An optimized proteomics-based approach to estimate blood contamination and cellular heterogeneity of frozen placental tissue

Kruger, Laken; Yue, Guihua; Paquette, Alison G.; Sathyanarayana, Sheela; Enquobahrie, Daniel A.; Bammler, Theo K.; MacDonald, James W.; Zhao, Qi; Prasad, Bhagwat

doi:10.1016/j.placenta.2022.12.007

Cited by 3 publications

(1 citation statement)

References 31 publications

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“…In vitro models used in drug metabolism and transport studies (e.g., for in vitro to in vivo extrapolation (IVIVE)) can be validated for protein abundance using quantitative proteomics. The technology is not only useful for protein abundance measurement, but it can also be used to assess quality and batch-to-batch variability of in vitro reagent preparation [e.g., microsomes and membrane preparations, (Xu et al, 2018;Leeder et al, 2022)] by detecting marker proteins and identifying contaminants in sample processing [e.g., placental preparations (Kruger et al, 2023)]. A recent study by Handin et al, demonstrates that a proteome, despite containing less data than the transcriptome, can accurately inform cell type deconvolution using different algorithms (Handin et al, 2023).…”

Section: What Is New In Quantitative Proteomics: Techniques and Appli...mentioning

confidence: 99%

Quantitative Proteomics for Translational Pharmacology and Precision Medicine: State of The Art and Future Outlook

Prasad,

Al-Majdoub,

Wegler

et al. 2024

Drug Metab Dispos

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Over the past 20 years, quantitative proteomics has contributed a wealth of protein expression data, which are currently used for a variety of systems pharmacology applications, as a complement or a surrogate for activity of the corresponding proteins. A symposium at the 25th North American ISSX meeting, in Boston, in September 2023, was held to explore current and emerging applications of quantitative proteomics in translational pharmacology and strategies for improved integration into model-informed drug development based on practical experience of each of the presenters. A summary of the talks and discussions is presented in this perspective alongside future outlooks that were outlined for future meetings. Significance StatementThis perspective explores current and emerging applications of quantitative proteomics in translational pharmacology and precision medicine and outlines outlooks for improved integration into model-informed drug development.

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Section: What Is New In Quantitative Proteomics: Techniques and Appli...mentioning

confidence: 99%

Quantitative Proteomics for Translational Pharmacology and Precision Medicine: State of The Art and Future Outlook

Prasad,

Al-Majdoub,

Wegler

et al. 2024

Drug Metab Dispos

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Studying the O-GlcNAcome of human placentas using banked tissue samples

Luna,

Malard,

Pereckas

et al. 2024

Glycobiology

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O-GlcNAcylation is a dynamic modulator of signaling pathways, equal in magnitude to the widely studied phosphorylation. With the rapid development of tools for its detection at the single protein level, the O-GlcNAc modification rapidly emerged as a novel diagnostic and therapeutic target in human diseases. Yet, mapping the human O-GlcNAcome in various tissues is essential for generating relevant biomarkers. In this study, we used human banked tissue as a sample source to identify O-GlcNAcylated protein targets relevant to human diseases. Using human term placentas, we propose (1) a method to clean frozen banked tissue of blood proteins; (2) an optimized protocol for the enrichment of O-GlcNAcylated proteins using immunoaffinity purification; and (3) a bioinformatic workflow to identify the most promising O-GlcNAc targets. As a proof-of-concept, we used 45 mg of banked placental samples from two pregnancies to generate intracellular protein extracts depleted of blood protein. Then, antibody-based O-GlcNAc enrichment on denatured samples yielded over 2000 unique HexNAc PSMs and 900 unique sites using 300 μg of protein lysate. Due to efficient sample cleanup, we also captured 82 HexNAc proteins with high placental expression. Finally, we provide a bioinformatic tool (CytOVS) to sort the HexNAc proteins based on their cellular localization and extract the most promising O-GlcNAc targets to explore further. To conclude, we provide a simple 3-step workflow to generate a manageable list of O-GlcNAc proteins from human tissue and improve our understanding of O-GlcNAcylation’s role in health and diseases.

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Placental Origins of Preeclampsia: Insights from Multi-Omic Studies

Cao,

Saxena,

Gray

2024

IJMS

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Preeclampsia (PE) is a major cause of maternal and neonatal morbidity and mortality worldwide, with the placenta playing a central role in disease pathophysiology. This review synthesizes recent advancements in understanding the molecular mechanisms underlying PE, focusing on placental genes, proteins, and genetic variants identified through multi-omic approaches. Transcriptomic studies in bulk placental tissue have identified many dysregulated genes in the PE placenta, including the PE signature gene, Fms-like tyrosine kinase 1 (FLT1). Emerging single-cell level transcriptomic data have revealed key cell types and molecular signatures implicated in placental dysfunction and PE. However, the considerable variability among studies underscores the need for standardized methodologies and larger sample sizes to enhance the reproducibility of results. Proteomic profiling of PE placentas has identified numerous PE-associated proteins, offering insights into potential biomarkers and pathways implicated in PE pathogenesis. Despite significant progress, challenges such as inconsistencies in study findings and lack of validation persist. Recent fetal genome-wide association studies have identified multiple genetic loci associated with PE, with ongoing efforts to elucidate their impact on placental gene expression and function. Future directions include the integration of multi-omic data, validation of findings in diverse PE populations and clinical subtypes, and the development of analytical approaches and experimental models to study the complex interplay of placental and maternal factors in PE etiology. These insights hold promise for improving risk prediction, diagnosis, and management of PE, ultimately reducing its burden on maternal and neonatal health.

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An optimized proteomics-based approach to estimate blood contamination and cellular heterogeneity of frozen placental tissue

Cited by 3 publications

References 31 publications

Quantitative Proteomics for Translational Pharmacology and Precision Medicine: State of The Art and Future Outlook

Quantitative Proteomics for Translational Pharmacology and Precision Medicine: State of The Art and Future Outlook

Studying the O-GlcNAcome of human placentas using banked tissue samples

Placental Origins of Preeclampsia: Insights from Multi-Omic Studies

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