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Shoaran M, Sabaie H, Mostafavi M, Rezazadeh M. A comprehensive review of the applications of RNA sequencing in celiac disease research. Gene 2024; 927:148681. [PMID: 38871036 DOI: 10.1016/j.gene.2024.148681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 06/06/2024] [Accepted: 06/10/2024] [Indexed: 06/15/2024]
Abstract
RNA sequencing (RNA-seq) has undergone substantial advancements in recent decades and has emerged as a vital technique for profiling the transcriptome. The transition from bulk sequencing to single-cell and spatial approaches has facilitated the achievement of higher precision at cell resolution. It provides valuable biological knowledge about individual immune cells and aids in the discovery of the molecular mechanisms that contribute to the development of autoimmune diseases. Celiac disease (CeD) is an autoimmune disorder characterized by a strong immune response to gluten consumption. RNA-seq has led to significantly advanced research in multiple fields, particularly in CeD research. It has been instrumental in studies involving comparative transcriptomics, nutritional genomics and wheat research, cancer research in the context of CeD, genetic and noncoding RNA-mediated epigenetic insights, disease monitoring and biomarker discovery, regulation of mitochondrial functions, therapeutic target identification and drug mechanism of action, dietary factors, immune cell profiling and the immune landscape. This review offers a comprehensive examination of recent RNA-seq technology research in the field of CeD, highlighting future challenges and opportunities for its application.
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Affiliation(s)
- Maryam Shoaran
- Pediatric Health Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hani Sabaie
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mehrnaz Mostafavi
- Faculty of Allied Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam Rezazadeh
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
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2
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Illescas O, Ferrero G, Belfiore A, Pardini B, Tarallo S, Ciniselli CM, Noci S, Daveri E, Signoroni S, Cattaneo L, Mancini A, Morelli D, Milione M, Cordero F, Rivoltini L, Verderio P, Pasanisi P, Vitellaro M, Naccarati A, Gariboldi M. Modulation of faecal miRNAs highlights the preventive effects of a Mediterranean low-inflammatory dietary intervention. Clin Nutr 2024; 43:951-959. [PMID: 38422953 DOI: 10.1016/j.clnu.2024.02.023] [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: 11/14/2023] [Revised: 02/22/2024] [Accepted: 02/23/2024] [Indexed: 03/02/2024]
Abstract
BACKGROUND Dietary interventions have been proposed as therapeutic approaches for several diseases, including cancer. A low-inflammatory Mediterranean dietary intervention, conducted as a pilot study in subjects with Familial Adenomatous Polyposis (FAP), reduced markers of local and systemic inflammation. We aim to determine whether this diet may modulate faecal microRNA (miRNA) and gene expression in the gut. METHODS Changes in the faecal miRNome were evaluated by small RNA sequencing at baseline (T0), after the three-month intervention (T1), and after an additional three months (T2). Changes in the transcriptome of healthy rectal mucosa and adenomas were evaluated by RNA sequencing at T0 and T2. The identification of validated miRNA-gene interactions and functional analysis of miRNA targets were performed using in silico approaches. RESULTS Twenty-seven subjects were included in this study. It was observed that the diet modulated 29 faecal miRNAs (p < 0.01; |log2 Fold Change|>1), and this modulation persisted for three months after the intervention. Levels of miR-3612-3p and miR-941 correlated with the adherence to the diet, miR-3670 and miR-4252-5p with faecal calprotectin, and miR-3670 and miR-6867 with serum calprotectin. Seventy genes were differentially expressed between adenoma and normal tissue, and most were different before the dietary intervention but reached similar levels after the diet. Functional enrichment analysis identified the proinflammatory ERK1/2, cell cycle regulation, and nutrient response pathways as commonly regulated by the modulated miRNAs and genes. CONCLUSIONS Faecal miRNAs modulated by the dietary intervention target genes that participate in inflammation. Changes in levels of miRNAs and genes with oncogenic and tumour suppressor functions further support the potential cancer-preventive effect of the low-inflammatory Mediterranean diet. CLINICAL TRIAL NUMBER REGISTRATION NCT04552405, Registered in ClinicalTrials.gov.
