Integrative Molecular Phenotyping
INTEGRATIVE MOLECULAR
PHENOTYPING
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY

PubMed

Blood microsampling technologies: Innovations and applications in 2022

Wed, 08/05/2024 - 12:00
Anal Sci Adv. 2023 May 18;4(5-6):154-180. doi: 10.1002/ansa.202300011. eCollection 2023 Jul.ABSTRACTWith the development of highly sensitive bioanalytical techniques, the volume of samples necessary for accurate analysis has reduced. Microsampling, the process of obtaining small amounts of blood, has thus gained popularity as it offers minimal-invasiveness, reduced logistical costs and biohazard risks while simultaneously showing increased sample stability and a potential for the decentralization of the approach and at-home self-sampling. Although the benefits of microsampling have been recognised, its adoption in clinical practice has been slow. Several microsampling technologies and devices are currently available and employed in research studies for various biomedical applications. This review provides an overview of the state-of-the-art in microsampling technology with a focus on the latest developments and advancements in the field of microsampling. Research published in the year 2022, including studies (i) developing strategies for the quantitation of analytes in microsamples and (ii) bridging and comparing the interchangeability between matrices and choice of technology for a given application, is reviewed to assess the advantages, challenges and limitations of the current state of microsampling. Successful implementation of microsampling in routine clinical care requires continued efforts for standardization and harmonization. Microsampling has been shown to facilitate data-rich studies and a patient-centric approach to healthcare and is foreseen to play a central role in the future digital revolution of healthcare through continuous monitoring to improve the quality of life.PMID:38716066 | PMC:PMC10989553 | DOI:10.1002/ansa.202300011

Profiling acidic metabolites by capillary electrophoresis-mass spectrometry in low numbers of mammalian cells using a novel chemical derivatization approach

Wed, 08/05/2024 - 12:00
Anal Sci Adv. 2021 Dec 14;3(1-2):3-13. doi: 10.1002/ansa.202100054. eCollection 2022 Feb.ABSTRACTThe simultaneous analysis of a broad range of polar ionogenic metabolites using capillary electrophoresis-mass spectrometry (CE-MS) can be challenging, as two different analytical methods are often required, that is, one for cations and one for anions. Even though CE-MS has shown to be an effective method for cationic metabolite profiling, the analysis of small anionic metabolites often results in relatively low sensitivity and poor repeatability. In this work, a novel derivatization strategy based on trimethylmethaneaminophenacetyl bromide was developed to enable CE-MS analysis of carboxylic acid metabolites using normal CE polarity (i.e., cathode in the outlet) and detection by mass spectrometry in positive ionization mode. Optimization of derivatization conditions was performed using a response surface methodology after which the optimized method (incubation time 50 min, temperature 90°C, and pH 10) was used for the analysis of carboxylic acid metabolites in extracts from HepG2 cells. For selected metabolites, detection limits were down to 8.2 nM, and intraday relative standard deviation values for replicates (n = 3) for peak areas were below 21.5%. Metabolites related to glycolysis, tricarboxylic acid cycle, and anaerobic respiration pathways were quantified in 250,000 cell lysates, and could still be detected in extracts from only 25,000 HepG2 cell lysates (∼70 cell lysates injected).PMID:38716053 | PMC:PMC10989665 | DOI:10.1002/ansa.202100054

Mass Sportrometry: An annual look back at applications of mass spectrometry in sport and exercise science

