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Liu X, Shi J, Jiao Y, An J, Tian J, Yang Y, Zhuo L. Integrated multi-omics with machine learning to uncover the intricacies of kidney disease. Brief Bioinform 2024; 25:bbae364. [PMID: 39082652 PMCID: PMC11289682 DOI: 10.1093/bib/bbae364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 06/20/2024] [Accepted: 07/17/2024] [Indexed: 08/03/2024] Open
Abstract
The development of omics technologies has driven a profound expansion in the scale of biological data and the increased complexity in internal dimensions, prompting the utilization of machine learning (ML) as a powerful toolkit for extracting knowledge and understanding underlying biological patterns. Kidney disease represents one of the major growing global health threats with intricate pathogenic mechanisms and a lack of precise molecular pathology-based therapeutic modalities. Accordingly, there is a need for advanced high-throughput approaches to capture implicit molecular features and complement current experiments and statistics. This review aims to delineate strategies for integrating multi-omics data with appropriate ML methods, highlighting key clinical translational scenarios, including predicting disease progression risks to improve medical decision-making, comprehensively understanding disease molecular mechanisms, and practical applications of image recognition in renal digital pathology. Examining the benefits and challenges of current integration efforts is expected to shed light on the complexity of kidney disease and advance clinical practice.
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Affiliation(s)
| | | | | | | | | | | | - Li Zhuo
- Corresponding author. Department of Nephrology, China-Japan Friendship Hospital, Beijing 100029, China; China-Japan Friendship Clinic Medical College, Beijing University of Chinese Medicine, 100029 Beijing, China. E-mail:
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Imaizumi T, Fujii N, Hamano T, Yang W, Taguri M, Kansal M, Mehta R, Shafi T, Taliercio J, Go A, Rao P, Hamm LL, Deo R, Maruyama S, Fukagawa M, Feldman HI. Excess risk of cardiovascular events in patients in the United States vs. Japan with chronic kidney disease is mediated mainly by left ventricular structure and function. Kidney Int 2023; 103:949-961. [PMID: 36738890 PMCID: PMC10869952 DOI: 10.1016/j.kint.2023.01.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 12/31/2022] [Accepted: 01/13/2023] [Indexed: 02/05/2023]
Abstract
While patients receiving dialysis therapy in the United States are more likely to develop cardiovascular disease (CVD) than those in Japan, direct comparisons of patients with predialysis chronic kidney disease (CKD) are rare. To study this, we compared various outcomes in patients with predialysis CKD using data from the Chronic Renal Insufficiency Cohort (CRIC) and CKD Japan Cohort (CKD-JAC) studies and determined mediators of any differences. Candidate mediators included left ventricular (LV) indices assessed by echocardiography. Among 3125 CRIC and 1097 CKD-JAC participants, the mean LV mass index (LVMI) and ejection fraction (EF) were 55.7 and 46.6 g/m2 and 54% and 65%, respectively (both significant). The difference in body mass index (32 and 24 kg/m2, respectively) largely accounted for the differences in LVMI and C-reactive protein levels across cohorts. Low EF and high LVMI were significantly associated with subsequent CVD in both cohorts. During a median follow-up of five years, CRIC participants were at higher risk for CVD (adjusted hazard ratio [95% confidence interval]: 3.66 [2.74-4.89]) and death (4.69 [3.05-7.19]). A three-fold higher C-reactive protein concentration and higher phosphate levels in the United States cohort were moderately strong mediators of the differences in CVD. However, echocardiographic parameters were stronger mediators than these laboratory measures. LVMI, EF and their combination mediated the observed difference in CVD (27%, 50%, and 57%, respectively) and congestive heart failure (33%, 62%, and 70%, respectively). Thus, higher LV mass and lower EF, even in the normal range, were found to be predictive of CVD in CKD.
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Affiliation(s)
- Takahiro Imaizumi
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA; Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania, Philadelphia, Pennsylvania, USA; Department of Advanced Medicine, Nagoya University Hospital, Nagoya, Aichi, Japan; Department of Nephrology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan; Department of Nephrology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Aichi, Japan
| | - Naohiko Fujii
- Medical and Research Center for Nephrology and Transplantation, Hyogo Prefectural Nishinomiya Hospital, Nishinomiya, Hyōgo, Japan
| | - Takayuki Hamano
- Department of Nephrology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Aichi, Japan; Department of Nephrology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan.
