1
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Patrício A, Costa RS, Henriques R. Pattern-centric transformation of omics data grounded on discriminative gene associations aids predictive tasks in TCGA while ensuring interpretability. Biotechnol Bioeng 2024; 121:2881-2892. [PMID: 38859573 DOI: 10.1002/bit.28758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 02/07/2024] [Accepted: 05/18/2024] [Indexed: 06/12/2024]
Abstract
The increasing prevalence of omics data sources is pushing the study of regulatory mechanisms underlying complex diseases such as cancer. However, the vast quantities of molecular features produced and the inherent interplay between them lead to a level of complexity that hampers both descriptive and predictive tasks, requiring custom-built algorithms that can extract relevant information from these sources of data. We propose a transformation that moves data centered on molecules (e.g., transcripts and proteins) to a new data space focused on putative regulatory modules given by statistically relevant co-expression patterns. To this end, the proposed transformation extracts patterns from the data through biclustering and uses them to create new variables with guarantees of interpretability and discriminative power. The transformation is shown to achieve dimensionality reductions of up to 99% and increase predictive performance of various classifiers across multiple omics layers. Results suggest that omics data transformations from gene-centric to pattern-centric data supports both prediction tasks and human interpretation, notably contributing to precision medicine applications.
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Affiliation(s)
- André Patrício
- INESC-ID and Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
- LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
| | - Rafael S Costa
- LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
| | - Rui Henriques
- INESC-ID and Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
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2
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Annesley SJ, Missailidis D, Heng B, Josev EK, Armstrong CW. Unravelling shared mechanisms: insights from recent ME/CFS research to illuminate long COVID pathologies. Trends Mol Med 2024; 30:443-458. [PMID: 38443223 DOI: 10.1016/j.molmed.2024.02.003] [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: 11/20/2023] [Revised: 01/29/2024] [Accepted: 02/13/2024] [Indexed: 03/07/2024]
Abstract
Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a debilitating chronic illness often triggered by an initiating acute event, mainly viral infections. The transition from acute to chronic disease remains unknown, but interest in this phenomenon has escalated since the COVID-19 pandemic and the post-COVID-19 illness, termed 'long COVID' (LC). Both ME/CFS and LC share many clinical similarities. Here, we present recent findings in ME/CFS research focussing on proposed disease pathologies shared with LC. Understanding these disease pathologies and how they influence each other is key to developing effective therapeutics and diagnostic tests. Given that ME/CFS typically has a longer disease duration compared with LC, with symptoms and pathologies evolving over time, ME/CFS may provide insights into the future progression of LC.
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Affiliation(s)
- Sarah J Annesley
- Department of Microbiology, Anatomy, Physiology and Pharmacology, La Trobe University, VIC, Australia.
| | - Daniel Missailidis
- Department of Microbiology, Anatomy, Physiology and Pharmacology, La Trobe University, VIC, Australia
| | - Benjamin Heng
- Macquarie Medical School, Faculty of Medicine, Human and Health Sciences, Macquarie University, Sydney, NSW, Australia
| | - Elisha K Josev
- Neurodisability & Rehabilitation, Clinical Sciences, Murdoch Children's Research Institute, Parkville, VIC, Australia; Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, VIC, Australia; Mercy Hospital for Women, Heidelberg, VIC, Australia
| | - Christopher W Armstrong
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, Australia
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Pietrangelo T, Cagnin S, Bondi D, Santangelo C, Marramiero L, Purcaro C, Bonadio RS, Di Filippo ES, Mancinelli R, Fulle S, Verratti V, Cheng X. Myalgic encephalomyelitis/chronic fatigue syndrome from current evidence to new diagnostic perspectives through skeletal muscle and metabolic disturbances. Acta Physiol (Oxf) 2024; 240:e14122. [PMID: 38483046 DOI: 10.1111/apha.14122] [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: 11/19/2023] [Revised: 02/01/2024] [Accepted: 02/19/2024] [Indexed: 04/17/2024]
Abstract
Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a demanding medical condition for patients and society. It has raised much more public awareness after the COVID-19 pandemic since ME/CFS and long-COVID patients share many clinical symptoms such as debilitating chronic fatigue. However, unlike long COVID, the etiopathology of ME/CFS remains a mystery despite several decades' research. This review moves from pathophysiology of ME/CFS through the compelling evidence and most interesting hypotheses. It focuses on the pathophysiology of skeletal muscle by proposing the hypothesis that skeletal muscle tissue offers novel opportunities for diagnosis and treatment of this syndrome and that new evidence can help resolve the long-standing debate on terminology.
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Affiliation(s)
- Tiziana Pietrangelo
- Department of Neuroscience, Imaging and Clinical Sciences, University "G. d'Annunzio" of Chieti-Pescara, Chieti, Italy
- IIM-Interuniversity Institute of Myology, University "G. d'Annunzio" of Chieti-Pescara, Chieti, Italy
| | - Stefano Cagnin
- Department of Biology, University of Padua, Padova, Italy
- CIR-Myo Myology Center, University of Padua, Padova, Italy
| | - Danilo Bondi
- Department of Neuroscience, Imaging and Clinical Sciences, University "G. d'Annunzio" of Chieti-Pescara, Chieti, Italy
- IIM-Interuniversity Institute of Myology, University "G. d'Annunzio" of Chieti-Pescara, Chieti, Italy
| | - Carmen Santangelo
- Department of Neuroscience, Imaging and Clinical Sciences, University "G. d'Annunzio" of Chieti-Pescara, Chieti, Italy
- IIM-Interuniversity Institute of Myology, University "G. d'Annunzio" of Chieti-Pescara, Chieti, Italy
| | - Lorenzo Marramiero
- Department of Neuroscience, Imaging and Clinical Sciences, University "G. d'Annunzio" of Chieti-Pescara, Chieti, Italy
- IIM-Interuniversity Institute of Myology, University "G. d'Annunzio" of Chieti-Pescara, Chieti, Italy
| | - Cristina Purcaro
- Department of Neuroscience, Imaging and Clinical Sciences, University "G. d'Annunzio" of Chieti-Pescara, Chieti, Italy