Wed, 08/05/2024 - 12:00
Anal Sci Adv. 2023 Mar 31;4(3-4):60-80. doi: 10.1002/ansa.202300003. eCollection 2023 May.ABSTRACTResearch in sport and exercise science (SES) is reliant on robust analyses of biomarker measurements to assist with the interpretation of physiological outcomes. Mass spectrometry (MS) is an analytical approach capable of highly sensitive, specific, precise, and accurate analyses of a range of biomolecules, many of which are of interest in SES including, but not limited to, endogenous metabolites, exogenously administered compounds (e.g. supplements), mineral ions, and circulating/tissue proteins. This annual review provides a summary of the applications of MS across studies investigating aspects related to sport or exercise in manuscripts published, or currently in press, in 2022. In total, 93 publications are included and categorized according to their methodologies including targeted analyses, metabolomics, lipidomics, proteomics, and isotope ratio/elemental MS. The advantageous analytical opportunities afforded by MS technologies are discussed across a selection of relevant articles. In addition, considerations for the future of MS in SES, including the need to improve the reporting of assay characteristics and validation data, are discussed, alongside the recommendation for selected current methods to be superseded by MS-based approaches where appropriate. The review identifies that a targeted, mostly quantitative, approach is the most commonly applied MS approach within SES, although there has also been a keen interest in the use of 'omics' to perform hypothesis-generating research studies. Nonetheless, MS is not commonplace in SES at this time, but its use to expand, and possibly improve, the analytical options should be continually considered to exploit the benefits of analytical chemistry in exercise/sports-based research. Overall, it is exciting to see the gradually increasing adoption of MS in SES and it is expected that the number, and quality, of MS-based assays in SES will increase over time, with the potential for 2023 to further establish this technique within the field.PMID:38715927 | PMC:PMC10989560 | DOI:10.1002/ansa.202300003

Pharmaco-metabolomics opportunities in drug development and clinical research

Wed, 08/05/2024 - 12:00
Anal Sci Adv. 2021 Sep 30;2(11-12):611-616. doi: 10.1002/ansa.202000178. eCollection 2021 Dec.ABSTRACTPharmaco-metabolomics uses metabolic phenotypes for the prediction of inter-individual variations in drug response and helps in understanding the mechanisms of drug action. The field has made significant progress over the last 14 years with numerous studies providing clinical evidence for personalised medicine. However, discovered pharmaco-metabolomic biomarkers are not yet translated into clinics due to a lack of large-scale validation. Integration of targeted and untargeted metabolomics workflows into pharmacokinetic analysis and drug development can advance the field from bench to bedside. Also, Indian pharmaceutical research and its bioanalytical infrastructure are in a position to take on these opportunities by addressing challenges such as appropriate training and regulatory compliance.PMID:38715865 | PMC:PMC10989535 | DOI:10.1002/ansa.202000178

NMR-based serum and muscle metabolomics for diagnosis and activity assessment in idiopathic inflammatory myopathies

Wed, 08/05/2024 - 12:00
Anal Sci Adv. 2021 Jun 6;2(11-12):515-526. doi: 10.1002/ansa.202000171. eCollection 2021 Dec.ABSTRACTOBJECTIVES: Differentiating smoldering disease activity from weakness due to fatty replacement of atrophied muscle can often be a challenge in the idiopathic inflammatory myositis (IIM). We aimed to identify the metabolic disturbances associated with IIM and if these changes can aid in the assessment of disease activity.METHODS: Metabolic profiles of sera (N = 99) and muscle (N = 21) from patients with IIM (ACR-EULAR criteria) were compared with healthy control (HC) samples (N = 75 for serum and N = 12 for muscle tissues) employing 800 MHz NMR (Nuclear Magnetic Resonance) spectroscopy. Metabolic disparity between IIM and HC was established based on Partial Least Squares Discriminant Analysis (PLS-DA) and the discriminatory metabolites were identified based on variable importance in projection (VIP) statistics (P-value < .05, corrected for false discovery rate (FDR)).RESULTS: Serum metabolomics profiles were distinctive in IIM as compared to HC, with a visible shift to anaerobic metabolism (increased lactate, low glucose), oxidative defect (high Phenylalanine/tyrosine), decreased muscle mass (low serum creatinine), increased muscle catabolism (increased branched-chain amino acids), and dyslipidemia (higher lipids, higher very low-density lipoprotein [VLDL]/low-density lipoprotein [LDL] ratio, lower polyunsaturated fatty acid [PUFA]). The sera of active IIM patients were characterized by anaerobic metabolism (low glucose), loss of muscle mass (low creatinine, amino acids), and oxidative defect (high Phenylalanine/tyrosine). Three metabolites (isopropanol, succinate, and glycine) were distinctive in muscle tissue metabolomics. NMR-based serum metabolic disparity was lacking between different clinical subsets of IIM.CONCLUSION: Serum and muscle tissue metabolomics have the potential to distinguish (a) IIM from HC and (b) active IIM from inactive IIM irrespective of disease subtype.PMID:38715864 | PMC:PMC10989623 | DOI:10.1002/ansa.202000171

