basic flavor of the Douchi fermented by A. niger, R. arrhizus, and B. circulans. Peptides, amines, and flavonoids, such as N-acetylhistamine, 7,3',4'-trihydroxyflavone, (3S,8As)-3-isobutylhexahydropyrrolo[1,2-a]pyrazine-1,4-dione might contribute to the basic function of the above three Douchi. The common metabolic pathways involved in the fermentation were isoflavonoid biosynthesis, flavonoid biosynthesis, etc. Ketones and esters such as 2,3-dihydro-3,5-dihydroxy-6-methyl-4H-pyran-4-one, 3-octanone, 5-methylfurfural and nonanal contributed to the unique flavor, while betaine, oleanolic acid, saikosaponin D and leucine might contribute to the unique function of A. niger fermented Douchi. Alkenes, pyrazine, and ketones such as α-terpinene, ethyl-pyrazine, dihydro-3-methyl-2(3H)-furanone, and linalool might contribute to unique flavor, while cordycepin, 2-Phenylacetamide might contributed to the unique function of R. arrhizus fermented Douchi. The unique flavor of B. circulans fermented Douchi might derived from ketones and esters such as 3-acetyl-2-butanone, 2-tridecanone, propionic acid-2-phenylethyl ester, while vitexin, astragalin, and phenethylamine might contribute to the unique function. Compared with single-strain fermented Douchi, the flavor substances and non-volatile components in multi-strain fermented Douchi were more abundant, such as hexadecanoic acid methyl ester, benzeneacetic acid ethyl ester, 9,12-octadecadienoic acid ethyl ester, nuciferine, and erucamide. It was speculated that there were common and differential substances in Douchi fermented by Aspergillus niger, Rhizopus arrhizus, and Bacillus circulans, which might contribute to the basic and unique flavor and function. Compared with single-strain fermented Douchi, the flavor substances and metabolites in multi-strain fermented Douchi were more abundant. This study provided a reference for the research of flavor and functional substances of Douchi.

Huangqin decoction inhibits colorectal inflammatory cancer transformation by improving gut microbiome-mediated metabolic dysfunction

Colorectal inflammatory cancer transformation poses a major risk to patients with colitis. Patients with chronic intestinal inflammation have an approximately 2-3fold increased risk of developing colorectal cancer (CRC). Unfortunately, there is currently no effective intervention available. Huangqin decoction (HQD), a well-known traditional Chinese medicine (TCM) formula, is frequently clinically prescribed for treating patients with colitis, and its active ingredients have effective antitumour efficacy. Nonetheless, the mechanism of HQD-mediated prevention of colorectal inflammatory cancer transformation remains unclear. A strategy integrating metagenomic, lipidomic, and messenger RNA (mRNA) sequencing analysis was used to investigate the regulatory effects of HQD on the gut microbiome, metabolism and potential mechanisms involved in colorectal inflammatory cancer transformation. Our study revealed that HQD suppressed colorectal inflammatory cancer transformation, which was associated with enhanced intestinal barrier function, decreased the inflammatory response, and regulation of the gut microbiome. Notably, cohousing experiments revealed that the transfer of the gut microbiome from HQD-treated mice largely inhibited the pathological transformation of colitis. Moreover, gut microbiome transfer from HQD-treated mice primarily resulted in the altered regulation of fatty acid metabolism, especially the remodeling of arachidonic acid metabolism, which was associated with the amelioration of pathological transformation. Arachidonic acid metabolism and the key metabolic enzyme arachidonic acid 12-lipoxygenase (ALOX12) were affected by HQD treatment, and no obvious protective effect of HQD was observed in ALOX12−/− mice, which revealed that ALOX12 was a critical mediator of HQD protection against colorectal inflammatory cancer transformation. In summary, multiple omics analyses were applied to produce valuable data and theoretical support for the application of HQD as a promising intervention for the transformation of inflammatory colorectal cancer.

Exosomes Derived from Antler Mesenchymal Stem Cells Promote Wound Healing by miR-21-5p/STAT3 Axis.