- IIM-Interuniversity Institute of Myology, University "G. d'Annunzio" of Chieti-Pescara, Chieti, Italy
| | | | - Ester Sara Di Filippo
- Department of Neuroscience, Imaging and Clinical Sciences, University "G. d'Annunzio" of Chieti-Pescara, Chieti, Italy
- IIM-Interuniversity Institute of Myology, University "G. d'Annunzio" of Chieti-Pescara, Chieti, Italy
| | - Rosa Mancinelli
- Department of Neuroscience, Imaging and Clinical Sciences, University "G. d'Annunzio" of Chieti-Pescara, Chieti, Italy
- IIM-Interuniversity Institute of Myology, University "G. d'Annunzio" of Chieti-Pescara, Chieti, Italy
| | - Stefania Fulle
- Department of Neuroscience, Imaging and Clinical Sciences, University "G. d'Annunzio" of Chieti-Pescara, Chieti, Italy
- IIM-Interuniversity Institute of Myology, University "G. d'Annunzio" of Chieti-Pescara, Chieti, Italy
| | - Vittore Verratti
- Department of Psychological, Health and Territorial Sciences, University "G. d'Annunzio" of Chieti-Pescara, Chieti, Italy
| | - Xuanhong Cheng
- Department of Bioengineering, Lehigh University, Bethlehem, Pennsylvania, USA
- Department of Materials Science and Engineering, Lehigh University, Bethlehem, Pennsylvania, USA
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4
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Sommen SL, Zhao Z, Segtnan S, Stiansen-Sonerud T, Selvakumar J, Beier Havdal L, Gjerstad J, Wyller VBB, Lund Berven L. Bulk RNA sequencing for analysis of post COVID-19 condition in adolescents and young adults. J Transl Med 2024; 22:312. [PMID: 38532465 PMCID: PMC10964710 DOI: 10.1186/s12967-024-05117-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 03/20/2024] [Indexed: 03/28/2024] Open
Abstract
BACKGROUND Post COVID-19 condition (PCC) is a complication of SARS-COV-2 infection and can lead to long-term disability. METHODS The present study was designed to analyse the gene expression patterns of PCC through bulk RNA sequencing of whole blood and to explore the potential molecular mechanisms of PCC. Whole blood was collected from 80 participants enrolled in a prospective cohort study following SARS-CoV-2 infected and non-infected individuals for 6 months after recruitment and was used for bulk RNA sequencing. Identification of differentially expressed genes (DEG), pathway enrichment and immune cell deconvolution was performed to explore potential biological pathways involved in PCC. RESULTS We have found 13 differentially expressed genes associated with PCC. Enriched pathways were related to interferon-signalling and anti-viral immune processes. CONCLUSION The PCC transcriptome is characterized by a modest overexpression of interferon-stimulated genes, pointing to a subtle ongoing inflammatory response.
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Affiliation(s)
- Silke Lauren Sommen
- Department of Pediatrics, Akershus University Hospital, Lørenskog, Norway
- University of Oslo, Oslo, Norway
| | - Zhi Zhao
- Oslo Centre for Biostatistics and Epidemiology (OCBE), Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
| | | | - Tonje Stiansen-Sonerud
- Department of Pediatrics, Akershus University Hospital, Lørenskog, Norway
- Department of Clinical Molecular Biology (EpiGen), University of Oslo and Akershus University Hospital, Lørenskog, Norway
| | - Joel Selvakumar
- Department of Pediatrics, Akershus University Hospital, Lørenskog, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Lise Beier Havdal
- Department of Pediatrics, Akershus University Hospital, Lørenskog, Norway
| | - Johannes Gjerstad
- Department of Behavioural Sciences, Faculty of Health Sciences, Oslo Metropolitan University, Oslo, Norway
| | - Vegard Bruun Bratholm Wyller
- Department of Pediatrics, Akershus University Hospital, Lørenskog, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Lise Lund Berven
- Department of Pediatrics, Akershus University Hospital, Lørenskog, Norway.
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Rojas-Velazquez D, Kidwai S, Kraneveld AD, Tonda A, Oberski D, Garssen J, Lopez-Rincon A. Methodology for biomarker discovery with reproducibility in microbiome data using machine learning. BMC Bioinformatics 2024; 25:26. [PMID: 38225565 PMCID: PMC10789030 DOI: 10.1186/s12859-024-05639-3] [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: 12/03/2023] [Accepted: 01/04/2024] [Indexed: 01/17/2024] Open
Abstract
BACKGROUND In recent years, human microbiome studies have received increasing attention as this field is considered a potential source for clinical applications. With the advancements in omics technologies and AI, research focused on the discovery for potential biomarkers in the human microbiome using machine learning tools has produced positive outcomes. Despite the promising results, several issues can still be found in these studies such as datasets with small number of samples, inconsistent results, lack of uniform processing and methodologies, and other additional factors lead to lack of reproducibility in biomedical research. In this work, we propose a methodology that combines the DADA2 pipeline for 16s rRNA sequences processing and the Recursive Ensemble Feature Selection (REFS) in multiple datasets to increase reproducibility and obtain robust and reliable results in biomedical research. RESULTS Three experiments were performed analyzing microbiome data from patients/cases in Inflammatory Bowel Disease (IBD), Autism Spectrum Disorder (ASD), and Type 2 Diabetes (T2D). In each experiment, we found a biomarker signature in one dataset and applied to 2 other as further validation. The effectiveness of the proposed methodology was compared with other feature selection methods such as K-Best with F-score and random selection as a base line. The Area Under the Curve (AUC) was employed as a measure of diagnostic accuracy and used as a metric for comparing the results of the proposed methodology with other feature selection methods. Additionally, we use the Matthews Correlation Coefficient (MCC) as a metric to evaluate the performance of the methodology as well as for comparison with other feature selection methods. CONCLUSIONS We developed a methodology for reproducible biomarker discovery for 16s rRNA microbiome sequence analysis, addressing the issues related with data dimensionality, inconsistent results and validation across independent datasets. The findings from the three experiments, across 9 different datasets, show that the proposed methodology achieved higher accuracy compared to other feature selection methods. This methodology is a first approach to increase reproducibility, to provide robust and reliable results.
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Affiliation(s)
- David Rojas-Velazquez
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, University of Utrecht, Utrecht, The Netherlands.