MR spectroscopy in breast cancer metabolomics

Wed, 08/05/2024 - 12:00
Anal Sci Adv. 2021 May 3;2(11-12):564-578. doi: 10.1002/ansa.202000160. eCollection 2021 Dec.ABSTRACTBreast cancer poses a significant health care challenge worldwide requiring early detection and effective treatment strategies for better patient outcome. A deeper understanding of the breast cancer biology and metabolism may help developing better diagnostic and therapeutic approaches. Metabolomic studies give a comprehensive analysis of small molecule metabolites present in human tissues in vivo. The changes in the level of these metabolites provide information on the complex mechanism of the development of the disease and its progression. Metabolomic approach using analytical techniques such as magnetic resonance spectroscopy (MRS) has evolved as an important tool for identifying clinically relevant metabolic biomarkers. The metabolic characterization of breast lesions using in-vivo MRS has shown that malignant breast tissues contain elevated levels of choline containing compounds (tCho), suggesting rapid proliferation of cancer cells and alterations in membrane metabolism. Also, tCho has been identified as one of the important biomarkers that help to enhance the diagnostic accuracy of dynamic contrast enhanced magnetic resonance imaging and also for monitoring treatment response. Further, metabolome of malignant tissues can be studied using ex vivo and in vitro MRS at high magnetic fields. This provided the advantage of detection of a large number of compounds that facilitated more comprehensive insight into the altered metabolic pathways associated with the cancer development and progression and also in identification of several metabolites as potential biomarkers. This article briefly reviews the role of MRS based metabolic profiling in the discovery of biomarkers and understanding of the altered metabolism in breast cancer.PMID:38715862 | PMC:PMC10989566 | DOI:10.1002/ansa.202000160

Applications of quantitative metabolomics to revolutionize early diagnosis of inborn errors of metabolism in India

Wed, 08/05/2024 - 12:00
Anal Sci Adv. 2021 Aug 5;2(11-12):546-563. doi: 10.1002/ansa.202100010. eCollection 2021 Dec.ABSTRACTInborn errors of metabolism (IEMs) are a group of disorders caused by disruption of metabolic pathways, which leads to accumulation, decreased circulating levels, or increased excretion of metabolites as a consequence of the underlying genetic defects. These heterogeneous groups of disorders cause significant neonatal and infant mortality across the whole world and it is of utmost concern for developing countries like India owing to lack of awareness and standard preventive strategies like newborn screening (NBS). Though the predictive cumulative incidence of IEMs is said to be ∼1:800 newborns, data pertaining to the true prevalence of individual IEMs is not available in the context of Indian population. There is a need for a large population-based study to get a clear picture of the prevalence of different IEMs. One of the best ways to screen for IEMs is by applying advanced liquid chromatography-mass spectrometry (LC-MS) technology using a quantitative metabolomics approaches such as selected or multiple reaction monitoring (SRM or MRM). Recent developments in LC-MS/MRM based quantification of marker metabolites in newborns have opened a novel opportunity to screen multiple disorders simultaneously from a minuscule volume of biological fluids. In this review article, we have highlighted how LC-MS/MRM based metabolomics approach with its high sensitivity and diagnostic capability can make an impact on the nation's public health through NBS programs.PMID:38715861 | PMC:PMC10989570 | DOI:10.1002/ansa.202100010

A conversation between hyphenated spectroscopic techniques and phytometabolites from medicinal plants