Deer antlers, unique among mammalian organs for their ability to regenerate annually without scar formation, provide an innovative model for regenerative medicine. This study explored the potential of exosomes derived from antler mesenchymal stem cells (AMSC-Exo) to enhance skin wound healing. We explored the proliferation, migration and angiogenesis effects of AMSC-Exo on HaCaT cells and HUVEC cells. To investigate the skin repairing effect of AMSC-Exo, we established a full-thickness skin injury mouse model. Then the skin thickness, the epidermis, collagen fibers, CD31 and collagen expressions were tested by H&E staining, Masson's trichrome staining and immunofluorescence experiments. MiRNA omics analysis was conducted to explore the mechanism of AMSC-Exo in skin repairing. AMSC-Exo stimulated the proliferation and migration of HaCaT cells, accelerated the migration and angiogenesis of HUVEC cells. In the mouse skin injury model, AMSC-Exo stimulated angiogenesis and regulated the extracellular matrix by facilitating the conversion of collagen type III to collagen type I, restoring epidermal thickness to normal state without aberrant hyperplasia. Notably, AMSC-Exo enhanced the quality of wound healing with increased vascularization and reduced scar formation. MiRNAs in AMSC-Exo, especially through the miR-21-5p/STAT3 signaling pathway, played a crucial role in these processes. This study underscores the efficacy of AMSC-Exo in treating skin wounds, suggesting a new approach for enhancing skin repair and regeneration.

Anti-inflammatory mechanism of Houttuynia cordata polysaccharides against ulcerative colitis based on multi-omics conjoint analysis

The Houttuynia cordata polysaccharide (HCP) was extracted from the traditional Chinese medicine, Houttuynia cordata, known for its anti-inflammatory properties. It has an acidic heteropolysaccharide with a molecular weight of approximately 13.38 kDa, consisting of 7 monosaccharides such as galactose, galacturonic acid, and glucose. Mouse ulcerative colitis (UC) model experiments demonstrated its effective anti-inflammatory activity at concentrations of 100 mg/kg and 300 mg/kg respectively. The objective of this study was to investigate the mechanism of action underlying the therapeutic effects of HCP in UC through omics analysis method. A total of 724 different metabolites and 246 differential lipids were identified. Through metabolomic analysis, six metabolic pathways including the linoleic acid metabolic pathway, caffeine metabolic pathway, mannose and fructose metabolic pathways, methyl histidine metabolic pathway and fatty acid biosynthesis, which were significantly associated with colon-related diseases. Subsequently, lipidomics analysis revealed that the metabolic pathways of α-linolenic and linoleic acid, fatty acid biosynthesis, and glycerolipid metabolism exhibited significant associations with serum lipid metabolism. These findings suggested that HCP had potential therapeutic effects in treating UC.

The Emerging Era of Molecular Medicine.

The era of molecular medicine arose as we began to diagnose and treat diseases based on understanding how genes, proteins, and cells work, providing optimal therapeutic care through molecular profiling. Central to molecular medicine is molecular recognition, which is underpinned by techniques involving omics analysis, gene editing, and targeted agents. Recent advancements in these tools not only expand our understanding of biological processes but also aid in the development of diagnostic and treatment modalities at the molecular level, thus bridging the gap between medical research and clinical applications. This perspective traces the development of molecular tools, highlighting, along the way, their pivotal role in advancing molecular medicine for the global health of people.

Long-term exposure to triclocarban induces splenic injuries in mice: Insights from spatial metabolomics and lipidomics

Triclocarban (TCC) is a widely used antimicrobial agent and known endocrine-disrupting chemical found in various products. While its potential toxicities on endocrine-related organs have been highlighted in previous studies, the effects of TCC on non-endocrine organs, particularly the spleen, remain largely unknown. Here, we employed a novel approach combining long-term TCC exposure in a mouse model with spatial metabolomics and lipidomics to investigate the effects of TCC on the spleen. Our results showed that TCC exposure significantly altered the splenic organ weight and coefficient and induced obvious pathological alterations. Omic analysis revealed that TCC exposure disrupted the splenic homeostasis, as indicated by the upregulation of glutathione metabolism, ceramide-to-sphingomyelin signaling and biosynthesis of glycerophospholipids. Notably, the data of mass spectrometry imaging (MSI) revealed that TCC accumulated in the red pulp of the mouse spleen, while its metabolites concentrated in the white pulp. Further MSI analyses identified region-specific metabolic disruptions, including upregulated ceramide signaling in the red pulp, indicating localized inflammation, and upregulated glutathione metabolism throughout the spleen, suggesting widespread oxidative damage. Our findings provide crucial insights into the spatial distribution and biochemical impact of TCC on mice spleens, highlighting the potential risks of long-term TCC exposure to immune function.