- Department of Data Science, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands.
| | - Sarah Kidwai
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, University of Utrecht, Utrecht, The Netherlands
| | - Aletta D Kraneveld
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, University of Utrecht, Utrecht, The Netherlands
- Department of Neuroscience, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Alberto Tonda
- UMR 518 MIA - PS, INRAE, Institut des Systèmes Complexes de Paris, Île - de - France (ISC-PIF) - UAR 3611 CNRS, Université Paris-Saclay, Paris, France
| | - Daniel Oberski
- Department of Data Science, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Johan Garssen
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, University of Utrecht, Utrecht, The Netherlands
- Global Centre of Excellence Immunology, Danone Nutricia Research, Utrecht, The Netherlands
| | - Alejandro Lopez-Rincon
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, University of Utrecht, Utrecht, The Netherlands
- Department of Data Science, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
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Maksoud R, Magawa C, Eaton-Fitch N, Thapaliya K, Marshall-Gradisnik S. Biomarkers for myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS): a systematic review. BMC Med 2023; 21:189. [PMID: 37226227 DOI: 10.1186/s12916-023-02893-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 05/09/2023] [Indexed: 05/26/2023] Open
Abstract
BACKGROUND Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a multifaceted condition that affects most body systems. There is currently no known diagnostic biomarker; instead, diagnosis is dependent on application of symptom-based case criteria following exclusion of any other potential medical conditions. While there are some studies that report potential biomarkers for ME/CFS, their efficacy has not been validated. The aim of this systematic review is to collate and appraise literature pertaining to a potential biomarker(s) which may effectively differentiate ME/CFS patients from healthy controls. METHODS This systematic review was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses and Cochrane review guidelines. PubMed, Embase and Scopus were systematically searched for articles containing "biomarker" and "ME/CFS" keywords in the abstract or title and if they included the following criteria: (1) were observational studies published between December 1994 and April 2022; (2) involved adult human participants; (3) full text is available in English (4) original research; (5) diagnosis of ME/CFS patients made according to the Fukuda criteria (1994), Canadian Consensus Criteria (2003), International Consensus Criteria (2011) or Institute of Medicine Criteria (2015); (6) study investigated potential biomarkers of ME/CFS compared to healthy controls. Quality and Bias were assessed using the Joanna Briggs Institute Critical Appraisal Checklist for Case Control Studies. RESULTS A total of 101 publications were included in this systematic review. Potential biomarkers ranged from genetic/epigenetic (19.8%), immunological (29.7%), metabolomics/mitochondrial/microbiome (14.85%), endovascular/circulatory (17.82%), neurological (7.92%), ion channel (8.91%) and physical dysfunction biomarkers (8.91%). Most of the potential biomarkers reported were blood-based (79.2%). Use of lymphocytes as a model to investigate ME/CFS pathology was prominent among immune-based biomarkers. Most biomarkers had secondary (43.56%) or tertiary (54.47%) selectivity, which is the ability for the biomarker to identify a disease-causing agent, and a moderate (59.40%) to complex (39.60%) ease-of-detection, including the requirement of specialised equipment. CONCLUSIONS All potential ME/CFS biomarkers differed in efficiency, quality, and translatability as a diagnostic marker. Reproducibility of findings between the included publications were limited, however, several studies validated the involvement of immune dysfunction in the pathology of ME/CFS and the use of lymphocytes as a model to investigate the pathomechanism of illness. The heterogeneity shown across many of the included studies highlights the need for multidisciplinary research and uniform protocols in ME/CFS biomarker research.
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Affiliation(s)
- Rebekah Maksoud
- National Centre for Neuroimmunology and Emerging Diseases (NCNED), Menzies Health Institute Queensland, Griffith University, Gold Coast, Australia.
- Consortium Health International for Myalgic Encephalomyelitis, Griffith University, Gold Coast, Australia.
- School of Pharmacy and Medical Science, Griffith University, Gold Coast, Australia.
| | - Chandi Magawa
- National Centre for Neuroimmunology and Emerging Diseases (NCNED), Menzies Health Institute Queensland, Griffith University, Gold Coast, Australia
- Consortium Health International for Myalgic Encephalomyelitis, Griffith University, Gold Coast, Australia
- School of Pharmacy and Medical Science, Griffith University, Gold Coast, Australia
| | - Natalie Eaton-Fitch
- National Centre for Neuroimmunology and Emerging Diseases (NCNED), Menzies Health Institute Queensland, Griffith University, Gold Coast, Australia
- Consortium Health International for Myalgic Encephalomyelitis, Griffith University, Gold Coast, Australia
| | - Kiran Thapaliya
- National Centre for Neuroimmunology and Emerging Diseases (NCNED), Menzies Health Institute Queensland, Griffith University, Gold Coast, Australia
- Consortium Health International for Myalgic Encephalomyelitis, Griffith University, Gold Coast, Australia
| | - Sonya Marshall-Gradisnik
- National Centre for Neuroimmunology and Emerging Diseases (NCNED), Menzies Health Institute Queensland, Griffith University, Gold Coast, Australia
- Consortium Health International for Myalgic Encephalomyelitis, Griffith University, Gold Coast, Australia
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Ferrier C, Bendifallah S, Suisse S, Dabi Y, Touboul C, Puchar A, Zarca K, Durand Zaleski I. Saliva microRNA signature to diagnose endometriosis: A cost-effectiveness evaluation of the Endotest®. BJOG 2023; 130:396-406. [PMID: 36424910 DOI: 10.1111/1471-0528.17348] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 11/03/2022] [Accepted: 11/05/2022] [Indexed: 11/26/2022]
Abstract
OBJECTIVE To evaluate a saliva diagnostic test (Endotest®) for endometriosis compared with the conventional algorithm. DESIGN A cost-effectiveness analysis with a decision-tree model based on literature data. SETTING France. POPULATION Women with chronic pelvic pain. METHODS Strategy I is the French algorithm, representing the comparator. For strategy II, all patients have an Endotest®. For strategy III, patients undergo ultrasonography to detect endometrioma and patients with no endometrioma detected have an Endotest®. For strategy IV, patients with no endometrioma detected on ultrasonography undergo pelvic magnetic resonance imaging (MRI) to detect endometrioma and/or deep endometriosis. An Endotest® is then performed for patients with a negative result on MRI. MAIN OUTCOMES MEASURES Costs and accuracy rates and incremental cost-effectiveness ratios (ICERs). Three analyses were performed with an Endotest® priced at €500, €750, and €1000. Probabilistic sensitivity analysis was conducted with Monte Carlo simulations. RESULTS With an Endotest® priced at €750, the cost per correctly diagnosed case was €1542, €990, €919 and €1000, respectively, for strategies I, II, III and IV. Strategy I was dominated by all other strategies. Strategies IV, III and II were, respectively, preferred for a willingness-to-pay threshold below €473, between €473 and €4670, and beyond €4670 per correctly diagnosed case. At a price of €500 per Endotest®, strategy I was dominated by all other strategies. At €1000, the ICERs of strategies II and III were €724 and €387 per correctly diagnosed case, respectively, compared with strategy I. CONCLUSION The present study demonstrates the value of the Endotest® from an economic perspective.