Wed, 08/05/2024 - 12:00
Anal Sci Adv. 2021 Sep 30;2(11-12):579-593. doi: 10.1002/ansa.202100021. eCollection 2021 Dec.ABSTRACTMedicinal plant metabolomics has emerged as a goldmine for the natural product chemists. It provides a pool of bioactive phytoconstituents leading to accelerated novel discoveries and the elucidation of a variety of biosynthetic pathways. Further, it also acts as an innovative tool for herbal medicine's scientific validation and quality assurance. This review highlights different strategies and analytical techniques employed in the practice of metabolomics. Further, it also discusses several other applications and advantages of metabolomics in the area of natural product chemistry. Additional examples of integrating metabolomics with multivariate data analysis techniques for some Indian medicinal plants are also reviewed. Recent technical advances in mass spectrometry-based hyphenated techniques, nuclear magnetic resonance-based techniques, and comprehensive hyphenated technologies for phytometabolite profiling studies have also been reviewed. Mass Spectral Imaging (MSI) has been presented as a highly promising method for high precision in situ spatiotemporal monitoring of phytometabolites. We conclude by introducing GNPS (Global Natural Products Social Molecular Networking) as an emerging platform to make social networks of related molecules, to explore data and to annotate more metabolites, and expand the networks to novel "predictive" metabolites that can be validated.PMID:38715860 | PMC:PMC10989556 | DOI:10.1002/ansa.202100021

Proteomic and metabolomic approach to rationalize the differential mosquito larvicidal toxicity in Bacillus sp. isolated from the mid-gut of Culex quinquefasciatus mosquito larvae

Wed, 08/05/2024 - 12:00
Anal Sci Adv. 2020 Oct 12;2(11-12):505-514. doi: 10.1002/ansa.202000081. eCollection 2021 Dec.ABSTRACTFrom the distinct wild locations of the Mumbai (India), dead Culex mosquito larvae were collected. The mid-gut micro-flora of these dead mosquito larvae was isolated on three different media that were selective for only the Gram-positive bacteria. These bacteria were tested against the third instar stage of Culex quinquefasciatus larvae, cultured in the laboratory, for their larvicidal activity. After performing the toxicity assay four times in duplicates, the average statistical values showed four bacteria exhibiting differential toxicities. Identification of these strains was done by 16S rRNA sequencing and their respective surface morphologies were studied by scanning electron microscopy (SEM). The differential toxicities of the four identified Bacillus strains were rationalized by performing differential proteomics and metabolomics approach using LC-MS and these results were analyzed against customized mosquito larvicidal toxin database which was further compared with the in silico p-BLAST data of that respective Bacillus sp. from the NCBI database. The presence and significance of the various mosquitocidal toxins in the identified Bacillus sp. are elucidated. The present study also attempted to identify new bacterial species exhibiting mosquitocidal toxicities that have not been reported earlier.PMID:38715859 | PMC:PMC10989537 | DOI:10.1002/ansa.202000081

Metabolomics of neurological disorders in India

Wed, 08/05/2024 - 12:00
Anal Sci Adv. 2021 Nov 28;2(11-12):594-610. doi: 10.1002/ansa.202000169. eCollection 2021 Dec.ABSTRACTMetabolomics is the comprehensive study of the metabolome and its alterations within biological fluids and tissues. Over the years, applications of metabolomics have been explored in several areas, including personalised medicine in diseases, metabolome-wide association studies (MWAS), pharmacometabolomics and in combination with other branches of omics such as proteomics, transcriptomics and genomics. Mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy are the major analytical techniques widely employed in metabolomics. In addition, MS is coupled with chromatography techniques like gas chromatography (GC) and liquid chromatography (LC) to separate metabolites before analysis. These analytical techniques have made possible identification and quantification of large numbers of metabolites, encompassing characterization of diseases and facilitating a systematic and rational therapeutic strategy based on metabolic patterns. In recent years, the metabolomics approach has been used to obtain a deeper insight into the underlying biochemistry of neurodegenerative disorders and the discovery of biomarkers of clinical implications. The current review mainly focuses on an Indian perspective of metabolomics for the identification of metabolites and metabolic alterations serving as potential diagnostic biomarkers for neurological diseases including acute spinal cord injury, amyotrophic lateral sclerosis, tethered cord syndrome, spina bifida, stroke, Parkinson's disease, glioblastoma and neurological disorders with inborn errors of metabolism.PMID:38715858 | PMC:PMC10989583 | DOI:10.1002/ansa.202000169

