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Liu Y, Fachrul M, Inouye M, Méric G. Harnessing human microbiomes for disease prediction. Trends Microbiol 2024; 32:707-719. [PMID: 38246848 DOI: 10.1016/j.tim.2023.12.004] [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: 09/12/2023] [Revised: 12/12/2023] [Accepted: 12/12/2023] [Indexed: 01/23/2024]
Abstract
The human microbiome has been increasingly recognized as having potential use for disease prediction. Predicting the risk, progression, and severity of diseases holds promise to transform clinical practice, empower patient decisions, and reduce the burden of various common diseases, as has been demonstrated for cardiovascular disease or breast cancer. Combining multiple modifiable and non-modifiable risk factors, including high-dimensional genomic data, has been traditionally favored, but few studies have incorporated the human microbiome into models for predicting the prospective risk of disease. Here, we review research into the use of the human microbiome for disease prediction with a particular focus on prospective studies as well as the modulation and engineering of the microbiome as a therapeutic strategy.
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Affiliation(s)
- Yang Liu
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK; Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia; Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Melbourne, Victoria, Australia; Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK; British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Muhamad Fachrul
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia; Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Melbourne, Victoria, Australia; Human Genomics and Evolution Unit, St Vincent's Institute of Medical Research, Victoria, Australia; Melbourne Integrative Genomics, University of Melbourne, Parkville, Victoria, Australia; School of BioSciences, University of Melbourne, Parkville, Victoria, Australia
| | - Michael Inouye
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK; Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia; Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK; British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK; Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK; British Heart Foundation Cambridge Centre of Research Excellence, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Guillaume Méric
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia; Department of Cardiometabolic Health, University of Melbourne, Melbourne, Victoria, Australia; Central Clinical School, Monash University, Melbourne, Victoria, Australia; Department of Medical Science, Molecular Epidemiology, Uppsala University, Uppsala, Sweden; Department of Cardiovascular Research, Translation, and Implementation, La Trobe University, Melbourne, Victoria, Australia.
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Fathi-Karkan S, Sargazi S, Shojaei S, Farasati Far B, Mirinejad S, Cordani M, Khosravi A, Zarrabi A, Ghavami S. Biotin-functionalized nanoparticles: an overview of recent trends in cancer detection. NANOSCALE 2024. [PMID: 38899396 DOI: 10.1039/d4nr00634h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Electrochemical bio-sensing is a potent and efficient method for converting various biological recognition events into voltage, current, and impedance electrical signals. Biochemical sensors are now a common part of medical applications, such as detecting blood glucose levels, detecting food pathogens, and detecting specific cancers. As an exciting feature, bio-affinity couples, such as proteins with aptamers, ligands, paired nucleotides, and antibodies with antigens, are commonly used as bio-sensitive elements in electrochemical biosensors. Biotin-avidin interactions have been utilized for various purposes in recent years, such as targeting drugs, diagnosing clinically, labeling immunologically, biotechnology, biomedical engineering, and separating or purifying biomolecular compounds. The interaction between biotin and avidin is widely regarded as one of the most robust and reliable noncovalent interactions due to its high bi-affinity and ability to remain selective and accurate under various reaction conditions and bio-molecular attachments. More recently, there have been numerous attempts to develop electrochemical sensors to sense circulating cancer cells and the measurement of intracellular levels of protein thiols, formaldehyde, vitamin-targeted polymers, huwentoxin-I, anti-human antibodies, and a variety of tumor markers (including alpha-fetoprotein, epidermal growth factor receptor, prostate-specific Ag, carcinoembryonic Ag, cancer antigen 125, cancer antigen 15-3, etc.). Still, the non-specific binding of biotin to endogenous biotin-binding proteins present in biological samples can result in false-positive signals and hinder the accurate detection of cancer biomarkers. This review summarizes various categories of biotin-functional nanoparticles designed to detect such biomarkers and highlights some challenges in using them as diagnostic tools.