Transcriptome and Metabolome Analyses Reveal High-Altitude Adaptation Mechanism of Epididymis Sperm Maturation in Tibetan Sheep.

In this study, the epididymal histology, caepididymal sperm physiological parameters, serum reproductive hormones, and antioxidant enzyme SOD levels of Tibetan sheep at a 2500 m and 3500 m altitude were compared by using a combination of transcriptome and metabolomics methods. This was conducted to investigate the effects of a high-altitude environment on spermatogenesis and the maturation of Tibetan sheep. The results showed that compared to the low-altitude group, the high-altitude group had a smaller epididymal lumen, thicker epididymal wall, significantly decreased sperm survival rate, and significantly increased sperm deformation rate, but no difference in sperm motility and sperm respiratory intensity. With increasing altitude, Tibetan sheep showed a decreasing trend in serum reproductive hormones (FSH and T), while the antioxidant enzyme SOD activity was significantly reduced. Transcriptomic analysis revealed 139 differentially expressed genes in the Tibetan sheep epididymis under high-altitude conditions. The SYCP2 gene is involved in multiple biological processes related to reproduction and plays an important role in the regulation of epididymal function and sperm quality in Tibetan sheep. Genes like ADCYAP1R1, CABP2, CALN1, and ATP6V1B1 can help maintain sperm viability and maturation by regulating the cAMP signaling pathway, calcium ion homeostasis, and cellular signaling. Metabolomic analysis found that the high-altitude group had increased adenosine content and decreased prostaglandin I2 content in the epididymis. These metabolites are involved in spermatogenesis, motility, fertilization, and early embryonic development. The integrated omics analysis suggests that Tibetan sheep adapt to the high-altitude hypoxic environment by regulating cAMP signaling pathway genes like ADCY and PRKACA, as well as metabolites like adenosine and prostaglandin I2, to maintain epididymal function and sperm motility. These genes and metabolites play an important role in maintaining normal epididymal function and sperm motility at high altitudes.

Multi-Omics Analysis Reveals the Mechanism by Which RpACBP3 Overexpression Contributes to the Response of Robinia pseudoacacia to Pb Stress.

Acyl-CoA-binding protein (ACBP) genes have been implicated in lead enrichment and translocation in plants; however, the mechanisms by which these genes contribute to the response to heavy metal stress in various taxa have not been determined. In this study, the molecular mechanisms underlying the response of Robinia pseudoacacia, an economically important deciduous tree, to Pb stress were examined using transcriptomic and metabolomic analyses. RpACBP3 overexpression increased Pb enrichment, translocation, and tolerance. After Pb stress for 3 days, 1125 differentially expressed genes (DEGs) and 485 differentially accumulated metabolites (DAMs) were identified between wild-type and RpACBP3-overexpressing R. pseudoacacia strains; after Pb stress for 45 days, 1746 DEGs and 341 DAMs were identified. Joint omics analyses showed that the DEGs and DAMs were co-enriched in α-linoleic acid metabolism and flavonoid biosynthesis pathways. In particular, DEGs and DAMs involved in α-linoleic acid metabolism and flavonoid biosynthesis were up- and down-regulated, respectively. Moreover, RpACBP3 overexpression enhanced the ability to scavenge reactive oxygen species and repair cell membranes under stress by regulating LOX gene expression and increasing the phosphatidylcholine content, thereby improving the tolerance to Pb stress. These findings lay a theoretical foundation for the future application of RpACBP3 genes in plant germplasm resource creation and phytoremediation of Pb contaminated soil in which R. pseudoacacia grow.

