Altered Amino Acid Research Articles

Biomarkers of Frailty in Patients with Advanced Chronic Liver Disease Undergoing a Multifactorial Intervention Consisting of Home Exercise, Branched-Chain Amino Acids, and Probiotics

Frailty in cirrhosis or advanced chronic liver disease (ACLD) is a relevant prognostic factor. In the present study, we aimed to analyze potential biomarkers associated with frailty and its improvement in patients with ACLD. We analyzed the serum of outpatients with ACLD who participated in a previous study (Román, Hepatol Commun 2024) in which frailty was assessed using the liver frailty index (LFI), and patients who were frail or prefrail were randomized to a multifactorial intervention (home exercise, branched-chain amino acids, and probiotics) or control for 12 months. We determined a biomarker battery of inflammation, bacterial translocation, and liver damage in blood and urine and blood metabolomics by 1H-NMR. Thirty-seven patients were included. According to the LFI, 32 patients were frail or prefrail, and 5 were robust. At baseline, LFI correlated with LBP, sCD163, mtDNA, FGF-21, urinary NGAL, urinary claudin-3, and the metabolites mannose, ethanol, and isoleucine. During the study, patients in the intervention group showed an improvement in LFI and a decrease in CRP, LBP, sCD163, and ccK18 compared to the control group. Metabolomics showed a decrease in dimethyl sulfone and creatinine and an increase in malonate, ornithine, isoleucine, and valine in the intervention group. We conclude that frailty in patients with ACLD is associated with biomarkers of systemic inflammation, bacterial translocation, and liver damage, and alterations of amino acid and short-chain fatty acid metabolism.

Transcriptional responses to diets without mineral phosphorus supplementation in the jejunum of two high-yielding laying hen strains

Phosphorus (P) is an essential mineral for all forms of life including laying hens, playing a crucial role in growth and efficient egg production. Recent studies suggest that current P recommendations might exceed the physiological demand, leading to unnecessarily high P excretions. This study on Lohmann Brown (LB) and Lohmann Selected Leghorn (LSL) laying hens (n=80; 10 replicates per strain, production period, and dietary group) investigates transcriptional changes in the jejunum, a critical intestinal segment for mineral absorption, in response to a diet either without (P-) or with (P+) a mineral supplement from monocalcium phosphate, administered over a 4-week period during the transition (15–19 weeks) or onset of laying (20–24 weeks). DESeq2 analysis of RNA sequencing data revealed that most differentially expressed genes (DEGs) varied between strains and age groups, with less pronounced effects from dietary mineral P content. The 19-week-old LB hens showed a stronger response to dietary mineral P removal, with transcripts affiliated with increased adaptation of the metabolism and decreased immune pathway activation. The identified pathways such as folate biosynthesis and p53 signaling, potentially link altered energy and amino acid metabolism (2-oxocarboxylic acid and arginine). Interestingly, genes involved in calcium transport (CALB1) and cellular signaling (PRKCA, STEAP4) along with tight junctions (CLDN2) were affected by complete removal of mineral P supplements, suggesting a promoted intestinal mineral uptake. Transcriptional regulation in the jejunum in response to low dietary mineral content is strain-specific when the laying phase begins, which may contribute to a physiological Ca:P ratio.

Metabolomics revealed pharmacodynamic effects of aspirin and indobufen in patients after percutaneous transluminal angioplasty surgery