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Affiliation(s)
- Clement Ferrier
- Department of Obstetrics and Reproductive Medicine, Hôpital Tenon, Paris, France.,Clinical Research Group (GRC) Paris 6: Centre Expert Endométriose (C3E), Sorbonne University (GRC6 C3E SU), Paris, France
| | - Sofiane Bendifallah
- Department of Obstetrics and Reproductive Medicine, Hôpital Tenon, Paris, France.,Clinical Research Group (GRC) Paris 6: Centre Expert Endométriose (C3E), Sorbonne University (GRC6 C3E SU), Paris, France
| | | | - Yohann Dabi
- Department of Obstetrics and Reproductive Medicine, Hôpital Tenon, Paris, France.,Clinical Research Group (GRC) Paris 6: Centre Expert Endométriose (C3E), Sorbonne University (GRC6 C3E SU), Paris, France
| | - Cyril Touboul
- Department of Obstetrics and Reproductive Medicine, Hôpital Tenon, Paris, France.,Clinical Research Group (GRC) Paris 6: Centre Expert Endométriose (C3E), Sorbonne University (GRC6 C3E SU), Paris, France
| | - Anne Puchar
- Department of Obstetrics and Reproductive Medicine, Hôpital Tenon, Paris, France.,Clinical Research Group (GRC) Paris 6: Centre Expert Endométriose (C3E), Sorbonne University (GRC6 C3E SU), Paris, France
| | - Kevin Zarca
- Assistance Publique-Hôpitaux de Paris, DRCI-URC Eco Ile-de-France, Paris, France.,Université de Paris, Research Centre of Research Epidemiology and Statistics (CRESS-UMR1153), Inserm, Paris, France
| | - Isabelle Durand Zaleski
- Assistance Publique-Hôpitaux de Paris, DRCI-URC Eco Ile-de-France, Paris, France.,Université de Paris, Research Centre of Research Epidemiology and Statistics (CRESS-UMR1153), Inserm, Paris, France
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Dabi Y, Suisse S, Puchar A, Delbos L, Poilblanc M, Descamps P, Haury J, Golfier F, Jornea L, Bouteiller D, Touboul C, Daraï E, Bendifallah S. Endometriosis-associated infertility diagnosis based on saliva microRNA signatures. Reprod Biomed Online 2023; 46:138-149. [PMID: 36411203 DOI: 10.1016/j.rbmo.2022.09.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 09/12/2022] [Accepted: 09/21/2022] [Indexed: 01/31/2023]
Abstract
RESEARCH QUESTION Can a saliva-based miRNA signature for endometriosis-associated infertility be designed and validated by analysing the human miRNome? DESIGN The prospective ENDOmiARN study (NCT04728152) included 200 saliva samples obtained between January 2021 and June 2021 from women with pelvic pain suggestive of endometriosis. All patients underwent either laparoscopy, magnetic resonance imaging, or both. Patients diagnosed with endometriosis were allocated to one of two groups according to their fertility status. Data analysis consisted of identifying a set of miRNA biomarkers using next-generation sequencing, and development of a saliva-based miRNA signature of infertility among patients with endometriosis based on a random forest model. RESULTS Among the 153 patients diagnosed with endometriosis, 24% (n = 36) were infertile and 76% (n = 117) were fertile. Small RNA-sequencing of the 153 saliva samples yielded approximately 3712 M raw sequencing reads (from ∼13.7 M to ∼39.3 M reads/sample). Of the 2561 known miRNAs, the feature selection method generated a signature of 34 miRNAs linked to endometriosis-associated infertility. After validation, the most accurate signature model had a sensitivity, specificity and area under the curve of 100%. CONCLUSION A saliva-based miRNA signature for endometriosis-associated infertility is reported. Although the results still require external validation before using the signature in routine practice, this non-invasive tool is likely to have a major effect on care provided to women with endometriosis.
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Affiliation(s)
- Yohann Dabi
- Sorbonne University, Department of Obstetrics and Reproductive Medicine, Hôpital Tenon, 4 rue de la Chine, Paris 75020; Clinical Research Group (GRC) Paris 6, Centre Expert Endométriose (C3E), Sorbonne University (GRC6 C3E SU); Cancer Biology and Therapeutics, Centre de Recherche Saint-Antoine (CRSA), Sorbonne University, INSERM UMR_S_938, Paris 75020, France
| | | | - Anne Puchar
- Sorbonne University, Department of Obstetrics and Reproductive Medicine, Hôpital Tenon, 4 rue de la Chine, Paris 75020
| | - Léa Delbos
- Department of Obstetrics and Reproductive Medicine, CHU d'Angers, Endometriosis Expert Center, Pays de la Loire, France
| | - Mathieu Poilblanc
- Department of Obstetrics and Reproductive Medicine, Lyon South University Hospital, Lyon Civil Hospices, Lyon, France; Endometriosis Expert Center, Steering Committee of the EndAURA Network
| | - Philippe Descamps
- Department of Obstetrics and Reproductive Medicine, CHU d'Angers, Endometriosis Expert Center, Pays de la Loire, France
| | - Julie Haury
- Sorbonne University, Department of Obstetrics and Reproductive Medicine, Hôpital Tenon, 4 rue de la Chine, Paris 75020
| | - Francois Golfier
- Department of Obstetrics and Reproductive Medicine, Lyon South University Hospital, Lyon Civil Hospices, Lyon, France; Endometriosis Expert Center, Steering Committee of the EndAURA Network
| | - Ludmila Jornea
- Sorbonne Université, Paris Brain Institute, Institut du Cerveau, ICM, Inserm U1127, CNRS UMR 7225, AP-HP, Hôpital Pitié-Salpêtrière, Paris, France
| | - Delphine Bouteiller
- Genotyping and Sequencing Core Facility, iGenSeq, Institut du Cerveau et de la Moelle Epinière, ICM, Hôpital Pitié-Salpêtrière, 47-83 Boulevard de l'Hôpital, Paris 75013, France
| | - Cyril Touboul
- Sorbonne University, Department of Obstetrics and Reproductive Medicine, Hôpital Tenon, 4 rue de la Chine, Paris 75020; Clinical Research Group (GRC) Paris 6, Centre Expert Endométriose (C3E), Sorbonne University (GRC6 C3E SU); Cancer Biology and Therapeutics, Centre de Recherche Saint-Antoine (CRSA), Sorbonne University, INSERM UMR_S_938, Paris 75020, France
| | - Emile Daraï
- Sorbonne University, Department of Obstetrics and Reproductive Medicine, Hôpital Tenon, 4 rue de la Chine, Paris 75020; Clinical Research Group (GRC) Paris 6, Centre Expert Endométriose (C3E), Sorbonne University (GRC6 C3E SU)
| | - Sofiane Bendifallah
- Sorbonne University, Department of Obstetrics and Reproductive Medicine, Hôpital Tenon, 4 rue de la Chine, Paris 75020; Clinical Research Group (GRC) Paris 6, Centre Expert Endométriose (C3E), Sorbonne University (GRC6 C3E SU); Cancer Biology and Therapeutics, Centre de Recherche Saint-Antoine (CRSA), Sorbonne University, INSERM UMR_S_938, Paris 75020, France.