Editorial for special issue: Metabolomics in India

Wed, 08/05/2024 - 12:00
Anal Sci Adv. 2021 Dec 23;2(11-12):495-496. doi: 10.1002/ansa.202100064. eCollection 2021 Dec.NO ABSTRACTPMID:38715857 | PMC:PMC10989613 | DOI:10.1002/ansa.202100064

Targeted NMR-based serum metabolic profiling of serine, glycine and methionine in acute-on-chronic liver failure patients: Possible insights into mitochondrial dysfunction

Wed, 08/05/2024 - 12:00
Anal Sci Adv. 2021 Jun 21;2(11-12):536-545. doi: 10.1002/ansa.202000167. eCollection 2021 Dec.ABSTRACTBACKGROUND: A recent study based on blood metabolomics analysis revealed inflammation-associated mitochondrial dysfunction as a potential mechanism underlying acute-on-chronic liver failure (ACLF) in cirrhotic patients. Serine, glycine, and methionine serve to maintain a healthy immune system and adequately sustain mitochondrial functionality in hepatocytes for regulating redox homeostasis through the production of antioxidant glutathione (GSH). Based on this, we hypothesized that the circulatory levels of serine, glycine and methionine will be altered in ACLF patients due to acute worsening of hepatic function and may provide novel insights into the mitochondrial dysfunction as well.METHODS: The circulatory concentrations of serine, glycine, and methionine were estimated in the sera of 40 ACLF patients and 49 normal controls (NC) subject using 1D 1H-CPMG NMR spectra recorded at 800 MHz NMR spectrometer. The resulting metabolite concentrations were compared using unpaired Student t-test and p-value < 0.05 was considered as the criterion of statistical significance. The diagnostic potential and statistical correlations were established using receiver-operating-characteristic (ROC) curve analysis and Pearson-r method, respectively.RESULTS: Circulating levels of serine and glycine were significantly decreased in ACLF patients (Ser = 23.06 ± 1.67 µM and Gly = 83.11±7.52 µM) compared to NC subjects (Ser = 55.61 ± 2.28 µM and Gly = 156.9±7.16 µM) with p-value < 0.0001, whereas those of methionine were significantly increased in ACLF (22.60 ± 2.49 µM) compared to NC subjects (=14.63 ± 0.85 µM) with p-value < 0.0015. Further, the ROC analysis yielded satisfactory sensitivity and specificity for serine, glycine, and methionine-to-glycine ratio (MGR) with area under ROC (AUROC) curve values equal to: 0.95 [95%CI = 0.91-0.99] for Ser; 0.87 [95%CI = 0.79-0.95] for Gly; and 0.90 [95%CI = 0.83-0.97] for MGR.CONCLUSION: Compared to NC subjects, the sera of ACLF patients were characterized by hypermethioninemia and aberrantly decreased levels of serine and glycine suggesting mitochondrial dysfunction as the possible mechanism for disturbed redox homeostasis and therefore depressed immune system in ACLF.PMID:38715854 | PMC:PMC10989557 | DOI:10.1002/ansa.202000167

Complementary approach for analysis of phospholipids by liquid chromatography hyphenated to elemental and molecular mass spectrometry