IntroductionAspirin and indobufen are commonly used therapeutic drugs for the prevention of vascular restenosis (VR) after percutaneous transluminal angioplasty surgery. They both exhibited antiplatelet effects but molecular mechanisms underlying metabolic changes induced by them remain unclear.MethodsIn this study, we collected plasma samples from patients on aspirin medication (n = 5), patients on indobufen medication, patients with no medication after PTA, and healthy controls (CKs) (n = 5). Our investigation aimed to reveal the metabolic processes in patients during vascular restenosis and its amelioration through drug therapy using liquid chromatography-tandem mass spectrometry (LC-MS/MS).ResultsOur data showed significant alterations in amino acid and choline metabolism in patients without medication after PTA. Aspirin and indobufen were able to regulate these metabolic pathways to alleviate VR symptoms. We identified several characteristic amino acids, including pro-leu, L-citrulline, his-glu, and L-glutamate, as important biomarkers for VR assessment in patients without medication after PTA. A total of 17 and 4 metabolites involved in arginine and phenylalanine metabolism were specifically induced by aspirin and indobufen, respectively. Their expression levels were significantly regulated by aspirin or indobufen, nearly reaching normal levels.DiscussionTaken together, our identification of metabolites involved in metabolic changes affected by aspirin and indobufen medication enhances the understanding of VR pathology after PTA. This may help identify early diagnostic biomarkers and therapeutic targets

Contaminant Exposure Profiles Demonstrate Similar Physiological Effects Across Environments Despite Unique Profile Composition in Formosa, Argentina, and Connecticut, USA.

Exposure to environmental contaminants is globally universal. However, communities vary in the specific combination of contaminants to which they are exposed, potentially contributing to variation in human health and creating "locally situated biologies." We investigated how environmental exposures differ across environments by comparing exposure profiles between two contexts that differ markedly across political, economic, and sociocultural factors-Namqom, Formosa, Argentina, and New Haven, Connecticut, United States. We collected infant urine, maternal urine, and human milk samples from mother-infant dyads in Formosa (n = 13) and New Haven (n = 21). We used untargeted liquid chromatography with high-resolution mass spectrometry (LC-HRMS) to annotate environmental contaminants and endogenous metabolites in these samples, and we analyzed the data using exposome-wide association studies (EWAS) followed by pathway enrichment. We found statistically significant differences between the chemical exposure profiles of the Argentinian and US mothers, mostly involving pesticides; however, we observed similarities in the infant urine and human milk environmental contaminant profiles, suggesting that the maternal body may buffer infant exposure through human milk. We also found that infants and mothers were exposed to contaminants that were associated with alterations in amino acid and carbohydrate metabolism. Infants additionally showed alterations in vitamin metabolism, including vitamins B1, B3, and B6. Differences in chemical exposure profiles may be related to structural factors. Despite variation in the composition of exposure profiles between the two study sites, environmental contaminant exposure was associated with similar patterns in human physiology when we considered contaminants comprehensively rather than individually, with implications for metabolic and cardiovascular disease risk as well as infant cognitive development.

Scutellarein inhibits lung cancer growth by inducing cell apoptosis and inhibiting glutamine metabolic pathway

Ethnopharmacological relevanceScutellaria baicalensis Georgi, a widely used Chinese medicinal herb, has shown effectiveness against lung cancer. Scutellarein, a key component of Scutellaria baicalensis, also demonstrates anticancer properties in lung cancer. However, the underlying mechanisms have not yet been clarified. Aim of the studyThis study aimed to investigate the effects of scutellarein in the treatment of NSCLC and its underlying mechanisms. MethodsThis study explored the effects of scutellarein on non–small cell lung cancer (NSCLC) and its mechanisms. A Lewis lung cancer mouse model was established to assess scutellarein's anticancer activity in vivo. Additionally, the compound's effects on cell proliferation, colony formation, migration, and apoptosis were evaluated in vitro using A549 and H1299 lung cancer cells. Metabolomics analysis was conducted to identify changes in cellular metabolism due to scutellarein, while molecular docking and western blotting techniques were employed to elucidate the molecular mechanisms of its anti-lung cancer effects. ResultsScutellarein significantly inhibited lung cancer xenograft tumor growth. In vitro studies showed that scutellarein suppressed migration and colony formation in A549 and H1299 cells, induced cell cycle arrest, and triggered cell apoptosis. Notably, scutellarein profoundly altered amino acid metabolism, particularly affecting glutamine metabolites. It affected key glutamine transporters ASCT2 and LAT1, as well as glutaminase GLS1, leading to their reduced expression. ConclusionScutellarein effectively inhibits lung cancer growth both in vivo and in vitro by inducing cell apoptosis and downregulating the glutamine metabolic pathway.

