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Maiti KS, Fill E, Strittmatter F, Volz Y, Sroka R, Apolonski A. Standard operating procedure to reveal prostate cancer specific volatile organic molecules by infrared spectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 304:123266. [PMID: 37657373 DOI: 10.1016/j.saa.2023.123266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 08/03/2023] [Accepted: 08/15/2023] [Indexed: 09/03/2023]
Abstract
The growing number of prostate cancer cases is a real concern in modern society. Over 1.4 million new cases and about 400 thousand (>26%) deaths were registered worldwide in 2020 due to prostate cancer. The high mortality rate of prostate cancer is due to the lack of reliable early detection of the disease. Till now the most reliable diagnosis of cancer is tissue biopsy, which is an invasive process. A non-invasive or minimally invasive technique could lead to a diagnostic tool that will allow for saving or prolonging the lifespan of millions of lives. Metabolite-based diagnostics may have a better chance of early cancer detection. However, reliable detection techniques need to be developed. Infrared spectroscopy based gaseous-biofluid holds great promise towards the development of non-invasive diagnostics. A pilot study based on breath analysis by infrared spectroscopy showed promising results in distinguishing prostate cancer patients from healthy volunteers. Details of the spectral metabolic analysis are presented.
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Affiliation(s)
- Kiran Sankar Maiti
- Max-Planck-Institut für Quantenoptik, Hans-Kopfermann-Straße 1, 85748 Garching, Germany; Lehrstuhl für Experimental Physik, Ludwig-Maximilians-Universität München, Am Couombwall 1, 85748 Garching, Germany; Department of Chemistry, Technical University of Munich, Lichtenbergstr. 4, Garching, 85747, Germany; Department of Anesthesiology and Intensive Care Medicine/Center for Sepsis Control and Care, Jena University Hospital, Am Klinikum 1, 07747 Jena, Germany.
| | - Ernst Fill
- Max-Planck-Institut für Quantenoptik, Hans-Kopfermann-Straße 1, 85748 Garching, Germany; Lehrstuhl für Experimental Physik, Ludwig-Maximilians-Universität München, Am Couombwall 1, 85748 Garching, Germany
| | - Frank Strittmatter
- Urologische Klinik und Poliklinik des Klinikums der Ludwig-Maximilians- Universität München in Großhadern, 81377 Munich, Germany
| | - Yannic Volz
- Urologische Klinik und Poliklinik des Klinikums der Ludwig-Maximilians- Universität München in Großhadern, 81377 Munich, Germany
| | - Ronald Sroka
- Urologische Klinik und Poliklinik des Klinikums der Ludwig-Maximilians- Universität München in Großhadern, 81377 Munich, Germany; Laser-Forschungslabor, LIFE Center, University Hospital, Ludwig-Maximilians-Universität München, 82152 Planegg, Germany
| | - Alexander Apolonski
- Max-Planck-Institut für Quantenoptik, Hans-Kopfermann-Straße 1, 85748 Garching, Germany; Lehrstuhl für Experimental Physik, Ludwig-Maximilians-Universität München, Am Couombwall 1, 85748 Garching, Germany; Institute of Automation and Electrometry SB RAS, 630090 Novosibirsk, Russia
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Sánchez-Valle J, Valencia A. Molecular bases of comorbidities: present and future perspectives. Trends Genet 2023; 39:773-786. [PMID: 37482451 DOI: 10.1016/j.tig.2023.06.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 06/12/2023] [Accepted: 06/12/2023] [Indexed: 07/25/2023]
Abstract
Co-occurrence of diseases decreases patient quality of life, complicates treatment choices, and increases mortality. Analyses of electronic health records present a complex scenario of comorbidity relationships that vary by age, sex, and cohort under study. The study of similarities between diseases using 'omics data, such as genes altered in diseases, gene expression, proteome, and microbiome, are fundamental to uncovering the origin of, and potential treatment for, comorbidities. Recent studies have produced a first generation of genetic interpretations for as much as 46% of the comorbidities described in large cohorts. Integrating different sources of molecular information and using artificial intelligence (AI) methods are promising approaches for the study of comorbidities. They may help to improve the treatment of comorbidities, including the potential repositioning of drugs.