| | - Wei Yang
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA; Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Masataka Taguri
- Department of Health Data Science, Tokyo Medical University, Tokyo, Japan
| | - Mayank Kansal
- Department of Medicine, School of Medicine, University of Illinois, Chicago, Illinois, USA
| | - Rupal Mehta
- Division of Nephrology and Hypertension, Department of Medicine and Center for Translational Metabolism and Health, Institute for Public Health and Medicine, Chicago, Illinois, USA; Department of Preventive Medicine Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Tariq Shafi
- School of Medicine, John Hopkins University, Baltimore, Maryland, USA
| | - Jonathan Taliercio
- Department of Nephrology and Hypertension, Cleveland Clinic, Cleveland, Ohio, USA
| | - Alan Go
- Departments of Epidemiology, Biostatistics and Medicine, University of California at San Francisco, San Francisco, California, USA
| | - Panduranga Rao
- Department of Internal Medicine, Division of Nephrology, University of Michigan Health System, Ann Arbor, Michigan, USA
| | - L Lee Hamm
- Department of Medicine, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Rajat Deo
- Departments of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Shoichi Maruyama
- Department of Nephrology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Masafumi Fukagawa
- Department of Internal Medicine, Division of Nephrology, Endocrinology and Metabolism, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Harold I Feldman
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA; Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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Hypomagnesemia as a Risk Factor and Accelerator for Vascular Aging in Diabetes Mellitus and Chronic Kidney Disease. Metabolites 2023; 13:metabo13020306. [PMID: 36837924 PMCID: PMC9959098 DOI: 10.3390/metabo13020306] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/17/2023] [Accepted: 02/18/2023] [Indexed: 02/22/2023] Open
Abstract
The age-old axiom that one is as old as his or her vessels are, calls for ongoing critical re-examination of modifiable risk factors of accelerated vascular ageing in chronic kidney diseases. Attempts to modulate vascular risk with cholesterol-lowering agents have largely failed in advanced chronic kidney disease (CKD). In addition to nitrogen waste products, many pathological biochemical processes also play a role in vascular calcification in chronic kidney damage. Magnesium, a cation vital for the body, may substantially reduce cardiovascular diseases' risk and progression. This narrative review aimed to address the relationship between hypomagnesemia and vascular calcification, which promotes further cardiovascular complications in diabetes, aging, and CKD. Articles with predefined keywords were searched for in the PubMed and Google Scholar databases with specific inclusion and exclusion criteria. We hypothesized that a decrease in serum magnesium levels contributes to increased vascular calcification and thereby increases cardiovascular mortality. In summary, based on existing evidence in the literature, it appears that simple and inexpensive oral magnesium supplementation may reduce the cardiovascular mortality of patients who are already severely affected by such diseases; in this context, the concept of 'normal' vs. 'ideal' serum magnesium levels should be carefully re-examined.
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Magnesium Depletion Score is Associated with Long-Term Mortality in Chronic Kidney Diseases: A Prospective Population-Based Cohort Study. J Nephrol 2022; 36:755-765. [PMID: 36378477 DOI: 10.1007/s40620-022-01489-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 10/08/2022] [Indexed: 11/16/2022]
Abstract
BACKGROUND Magnesium deficiency is common in patients with chronic kidney diseases (CKD) due to restricted magnesium intake and impaired magnesium reabsorption. Based on pathophysiological risk factors influencing kidney magnesium reabsorption, a magnesium depletion score (MDS) was developed. Using MDS as a novel indicator for assessing body magnesium status, we hypothesized that it was associated with clinical prognosis. METHODS We conducted a prospective population-based cohort study using data from the National Health and Nutrition Examination Survey 1999-2014 to explore the impact of MDS on the clinical outcomes of CKD patients. Propensity score-matched analyses were conducted to increase comparability. The primary outcome was all-cause mortality, and the secondary outcomes were cardiovascular-cause and cancer-cause mortality. RESULTS After propensity score matching, 3294 CKD patients were divided into 2 groups: MDS ≤ 2 (N = 1647), and MDS > 2 (N = 1647). During a median follow-up of 75 months, Kaplan-Meier analyses showed that MDS > 2 was associated with worse 5- and 10-year overall survival (78.5% vs 73.4%; 53.1% vs 43.1%, P < 0.001). After adjusting for confounding variables, MDS was found to be an independent risk factor for all-cause mortality (HR:1.34, 95% CI 1.20-1.50, P < 0.001). MDS > 2 was also associated with higher cardiovascular-cause mortality (16.2% VS 11.6%, P = 0.005). Multivariate competing risk analysis revealed that MDS > 2 was an independent risk factor (HR: 1.33, 95% CI 1.06-1.66, P = 0.012). Subgroup analyses reported that MDS > 2 increased all-cause mortality and cardiovascular-cause mortality only in patients with inadequate magnesium intake (P < 0.001, P < 0.001) but not in those with adequate intake (P = 0.068, P = 0.920). CONCLUSIONS A magnesium depletion score > 2 was independently associated with higher long-term cardiovascular-cause and all-cause mortality in CKD patients.