Comprehensive structure-function analysis reveals gain- and loss-of-function mechanisms impacting oncogenic KRAS activity.

To dissect variant-function relationships in the KRAS oncoprotein, we performed deep mutational scanning (DMS) screens for both wild-type and KRAS G12D mutant alleles. We defined the spectrum of oncogenic potential for nearly all possible KRAS variants, identifying several novel transforming alleles and elucidating a model to describe the frequency of KRAS mutations in human cancer as a function of transforming potential, mutational probability, and tissue-specific mutational signatures. Biochemical and structural analyses of variants identified in a KRAS G12D second-site suppressor DMS screen revealed that attenuation of oncogenic KRAS can be mediated by protein instability and conformational rigidity, resulting in reduced binding affinity to effector proteins, such as RAF and PI3-kinases, or reduced SOS-mediated nucleotide exchange activity. These studies define the landscape of single amino acid alterations that modulate the function of KRAS, providing a resource for the clinical interpretation of KRAS variants and elucidating mechanisms of oncogenic KRAS inactivation for therapeutic exploitation.

Branched-chain amino acid catabolism promotes ovarian cancer cell proliferation via phosphorylation of mTOR.

This study uncovers altered amino acid metabolism, specifically increased BCAA catabolism, at the interface of ovarian cancer cells and omental tissue in a coculture model of HGSOC secondary metastasis. Enhanced BCAA catabolism may promote cancer cell proliferation through mTOR signaling, presenting potential therapeutic value. These findings deepen our understanding of HGSOC pathogenesis and the metastatic tumor microenvironment, offering insights for developing new treatment strategies.

Transcriptional variation and RNA polymorphism among different Lentinula edodes (Berk.) Pegler strains.

Lentinula edodes is a commercially important mushroom known for its nutritional and therapeutic values. However, the molecular mechanisms underlying the distinct nutritional and physiological attributes of various L. edodes strains are not well understood. This study focused on three Lentinula strains (DMRO-356, DMRO-623, and DMRO-388s) with different nutritional and productivity profiles. Illumina sequencing was used to perform a whole-transcriptome analysis, conducting 100-base pair paired-end sequencing of total messenger RNA (mRNA) in duplicate, resulting in 28-48 million sequencing reads per strain. After rigorous data filtering, over 99% of high-quality reads were retained, and more than 95% were aligned to the Lentinula genome. Differential gene expression analyses identified 2210 differentially expressed genes between DMRO-356 and DMRO-623, 862 between DMRO-356 and DMRO-388s, and 2212 between DMRO-623 and DMRO-388s. Significant genetic variations were found among the strains, including 7753 single nucleotide polymorphisms (SNPs) in DMRO-356 versus DMRO-623 and 4080 SNPs in DMRO-356 versus DMRO-388s. Additionally, 349 insertions/deletions (InDels) were found in DMRO-356/DMRO-623 and 218 in DMRO-356/DMRO-388 s. Non-synonymous SNPs, which alter amino acid compositions, were analyzed, showing a preference for polar over charged amino acids. These differentially expressed genes were associated with various nutritional and developmental processes, highlighting the importance of genetic variations in shaping amino acid composition and potentially affecting protein function. This study is the first comprehensive exploration of transcriptional differences among Lentinula strains available for its cultivation, providing valuable insights to enhance mushroom quality and productivity. © 2024 Society of Chemical Industry.

Metabolic adaptations of Shewanella eurypsychrophilus YLB-09 for survival in the high-pressure environment of the deep sea.