Aortic valve disease augments vesicular microRNA-145-5p to regulate the calcification of valvular interstitial cells via cellular crosstalk

Abstract Rationale: Aortic valve stenosis (AVS) is a major contributor to cardiovascular death in the elderly population worldwide. MicroRNAs (miRNAs) are highly dysregulated in patients with AVS undergoing surgical aortic valve replacement (SAVR). However, miRNA-dependent mechanisms regulating inflammation and calcification or miRNA-mediated cell-cell crossstalk during the pathogenesis of AVS are still poorly understood. Here, we explored the role of extracellular vesicles (EV)-associated miR-145-5p, which we showed to be highly upregulated upon valvular calcification in AVS in mice and humans. Methods Human TaqMan miRNA arrays identified dysregulated miRNAs in aortic valve tissue explants from AVS patients compared to non-calcified valvular tissue explants of patients undergoing SAVR. Echocardiographic parameters were measured in association with the quantification of dysregulated miRNAs in a murine AVS model. In vitro calcification experiments were performed to explore the effects of EV-miR-145-5p on calcification and crosstalk in valvular cells. To dissect molecular miRNA signatures and their effect on signaling pathways, integrated OMICS analyses were performed. RNA sequencing (RNA-seq), high-throughput transcription factor (TF) and proteome arrays showed that a number of genes, miRNAs, TFs, and proteins are crucial for calcification and apoptosis, which are involved in the pathogenesis of AVS. Results Among several miRNAs dysregulated in valve explants of AVS patients, miR-145-5p was the most highly gender-independently dysregulated miRNA (AUC, 0.780, p-value, 0.01). MiRNA arrays utilizing patient-derived- and murine aortic-stenosis samples demonstrated that the expression of miR-145-5p is significantly upregulated and correlates positively with cardiac function based on echocardiography. In vitro experiments confirmed that miR-145-5p is encapsulated into EVs and shuttled into valvular interstitial cells. Based on the integrated OMICs results, miR-145-5p interrelates with markers of inflammation, calcification, and apoptosis. In vitro calcification experiments demonstrated that miR-145-5p regulates the ALPL gene, a hallmark of calcification in vascular and valvular cells. EV-mediated shuttling of miR-145-5p suppressed the expression of ZEB2, a negative regulator of the ALPL gene, by binding to its 3' untranslated region to inhibit its translation, thereby diminishing the calcification of target valvular interstitial cells. Conclusion Elevated levels of pro-calcific and pro-apoptotic EV-associated miR-145-5p contribute to the progression of AVS via the ZEB2-ALPL axis, which could potentially be therapeutically targeted to minimize the burden of AVS.

Multiple Omics Analyses Reveal Activation of Nitrogen Metabolism and Flavonoid Glycosylation in Toxicodendron vernicifluum Under High Temperature

Lacquer trees (Toxicodendron vernicifluum), economically vital, face high-temperature stress in summer. Transcriptomic, proteomic, and metabolomic analyses were employed to investigate the mechanisms by which lacquer trees respond to high temperatures. High-temperature treatment led to notable metabolite changes with 224 upregulated and 69 downregulated. Indole-3-acetic acid remained stable while abscisic acid decreased, with increases in jasmonic acid and jasmonoyl-L-isoleucine indicating complex hormonal responses. JAR1 and ABA 8′-hydroxylase encoding genes were upregulated. The rise in JAs boosted the alkaloid content and activated nitrogen transport. High temperatures also increased specific amino acids and upregulated aminotransferase and protease-encoding genes. Metabolomic analysis showed elevated flavonoid glycosides and the upregulation of glycosyltransferase genes. WPCNA found 35 protein modules involved in secondary metabolite biosynthesis, protein phosphorylation, and signal transduction. Protein–protein interaction analysis revealed MYC6’s link with flavonoid biosynthesis, indicating its role in promoting flavonoids.