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Nephrolithiasis: A Red Flag for Cardiovascular Risk. J Clin Med 2022; 11:jcm11195512. [PMID: 36233380 PMCID: PMC9573143 DOI: 10.3390/jcm11195512] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/13/2022] [Accepted: 09/16/2022] [Indexed: 02/05/2023] Open
Abstract
Epidemiological evidence shows that nephrolithiasis is associated with cardiovascular (CV) morbidities. The association between nephrolithiasis and CV disease is not surprising because both diseases share conditions that facilitate their development. Metabolic conditions, encompassed in the definition of metabolic syndrome (MS), and habits that promote nephrolithiasis by altering urine composition also promote clinical manifestations of CV disease. By inducing oxidative stress, these conditions cause endothelial dysfunction and increased arterial stiffness, which are both well-known predictors of CV disease. Furthermore, the subtle systemic metabolic acidosis observed in stone formers with CV disease may have a pathogenic role by increasing bone turnover and leading to reduced mineral content and osteoporosis/osteopenia. Heart valves and/or coronary artery and aortic calcifications are frequently associated with reduced mineral density. This is known as the 'calcification paradox' in osteoporosis and has also been observed in subjects with calcium nephrolithiasis. Evidence supports the hypothesis that osteoporosis/osteopenia is an independent risk factor for the development of CV calcifications. In the long term, episodes of renal stones may occur from the onset of metabolic derangements/MS to arterial stiffness/atherosclerosis and CV morbidities. These episodes should be considered a warning sign of an ongoing and silent atherosclerotic process. The evaluation of cardiometabolic risk factors and MS components should be routine in the assessment of renal stone formers. This would allow for treatment and prevention of the development of CV complications, which are much more severe for the patient and for public health.
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Bargagli M, Moochhala S, Robertson WG, Gambaro G, Lombardi G, Unwin RJ, Ferraro PM. Urinary metabolic profile and stone composition in kidney stone formers with and without heart disease. J Nephrol 2021; 35:851-857. [PMID: 34152561 PMCID: PMC8995244 DOI: 10.1007/s40620-021-01096-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 06/09/2021] [Indexed: 11/09/2022]
Abstract
Objective Kidney stone disease seems to be associated with an increased risk of incident cardiovascular outcomes; the aim of this study is to identify differences in 24-h urine excretory profiles and stone composition among stone formers with and without cardiovascular disease (CVD). Methods Data from patients attending the Department of Renal Medicine’s metabolic stone clinic from 1995 to 2012 were reviewed. The sample was divided according to the presence or absence of CVD (myocardial infarction, angina, coronary revascularization, or surgery for calcified heart valves). Univariable and multivariable regression models, adjusted for age, sex, BMI, hypertension, diabetes, eGFR, plasma bicarbonate and potential renal acid load of foods were used to investigate differences across groups. Results 1826 patients had available data for 24-h urine analysis. Among these, 108 (5.9%) had a history of CVD. Those with CVD were older, have higher prevalence of hypertension and diabetes and lower eGFR. Univariable analysis showed that patients with CVD had significantly lower 24-h urinary excretions for citrate (2.4 vs 2.6 mmol/24 h, p = 0.04), magnesium (3.9 vs 4.2 mmol/24 h, p = 0.03) and urinary pH (6.1 vs 6.2, p = 0.02). After adjustment for confounders, differences in urinary citrate and magnesium excretions remained significant. No differences in the probability of stone formation or stone compositions were found. Conclusions Stone
formers with CVD have lower renal alkali excretion, possibly suggesting higher
acid retention in stone formers with cardiovascular comorbidities. Randomized
clinical trials including medications and a controlled diet design are needed
to confirm the results presented here. Graphic abstract ![]()
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Affiliation(s)
- Matteo Bargagli
- U.O.S. Terapia Conservativa della Malattia Renale Cronica, U.O.C. Nefrologia, Fondazione Policlinico Universitario A. Gemelli IRCCS, Università Cattolica del Sacro Cuore, Largo Agostino Gemelli 8, 00168, Rome, Italy
| | - Shabbir Moochhala
- Department of Renal Medicine, Royal Free Campus Medical School, University College Hospital, London, UK
| | - William G Robertson
- Department of Renal Medicine, Royal Free Campus Medical School, University College Hospital, London, UK
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Giovanni Gambaro
- Renal Unit, Division of Nephrology and Dialysis, Department of Medicine, University of Verona, Verona, Italy
| | - Gianmarco Lombardi
- Renal Unit, Division of Nephrology and Dialysis, Department of Medicine, University of Verona, Verona, Italy
| | - Robert J Unwin
- Department of Renal Medicine, Royal Free Campus Medical School, University College Hospital, London, UK
| | - Pietro Manuel Ferraro
- U.O.S. Terapia Conservativa della Malattia Renale Cronica, U.O.C. Nefrologia, Fondazione Policlinico Universitario A. Gemelli IRCCS, Università Cattolica del Sacro Cuore, Largo Agostino Gemelli 8, 00168, Rome, Italy.
- Dipartimento Universitario di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Rome, Italy.
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