Elucidation of the adaptation mechanisms and survival strategies of deep-sea microorganisms to extreme environments could provide a theoretical basis for the industrial development of extreme enzymes. There is currently a lack of understanding of the metabolic adaptation mechanisms of deep-sea microorganisms to high-pressure environments. The objective of this study was to investigate the metabolic regulatory mechanisms enabling a strain of the deep-sea bacterium Shewanella eurypsychrophilus to thrive under high-pressure conditions. To achieve this, we used nuclear magnetic resonance-based metabolomic and RNA sequencing-based transcriptomic analyses of S. eurypsychrophilus strain YLB-09, which was previously isolated by our research group and shown to be capable of tolerating high pressure levels and low temperatures. We found that high-pressure conditions had pronounced impacts on the metabolic pattern of YLB-09, as evidenced by alterations in energy, amino acid, and glycerolipid metabolism, among other processes. YLB-09 adapted to the high-pressure conditions of the deep sea by switching from aerobic intracellular energy metabolism to trimethylamine N-oxide respiration, altering the amino acid profile, and regulating the composition and the fluidity of cell membrane. The findings of our study demonstrate the capacity of microorganisms to alter their metabolism in response to elevated pressure, thereby establishing a foundation for a more profound understanding of the survival mechanisms of life in high-pressure environments.

Detrimental effects of glyphosate on muscle metabolism in grass carp (Ctenopharyngodon idellus)

Glyphosate, a commonly used herbicide, has been associated with environmental pollution and potential health risks to aquatic organisms. This study investigated the effects of glyphosate on the muscle metabolism of grass carp (Ctenopharyngodon idellus) following exposure to environmentally relevant concentrations. Over a 14-day exposure period to varying glyphosate levels, significant disruptions were observed in antioxidant capacity and muscle health. These disruptions were evidenced by reductions in total antioxidant capacity (T-AOC), increases in malondialdehyde (MDA) levels, and decreases in activities of glutathione peroxidase (GSH-PX) and catalase (CAT). Furthermore, exposure to glyphosate resulted in a reduction of vitamin E content and an elevation of hormonal levels, suggesting the potential for endocrine disruption. Metabolomics analysis identified 605 distinct metabolites, with notable alterations in amino acid, carbohydrate, and nucleotide metabolism pathways. Specifically, arginine and glutathione metabolisms were severely impacted, with decreases in key amino acids such as glycine and glutathione at higher glyphosate concentrations. Nucleotide metabolism, particularly purine synthesis, was also significantly affected, with reduced levels of deoxyguanosine and other purine-related compounds. The study further investigated the origins of these differential metabolites using the MetOrigin platform, suggesting a potential involvement of the intestinal microbiota in the metabolic response to glyphosate. These findings highlight the multifaceted adverse effects of glyphosate on fish muscle, including oxidative stress and metabolic dysregulation, which may contribute to diminished muscle quality and health risks for aquatic organisms.

Amino acid metabolites profiling in unpredictable chronic mild stress-induced depressive rats and the protective effects of Gastrodia elata Blume and gastrodin

Ethnopharmacological relevanceMajor depressive disorder (MDD) is a prevalent condition that affects approximately 350 million people worldwide. Several studies have identified changes in amino acids in the blood of MDD patients, suggesting their potential as biomarkers to better understand their role in depression. Gastrodia elata Blume (GEB) and its active compound gastrodin (GAS) are recognized for their antidepressant properties. However, their effects on amino acid profiles and their potential role in alleviating depression remain poorly understood. Understanding how GEB and GAS influence amino acid metabolism may offer novel insights into their mechanisms in alleviating depression, potentially leading to more targeted therapeutic strategies. Aim of the studyThis study aimed to investigate the potential role of supplementing GEB and its active compound GAS to reverse altered amino acid profiles in depressed rats. Materials and methodsTo achieve this, six-week-old SD rats were induced depressive-like behaviors by the UCMS rat model for 5 weeks. Groups receiving GEB or GAS were administered orally via gavage daily within the UCMS model. Serum samples were collected and analyzed using a targeted metabolomics approach employing LC-MS for amino acid profiling. ResultsA total of 38 amino acid metabolites were identified, 17 of which were significantly altered following UCMS. UCMS rats exhibited perturbed arginine biosynthesis, arginine and proline metabolism pathways. Changes in key amino acids in these metabolic pathways were reversed following supplementation with GEB and GAS, which also alleviated depressive symptoms. ConclusionsIn conclusion, UCMS-induced depression in rats causes changes in some amino acid metabolites similar to those found in human depression, validating its relevance as a model for studying depression. Additionally, the research suggests that GEB and GAS may exert antidepressant effects by regulating amino acid metabolism.