Multi-omics analysis uncovers the transcriptional regulatory mechanism of magnesium Ions in the synthesis of active ingredients in Sophora tonkinensis

Magnesium (Mg) plays a pivotal role as an essential component of plant chlorophyll and functions as a critical coenzyme. However, research exploring the regulatory mechanisms of magnesium ions on the synthesis of secondary metabolites is still in its early stages. Sophora tonkinensis is a widely utilized medicinal plant in China, recognized for its diverse secondary metabolites with active properties. This study investigates variations in these ingredients in tissue-cultured seedlings under varying magnesium concentrations. Simultaneously, an omics data analysis was conducted on tissue-cultured seedlings subjected to treatments with magnesium and low magnesium. These comprehensive omics analyses aimed to elucidate the mechanisms through which magnesium influences active components, growth, and development. Magnesium exerts a pervasive influence on various metabolic pathways, forming an intricate network. Research findings indicate that magnesium impacts diverse metabolic processes, including the absorption of potassium and calcium, as well as photosynthetic activity. Consequently, these influences lead to discernible changes in the levels of pharmacologically active compounds and the growth and developmental status.This study is the first to employ a multi-omics data analysis in S. tonkinensis. This methodology allows us to uncover the overarching impact of metabolic networks on the levels of various active ingredients and specific phenotypes.

Integrative Metabolome and Proteome Analysis of Cerebrospinal Fluid in Parkinson's Disease.

Parkinson's disease (PD) is a common neurodegenerative disorder characterized by the loss of dopaminergic neurons in the substantia nigra. Recent studies have highlighted the significant role of cerebrospinal fluid (CSF) in reflecting pathophysiological PD brain conditions by analyzing the components of CSF. Based on the published literature, we created a single network with altered metabolites in the CSF of patients with PD. We analyzed biological functions related to the transmembrane of mitochondria, respiration of mitochondria, neurodegeneration, and PD using a bioinformatics tool. As the proteome reflects phenotypes, we collected proteome data based on published papers, and the biological function of the single network showed similarities with that of the metabolomic network. Then, we analyzed the single network of integrated metabolome and proteome. In silico predictions based on the single network with integrated metabolomics and proteomics showed that neurodegeneration and PD were predicted to be activated. In contrast, mitochondrial transmembrane activity and respiration were predicted to be suppressed in the CSF of patients with PD. This review underscores the importance of integrated omics analyses in deciphering PD's complex biochemical networks underlying neurodegeneration.

Stratification according to autoantibody status in systemic sclerosis reveals distinct molecular signatures

ObjectivesSystemic sclerosis (SSc) is a heterogeneous disease, complicating its management. Its complexity and the insufficiency of clinical manifestations alone to delineate homogeneous patient groups further challenge this task. However, autoantibodies...

Serum metabolite and metal ions profiles for breast cancer screening

Enhancing early-stage breast cancer detection requires integrating additional screening methods with current diagnostic imaging. Omics screening, using easily collectible serum samples, could serve as an initial step. Alongside biomarker identification capabilities, omics analysis allows for a comprehensive analysis of prevalent histological types—DCIS and IDC. Employing metabolomics, metallomics, and machine learning, could yield accurate screening models with valuable insights into organism responses. Serum samples of confirmed breast cancer patients were utilized to analyze metabolite and metal ion profiles, using two distinct analysis methods, proton NMR for metabolomics and ICP-OES for metallomics. The resulting responses were then subjected to discriminant analysis, progression biomarker exploration, examination of correlations between patients’ metabolites and metal ions, and the impact of age and menopause status. Measured NMR spectra and metabolite relative integrals were used to achieve statistically significant discrimination through MVA between breast cancer and control groups. The analysis identified 24 metabolites and 4 metal ions crucial for discrimination. Furthermore, four metabolites were associated with disease progression. Additionally, there were important correlations and relationships between metabolite relative integrals, metal ion concentrations, and age/menopausal status subgroups. Quantified relative integrals allowed for discrimination between studied subgroups, validated with a holdout set. Feature importance and statistical analysis for metabolomics and metallomics extracted a set of common entities which in combination provides valuable insights into ongoing molecular disturbances and disease progression.

Building a community-driven bioinformatics platform to facilitate Cannabis sativa multi-omics research.

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