Wed, 08/05/2024 - 12:00
Anal Sci Adv. 2020 Apr 22;1(1):46-55. doi: 10.1002/ansa.20190009. eCollection 2020 Jun.ABSTRACTPhospholipids are one of the most important lipid categories with multiple functions in biological systems. Their analysis can contribute to a better understanding of metabolomic and kinetic processes in living cells. Comprehensive methods based on liquid chromatography coupled to mass spectrometry are available for phospholipid identification and quantification. However, quantification of phospholipids using electrospray ionization-mass spectrometry with internal standards is still challenging due to several reasons. In particular, the detector response of phospholipid species differs with variation of the head group as well as the fatty acid chain length and double bond number. Inductively coupled plasma-tandem mass spectrometry (ICP-MS/MS) provides an alternative approach for their absolute quantification with universal detector response for phosphorus independent of its chemical form and proportional to its quantity. Therefore, a quantification method based on compound-independent calibration using hydrophilic interaction liquid chromatography (HILIC) coupled to ICP-MS/MS was developed. An inverse gradient system was implemented for constant mobile phase composition after HILIC separation, which provides steady plasma ionization conditions. Isobaric phosphorus interferences were decreased by using the oxygen reaction mode of the triple quadrupole based ICP-MS/MS instrument. Complementary molecular information was obtained by ESI-high-resolution MS and MS/MS. The applicability of this approach was demonstrated in a proof of concept by complementary analysis of a total lipid extract of baker's yeast.PMID:38715851 | PMC:PMC10989138 | DOI:10.1002/ansa.20190009

Comparative metabolomics of MCF-7 and MCF-7/TAMR identifies potential metabolic pathways in tamoxifen resistant breast cancer cells

Wed, 08/05/2024 - 12:00
Am J Transl Res. 2024 Apr 15;16(4):1337-1352. doi: 10.62347/MJLN5908. eCollection 2024.ABSTRACTOBJECTIVES: Breast cancer is the most common cancer and the leading cause of cancer-related death among women. An Estrogen Receptor (ER) antagonist called tamoxifen is used as an adjuvant therapy for ER-positive breast cancers. Approximately 40% of patients develop tamoxifen resistance (TAMR) while receiving treatment. Cancer cells can rewire their metabolism to develop resistant phenotypes, and their metabolic state determines how receptive they are to chemotherapy.METHODS: Metabolite extraction from human MCF-7 and MCF-7/TAMR cells was done using the methanol-methanol-water extraction method. After treating the dried samples with methoxamine hydrochloride in pyridine, the samples were derivatized with 2,2,2-Trifluoro-N-methyl-N-(trimethylsilyl)-acetamide, and Chlorotrimethylsilane (MSTFA + 1% TMCS). The Gas chromatography/mass spectrometry (GC-MS) raw data were processed using MSdial and Metaboanalyst for analysis.RESULTS: Univariate analysis revealed that 35 metabolites were elevated in TAMR cells whereas 25 metabolites were downregulated. N-acetyl-D-glucosamine, lysine, uracil, tyrosine, alanine, and o-phosphoserine were upregulated in TAMR cells, while hydroxyproline, glutamine, N-acetyl-L-aspartic acid, threonic acid, pyroglutamic acid, glutamine, o-phosphoethanolamine, oxoglutaric acid, and myoinositol were found to be downregulated. Multivariate analysis revealed a distinct separation between the two cell lines, as evidenced by their metabolite levels. The enriched pathways of deregulated metabolites included valine, leucine, and isoleucine degradation, Citric Acid Cycle, Warburg effect, Malate-Aspartate shuttle, glucose-alanine cycle, propanoate metabolism, and Phospholipid biosynthesis.CONCLUSION: This study revealed dysregulation of various metabolic processes in TAMR cells, which may be crucial in elucidating the molecular basis of the mechanisms underlying acquired tamoxifen resistance.PMID:38715825 | PMC:PMC11070380 | DOI:10.62347/MJLN5908

A review of retention mechanism studies for packed column supercritical fluid chromatography