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Affiliation(s)
- Oscar Illescas
- Molecular Epigenomics Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Giulio Ferrero
- Dept. of Clinical and Biological Sciences, University of Turin, Turin, Italy; Dept. of Computer Science, University of Turin, Turin, Italy
| | - Antonino Belfiore
- First Pathology Division, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Barbara Pardini
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Turin, Italy; Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy
| | - Sonia Tarallo
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Turin, Italy; Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy
| | - Chiara M Ciniselli
- Bioinformatics and Biostatistics Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Sara Noci
- Molecular Epigenomics Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Elena Daveri
- Unit of Immunotherapy of Human Tumors, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Stefano Signoroni
- Hereditary Digestive Tract Tumors Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Laura Cattaneo
- First Pathology Division, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Andrea Mancini
- Diagnostic and Therapeutic Endoscopy Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Daniele Morelli
- Laboratory Medicine Division, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Massimo Milione
- First Pathology Division, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Francesca Cordero
- Dept. of Clinical and Biological Sciences, University of Turin, Turin, Italy; Dept. of Computer Science, University of Turin, Turin, Italy
| | - Licia Rivoltini
- Unit of Immunotherapy of Human Tumors, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Paolo Verderio
- Bioinformatics and Biostatistics Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Patrizia Pasanisi
- Unit of Epidemiology and Prevention, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Marco Vitellaro
- Hereditary Digestive Tract Tumors Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Alessio Naccarati
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Turin, Italy; Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy
| | - Manuela Gariboldi
- Molecular Epigenomics Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy.
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3
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Pardini B, Ferrero G, Naccarati A. Reply. Gastroenterology 2024; 166:358-359. [PMID: 37972822 DOI: 10.1053/j.gastro.2023.11.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 11/09/2023] [Accepted: 11/10/2023] [Indexed: 11/19/2023]
Affiliation(s)
- Barbara Pardini
- Genetic and Molecular Epidemiology Research Unit, Italian Institute for Genomic Medicine, Turin, Italy; Candiolo Cancer Institute, FPO IRCCS, Turin, Italy
| | - Giulio Ferrero
- Department of Clinical and Biological Sciences; Department of Computer Science, University of Torino, Turin, Italy
| | - Alessio Naccarati
- Genetic and Molecular Epidemiology Research Unit, Italian Institute for Genomic Medicine, Turin, Italy; Candiolo Cancer Institute, FPO IRCCS, Turin, Italy
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4
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Ferrero G, Festa R, Follia L, Lettieri G, Tarallo S, Notari T, Giarra A, Marinaro C, Pardini B, Marano A, Piaggeschi G, Di Battista C, Trifuoggi M, Piscopo M, Montano L, Naccarati A. Small noncoding RNAs and sperm nuclear basic proteins reflect the environmental impact on germ cells. Mol Med 2024; 30:12. [PMID: 38243211 PMCID: PMC10799426 DOI: 10.1186/s10020-023-00776-6] [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] [Accepted: 12/26/2023] [Indexed: 01/21/2024] Open
Abstract
BACKGROUND Molecular techniques can complement conventional spermiogram analyses to provide new information on the fertilizing potential of spermatozoa and to identify early alterations due to environmental pollution. METHODS Here, we present a multilevel molecular profiling by small RNA sequencing and sperm nuclear basic protein analysis of male germ cells from 33 healthy young subjects residing in low and high-polluted areas. RESULTS Although sperm motility and sperm concentration were comparable between samples from the two sites, those from the high-pollution area had a higher concentration of immature/immune cells, a lower protamine/histone ratio, a reduced ability of sperm nuclear basic proteins to protect DNA from oxidative damage, and an altered copper/zinc ratio in sperm. Sperm levels of 32 microRNAs involved in intraflagellar transport, oxidative stress response, and spermatogenesis were different between the two areas. In parallel, a decrease of Piwi-interacting RNA levels was observed in samples from the high-polluted area. CONCLUSIONS This comprehensive analysis provides new insights into pollution-driven epigenetic alterations in sperm not detectable by spermiogram.