Evaluation of the role of EGFR exon 19 747-750 deletion mutation and plasma amino acid profile in the development of lung cancer.

Lung cancer (LC) is the most common form of cancer in the world. Of the proteins involved in cell differentiation and proliferation, the epidermal growth factor receptor (EGFR) is among the most significant. Amino acids play a crucial role in cell physiology as metabolic regulators. The benefits of liquid biopsies are their non-invasive nature, ease of collection, and ability to depict the entire tumor's status. The present study is designed to detect the relation between the EGFR exon 19 747-750 deletion mutation and lung cancer and investigate the patterns of alterations of plasma-free amino acids (PFAA) in lung cancer patients of different histopathological types and stages as biomarkers for early detection of lung cancer. The study sample comprised 60 lung cancer patients and 60 age- and sex-matched healthy individuals as the control group. Polymerase chain reaction and restriction fragment length polymorphism (PCR-RFLP) were used to examine the EGFR exon 19 747-750 deletion mutation, and an AA analyzer was used to quantify the plasma free amino acid (PFAA) profile. Compared with controls, LC patients had significantly higher levels of three AAs and significantly lower levels of fifteen AAs. Thirteen AAs varied significantly between stages I and II. In the lung cancer group, the percentage of cases of mutant EGFR exon-19 deletion increased to 30% from 13.3% in the control group. The histological forms of lung cancer did not significantly differ in this rise. Valine and citrulline plasma levels were substantially greater in the mutant than in the wild-type. Lysine, histidine, and methionine were the independent predictors of the LC group in multivariate analysis. Lung cancer development is influenced by the EGFR exon 19 747-750 deletion mutation, and the prognosis and early prediction of lung cancer are greatly affected by the amino acid profile concentrations.

The genetic diversity of genogroup I noroviruses causing acute gastroenteritis outbreaks in Beijing between 2014 and 2023

BackgroundIn the past decade, we have continuously conducted sporadic monitoring and outbreak detection of norovirus (NoV), which causes human acute gastroenteritis (AGE) in the capital of China. Accumulated data have shown that genogroup I (GI) NoVs not only cause sporadic cases but also cannot be ignored during outbreaks. This study aimed to update the genetic diversity of GI NoVs in the capital of China from 2014 to 2023. MethodsFecal or anal swab samples were collected from AGE outbreaks triggered by GI NoVs in Beijing Chaoyang District from 2014 to 2023. Both the partial coding genes of RNA-dependent RNA polymerase (RdRp) (∼283 bp) and viral protein 1 (VP1) (∼303 bp) were amplified via reverse transcription polymerase chain reaction (RT-PCR) and sequenced, followed by genotyping and phylogenetic analysis. ResultsA total of 421 fecal or anal swab samples were collected from 59 AGE outbreaks caused by GI NoVs. Genetic diversity was observed, with nine genotypes reported, including recombinant strains of GI.6[P11] and GI.3[P13], as well as multiple subtypes that cocirculated. In addition, we also reported a shift in the dominant genotype, with GI.6 [P11] in 2015–2018, GI.3 [P13] in 2019–2021, and GI.4 [P4] in 2023. Furthermore, alterations in amino acids were indirectly indicated through single nucleotide polymorphisms (SNPs) in certain VP1 areas of strains GI.3[P13] and GI.6[P11]. Epidemiologically, the peak of infection induced by GI NoVs occurs from March to May. ConclusionsThe sustained circulation and obvious genotype shift of GI NoVs in this region cannot be ignored, and GI.4[P4] NoVs are highly likely to become the main epidemic strain in the following years.