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Affiliation(s)
- Jon Sánchez-Valle
- Life Sciences Department, Barcelona Supercomputing Center, Barcelona, 08034, Spain.
| | - Alfonso Valencia
- Life Sciences Department, Barcelona Supercomputing Center, Barcelona, 08034, Spain; ICREA, Barcelona, 08010, Spain.
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Zhao Y, Ma Y, Zhang Q. Metabolite-disease interaction prediction based on logistic matrix factorization and local neighborhood constraints. Front Psychiatry 2023; 14:1149947. [PMID: 37342171 PMCID: PMC10277486 DOI: 10.3389/fpsyt.2023.1149947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 05/10/2023] [Indexed: 06/22/2023] Open
Abstract
Background Increasing evidence indicates that metabolites are closely related to human diseases. Identifying disease-related metabolites is especially important for the diagnosis and treatment of disease. Previous works have mainly focused on the global topological information of metabolite and disease similarity networks. However, the local tiny structure of metabolites and diseases may have been ignored, leading to insufficiency and inaccuracy in the latent metabolite-disease interaction mining. Methods To solve the aforementioned problem, we propose a novel metabolite-disease interaction prediction method with logical matrix factorization and local nearest neighbor constraints (LMFLNC). First, the algorithm constructs metabolite-metabolite and disease-disease similarity networks by integrating multi-source heterogeneous microbiome data. Then, the local spectral matrices based on these two networks are established and used as the input of the model, together with the known metabolite-disease interaction network. Finally, the probability of metabolite-disease interaction is calculated according to the learned latent representations of metabolites and diseases. Results Extensive experiments on the metabolite-disease interaction data were conducted. The results show that the proposed LMFLNC method outperformed the second-best algorithm by 5.28 and 5.61% in the AUPR and F1, respectively. The LMFLNC method also exhibited several potential metabolite-disease interactions, such as "Cortisol" (HMDB0000063), relating to "21-Hydroxylase deficiency," and "3-Hydroxybutyric acid" (HMDB0000011) and "Acetoacetic acid" (HMDB0000060), both relating to "3-Hydroxy-3-methylglutaryl-CoA lyase deficiency." Conclusion The proposed LMFLNC method can well preserve the geometrical structure of original data and can thus effectively predict the underlying associations between metabolites and diseases. The experimental results show its effectiveness in metabolite-disease interaction prediction.
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Affiliation(s)
- Yongbiao Zhao
- National Engineering Research Center for E-Learning, Central China Normal University, Wuhan, Hubei, China
- School of Computer Engineering, Hubei University of Arts and Science, Xiangyang, Hubei, China
| | - Yuanyuan Ma
- School of Computer Engineering, Hubei University of Arts and Science, Xiangyang, Hubei, China
| | - Qilin Zhang
- School of Computer Engineering, Hubei University of Arts and Science, Xiangyang, Hubei, China
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Maiti KS. Non-Invasive Disease Specific Biomarker Detection Using Infrared Spectroscopy: A Review. Molecules 2023; 28:2320. [PMID: 36903576 PMCID: PMC10005715 DOI: 10.3390/molecules28052320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/22/2023] [Accepted: 02/22/2023] [Indexed: 03/06/2023] Open
Abstract
Many life-threatening diseases remain obscure in their early disease stages. Symptoms appear only at the advanced stage when the survival rate is poor. A non-invasive diagnostic tool may be able to identify disease even at the asymptotic stage and save lives. Volatile metabolites-based diagnostics hold a lot of promise to fulfil this demand. Many experimental techniques are being developed to establish a reliable non-invasive diagnostic tool; however, none of them are yet able to fulfil clinicians' demands. Infrared spectroscopy-based gaseous biofluid analysis demonstrated promising results to fulfil clinicians' expectations. The recent development of the standard operating procedure (SOP), sample measurement, and data analysis techniques for infrared spectroscopy are summarized in this review article. It has also outlined the applicability of infrared spectroscopy to identify the specific biomarkers for diseases such as diabetes, acute gastritis caused by bacterial infection, cerebral palsy, and prostate cancer.
