Failure to apply standard limit-of-detection or limit-of-quantitation criteria to specialized pro-resolving mediator analysis incorrectly characterizes their presence in biological samples

O’Donnell, Valerie B.; Schebb, Nils H.; Milne, Ginger L.; Murphy, Michael P.; Thomas, Christopher P.; Steinhilber, Dieter; Gelhaus, Stacy L.; Kühn, Hartmut; Gelb, Michael H.; Jakobsson, Per-Johan; Blair, Ian A.; Murphy, Robert C.; Freeman, Bruce A.; Brash, Alan R.; FitzGerald, Garret A.

doi:10.1038/s41467-023-41766-w

Cited by 22 publications

(9 citation statements)

References 12 publications

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“…Ein aktueller Artikel bestätigt diese Kritik: 2) "Failure to apply standard limit-of-detection or limitof-quantitation criteria to specialized pro-resolving mediator analysis incorrectly characterizes their presence in biological samples", lautet der Titel des Matters-Arising-Artikels in Nature Communications. 2) Wird das international akzeptierte s/n-Verhältnis zur Bestimmung genutzt, lässt sich somit nicht belegen, dass viele der SPMs in Proben vorkommen oder gar mit einer biologischen Wirkung im Zusammenhang stehen.…”

Section: Was Ist Messbar Was Nichtunclassified

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Steinhilber,

Weylandt,

Schebb

2024

Nachr Chem

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Section: Was Ist Messbar Was Nichtunclassified

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Steinhilber,

Weylandt,

Schebb

2024

Nachr Chem

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“…151 In any case, users should always review latest recommendations and carefully design their pipelines, to avoid major errors in data analyses that may invalidate results, as it has also been shown in meta-metabolomics studies. 158 Box 5 and ►Fig. 2 show the pros and cons of this methodology.…”

Section: Advantagesmentioning

confidence: 99%

Exploring the Microbiome in Human Reproductive Tract: High-Throughput Methods for the Taxonomic Characterization of Microorganisms

Salas-Espejo,

Terrón-Camero,

Ruiz

et al. 2023

Semin Reprod Med

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Microorganisms are important due to their widespread presence and multifaceted roles across various domains of life, ecology, and industries. In humans, they underlie the proper functioning of multiple systems crucial to well-being, including immunological and metabolic functions. Emerging research addressing the presence and roles of microorganisms within human reproduction is increasingly relevant. Studies implementing new methodologies (e.g., to investigate vaginal, uterine, and semen microenvironments) can now provide relevant insights into fertility, reproductive health, or pregnancy outcomes. In that sense, cutting-edge sequencing techniques, as well as others such as meta-metabolomics, culturomics, and meta-proteomics, are becoming more popular and accessible worldwide, allowing the characterization of microbiomes at unprecedented resolution. However, they frequently involve rather complex laboratory protocols and bioinformatics analyses, for which researchers may lack the required expertise. A suitable pipeline would successfully enable both taxonomic classification and functional profiling of the microbiome, providing easy-to-understand biological interpretations. However, the selection of an appropriate methodology would be crucial, as it directly impacts the reproducibility, accuracy, and quality of the results and observations. This review focuses on the different current microbiome-related techniques in the context of human reproduction, encompassing niches like vagina, endometrium, and seminal fluid. The most standard and reliable methods are 16S rRNA gene sequencing, metagenomics, and meta-transcriptomics, together with complementary approaches including meta-proteomics, meta-metabolomics, and culturomics. Finally, we also offer case examples and general recommendations about the most appropriate methods and workflows and discuss strengths and shortcomings for each technique.

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“…There is currently a debate on whether most SPMS can be reliably measured in open circulation using current analytical techniques (O’Donnell et al, 2023; Schebb et al, 2022), possibly due to their short half-life and rapid elimination (Psychogios et al, 2011; Skarke et al, 2015). However, the immunomodulatory roles for lipoxins and fatty acid epoxides are well established (Chandrasekharan & Sharma-Walia, 2015), and collections of resolvin-, protectin- and maresin-sensitive receptors have been reported (Ferguson et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

Blood-based targeted metabolipidomics reveals altered omega fatty acid-derived lipid mediators in relapsing-remitting multiple sclerosis patients

Zahoor,

Waters,

Ata

et al. 2024

Preprint

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Unresolved and uncontrolled inflammation is considered a hallmark of pathogenesis in chronic inflammatory diseases like multiple sclerosis (MS), suggesting a defective resolution process. Inflammatory resolution is an active process partially mediated by endogenous metabolites of dietary polyunsaturated fatty acids (PUFA), collectively termed specialized pro-resolving lipid mediators (SPMs). Altered levels of resolution mediators have been reported in several inflammatory diseases and may partly explain impaired inflammatory resolution. Performing LC-MS/MS-based targeted lipid mediator profiling, we observed distinct changes in fatty acid metabolites in serum from 30 relapsing-remitting MS (RRMS) patients relative to 30 matched healthy subjects (HS). Robust linear regression revealed 12 altered lipid mediators after adjusting for confounders (p <0.05). Of these, 15d-PGJ2, PGE3, and LTB5 were increased in MS while PGF2a, 8,9-DiHETrE, 5,6-DiHETrE, 20-HETE, 15-HETE, 12-HETE, 12-HEPE, 14-HDoHE, and DHEA were decreased in MS compared to HS. In addition, 12,13-DiHOME and 12,13-DiHODE were positively correlated with expanded disability status scale values (EDSS). Using Partial Least Squares, we identified several lipid mediators with high VIP scores (VIP > 1: 32% - 52%) of which POEA, PGE3, DHEA, LTB5, and 12-HETE were top predictors for distinguishing between RRMS and HS (AUC =0.75) based on the XGBoost Classifier algorithm. Collectively, these findings suggest an imbalance between inflammation and resolution. Altogether, lipid mediators appear to have potential as diagnostic and prognostic biomarkers for RRMS.

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Failure to apply standard limit-of-detection or limit-of-quantitation criteria to specialized pro-resolving mediator analysis incorrectly characterizes their presence in biological samples

Cited by 22 publications

References 12 publications

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Exploring the Microbiome in Human Reproductive Tract: High-Throughput Methods for the Taxonomic Characterization of Microorganisms

Blood-based targeted metabolipidomics reveals altered omega fatty acid-derived lipid mediators in relapsing-remitting multiple sclerosis patients

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