Novel ryanodine receptor 1 (RYR1) missense gene variants in two pet dogs with fatal malignant hyperthermia identified by next-generation sequencing

ObjectiveEvaluate a precision medicine approach to confirm a tentative diagnosis of fatal malignant hyperthermia (MH) in isoflurane-anesthetized pet dogs by identifying novel risk variants in known MH susceptibility genes. Study designRetrospective case series. AnimalsA male Pit Bull mix aged 7 years (case #1), a male Golden Retriever aged 12 months (case #2) and the dam and sire of case #2. MethodsAvailable case histories and medical records were reviewed. Missense variants in MH susceptibility genes RYR-1, CACNA1S and STAC3 (case #2 only) were identified by next-generation sequencing of DNA from each case and the parents of case #2 with confirmation by Sanger sequencing. The pathogenicity of variants was evaluated by multiple in silico approaches. ResultsBoth cases demonstrated clinical signs during isoflurane anesthesia consistent with volatile anesthetic-induced MH, including tachypnea, tachycardia, severe hyperthermia and muscle rigidity. Despite whole body cooling and other treatments, both dogs died after cardiac arrest within 15 minutes of detecting hyperthermia. Gene sequencing identified novel missense RYR-1 variants in case #1 (p.Gly2375Arg) and case #2 (p.Pro152Leu). Both variants were likely pathogenic based on multiple criteria, including gene location, amino acid alteration and population allele frequency. The case #1 variant was identical to a known human diagnostic MH variant (p.Gly2375Arg). Neither parent of case #2 had the case #2 variant, indicating this variant was not inherited, but arose de novo in a germ cell of either parent or early in embryogenesis. Whole genome sequence analysis confirmed parentage. Two missense variants were identified in CACNA1S. Both variants were considered nonpathogenic. No variants were identified in STAC3. Conclusions and clinical relevanceLike humans, MH susceptibility in dogs is associated with different rare variants located in pathogenic hotspots in the RYR-1 gene. Next-generation sequencing is a useful tool to assist in the definitive diagnosis of MH in dogs.

‘GGFGGQ’ repeats in Hfq of Acinetobacter baumannii are essential for nutrient utilization and virulence

The nosocomial pathogen Acinetobacter baumannii is known for causing lung and soft tissue infections in immunocompromised hosts. Its ability to adapt to various environments through post-transcriptional gene regulation is key to its success. Central to this regulation is the RNA chaperone Hfq, which facilitates interactions between mRNA targets and their small RNA (sRNA) partners through a Sm-core domain. Notably, the A. baumannii Hfq protein has a uniquely long C-terminal domain (CTD) with GGFGGQ amino acid repeats and an acidic amino acid-rich C-terminal tip (C-tip). Previous research has shown the importance of the intact CTD for Hfq's functionality. Given the significance of the C-tip in E. coli Hfq, we examined the pathophysiological roles of the redundant 'GGFGGQ' repeats along with the C-tip of A. baumannii Hfq. We constructed several variations of Hfq protein with fewer 'GGFGGQ' repeats while preserving the C-tip, and variants with altered C-tip amino acid composition. We then studied their RNA interaction abilities and assessed the pathophysiological fitness and virulence of genome-complemented A. baumannii mutants. Our findings reveal that the redundancy of the 'GGFGGQ' repeats is crucial for Hfq's role in pathophysiological fitness and negatively impacts A. baumannii's virulence in a murine lung infection model. In addition, C-tip mutants exhibited a negative effect on both fitness and virulence, however, to a lesser extent than the other variants. These results underscore the importance of 'GGFGGQ' redundancy and acidic residues in Hfq's ribo-regulation and autoregulation, suggesting their critical role in establishing regulatory networks.