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Affiliation(s)
- Kiran Sankar Maiti
- Max–Planck–Institut für Quantenoptik, Hans-Kopfermann-Straße 1, 85748 Garching, Germany; ; Tel.: +49-289-14054
- Lehrstuhl für Experimental Physik, Ludwig-Maximilians-Universität München, Am Coulombwall 1, 85748 Garching, Germany
- Laser-Forschungslabor, Klinikum der Universität München, Fraunhoferstrasse 20, 82152 Planegg, Germany
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Schifano E, Conta G, Preziosi A, Ferrante C, Batignani G, Mancini P, Tomassini A, Sciubba F, Scopigno T, Uccelletti D, Miccheli A. 2-hydroxyisobutyric acid (2-HIBA) modulates ageing and fat deposition in Caenorhabditis elegans. Front Mol Biosci 2022; 9:986022. [PMID: 36533081 PMCID: PMC9749906 DOI: 10.3389/fmolb.2022.986022] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 11/07/2022] [Indexed: 06/30/2024] Open
Abstract
High levels of 2-hydroxyisobutyric acid (2-HIBA) were found in urines of patients with obesity and hepatic steatosis, suggesting a potential involvement of this metabolite in clinical conditions. The gut microbial origin of 2-HIBA was hypothesized, however its actual origin and role in biological processes are still not clear. We investigated how treatment with 2-HIBA affected the physiology of the model organism Caenorhabditis elegans, in both standard and high-glucose diet (HGD) growth conditions, by targeted transcriptomic and metabolomic analyses, Coherent Anti-Stokes Raman Scattering (CARS) and two-photon fluorescence microscopy. In standard conditions, 2-HIBA resulted particularly effective to extend the lifespan, delay ageing processes and stimulate the oxidative stress resistance in wild type nematodes through the activation of insulin/IGF-1 signaling (IIS) and p38 MAPK pathways and, consequently, through a reduction of ROS levels. Moreover, variations of lipid accumulation observed in treated worms correlated with transcriptional levels of fatty acid synthesis genes and with the involvement of peptide transporter PEP-2. In HGD conditions, the effect of 2-HIBA on C. elegans resulted in a reduction of the lipid droplets deposition, accordingly with an increase of acs-2 gene transcription, involved in β-oxidation processes. In addition, the pro-longevity effect appeared to be correlated to higher levels of tryptophan, which may play a role in restoring the decreased viability observed in the HGD untreated nematodes.
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Affiliation(s)
- Emily Schifano
- Department of Biology and Biotechnology “C. Darwin”, Sapienza University of Rome, Rome, Italy
| | - Giorgia Conta
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
- NMR-based Metabolomics Laboratory of Sapienza (NMLab), Sapienza University of Rome, Rome, Italy
| | - Adele Preziosi
- Department of Biology and Biotechnology “C. Darwin”, Sapienza University of Rome, Rome, Italy
| | - Carino Ferrante
- Department of Physics, Sapienza University of Rome, Rome, Italy
- Center for Life Nano- and Neuro-science, Istituto Italiano di Tecnologia, Rome, Italy
| | - Giovanni Batignani
- Department of Physics, Sapienza University of Rome, Rome, Italy
- Center for Life Nano- and Neuro-science, Istituto Italiano di Tecnologia, Rome, Italy
| | - Patrizia Mancini
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Alberta Tomassini
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
- NMR-based Metabolomics Laboratory of Sapienza (NMLab), Sapienza University of Rome, Rome, Italy
| | - Fabio Sciubba
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
- NMR-based Metabolomics Laboratory of Sapienza (NMLab), Sapienza University of Rome, Rome, Italy
| | - Tullio Scopigno
- Department of Physics, Sapienza University of Rome, Rome, Italy
- Center for Life Nano- and Neuro-science, Istituto Italiano di Tecnologia, Rome, Italy
| | - Daniela Uccelletti
- Department of Biology and Biotechnology “C. Darwin”, Sapienza University of Rome, Rome, Italy
| | - Alfredo Miccheli
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
- NMR-based Metabolomics Laboratory of Sapienza (NMLab), Sapienza University of Rome, Rome, Italy
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Banimfreg BH, Shamayleh A, Alshraideh H. Survey for Computer-Aided Tools and Databases in Metabolomics. Metabolites 2022; 12:metabo12101002. [PMID: 36295904 PMCID: PMC9610953 DOI: 10.3390/metabo12101002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 10/08/2022] [Accepted: 10/12/2022] [Indexed: 11/14/2022] Open
Abstract
Metabolomics has advanced from innovation and functional genomics tools and is currently a basis in the big data-led precision medicine era. Metabolomics is promising in the pharmaceutical field and clinical research. However, due to the complexity and high throughput data generated from such experiments, data mining and analysis are significant challenges for researchers in the field. Therefore, several efforts were made to develop a complete workflow that helps researchers analyze data. This paper introduces a review of the state-of-the-art computer-aided tools and databases in metabolomics established in recent years. The paper provides computational tools and resources based on functionality and accessibility and provides hyperlinks to web pages to download or use. This review aims to present the latest computer-aided tools, databases, and resources to the metabolomics community in one place.