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Affiliation(s)
- Giulio Ferrero
- Department of Clinical and Biological Sciences, University of Turin, Regione Gonzole 10, 10043, Orbassano, Turin, Italy
- Department of Computer Science, University of Turin, Corso Svizzera, 185, 10149, Turin, Italy
| | - Rosaria Festa
- Department of Biology, University of Naples Federico II, Via Cinthia, 21, 80126, Naples, Italy
| | - Laura Follia
- Department of Clinical and Biological Sciences, University of Turin, Regione Gonzole 10, 10043, Orbassano, Turin, Italy
| | - Gennaro Lettieri
- Department of Biology, University of Naples Federico II, Via Cinthia, 21, 80126, Naples, Italy
| | - Sonia Tarallo
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, SP 142 Km. 3,95, 10060, Candiolo, Turin, Italy
| | - Tiziana Notari
- Check-Up PolyDiagnostic and Research Laboratory, Andrology Unit, Viale Andrea De Luca 5, 84131, Salerno, Italy
| | - Antonella Giarra
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia, 21, 80126, Naples, Italy
| | - Carmela Marinaro
- Department of Biology, University of Naples Federico II, Via Cinthia, 21, 80126, Naples, Italy
| | - Barbara Pardini
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, SP 142 Km. 3,95, 10060, Candiolo, Turin, Italy
| | - Alessandra Marano
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia, 21, 80126, Naples, Italy
| | - Giulia Piaggeschi
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, SP 142 Km. 3,95, 10060, Candiolo, Turin, Italy
| | - Carla Di Battista
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, SP 142 Km. 3,95, 10060, Candiolo, Turin, Italy
| | - Marco Trifuoggi
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia, 21, 80126, Naples, Italy
| | - Marina Piscopo
- Department of Biology, University of Naples Federico II, Via Cinthia, 21, 80126, Naples, Italy.
| | - Luigi Montano
- Andrology Unit and Service of Lifestyle Medicine in UroAndrology, Local Health Authority (ASL) Salerno, Coordination Unit of the Network for Environmental and Reproductive Health (Eco-FoodFertility Project), S. Francesco di Assisi Hospital, 84020, Oliveto Citra, Salerno, Italy.
- PhD Program in Evolutionary Biology and Ecology, University of Rome Tor Vergata, 00133, Rome, Italy.
| | - Alessio Naccarati
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, SP 142 Km. 3,95, 10060, Candiolo, Turin, Italy
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Li C, Lin Y, Lin R, Chen Z, Zhou Q, Luo C, Mo Z. Host miR-129-5p reverses effects of ginsenoside Rg1 on morphine reward possibly mediated by changes in B. vulgatus and serotonin metabolism in hippocampus. Gut Microbes 2023; 15:2254946. [PMID: 37698853 PMCID: PMC10498813 DOI: 10.1080/19490976.2023.2254946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 07/31/2023] [Accepted: 08/30/2023] [Indexed: 09/13/2023] Open
Abstract
Morphine addiction is closely associated with dysbiosis of the gut microbiota. miRNAs play a crucial role in regulating intestinal bacterial growth and are involved in the development of disease. Ginsenoside Rg1 exhibits an anti-addiction effect and significantly improves intestinal microbiota disorders. In pseudo-germfree mice, supplementation with Bacteroides vulgatus (B. vulgatus) synergistically enhanced Rg1 to alleviate morphine addiction. However, it is currently unknown the relationship between fecal miRNAs in morphine-exposed mice and their potential modulation of gut microbiome, as well as their role in mediating the resistance of ginsenoside Rg1 to drug addiction. Here, we studied the fecal miRNA abundance in mice treated with morphine to explore the different miRNAs expressed, their association with B. vulgatus and their role in the amelioration of morphine reward by ginsenoside Rg1. Our results indicated ginsenoside Rg1 attenuated the significant increase in miR-129-5p expression observed in the feces of morphine-treated mice. The miR-129-5p, specifically, inhibited the growth of B. vulgatus by modulating the transcript of the site-tag BVU_RS11835 and increased the levels of 5-hydroxytryptophan and indole-3-carboxaldehyde in vitro. Subsequently, we noticed that oral administration of synthetic miR-129-5p increased 5-HT levels in the hippocampus and inhibited the reversal effect of ginsenoside Rg1 both on the relative abundance of B. vulgatus in the feces and CPP effect induced by morphine exposure. In short, Ginsenoside Rg1 might play an indirect role in remodeling the B. vulgatus against morphine reward by suppressing miR-129-5p expression. These results highlight the role of miR-129-5p and B. vulgatus in morphine reward and the anti-morphine addiction of ginsenoside Rg1.