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Affiliation(s)
- Sonia Fathi-Karkan
- Natural Products and Medicinal Plants Research Center, North Khorasan University of Medical Sciences, Bojnurd, 94531-55166 Iran.
- Department of Advanced Sciences and Technologies in Medicine, School of Medicine, North Khorasan University of Medical Sciences, Bojnurd 9414974877, Iran.
| | - Saman Sargazi
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran.
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran.
| | - Shirin Shojaei
- Nano Drug Delivery Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Bahareh Farasati Far
- Department of Chemistry, Iran University of Science and Technology, Tehran, Iran.
| | - Shekoufeh Mirinejad
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran.
| | - Marco Cordani
- Department of Biochemistry and Molecular Biology, Faculty of Biology, Complutense University, 28040 Madrid, Spain
- Instituto de Investigaciones Sanitarias San Carlos (IdISSC), 28040 Madrid, Spain
| | - Arezoo Khosravi
- Department of Genetics and Bioengineering, Faculty of Engineering and Natural Sciences, Istanbul Okan University, Istanbul 34959, Turkiye.
| | - Ali Zarrabi
- Department of Biomedical Engineering, Faculty of Engineering and Natural Sciences, Istinye University, Istanbul 34396, Turkiye.
- Department of Research Analytics, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai - 600 077, India
- Graduate School of Biotechnology and Bioengineering, Yuan Ze University, Taoyuan 320315, Taiwan
| | - Saeid Ghavami
- Department of Human Anatomy and Cell Science, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.
- Faculty of Medicine in Zabrze, University of Technology in Katowice, 41-800 Zabrze, Poland
- Research Institute of Oncology and Hematology, Cancer Care Manitoba, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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Drent M, Wijnen P, Bekers O, Bast A. Is a Vitamin K Epoxide Reductase Complex Subunit 1 ( VKORC1) Polymorphism a Risk Factor for Nephrolithiasis in Sarcoidosis? Int J Mol Sci 2024; 25:4448. [PMID: 38674033 PMCID: PMC11050420 DOI: 10.3390/ijms25084448] [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: 03/14/2024] [Revised: 04/11/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
Sarcoidosis is a systemic inflammatory disorder characterized by granuloma formation in various organs. It has been associated with nephrolithiasis. The vitamin K epoxide reductase complex subunit 1 (VKORC1) gene, which plays a crucial role in vitamin K metabolism, has been implicated in the activation of proteins associated with calcification, including in the forming of nephrolithiasis. This study aimed to investigate the VKORC1 C1173T polymorphism (rs9934438) in a Dutch sarcoidosis cohort, comparing individuals with and without a history of nephrolithiasis. Retrospectively, 424 patients with sarcoidosis were divided into three groups: those with a history of nephrolithiasis (Group I: n = 23), those with hypercalcemia without nephrolithiasis (Group II: n = 38), and those without nephrolithiasis or hypercalcemia (Group III: n = 363). Of the 424 sarcoidosis patients studied, 5.4% had a history of nephrolithiasis (Group I), only two of whom possessed no VKORC1 polymorphisms (OR = 7.73; 95% CI 1.79-33.4; p = 0.001). The presence of a VKORC1 C1173T variant allele was found to be a substantial risk factor for the development of nephrolithiasis in sarcoidosis patients. This study provides novel insights into the genetic basis of nephrolithiasis in sarcoidosis patients, identifying VKORC1 C1173T as a potential contributor. Further research is warranted to elucidate the precise mechanisms and explore potential therapeutic interventions based on these genetic findings.
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Affiliation(s)
- Marjolein Drent
- ILD Center of Excellence, Department of Respiratory Medicine, St. Antonius Hospital, 3435 CM Nieuwegein, The Netherlands;
- Department of Pharmacology and Toxicology, Faculty of Health, Medicine, and Life Science, Maastricht University, 6200 MD Maastricht, The Netherlands; (O.B.); (A.B.)