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7
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Granata I, Manipur I, Giordano M, Maddalena L, Guarracino MR. TumorMet: A repository of tumor metabolic networks derived from context-specific Genome-Scale Metabolic Models. Sci Data 2022; 9:607. [PMID: 36207341 PMCID: PMC9547001 DOI: 10.1038/s41597-022-01702-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 09/15/2022] [Indexed: 11/25/2022] Open
Abstract
Studies about the metabolic alterations during tumorigenesis have increased our knowledge of the underlying mechanisms and consequences, which are important for diagnostic and therapeutic investigations. In this scenario and in the era of systems biology, metabolic networks have become a powerful tool to unravel the complexity of the cancer metabolic machinery and the heterogeneity of this disease. Here, we present TumorMet, a repository of tumor metabolic networks extracted from context-specific Genome-Scale Metabolic Models, as a benchmark for graph machine learning algorithms and network analyses. This repository has an extended scope for use in graph classification, clustering, community detection, and graph embedding studies. Along with the data, we developed and provided Met2Graph, an R package for creating three different types of metabolic graphs, depending on the desired nodes and edges: Metabolites-, Enzymes-, and Reactions-based graphs. This package allows the easy generation of datasets for downstream analysis. Measurement(s) | gene expression, metabolic relationships | Technology Type(s) | Genome Scale Metabolic Models; Computational network biology | Sample Characteristic - Organism | Homo sapiens |
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8
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Khosla NK, Lesinski JM, Colombo M, Bezinge L, deMello AJ, Richards DA. Simplifying the complex: accessible microfluidic solutions for contemporary processes within in vitro diagnostics. LAB ON A CHIP 2022; 22:3340-3360. [PMID: 35984715 PMCID: PMC9469643 DOI: 10.1039/d2lc00609j] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 08/15/2022] [Indexed: 05/02/2023]
Abstract
In vitro diagnostics (IVDs) form the cornerstone of modern medicine. They are routinely employed throughout the entire treatment pathway, from initial diagnosis through to prognosis, treatment planning, and post-treatment surveillance. Given the proven links between high quality diagnostic testing and overall health, ensuring broad access to IVDs has long been a focus of both researchers and medical professionals. Unfortunately, the current diagnostic paradigm relies heavily on centralized laboratories, complex and expensive equipment, and highly trained personnel. It is commonly assumed that this level of complexity is required to achieve the performance necessary for sensitive and specific disease diagnosis, and that making something affordable and accessible entails significant compromises in test performance. However, recent work in the field of microfluidics is challenging this notion. By exploiting the unique features of microfluidic systems, researchers have been able to create progressively simple devices that can perform increasingly complex diagnostic assays. This review details how microfluidic technologies are disrupting the status quo, and facilitating the development of simple, affordable, and accessible integrated IVDs. Importantly, we discuss the advantages and limitations of various approaches, and highlight the remaining challenges within the field.