Wed, 08/05/2024 - 12:00
Anal Sci Adv. 2021 Jan 21;2(1-2):47-67. doi: 10.1002/ansa.202000144. eCollection 2021 Feb.ABSTRACTThe packed column supercritical fluid chromatography has risen as a promising alternative separation technique to the conventional liquid chromatography and gas chromatography. Although the packed column supercritical fluid chromatography has many advantages compared to other chromatographic techniques, its separation mechanism is not fully understood due to the complex combination effects of many chromatographic parameters on separation quality and the lacking of global strategies for studying separation mechanisms. This review aims to provide recent information regarding the chromatographic behaviors and the effects of the parameters on the separation, discuss the results, and point out the remaining bottlenecks in the packed column supercritical fluid chromatography retention mechanism studies.PMID:38715740 | PMC:PMC10989630 | DOI:10.1002/ansa.202000144

Hidden in the photograph: The myth of complete metabolic coverage possible in metabolomics investigations

Wed, 08/05/2024 - 12:00
Anal Sci Adv. 2023 Mar 21;4(11-12):319-323. doi: 10.1002/ansa.202200055. eCollection 2023 Dec.ABSTRACTSince the late 1970s, many 'omics-style investigations have advanced our understanding of systems at all levels, from community level, through organismal, to individual cellular processes. Beginning with genomics and progressing through transcriptomics, proteomics and finally to metabolomics, the scope of interest shifts significantly from what is genetically possible to what is currently expressed, produced and measurable in a system. While the ideal goal of any 'omics investigation is to fully describe a system, loss of information occurs at each decision-making juncture. These losses are often not considered in the experimental planning stage but, when combined, they drastically affect the power of an investigation and the conclusions that can be drawn from it. Herein we discuss through the analogy of photography many of the decision-making junctures of metabolomics investigations and the resultant losses of information occurring at each.PMID:38715650 | PMC:PMC10989593 | DOI:10.1002/ansa.202200055

Metabolomic analysis of rumen-protected branched-chain amino acids in primiparous dairy cows

Wed, 08/05/2024 - 12:00
Front Immunol. 2024 Apr 23;15:1385896. doi: 10.3389/fimmu.2024.1385896. eCollection 2024.ABSTRACTINTRODUCTION: Peripartal cows are susceptible to a negative energy balance due to inadequate nutrient intake and high energy requirements for lactation. Improving the energy metabolism of perinatal dairy cows is crucial in increasing production in dairy cows.METHODS: In this study, we investigated the impact of rumen-protected branched-chain amino acid (RPBCAA) on the production performance, energy and lipid metabolism, oxidative stress, and immune function of primiparous dairy cows using metabolomics through a single-factor experiment. Twenty healthy primiparous Holstein cows were selected based on body condition scores and expected calving date, and were randomly divided into RPBCAA (n = 10) and control (n = 10) groups. The control group received a basal diet from calving until 21 d in milk, and the RPBCAA group received the basal diet and 44.6 g/d RPLeu, 25.14 g/d RPIle, and 25.43 g/d RPVal.RESULTS: In comparison to the control group, the supplementation of RPBCAA had no significant effect on milk yield and milk composition of the dairy cows. Supplementation with RPBCAA significantly increased the concentrations of insulin, insulin growth factor 1, glucagon, and growth hormones, which are indicators of energy metabolism in postpartum cows. The very low density lipoprotein, fatty acid synthase, acetyl coenzyme A carboxylase, and hormone-sensitive lipase contents of the RPBCAA group were significantly greater than that of the control group; these metrics are related to lipid metabolism. In addition, RPBCAA supplementation significantly increased serum glutathione peroxidase and immunoglobulin G concentrations and decreased malondialdehyde concentrations. Liquid chromatography-mass spectrometry (LC-MS) analysis revealed 414 serum and 430 milk metabolic features. Supplementation with RPBCAA primarily increased concentrations of amino acid and lipid metabolism pathways and upregulated the abundance of serotonin, glutamine, and phosphatidylcholines.DISCUSSION: In summary, adding RPBCAA to the daily ration can influence endocrine function and improve energy metabolism, regulate amino acid and lipid metabolism, mitigate oxidative stress and maintain immune function on primiparous cows in early lactation.PMID:38715606 | PMC:PMC11075066 | DOI:10.3389/fimmu.2024.1385896