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9
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Bendifallah S, Dabi Y, Suisse S, Jornea L, Bouteiller D, Touboul C, Puchar A, Daraï E. A Bioinformatics Approach to MicroRNA-Sequencing Analysis Based on Human Saliva Samples of Patients with Endometriosis. Int J Mol Sci 2022; 23:ijms23148045. [PMID: 35887388 PMCID: PMC9317484 DOI: 10.3390/ijms23148045] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/16/2022] [Accepted: 07/16/2022] [Indexed: 02/01/2023] Open
Abstract
Endometriosis, defined by the presence of endometrium-like tissue outside the uterus, affects 2–10% of the female population, i.e., around 190 million women, worldwide. The aim of the prospective ENDO-miRNA study was to develop a bioinformatics approach for microRNA-sequencing analysis of 200 saliva samples for miRNAome expression and to test its diagnostic accuracy for endometriosis. Among the 200 patients, 76.5% (n = 153) had confirmed endometriosis and 23.5% (n = 47) had no endometriosis (controls). Small RNA-seq of 200 saliva samples yielded ~4642 M raw sequencing reads (from ~13.7 M to ~39.3 M reads/sample). The number of expressed miRNAs ranged from 1250 (outlier) to 2561 per sample. Some 2561 miRNAs were found to be differentially expressed in the saliva samples of patients with endometriosis compared with the control patients. Among these, 1.17% (n = 30) were up- or downregulated. Among these, the F1-score, sensitivity, specificity, and AUC ranged from 11–86.8%, 5.8–97.4%, 10.6–100%, and 39.3–69.2%, respectively. Here, we report a bioinformatic approach to saliva miRNA sequencing and analysis. We underline the advantages of using saliva over blood in terms of ease of collection, reproducibility, stability, safety, non-invasiveness. This report describes the whole saliva transcriptome to make miRNA quantification a validated, standardized, and reliable technique for routine use. The methodology could be applied to build a saliva signature of endometriosis.
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Affiliation(s)
- Sofiane Bendifallah
- Department of Obstetrics and Reproductive Medicine, Hospital Tenon, Sorbonne University, 4 rue de la Chine, 75020 Paris, France; (Y.D.); (C.T.); (A.P.); (E.D.)
- Clinical Research Group (GRC) Paris 6: Endometriosis Expert Center (C3E), Sorbonne University (GRC6 C3E SU), 75020 Paris, France
- Cancer Biology and Therapeutics, Centre de Recherche Saint-Antoine (CRSA), Sorbonne University, INSERM UMR_S_938, 75020 Paris, France
- Correspondence: ; Tel.: +33-1-56-01-73-18
| | - Yohann Dabi
- Department of Obstetrics and Reproductive Medicine, Hospital Tenon, Sorbonne University, 4 rue de la Chine, 75020 Paris, France; (Y.D.); (C.T.); (A.P.); (E.D.)
- Clinical Research Group (GRC) Paris 6: Endometriosis Expert Center (C3E), Sorbonne University (GRC6 C3E SU), 75020 Paris, France
- Cancer Biology and Therapeutics, Centre de Recherche Saint-Antoine (CRSA), Sorbonne University, INSERM UMR_S_938, 75020 Paris, France
| | | | - Ludmila Jornea
- Paris Brain Institute-Institut du Cerveau-ICM, Sorbonne University, Inserm U1127, CNRS UMR 7225, AP-HP-Hôpital Pitié-Salpêtrière, 75013 Paris, France;
| | - Delphine Bouteiller
- Gentoyping and Sequencing Core Facility, iGenSeq, Institut du Cerveau et de la Moelle Épinière, ICM, Hôpital Pitié-Salpêtrière, 47-83 Boulevard de l’Hôpital, 75013 Paris, France;
| | - Cyril Touboul
- Department of Obstetrics and Reproductive Medicine, Hospital Tenon, Sorbonne University, 4 rue de la Chine, 75020 Paris, France; (Y.D.); (C.T.); (A.P.); (E.D.)
- Clinical Research Group (GRC) Paris 6: Endometriosis Expert Center (C3E), Sorbonne University (GRC6 C3E SU), 75020 Paris, France
- Cancer Biology and Therapeutics, Centre de Recherche Saint-Antoine (CRSA), Sorbonne University, INSERM UMR_S_938, 75020 Paris, France
| | - Anne Puchar
- Department of Obstetrics and Reproductive Medicine, Hospital Tenon, Sorbonne University, 4 rue de la Chine, 75020 Paris, France; (Y.D.); (C.T.); (A.P.); (E.D.)
| | - Emile Daraï
- Department of Obstetrics and Reproductive Medicine, Hospital Tenon, Sorbonne University, 4 rue de la Chine, 75020 Paris, France; (Y.D.); (C.T.); (A.P.); (E.D.)
- Clinical Research Group (GRC) Paris 6: Endometriosis Expert Center (C3E), Sorbonne University (GRC6 C3E SU), 75020 Paris, France
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10
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Bendifallah S, Dabi Y, Suisse S, Jornea L, Bouteiller D, Touboul C, Puchar A, Daraï E. MicroRNome analysis generates a blood-based signature for endometriosis. Sci Rep 2022; 12:4051. [PMID: 35260677 PMCID: PMC8902281 DOI: 10.1038/s41598-022-07771-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 02/16/2022] [Indexed: 02/07/2023] Open
Abstract
Endometriosis, characterized by endometrial-like tissue outside the uterus, is thought to affect 2–10% of women of reproductive age: representing about 190 million women worldwide. Numerous studies have evaluated the diagnostic value of blood biomarkers but with disappointing results. Thus, the gold standard for diagnosing endometriosis remains laparoscopy. We performed a prospective trial, the ENDO-miRNA study, using both Artificial Intelligence (AI) and Machine Learning (ML), to analyze the current human miRNome to differentiate between patients with and without endometriosis, and to develop a blood-based microRNA (miRNA) diagnostic signature for endometriosis. Here, we present the first blood-based diagnostic signature obtained from a combination of two robust and disruptive technologies merging the intrinsic quality of miRNAs to condense the endometriosis phenotype (and its heterogeneity) with the modeling power of AI. The most accurate signature provides a sensitivity, specificity, and Area Under the Curve (AUC) of 96.8%, 100%, and 98.4%, respectively, and is sufficiently robust and reproducible to replace the gold standard of diagnostic surgery. Such a diagnostic approach for this debilitating disorder could impact recommendations from national and international learned societies.