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Affiliation(s)
- Nathan K Khosla
- Institute for Chemical and Bioengineering, ETH Zürich, Vladimir Prelog Weg 1, Zürich, 8093, Switzerland.
| | - Jake M Lesinski
- Institute for Chemical and Bioengineering, ETH Zürich, Vladimir Prelog Weg 1, Zürich, 8093, Switzerland.
| | - Monika Colombo
- Institute for Chemical and Bioengineering, ETH Zürich, Vladimir Prelog Weg 1, Zürich, 8093, Switzerland.
| | - Léonard Bezinge
- Institute for Chemical and Bioengineering, ETH Zürich, Vladimir Prelog Weg 1, Zürich, 8093, Switzerland.
| | - Andrew J deMello
- Institute for Chemical and Bioengineering, ETH Zürich, Vladimir Prelog Weg 1, Zürich, 8093, Switzerland.
| | - Daniel A Richards
- Institute for Chemical and Bioengineering, ETH Zürich, Vladimir Prelog Weg 1, Zürich, 8093, Switzerland.
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9
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Arruda MAZ, de Jesus JR, Blindauer CA, Stewart AJ. Speciomics as a concept involving chemical speciation and omics. J Proteomics 2022; 263:104615. [PMID: 35595056 DOI: 10.1016/j.jprot.2022.104615] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/29/2022] [Accepted: 05/03/2022] [Indexed: 10/18/2022]
Abstract
The study of chemical speciation and the refinement and expansion of omics-based methods are both consolidated and highly active research fields. Although well established, such fields are extremely dynamic and are driven by the emergence of new strategies and improvements in instrumentation. In the case of omics-based studies, subareas including lipidomics, proteomics, metallomics, metabolomics and foodomics have emerged. Here, speciomics is being proposed as an "umbrella" term, that incorporates all of these subareas, to capture studies where the evaluation of chemical species is carried out using omics approaches. This paper contextualizes both speciomics and the speciome, and reviews omics applications used for species identification through examination of proteins, metalloproteins, metabolites, and nucleic acids. In addition, some implications from such studies and a perspective for future development of this area are provided. SIGNIFICANCE: The synergic effect between chemical speciation and omics is highlighted in this work, demonstrating an emerging area of research with a multitude of possibilities in terms of applications and further developments. This work not only defines and contextualizes speciomics and individual speciomes, but also demonstrates with some examples the great potential of this new interdisciplinary area of research.
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Affiliation(s)
- Marco Aurélio Zezzi Arruda
- Spectrometry, Sample Preparation and Mechanization Group, Institute of Chemistry, University of Campinas - Unicamp, P.O. Box 6154, Campinas, SP 13083-970, Brazil; National Institute of Science and Technology for Bioanalytics, Institute of Chemistry, University of Campinas - Unicamp, P.O. Box 6154, Campinas, SP 13083-970, Brazil.
| | - Jemmyson Romário de Jesus
- Research Laboratory in bionanomaterials, LPbio, Chemistry Department, Federal University of Viçosa, UFV, Viçosa, Minas Gerais, Brazil
| | | | - Alan James Stewart
- School of Medicine, University of St Andrews, North Haugh, St Andrews KY16 9TF, United Kingdom
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10
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Yu M, Teitelbaum SL, Dolios G, Dang LHT, Tu P, Wolff MS, Petrick LM. Molecular Gatekeeper Discovery: Workflow for Linking Multiple Exposure Biomarkers to Metabolomics. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:6162-6171. [PMID: 35129943 PMCID: PMC9164279 DOI: 10.1021/acs.est.1c04039] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The exposome reflects multiple exposures across the life-course that can affect health. Metabolomics can reveal the underlying molecular basis linking exposures to health conditions. Here, we explore the concept and general data analysis framework of "molecular gatekeepers"─key metabolites that link single or multiple exposure biomarkers with correlated clusters of endogenous metabolites─to inform health-relevant biological targets. We performed untargeted metabolomics on plasma from 152 adolescent girls participating in the Growing Up Healthy Study in New York City. We then performed network analysis to link metabolites to exposure biomarkers including five trace elements (Cd, Mn, Pb, Se, and Hg) and five perfluorinated chemicals (PFCs; n-PFOS, Sm-PFOS, n-PFOA, PFHxS, and PFNA). We found 144 molecular gatekeepers and annotated 22 of them. Lysophosphatidylcholine (16:0) and taurodeoxycholate were correlated with both n-PFOA and n-PFOS, suggesting a shared dysregulation from multiple xenobiotic exposures. Sphingomyelin (d18:2/14:0) was significantly associated with age at menarche; yet, no direct association was detected between any exposure biomarkers and age at menarche. Thus, molecular gatekeepers can also discover molecular linkages between exposure biomarkers and health outcomes that may otherwise be obscured by complex interactions in direct measurements.