Microbial Coadaptation Drives the Dynamic Stability of Microecology in Mainstream and Sidestream Anammox Systems Under Exposure of Progesterone

Microbial cooperation determines the efficacy of wastewater biological treatment, and the adaptability of microorganisms to environmental stresses varies. Recently, extensive use of hormones results in their inevitable discharge into aquatic environment. Therefore, mainstream and sidestream anammox reactors were constructed in this study to evaluate their removal performance of progesterone and nitrogen simultaneously, the adaptability of anammox consortia to progesterone stress and the corresponding regulation mechanism. Both anammox processes had the resilience to progesterone stress, with the average nitrogen removal efficiency exceeding 90%. At the same time, progesterone removal efficiency also exceeded 70%. In contrast, microbial community in the mainstream reactors was more susceptible to progesterone interference. The adaptation of anammox consortia mainly depended on microbial cooperation and molecular regulation. Initially, bacteria secreted more extracellular polymeric substances to detain progesterone. Biodegradation also contributed to mitigating the side effect of progesterone, which was demonstrated by the proliferation of potential degrading bacteria such as Bacillus salacetis, Bacillus wiedmannii and Rhodococcus erythropolis. In addition, the enhancement of microbial interaction intensity drove their cooperation to enhance adaptability and maintain stable performance. Combined with metagenomic and metatranscriptomic analyses, such microbial adaptability was enhanced through molecular regulations, including the energy redistribution for amino acid synthesis and alteration of key metabolic pathways. Related functional gene expressions and microbial interactions were, in turn, regulated by quorum sensing. This work verifies the feasibility of anammox process in hormone-containing wastewater treatment and provides a holistic understanding of molecular mechanism of microbial interaction and coadaptation to stress.

The Use of Patient-Derived Organoids in the Study of Molecular Metabolic Adaptation in Breast Cancer

Around 13% of women will likely develop breast cancer during their lifetime. Advances in cancer metabolism research have identified a range of metabolic reprogramming events, such as altered glucose and amino acid uptake, increased reliance on glycolysis, and interactions with the tumor microenvironment (TME), all of which present new opportunities for targeted therapies. However, studying these metabolic networks is challenging in traditional 2D cell cultures, which often fail to replicate the three-dimensional architecture and dynamic interactions of real tumors. To address this, organoid models have emerged as powerful tools. Tumor organoids are 3D cultures, often derived from patient tissue, that more accurately mimic the structural and functional properties of actual tumor tissues in vivo, offering a more realistic model for investigating cancer metabolism. This review explores the unique metabolic adaptations of breast cancer and discusses how organoid models can provide deeper insights into these processes. We evaluate the most advanced tools for studying cancer metabolism in three-dimensional culture models, including optical metabolic imaging (OMI), matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI), and recent advances in conventional techniques applied to 3D cultures. Finally, we explore the progress made in identifying and targeting potential therapeutic targets in breast cancer metabolism.

Application of Eight Machine Learning Algorithms in the Establishment of Infertility and Pregnancy Diagnostic Models: A Comprehensive Analysis of Amino Acid and Carnitine Metabolism.

To explore the effects of altered amino acids (AAs) and the carnitine metabolism in non-pregnant women with infertility (NPWI), pregnant women without infertility (PWI) and infertility-treated pregnant women (ITPW) compared with non-pregnant women (NPW, control), and develop more efficient models for the diagnosis of infertility and pregnancy, 496 samples were evaluated for levels of 21 AAs and 55 carnitines using targeted high-performance liquid chromatography with tandem mass spectrometry (HPLC-MS/MS). Three methods were used to screen the biomarkers for modeling, with eight algorithms used to build and validate the model. The ROC, sensitivity, specificity, and accuracy of the infertility diagnosis training model were higher than 0.956, 82.89, 66.64, and 82.57%, respectively, whereas those of the validated model were higher than 0.896, 77.67, 69.72, and 83.38%, respectively. The ROC, sensitivity, specificity, and accuracy of the pregnancy diagnosis training model were >0.994, 96.23, 97.79, and 97.69%, respectively, whereas those of the validated model were >0.572, 96.39, 93.03, and 94.71%, respectively. Our findings indicate that pregnancy may alter the AA and carnitine metabolism in women with infertility to match the internal environment of PWI. The developed model demonstrated good performance and high sensitivity for facilitating infertility and pregnancy diagnosis.