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Affiliation(s)
- Sofiane Bendifallah
- Department of Obstetrics and Reproductive Medicine, Hôpital Tenon, 4 rue de la Chine, 75020, Paris, France. .,Clinical Research Group (GRC) Paris 6: Centre Expert Endométriose (C3E), Sorbonne University (GRC6 C3E SU), Paris, France.
| | - Yohann Dabi
- Department of Obstetrics and Reproductive Medicine, Hôpital Tenon, 4 rue de la Chine, 75020, Paris, France.,Clinical Research Group (GRC) Paris 6: Centre Expert Endométriose (C3E), Sorbonne University (GRC6 C3E SU), Paris, France.,Cancer Biology and Therapeutics, Centre de Recherche Saint-Antoine (CRSA), Sorbonne University, INSERM UMR_S_938, 75020, Paris, France
| | - Stéphane Suisse
- Clinical Research Group (GRC) Paris 6: Centre Expert Endométriose (C3E), Sorbonne University (GRC6 C3E SU), Paris, France
| | - Ludmila Jornea
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Delphine Bouteiller
- Gentoyping and Sequencing Core Facility, iGenSeq, Institut du Cerveau et de la Moelle épinière, ICM, Hôpital Pitié-Salpêtrière, 47-83 Boulevard de l'Hôpital, 75013, Paris, France
| | - Cyril Touboul
- Department of Obstetrics and Reproductive Medicine, Hôpital Tenon, 4 rue de la Chine, 75020, Paris, France.,Clinical Research Group (GRC) Paris 6: Centre Expert Endométriose (C3E), Sorbonne University (GRC6 C3E SU), Paris, France
| | - Anne Puchar
- Department of Obstetrics and Reproductive Medicine, Hôpital Tenon, 4 rue de la Chine, 75020, Paris, France.,Clinical Research Group (GRC) Paris 6: Centre Expert Endométriose (C3E), Sorbonne University (GRC6 C3E SU), Paris, France
| | - Emile Daraï
- Department of Obstetrics and Reproductive Medicine, Hôpital Tenon, 4 rue de la Chine, 75020, Paris, France.,Clinical Research Group (GRC) Paris 6: Centre Expert Endométriose (C3E), Sorbonne University (GRC6 C3E SU), Paris, France
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11
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van Stigt AH, Oude Rengerink K, Bloemenkamp KWM, de Waal W, Prevaes SMPJ, Le TM, van Wijk F, Nederend M, Hellinga AH, Lammers CS, den Hartog G, van Herwijnen MJC, Garssen J, Knippels LMJ, Verhagen LM, de Theije CGM, Lopez-Rincon A, Leusen JHW, Van't Land B, Bont L. Analysing the protection from respiratory tract infections and allergic diseases early in life by human milk components: the PRIMA birth cohort. BMC Infect Dis 2022; 22:152. [PMID: 35164699 PMCID: PMC8842741 DOI: 10.1186/s12879-022-07107-w] [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: 12/22/2020] [Accepted: 01/29/2022] [Indexed: 11/28/2022] Open
Abstract
Background Many studies support the protective effect of breastfeeding on respiratory tract infections. Although infant formulas have been developed to provide adequate nutritional solutions, many components in human milk contributing to the protection of newborns and aiding immune development still need to be identified. In this paper we present the methodology of the “Protecting against Respiratory tract lnfections through human Milk Analysis” (PRIMA) cohort, which is an observational, prospective and multi-centre birth cohort aiming to identify novel functions of components in human milk that are protective against respiratory tract infections and allergic diseases early in life. Methods For the PRIMA human milk cohort we aim to recruit 1000 mother–child pairs in the first month postpartum. At one week, one, three, and six months after birth, fresh human milk samples will be collected and processed. In order to identify protective components, the level of pathogen specific antibodies, T cell composition, Human milk oligosaccharides, as well as extracellular vesicles (EVs) will be analysed, in the milk samples in relation to clinical data which are collected using two-weekly parental questionnaires. The primary outcome of this study is the number of parent-reported medically attended respiratory infections. Secondary outcomes that will be measured are physician diagnosed (respiratory) infections and allergies during the first year of life. Discussion The PRIMA human milk cohort will be a large prospective healthy birth cohort in which we will use an integrated, multidisciplinary approach to identify the longitudinal effect human milk components that play a role in preventing (respiratory) infections and allergies during the first year of life. Ultimately, we believe that this study will provide novel insights into immunomodulatory components in human milk. This may allow for optimizing formula feeding for all non-breastfed infants. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-022-07107-w.
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Affiliation(s)
- Arthur H van Stigt
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Katrien Oude Rengerink
- Department of Biostatistics and Research Support, Clinical Trial Methodology, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Kitty W M Bloemenkamp
- Department of Gynaecology and Obstetrics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Wouter de Waal
- Department of Pediatrics, Diakonessenhuis, Utrecht, The Netherlands
| | - Sabine M P J Prevaes
- Department of Pediatric Pulmonology and Allergology, Wilhelmina Children's Hospital/University Medical Center, Utrecht University, Utrecht, The Netherlands
| | - Thuy-My Le
- Department of Dermatology/Allergology, University Medical Center Utrecht, University of Utrecht, Utrecht, The Netherlands
| | - Femke van Wijk
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Maaike Nederend
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Anneke H Hellinga
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Christianne S Lammers
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Gerco den Hartog
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Martijn J C van Herwijnen
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Johan Garssen
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands.,Danone Nutricia Research, Utrecht, The Netherlands
| | - Léon M J Knippels
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands.,Danone Nutricia Research, Utrecht, The Netherlands
| | - Lilly M Verhagen
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht, The Netherlands
| | - Caroline G M de Theije
- Department of Neonatology, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Alejandro Lopez-Rincon
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Jeanette H W Leusen
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Belinda Van't Land
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, The Netherlands.,Danone Nutricia Research, Utrecht, The Netherlands
| | - Louis Bont
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, The Netherlands. .,Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht, The Netherlands. .,ReSViNET Foundation, Zeist, The Netherlands.