- Research Team, ILD Care Foundation, 6711 NR Ede, The Netherlands
| | - Petal Wijnen
- ILD Center of Excellence, Department of Respiratory Medicine, St. Antonius Hospital, 3435 CM Nieuwegein, The Netherlands;
- Research Team, ILD Care Foundation, 6711 NR Ede, The Netherlands
- Department of Clinical Chemistry, Central Diagnostic Laboratory, Maastricht University Medical Centre, 6229 HX Maastricht, The Netherlands
| | - Otto Bekers
- Department of Pharmacology and Toxicology, Faculty of Health, Medicine, and Life Science, Maastricht University, 6200 MD Maastricht, The Netherlands; (O.B.); (A.B.)
- Department of Clinical Chemistry, Central Diagnostic Laboratory, Maastricht University Medical Centre, 6229 HX Maastricht, The Netherlands
| | - Aalt Bast
- Department of Pharmacology and Toxicology, Faculty of Health, Medicine, and Life Science, Maastricht University, 6200 MD Maastricht, The Netherlands; (O.B.); (A.B.)
- Research Team, ILD Care Foundation, 6711 NR Ede, The Netherlands
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dos Santos Junior ACS, Foligno NE, Vezzoli G. The Implications of the Vitamin D Metabolite Diagnostic Ratio in the Assessment of Patients With Idiopathic Hypercalciuria. Kidney Int Rep 2024; 9:743-745. [PMID: 38765587 PMCID: PMC11101799 DOI: 10.1016/j.ekir.2024.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024] Open
Affiliation(s)
| | - Nadia Edvige Foligno
- Nephrology and Dialysis Unit, IRCCS San Raffaele Scientific Institute; Vita Salute San Raffaele University, Milan, Italy
| | - Giuseppe Vezzoli
- Nephrology and Dialysis Unit, IRCCS San Raffaele Scientific Institute; Vita Salute San Raffaele University, Milan, Italy
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Srikrishnaraj A, Lanting BA, Burton JP, Teeter MG. The Microbial Revolution in the World of Joint Replacement Surgery. JB JS Open Access 2024; 9:e23.00153. [PMID: 38638595 PMCID: PMC11023614 DOI: 10.2106/jbjs.oa.23.00153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/20/2024] Open
Abstract
Background The prevalence of revision surgery due to aseptic loosening and periprosthetic joint infection (PJI) following total hip and knee arthroplasty is growing. Strategies to prevent the need for revision surgery and its associated health-care costs and patient morbidity are needed. Therapies that modulate the gut microbiota to influence bone health and systemic inflammation are a novel area of research. Methods A literature review of preclinical and clinical peer-reviewed articles relating to the role of the gut microbiota in bone health and PJI was performed. Results There is evidence that the gut microbiota plays a role in maintaining bone mineral density, which can contribute to osseointegration, osteolysis, aseptic loosening, and periprosthetic fractures. Similarly, the gut microbiota influences gut permeability and the potential for bacterial translocation to the bloodstream, increasing susceptibility to PJI. Conclusions Emerging evidence supports the role of the gut microbiota in the development of complications such as aseptic loosening and PJI after total hip or knee arthroplasty. There is a potential for microbial therapies such as probiotics or fecal microbial transplantation to moderate the risk of developing these complications. However, further investigation is required. Clinical Relevance Modulation of the gut microbiota may influence patient outcomes following total joint arthroplasty.