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Affiliation(s)
- Chan Li
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Yingbo Lin
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
- Department of Pharmacy, Jiangmen Central Hospital, Jiangmen, China
| | - Rukun Lin
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Zhijie Chen
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Qichun Zhou
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Chaohua Luo
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Zhixian Mo
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
- Department of Chinese Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
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Zolnikova O, Dzhakhaya N, Bueverova E, Sedova A, Kurbatova A, Kryuchkova K, Butkova T, Izotov A, Kulikova L, Yurku K, Chekulaev P, Zaborova V. The Contribution of the Intestinal Microbiota to the Celiac Disease Pathogenesis along with the Effectiveness of Probiotic Therapy. Microorganisms 2023; 11:2848. [PMID: 38137992 PMCID: PMC10745538 DOI: 10.3390/microorganisms11122848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/15/2023] [Accepted: 11/20/2023] [Indexed: 12/24/2023] Open
Abstract
The development of many human disorders, including celiac disease (CD), is thought to be influenced by the microbiota of the gastrointestinal tract and its metabolites, according to current research. This study's goal was to provide a concise summary of the information on the contribution of the intestinal microbiota to the CD pathogenesis, which was actively addressed while examining the reported pathogenesis of celiac disease (CD). We assumed that a change in gluten tolerance is formed under the influence of a number of different factors, including genetic predisposition and environmental factors. In related investigations, researchers have paid increasing attention to the study of disturbances in the composition of the intestinal microbiota and its functional activity in CD. A key finding of our review is that the intestinal microbiota has gluten-degrading properties, which, in turn, may have a protective effect on the development of CD. The intestinal microbiota contributes to maintaining the integrity of the intestinal barrier, preventing the formation of a "leaky" intestine. On the contrary, a change in the composition of the microbiota can act as a significant link in the pathogenesis of gluten intolerance and exacerbate the course of the disease. The possibility of modulating the composition of the microbiota by prescribing probiotic preparations is being considered. The effectiveness of the use of probiotics containing Lactobacillus and Bifidobacterium bacteria in experimental and clinical studies as a preventive and therapeutic agent has been documented.
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Affiliation(s)
- Oxana Zolnikova
- Institute of Clinical Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia; (O.Z.); (N.D.); (E.B.); (A.S.); (A.K.); (P.C.)
| | - Natiya Dzhakhaya
- Institute of Clinical Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia; (O.Z.); (N.D.); (E.B.); (A.S.); (A.K.); (P.C.)
| | - Elena Bueverova
- Institute of Clinical Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia; (O.Z.); (N.D.); (E.B.); (A.S.); (A.K.); (P.C.)
| | - Alla Sedova
- Institute of Clinical Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia; (O.Z.); (N.D.); (E.B.); (A.S.); (A.K.); (P.C.)