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Affiliation(s)
- Miao Yu
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Susan L Teitelbaum
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Georgia Dolios
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Lam-Ha T Dang
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Peijun Tu
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Mary S Wolff
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Lauren M Petrick
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
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11
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Metabolomics Signatures and Subsequent Maternal Health among Mothers with a Congenital Heart Defect-Affected Pregnancy. Metabolites 2022; 12:metabo12020100. [PMID: 35208175 PMCID: PMC8877777 DOI: 10.3390/metabo12020100] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 01/13/2022] [Accepted: 01/15/2022] [Indexed: 12/24/2022] Open
Abstract
Congenital heart defects (CHDs) are the most prevalent and serious of all birth defects in the United States. However, little is known about the impact of CHD-affected pregnancies on subsequent maternal health. Thus, there is a need to characterize the metabolic alterations associated with CHD-affected pregnancies. Fifty-six plasma samples were identified from post-partum women who participated in the National Birth Defects Prevention Study between 1997 and 2011 and had (1) unaffected control offspring (n = 18), (2) offspring with tetralogy of Fallot (ToF, n = 22), or (3) hypoplastic left heart syndrome (HLHS, n = 16) in this pilot study. Absolute concentrations of 408 metabolites using the AbsoluteIDQ® p400 HR Kit (Biocrates) were evaluated among case and control mothers. Twenty-six samples were randomly selected from above as technical repeats. Analysis of covariance (ANCOVA) and logistic regression models were used to identify significant metabolites after controlling for the maternal age at delivery and body mass index. The receiver operating characteristic (ROC) curve and area-under-the-curve (AUC) are reported to evaluate the performance of significant metabolites. Overall, there were nine significant metabolites (p < 0.05) identified in HLHS case mothers and 30 significant metabolites in ToF case mothers. Statistically significant metabolites were further evaluated using ROC curve analyses with PC (34:1), two sphingolipids SM (31:1), SM (42:2), and PC-O (40:4) elevated in HLHS cases; while LPC (18:2), two triglycerides: TG (44:1), TG (46:2), and LPC (20:3) decreased in ToF; and cholesterol esters CE (22:6) were elevated among ToF case mothers. The metabolites identified in the study may have profound structural and functional implications involved in cellular signaling and suggest the need for postpartum dietary supplementation among women who gave birth to CHD offspring.
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12
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Wu S, Chen D, Snyder MP. Network biology bridges the gaps between quantitative genetics and multi-omics to map complex diseases. Curr Opin Chem Biol 2021; 66:102101. [PMID: 34861483 DOI: 10.1016/j.cbpa.2021.102101] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 10/17/2021] [Accepted: 10/27/2021] [Indexed: 12/27/2022]
Abstract
With advances in high-throughput sequencing technologies, quantitative genetics approaches have provided insights into genetic basis of many complex diseases. Emerging in-depth multi-omics profiling technologies have created exciting opportunities for systematically investigating intricate interaction networks with different layers of biological molecules underlying disease etiology. Herein, we summarized two main categories of biological networks: evidence-based and statistically inferred. These different types of molecular networks complement each other at both bulk and single-cell levels. We also review three main strategies to incorporate quantitative genetics results with multi-omics data by network analysis: (a) network propagation, (b) functional module-based methods, (c) comparative/dynamic networks. These strategies not only aid in elucidating molecular mechanisms of complex diseases but can guide the search for therapeutic targets.
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Affiliation(s)
- Si Wu
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Dijun Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
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