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Affiliation(s)
- Arjuna Srikrishnaraj
- Department of Surgery, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
| | - Brent A. Lanting
- Department of Surgery, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
- Bone and Joint Institute, Western University, London, Ontario, Canada
| | - Jeremy P. Burton
- Department of Surgery, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
- Bone and Joint Institute, Western University, London, Ontario, Canada
| | - Matthew G. Teeter
- Department of Surgery, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
- Bone and Joint Institute, Western University, London, Ontario, Canada
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Al KF, Joris BR, Daisley BA, Chmiel JA, Bjazevic J, Reid G, Gloor GB, Denstedt JD, Razvi H, Burton JP. Multi-site microbiota alteration is a hallmark of kidney stone formation. MICROBIOME 2023; 11:263. [PMID: 38007438 PMCID: PMC10675928 DOI: 10.1186/s40168-023-01703-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 10/17/2023] [Indexed: 11/27/2023]
Abstract
BACKGROUND Inquiry of microbiota involvement in kidney stone disease (KSD) has largely focussed on potential oxalate handling abilities by gut bacteria and the increased association with antibiotic exposure. By systematically comparing the gut, urinary, and oral microbiota of 83 stone formers (SF) and 30 healthy controls (HC), we provide a unified assessment of the bacterial contribution to KSD. RESULTS Amplicon and shotgun metagenomic sequencing approaches were consistent in identifying multi-site microbiota disturbances in SF relative to HC. Biomarker taxa, reduced taxonomic and functional diversity, functional replacement of core bioenergetic pathways with virulence-associated gene markers, and community network collapse defined SF, but differences between cohorts did not extend to oxalate metabolism. CONCLUSIONS We conclude that multi-site microbiota alteration is a hallmark of SF, and KSD treatment should consider microbial functional restoration and the avoidance of aberrant modulators such as poor diet and antibiotics where applicable to prevent stone recurrence. Video Abstract.
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Affiliation(s)
- Kait F Al
- Centre for Human Microbiome and Probiotic Research, Lawson Health Research Institute, London, ON, Canada
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada
| | - Benjamin R Joris
- Department of Biochemistry, The University of Western Ontario, London, ON, Canada
| | - Brendan A Daisley
- Molecular and Cellular Biology Department, University of Guelph, Guelph, ON, Canada
| | - John A Chmiel
- Centre for Human Microbiome and Probiotic Research, Lawson Health Research Institute, London, ON, Canada
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada
| | - Jennifer Bjazevic
- Division of Urology, Department of Surgery, The University of Western Ontario, London, ON, Canada
| | - Gregor Reid
- Centre for Human Microbiome and Probiotic Research, Lawson Health Research Institute, London, ON, Canada
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada
- Division of Urology, Department of Surgery, The University of Western Ontario, London, ON, Canada
| | - Gregory B Gloor
- Department of Biochemistry, The University of Western Ontario, London, ON, Canada
| | - John D Denstedt
- Division of Urology, Department of Surgery, The University of Western Ontario, London, ON, Canada
| | - Hassan Razvi
- Division of Urology, Department of Surgery, The University of Western Ontario, London, ON, Canada
| | - Jeremy P Burton
- Centre for Human Microbiome and Probiotic Research, Lawson Health Research Institute, London, ON, Canada.
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada.
- Division of Urology, Department of Surgery, The University of Western Ontario, London, ON, Canada.
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Stepanova N. Oxalate Homeostasis in Non-Stone-Forming Chronic Kidney Disease: A Review of Key Findings and Perspectives. Biomedicines 2023; 11:1654. [PMID: 37371749 DOI: 10.3390/biomedicines11061654] [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: 05/18/2023] [Revised: 06/03/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Chronic kidney disease (CKD) is a significant global public health concern associated with high morbidity and mortality rates. The maintenance of oxalate homeostasis plays a critical role in preserving kidney health, particularly in the context of CKD. Although the relationship between oxalate and kidney stone formation has been extensively investigated, our understanding of oxalate homeostasis in non-stone-forming CKD remains limited. This review aims to present an updated analysis of the existing literature, focusing on the intricate mechanisms involved in oxalate homeostasis in patients with CKD. Furthermore, it explores the key factors that influence oxalate accumulation and discusses the potential role of oxalate in CKD progression and prognosis. The review also emphasizes the significance of the gut-kidney axis in CKD oxalate homeostasis and provides an overview of current therapeutic strategies, as well as potential future approaches. By consolidating important findings and perspectives, this review offers a comprehensive understanding of the present knowledge in this field and identifies promising avenues for further research.
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Affiliation(s)
- Natalia Stepanova
- State Institution «Institute of Nephrology of the National Academy of Medical Sciences of Ukraine», 04050 Kyiv, Ukraine
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