| | - Anastasia Kurbatova
- Institute of Clinical Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia; (O.Z.); (N.D.); (E.B.); (A.S.); (A.K.); (P.C.)
| | - Kira Kryuchkova
- Institute of Public Health, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia;
| | - Tatyana Butkova
- Institute of Biomedical Chemistry, Biobanking Group, 109028 Moscow, Russia; (T.B.); (A.I.); (L.K.)
| | - Alexander Izotov
- Institute of Biomedical Chemistry, Biobanking Group, 109028 Moscow, Russia; (T.B.); (A.I.); (L.K.)
| | - Ludmila Kulikova
- Institute of Biomedical Chemistry, Biobanking Group, 109028 Moscow, Russia; (T.B.); (A.I.); (L.K.)
- Institute of Mathematical Problems of Biology RAS—The Branch of Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, 142290 Pushchino, Russia
| | - Kseniya Yurku
- State Research Center—Burnasyan Federal Medical Biophysical Center of Federal Medical Biological Agency, 123098 Moscow, Russia;
| | - Pavel Chekulaev
- Institute of Clinical Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia; (O.Z.); (N.D.); (E.B.); (A.S.); (A.K.); (P.C.)
| | - Victoria Zaborova
- Institute of Clinical Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia; (O.Z.); (N.D.); (E.B.); (A.S.); (A.K.); (P.C.)
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Saviano A, Petruzziello C, Brigida M, Morabito Loprete MR, Savioli G, Migneco A, Ojetti V. Gut Microbiota Alteration and Its Modulation with Probiotics in Celiac Disease. Biomedicines 2023; 11:2638. [PMID: 37893012 PMCID: PMC10603901 DOI: 10.3390/biomedicines11102638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/03/2023] [Accepted: 08/14/2023] [Indexed: 10/29/2023] Open
Abstract
Celiac disease (CD) is a chronic inflammation of the small intestine triggered by gluten ingestion in genetically predisposed people. Recent literature studies highlight the possible role of the gut microbiota in the pathogenesis of this disease. The gut microbiota is a complex community of microorganisms that can interact with the innate and adaptative immune systems. A condition of dysbiosis, which refers to an alteration in the composition and function of the human gut microbiota, can lead to a dysregulated immune response. This condition may contribute to triggering gluten intolerance, favoring the development and/or progression of CD in genetically susceptible patients. Interestingly, studies on children and adults with CD showed a different microbiome profile in fecal samples, with a different degree of "activity" for the disease. From this point of view, our review aimed to collect and discuss modern evidence about the alteration of the gut microbiota and its modulation with probiotics, with possible future indications in the management of patients affected by CD.
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Affiliation(s)
- Angela Saviano
- Department of Emergency Medicine, Fondazione Policlinico Universitario A. Gemelli, IRCCS, 00168 Rome, Italy; (A.S.); (A.M.)
| | - Carmine Petruzziello
- Department of Emergency Medicine, Ospedale San Carlo di Nancy, GVM Care and Research, 00165 Rome, Italy
| | - Mattia Brigida
- Gastroenterology Unit, Policlinico Universitario Tor Vergata, 00133 Rome, Italy
| | - Maria Rita Morabito Loprete
- Department of Emergency Medicine, Fondazione Policlinico Universitario A. Gemelli, IRCCS, 00168 Rome, Italy; (A.S.); (A.M.)
| | - Gabriele Savioli
- Department of Emergency Medicine, Fondazione Policlinico San Matteo University Hospital, 27100 Pavia, Italy;
| | - Alessio Migneco
- Department of Emergency Medicine, Fondazione Policlinico Universitario A. Gemelli, IRCCS, 00168 Rome, Italy; (A.S.); (A.M.)