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12
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Bendifallah S, Suisse S, Puchar A, Delbos L, Poilblanc M, Descamps P, Golfier F, Jornea L, Bouteiller D, Touboul C, Dabi Y, Daraï E. Salivary MicroRNA Signature for Diagnosis of Endometriosis. J Clin Med 2022; 11:jcm11030612. [PMID: 35160066 PMCID: PMC8836532 DOI: 10.3390/jcm11030612] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/22/2022] [Accepted: 01/24/2022] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Endometriosis diagnosis constitutes a considerable economic burden for the healthcare system with diagnostic tools often inconclusive with insufficient accuracy. We sought to analyze the human miRNAome to define a saliva-based diagnostic miRNA signature for endometriosis. METHODS We performed a prospective ENDO-miRNA study involving 200 saliva samples obtained from 200 women with chronic pelvic pain suggestive of endometriosis collected between January and June 2021. The study consisted of two parts: (i) identification of a biomarker based on genome-wide miRNA expression profiling by small RNA sequencing using next-generation sequencing (NGS) and (ii) development of a saliva-based miRNA diagnostic signature according to expression and accuracy profiling using a Random Forest algorithm. RESULTS Among the 200 patients, 76.5% (n = 153) were diagnosed with endometriosis and 23.5% (n = 47) without (controls). Small RNA-seq of 200 saliva samples yielded ~4642 M raw sequencing reads (from ~13.7 M to ~39.3 M reads/sample). Quantification of the filtered reads and identification of known miRNAs yielded ~190 M sequences that were mapped to 2561 known miRNAs. Of the 2561 known miRNAs, the feature selection with Random Forest algorithm generated after internally cross validation a saliva signature of endometriosis composed of 109 miRNAs. The respective sensitivity, specificity, and AUC for the diagnostic miRNA signature were 96.7%, 100%, and 98.3%. CONCLUSIONS The ENDO-miRNA study is the first prospective study to report a saliva-based diagnostic miRNA signature for endometriosis. This could contribute to improving early diagnosis by means of a non-invasive tool easily available in any healthcare system.
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Affiliation(s)
- Sofiane Bendifallah
- Department of Obstetrics and Reproductive Medicine, Hôpital Tenon, 4 Rue de la Chine, 75020 Paris, France; (A.P.); (C.T.); (Y.D.); (E.D.)
- Clinical Research Group (GRC) Paris 6, Centre Expert Endométriose (C3E), Sorbonne University (GRC6 C3E SU), 4 Rue de la Chine, 75020 Paris, France
- Correspondence: ; Tel.: +33-1-56-01-73-18; Fax: +33-1-56-01-73-17
| | | | - Anne Puchar
- Department of Obstetrics and Reproductive Medicine, Hôpital Tenon, 4 Rue de la Chine, 75020 Paris, France; (A.P.); (C.T.); (Y.D.); (E.D.)
- Clinical Research Group (GRC) Paris 6, Centre Expert Endométriose (C3E), Sorbonne University (GRC6 C3E SU), 4 Rue de la Chine, 75020 Paris, France
| | - Léa Delbos
- Department of Obstetrics and Reproductive Medicine, Centre Hospitalier Universitaire, 49000 Angers, France; (L.D.); (P.D.)
- Endometriosis Expert Center, Pays de la Loire, 49000 Angers, France
| | - Mathieu Poilblanc
- Department of Obstetrics and Reproductive Medicine, Lyon South University Hospital, Lyon Civil Hospices, 69008 Lyon, France; (M.P.); (F.G.)
- Endometriosis Expert Center, Steering Committee of the EndAURA Network, 75020 Paris, France
| | - Philippe Descamps
- Department of Obstetrics and Reproductive Medicine, Centre Hospitalier Universitaire, 49000 Angers, France; (L.D.); (P.D.)
- Endometriosis Expert Center, Pays de la Loire, 49000 Angers, France
| | - Francois Golfier
- Department of Obstetrics and Reproductive Medicine, Lyon South University Hospital, Lyon Civil Hospices, 69008 Lyon, France; (M.P.); (F.G.)
- Endometriosis Expert Center, Steering Committee of the EndAURA Network, 75020 Paris, France
| | - Ludmila Jornea
- Paris Brain Institute—Institut du Cerveau—ICM, Inserm U1127, CNRS UMR 7225, AP-HP—Hôpital Pitié-Salpêtrière, Sorbonne University, 75020 Paris, France;
| | - Delphine Bouteiller
- Genotyping and Sequencing Core Facility, iGenSeq, Institut du Cerveau et de la Moelle Epinière, Institut du Cerveau, Hôpital Pitié-Salpêtrière, 47-83 Boulevard de l’Hôpital, 75013 Paris, France;
| | - Cyril Touboul
- Department of Obstetrics and Reproductive Medicine, Hôpital Tenon, 4 Rue de la Chine, 75020 Paris, France; (A.P.); (C.T.); (Y.D.); (E.D.)
- Clinical Research Group (GRC) Paris 6, Centre Expert Endométriose (C3E), Sorbonne University (GRC6 C3E SU), 4 Rue de la Chine, 75020 Paris, France
| | - Yohann Dabi
- Department of Obstetrics and Reproductive Medicine, Hôpital Tenon, 4 Rue de la Chine, 75020 Paris, France; (A.P.); (C.T.); (Y.D.); (E.D.)
- Clinical Research Group (GRC) Paris 6, Centre Expert Endométriose (C3E), Sorbonne University (GRC6 C3E SU), 4 Rue de la Chine, 75020 Paris, France
| | - Emile Daraï
- Department of Obstetrics and Reproductive Medicine, Hôpital Tenon, 4 Rue de la Chine, 75020 Paris, France; (A.P.); (C.T.); (Y.D.); (E.D.)