Analytics for Grannies 001: Metabolomics

Wed, 08/05/2024 - 12:00
Anal Sci Adv. 2022 Nov 8;4(1-2):1-3. doi: 10.1002/ansa.202200901. eCollection 2023 Feb.NO ABSTRACTPMID:38715587 | PMC:PMC10989530 | DOI:10.1002/ansa.202200901

Dried blood spot characterization of sex-based metabolic responses to acute running exercise

Wed, 08/05/2024 - 12:00
Anal Sci Adv. 2023 Feb 5;4(1-2):37-48. doi: 10.1002/ansa.202200039. eCollection 2023 Feb.ABSTRACTMetabolomics and lipidomics techniques are capable of comprehensively measuring hundreds to thousands of small molecules in single analytical runs and have been used to characterize responses to exercise traditionally using venipuncture-produced liquid samples. Advanced microsampling devices offer an alternative by circumventing the requirement to maintain frozen samples. This approach combines a microneedle puncture for blood draw with microfluidic sample collection onto a dried carrier and has thus far been employed for targeted measurements of a few analytes. To demonstrate the utility of advanced dried microsampling to characterize metabolomic and lipidomic changes during exercise, we obtained samples before and after a 2-mile run from twelve (8 male, 4 female) healthy volunteers with various ranges in activity levels. Results highlighted significant changes in whole blood levels of several metabolites associated with energy (glycolysis and Tricarboxylic Acid cycle) and redox (Pentose Phosphate Pathway) metabolism. Lipid changes during this same period were individualized and less uniform. Sex-based differences in response to running highlighted reliance on carbohydrate or fat substrate utilization in males or females, respectively. The results presented herein illustrate the ability of this approach to monitor circulating metabolome and lipidome profiles from field sampled blood in response to exercise.PMID:38715582 | PMC:PMC10989637 | DOI:10.1002/ansa.202200039

Metabolomic Alterations in Methotrexate Treatment of Moderate-to-Severe Psoriasis

Wed, 08/05/2024 - 12:00
Med Sci Monit. 2024 May 8;30:e943360. doi: 10.12659/MSM.943360.ABSTRACTBACKGROUND Aberrant lipid metabolism alterations in skin tissue, blood, or urine have been implicated in psoriasis. Here, we examined lipid metabolites related to psoriasis and their association with the age of disease onset. MATERIAL AND METHODS Differences in lipid metabolites before and after methotrexate (MTX) treatment were evaluated. The discovery cohort and validation cohort consisted of 50 and 46 patients, respectively, with moderate-to-severe psoriasis. After MTX treatment, the patients were divided into response (Psoriasis Area and Severity Index [PASI] 75 and above) and non-response (PASI below 75) groups, blood was collected for serum metabolomics, and multivariate statistical analysis was performed. RESULTS We detected 1546 lipid metabolites. The proportion of the top 3 metabolites was as follows: triglycerides (TG, 34.8%), phospholipids (PE, 14.5%), phosphatidylcholine (PC, 12.4%); diglycerides (DG) (16: 1/18: 1), and DG (18: 1/18: 1) showed strong positive correlations with onset age. There were marked changes in TG (16: 0/18: 0/20: 0), TG (18: 0/18: 0/22: 0), TG (14: 0/18: 0/22: 0), TG (14: 0/20: 0/20: 0), lysophosphatidylcholine (LPC) (16: 0/0: 0), LPC (18: 0/0: 0), LPC (14: 0/0: 0), and LPC (18: 1/0: 0) levels before and after 12 weeks of MTX treatment. The glycerophospholipid metabolic pathway was implicated in psoriasis development. Of the 96 recruited patients, 35% were MTX responders and 65% non-responders. PE (34: 4) and PE (38: 1) levels were significantly different between the groups. Obvious differences in lipid metabolism were found between early-onset (<40 years) and late-onset (≥40 years) psoriasis. Significant changes in serum lipid profile before and after MTX treatment were observed. CONCLUSIONS The specific lipid level changes in responders may serve as an index for MTX treatment efficacy evaluation.PMID:38715343 | DOI:10.12659/MSM.943360

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