| | - Veronica Ojetti
- Department of Emergency Medicine-Fondazione Policlinico Universitario A. Gemelli, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
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8
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Pardini B, Ferrero G, Tarallo S, Gallo G, Francavilla A, Licheri N, Trompetto M, Clerico G, Senore C, Peyre S, Vymetalkova V, Vodickova L, Liska V, Vycital O, Levy M, Macinga P, Hucl T, Budinska E, Vodicka P, Cordero F, Naccarati A. A Fecal MicroRNA Signature by Small RNA Sequencing Accurately Distinguishes Colorectal Cancers: Results From a Multicenter Study. Gastroenterology 2023; 165:582-599.e8. [PMID: 37263306 DOI: 10.1053/j.gastro.2023.05.037] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 04/18/2023] [Accepted: 05/24/2023] [Indexed: 06/03/2023]
Abstract
BACKGROUND & AIMS Fecal tests currently used for colorectal cancer (CRC) screening show limited accuracy in detecting early tumors or precancerous lesions. In this respect, we comprehensively evaluated stool microRNA (miRNA) profiles as biomarkers for noninvasive CRC diagnosis. METHODS A total of 1273 small RNA sequencing experiments were performed in multiple biospecimens. In a cross-sectional study, miRNA profiles were investigated in fecal samples from an Italian and a Czech cohort (155 CRCs, 87 adenomas, 96 other intestinal diseases, 141 colonoscopy-negative controls). A predictive miRNA signature for cancer detection was defined by a machine learning strategy and tested in additional fecal samples from 141 CRC patients and 80 healthy volunteers. miRNA profiles were compared with those of 132 tumors/adenomas paired with adjacent mucosa, 210 plasma extracellular vesicle samples, and 185 fecal immunochemical test leftover samples. RESULTS Twenty-five miRNAs showed altered levels in the stool of CRC patients in both cohorts (adjusted P < .05). A 5-miRNA signature, including miR-149-3p, miR-607-5p, miR-1246, miR-4488, and miR-6777-5p, distinguished patients from control individuals (area under the curve [AUC], 0.86; 95% confidence interval [CI], 0.79-0.94) and was validated in an independent cohort (AUC, 0.96; 95% CI, 0.92-1.00). The signature classified control individuals from patients with low-/high-stage tumors and advanced adenomas (AUC, 0.82; 95% CI, 0.71-0.97). Tissue miRNA profiles mirrored those of stool samples, and fecal profiles of different gastrointestinal diseases highlighted miRNAs specifically dysregulated in CRC. miRNA profiles in fecal immunochemical test leftover samples showed good correlation with those of stool collected in preservative buffer, and their alterations could be detected in adenoma or CRC patients. CONCLUSIONS Our comprehensive fecal miRNome analysis identified a signature accurately discriminating cancer aimed at improving noninvasive diagnosis and screening strategies.
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Affiliation(s)
- Barbara Pardini
- Italian Institute for Genomic Medicine, Turin, Italy; Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy.
| | - Giulio Ferrero
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy; Department of Computer Science, University of Turin, Turin, Italy
| | - Sonia Tarallo
- Italian Institute for Genomic Medicine, Turin, Italy; Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
| | - Gaetano Gallo
- Department of Surgery, Sapienza University of Rome, Rome, Italy; Department of Colorectal Surgery, Clinica S. Rita, Vercelli, Italy
| | | | - Nicola Licheri
- Department of Computer Science, University of Turin, Turin, Italy
| | - Mario Trompetto
- Department of Colorectal Surgery, Clinica S. Rita, Vercelli, Italy
| | - Giuseppe Clerico
- Department of Colorectal Surgery, Clinica S. Rita, Vercelli, Italy
| | - Carlo Senore
- Epidemiology and Screening Unit-CPO, University Hospital Città della Salute e della Scienza, Turin, Italy
| | - Sergio Peyre
- LILT (Lega Italiana Lotta contro i Tumori), associazione provinciale di Biella, Biella, Italy
| | - Veronika Vymetalkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic; Institute of Biology and Medical Genetics, 1st Medical Faculty, Charles University, Prague, Czech Republic; Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Ludmila Vodickova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic; Institute of Biology and Medical Genetics, 1st Medical Faculty, Charles University, Prague, Czech Republic; Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Vaclav Liska
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic; Department of Surgery, University Hospital and Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Ondrej Vycital
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic; Department of Surgery, University Hospital and Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Miroslav Levy
- Department of Surgery, First Faculty of Medicine, Charles University and Thomayer Hospital, Prague, Czech Republic
| | - Peter Macinga
- Department of Gastroenterology and Hepatology, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Tomas Hucl
- Department of Gastroenterology and Hepatology, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Eva Budinska
- RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic; Institute of Biology and Medical Genetics, 1st Medical Faculty, Charles University, Prague, Czech Republic; Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | | | - Alessio Naccarati
- Italian Institute for Genomic Medicine, Turin, Italy; Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy.