Nutritional status and extended metabolic screening in Egyptian children with uncomplicated type 1 diabetes

Nutritional status assessment, including amino acids, carnitine, and acylcarnitine profile, is an important component of diabetes care management, influencing growth and metabolic regulation. A designed case–control research included 100 Egyptian participants (50 T1DM and 50 healthy controls) aged 6 to 18 years old. The participants' nutritional status was assessed using the Body Mass Index (BMI) Z-score. Extended metabolic screening (EMS) was performed using a high-performance liquid chromatography-electrospray ionization-mass spectroscopy system to evaluate the levels of 14 amino acids, free carnitine, and 27 carnitine esters. T1DM children had considerably lower anthropometric Z-scores than the control group, with 16% undernutrition and 32% short stature. Total aromatic amino acids, phenylalanine, phenylalanine/tyrosine ratio, proline, arginine, leucine, isoleucine, free carnitine, and carnitine esters levels were considerably lower in the diabetic group, suggesting an altered amino acid and carnitine metabolism in type 1 diabetes. BMI Z-score showed a significant positive correlation with Leucine, Isoleucine, Phenylalanine, Citrulline, Tyrosine, Arginine, Proline, free carnitine, and some carnitine esters (Acetylcarnitine, Hydroxy-Isovalerylcarnitine, Hexanoylcarnitine, Methylglutarylcarnitine, Dodecanoylcarnitine, Tetradecanoylcarnitine, and Hexadecanoylcarnitine). HbA1c% had a significant negative correlation with Total aromatic amino acids, Branched-chain amino acid/Total aromatic amino acids ratio, Glutamic Acid, Citrulline, Tyrosine, Arginine, Proline, and certain carnitine esters (Propionylcarnitine, Methylglutarylcarnitine, Decanoylcarnitine, Octadecanoylcarnitine and Octadecenoylcarnitine), suggest that dysregulated amino acid and carnitine metabolism may be negatively affect the glycaemic control in children with TIDM. In conclusion, regular nutritional assessments including EMS of T1DM patients are critical in terms of diet quality and protein content for improved growth and glycemic management.

SARS-CoV-2 Genotyping Highlights the Challenges in Spike Protein Drift Independent of Other Essential Proteins.

As of 2024, SARS-CoV-2 continues to propagate and drift as an endemic virus, impacting healthcare for years. The largest sequencing initiative for any species was initiated to combat the virus, tracking changes over time at a full virus base-pair resolution. The SARS-CoV-2 sequencing represents a unique opportunity to understand selective pressures and viral evolution but requires cross-disciplinary approaches from epidemiology to functional protein biology. Within this work, we integrate a two-year genotyping window with structural biology to explore the selective pressures of SARS-CoV-2 on protein insights. Although genotype and the Spike (Surface Glycoprotein) protein continue to drift, most SARS-CoV-2 proteins have had few amino acid alterations. Within Spike, the high drift rate of amino acids involved in antibody evasion also corresponds to changes within the ACE2 binding pocket that have undergone multiple changes that maintain functional binding. The genotyping suggests selective pressure for receptor specificity that could also confer changes in viral risk. Mapping of amino acid changes to the structures of the SARS-CoV-2 co-transcriptional complex (nsp7-nsp14), nsp3 (papain-like protease), and nsp5 (cysteine protease) proteins suggest they remain critical factors for drug development that will be sustainable, unlike those strategies targeting Spike.