- Clinical Research Group (GRC) Paris 6, Centre Expert Endométriose (C3E), Sorbonne University (GRC6 C3E SU), 4 Rue de la Chine, 75020 Paris, France
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Szklany K, Engen PA, Naqib A, Green SJ, Keshavarzian A, Lopez Rincon A, Siebrand CJ, Diks MAP, van de Kaa M, Garssen J, Knippels LMJ, Kraneveld AD. Dietary Supplementation throughout Life with Non-Digestible Oligosaccharides and/or n-3 Poly-Unsaturated Fatty Acids in Healthy Mice Modulates the Gut-Immune System-Brain Axis. Nutrients 2021; 14:173. [PMID: 35011046 PMCID: PMC8746884 DOI: 10.3390/nu14010173] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/20/2021] [Accepted: 12/24/2021] [Indexed: 12/11/2022] Open
Abstract
The composition and activity of the intestinal microbial community structures can be beneficially modulated by nutritional components such as non-digestible oligosaccharides and omega-3 poly-unsaturated fatty acids (n-3 PUFAs). These components affect immune function, brain development and behaviour. We investigated the additive effect of a dietary combination of scGOS:lcFOS and n-3 PUFAs on caecal content microbial community structures and development of the immune system, brain and behaviour from day of birth to early adulthood in healthy mice. Male BALB/cByJ mice received a control or enriched diet with a combination of scGOS:lcFOS (9:1) and 6% tuna oil (n-3 PUFAs) or individually scGOS:lcFOS (9:1) or 6% tuna oil (n-3 PUFAs). Behaviour, caecal content microbiota composition, short-chain fatty acid levels, brain monoamine levels, enterochromaffin cells and immune parameters in the mesenteric lymph nodes (MLN) and spleen were assessed. Caecal content microbial community structures displayed differences between the control and dietary groups, and between the dietary groups. Compared to control diet, the scGOS:lcFOS and combination diets increased caecal saccharolytic fermentation activity. The diets enhanced the number of enterochromaffin cells. The combination diet had no effects on the immune cells. Although the dietary effect on behaviour was limited, serotonin and serotonin metabolite levels in the amygdala were increased in the combination diet group. The combination and individual interventions affected caecal content microbial profiles, but had limited effects on behaviour and the immune system. No apparent additive effect was observed when scGOS:lcFOS and n-3 PUFAs were combined. The results suggest that scGOS:lcFOS and n-3 PUFAs together create a balance-the best of both in a healthy host.
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Affiliation(s)
- Kirsten Szklany
- Division of Pharmacology, Utrecht Institute of Pharmaceutical Sciences, Faculty of Science, Utrecht University, 3584 CG Utrecht, The Netherlands; (K.S.); (A.L.R.); (C.J.S.); (M.A.P.D.); (M.v.d.K.); (J.G.); (L.M.J.K.)
| | - Phillip A. Engen
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush Medical College, Rush University Medical Center, Chicago, IL 60602, USA; (P.A.E.); (A.N.); (A.K.)
| | - Ankur Naqib
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush Medical College, Rush University Medical Center, Chicago, IL 60602, USA; (P.A.E.); (A.N.); (A.K.)
| | - Stefan J. Green
- Genomics and Microbiome Core Facility, Rush University Medical Center, Chicago, IL 60602, USA;
| | - Ali Keshavarzian
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush Medical College, Rush University Medical Center, Chicago, IL 60602, USA; (P.A.E.); (A.N.); (A.K.)
- Department of Medicine & Physiology, Rush University Medical Center, Chicago, IL 60602, USA
| | - Alejandro Lopez Rincon
- Division of Pharmacology, Utrecht Institute of Pharmaceutical Sciences, Faculty of Science, Utrecht University, 3584 CG Utrecht, The Netherlands; (K.S.); (A.L.R.); (C.J.S.); (M.A.P.D.); (M.v.d.K.); (J.G.); (L.M.J.K.)
- Department of Data Science, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, 3584 EA Utrecht, The Netherlands
| | - Cynthia J. Siebrand
- Division of Pharmacology, Utrecht Institute of Pharmaceutical Sciences, Faculty of Science, Utrecht University, 3584 CG Utrecht, The Netherlands; (K.S.); (A.L.R.); (C.J.S.); (M.A.P.D.); (M.v.d.K.); (J.G.); (L.M.J.K.)
| | - Mara A. P. Diks
- Division of Pharmacology, Utrecht Institute of Pharmaceutical Sciences, Faculty of Science, Utrecht University, 3584 CG Utrecht, The Netherlands; (K.S.); (A.L.R.); (C.J.S.); (M.A.P.D.); (M.v.d.K.); (J.G.); (L.M.J.K.)
| | - Melanie van de Kaa
- Division of Pharmacology, Utrecht Institute of Pharmaceutical Sciences, Faculty of Science, Utrecht University, 3584 CG Utrecht, The Netherlands; (K.S.); (A.L.R.); (C.J.S.); (M.A.P.D.); (M.v.d.K.); (J.G.); (L.M.J.K.)
| | - Johan Garssen
- Division of Pharmacology, Utrecht Institute of Pharmaceutical Sciences, Faculty of Science, Utrecht University, 3584 CG Utrecht, The Netherlands; (K.S.); (A.L.R.); (C.J.S.); (M.A.P.D.); (M.v.d.K.); (J.G.); (L.M.J.K.)
- Global Centre of Excellence Immunology, Nutricia Danone Research, 3584 CT Utrecht, The Netherlands
| | - Leon M. J. Knippels
- Division of Pharmacology, Utrecht Institute of Pharmaceutical Sciences, Faculty of Science, Utrecht University, 3584 CG Utrecht, The Netherlands; (K.S.); (A.L.R.); (C.J.S.); (M.A.P.D.); (M.v.d.K.); (J.G.); (L.M.J.K.)
- Global Centre of Excellence Immunology, Nutricia Danone Research, 3584 CT Utrecht, The Netherlands
| | - Aletta D. Kraneveld
- Division of Pharmacology, Utrecht Institute of Pharmaceutical Sciences, Faculty of Science, Utrecht University, 3584 CG Utrecht, The Netherlands; (K.S.); (A.L.R.); (C.J.S.); (M.A.P.D.); (M.v.d.K.); (J.G.); (L.M.J.K.)
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14
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ME/CFS: Past, Present and Future. Healthcare (Basel) 2021; 9:healthcare9080984. [PMID: 34442121 PMCID: PMC8394918 DOI: 10.3390/healthcare9080984] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/23/2021] [Accepted: 07/25/2021] [Indexed: 01/16/2023] Open
Abstract
This review raises a number of compelling issues related to the condition of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS). Some historical perspective is necessary in order to highlight the nature of the controversy concerning its causation. Throughout history, a pattern tends to repeat itself when natural phenomena require explanation. Dogma usually arrives first, then it is eventually replaced by scientific understanding. The same pattern is unfolding in relation to ME/CFS, but supporters of the psychological dogma surrounding its causation remain stubbornly resistant, even in the face of compelling scientific evidence to the contrary. Acceptance of the latter is not just an academic issue; the route to proper understanding and treatment of ME/CFS is through further scientific research rather than psychological theorisation. Only then will a long-suffering patient group benefit.
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