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Turjeman S, Sharon E, Levin R, Oralewska B, Szaflarska-Popławska A, Bierła JB, Cukrowska B, Koren O. Celiac-the lone horse? An autoimmune condition without signals of microbiota dysbiosis. Microbiol Spectr 2023; 11:e0146323. [PMID: 37565758 PMCID: PMC10581062 DOI: 10.1128/spectrum.01463-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 06/29/2023] [Indexed: 08/12/2023] Open
Abstract
Accumulating evidence supports the role of microbiota in autoimmune processes, but research regarding the role of the gut microbiota in celiac disease (CD) is still emerging, and a consistent CD-associated dysbiosis pattern has not yet been defined. Here, we characterized the microbiota of children newly diagnosed with CD, with their unaffected family members as a healthy control group to reduce confounding factors including genetic background, hygiene, dietary habits, and environment, and followed children with CD over 1 year of dietary intervention (exclusion of gluten) to understand if the microbiota is associated with CD and its mediation. We did not find differences in the microbiota of siblings with and without CD, despite a wealth of evidence in the literature supporting CD-specific microbiota. CD is common among first-degree relatives, so this could suggest that unaffected family members in this study may be living in a pre-CD state, currently below clinical detection. Interestingly, despite the effectiveness of diet in CD control, we did not observe diet-mediated microbiota changes, except for short-term increase in Akkermansia muciniphila. This lack of effect could suggest a very strong CD microbial signature even when controlled or could be a technical shortcoming. Expanded future studies with both related and unrelated controls and diet interventions in both the CD and control arms can provide further context to our findings. IMPORTANCE The microbiota is the community of microbes that live in and on us. These microbes are essential to our health and everyday function. Disruption of the community is associated with diseases ranging from metabolic syndrome to autoimmune diseases to mental disorders. In the case of celiac disease (CD), research remains inconclusive regarding implications of the microbiota in etiology. Here, we compared microbiota of children with CD to those of their unaffected family members and found very few differences in microbiota profiles. We next examined how gluten elimination in CD patients affects the microbiota. Surprisingly, despite diet adherence, microbiota shifts were minimal, with only a short-term increase in Akkermansia muciniphila. Previous studies suggest that family members of CD patients may be living in a pre-CD state, which could explain their microbial similarity. A larger study with unrelated controls and increased microbiota monitoring during diet intervention should give our findings more perspective.
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Affiliation(s)
- Sondra Turjeman
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Efrat Sharon
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Rachel Levin
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Beata Oralewska
- Department of Gastroenterology, Hepatology, Nutritional Disorders and Pediatrics, The Children’s Memorial Health Institute, Warsaw, Poland
| | - Anna Szaflarska-Popławska
- Department of Pediatric Endoscopy and Gastrointestinal Function Testing, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Bydgoszcz, Poland
| | - Joanna B. Bierła
- Department of Pathomorphology, The Children’s Memorial Health Institute, Warsaw, Poland
| | - Bożena Cukrowska
- Department of Pathomorphology, The Children’s Memorial Health Institute, Warsaw, Poland
| | - Omry Koren
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
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