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Hou L, Geng Z, Yuan Z, Shi X, Wang C, Chen F, Li H, Xue F. MRSL: a causal network pruning algorithm based on GWAS summary data. Brief Bioinform 2024; 25:bbae086. [PMID: 38487847 PMCID: PMC10940843 DOI: 10.1093/bib/bbae086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 02/01/2024] [Accepted: 02/15/2024] [Indexed: 03/18/2024] Open
Abstract
Causal discovery is a powerful tool to disclose underlying structures by analyzing purely observational data. Genetic variants can provide useful complementary information for structure learning. Recently, Mendelian randomization (MR) studies have provided abundant marginal causal relationships of traits. Here, we propose a causal network pruning algorithm MRSL (MR-based structure learning algorithm) based on these marginal causal relationships. MRSL combines the graph theory with multivariable MR to learn the conditional causal structure using only genome-wide association analyses (GWAS) summary statistics. Specifically, MRSL utilizes topological sorting to improve the precision of structure learning. It proposes MR-separation instead of d-separation and three candidates of sufficient separating set for MR-separation. The results of simulations revealed that MRSL had up to 2-fold higher F1 score and 100 times faster computing time than other eight competitive methods. Furthermore, we applied MRSL to 26 biomarkers and 44 International Classification of Diseases 10 (ICD10)-defined diseases using GWAS summary data from UK Biobank. The results cover most of the expected causal links that have biological interpretations and several new links supported by clinical case reports or previous observational literatures.
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Affiliation(s)
- Lei Hou
- Beijing International Center for Mathematical Research, Peking University, Beijing, People’s Republic of China, 100871
| | - Zhi Geng
- School of Mathematics and Statistics, Beijing Technology and Business University, Beijing, People’s Republic of China, 100048
| | - Zhongshang Yuan
- Department of Epidemiology and Health Statistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, People’s Republic of China, 250000
- Institute for Medical Dataology, Cheeloo College of Medicine, Shandong University, Jinan, People’s Republic of China, 250000
| | - Xu Shi
- Department of Biostatistics, University of Michigan, Ann Arbor, USA
| | - Chuan Wang
- Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, People's Republic of China, 250000
| | - Feng Chen
- School of Public Health, Nanjing Medical University, Nanjing, China, 211166
| | - Hongkai Li
- Department of Epidemiology and Health Statistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, People’s Republic of China, 250000
- Institute for Medical Dataology, Cheeloo College of Medicine, Shandong University, Jinan, People’s Republic of China, 250000
| | - Fuzhong Xue
- Department of Epidemiology and Health Statistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, People’s Republic of China, 250000
- Institute for Medical Dataology, Cheeloo College of Medicine, Shandong University, Jinan, People’s Republic of China, 250000
- Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, People's Republic of China, 250000
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Prasad N, Hamosh A, Sponseller P. Orthopaedic Manifestations of Inborn Errors of Metabolism. JBJS Rev 2021; 9:01874474-202107000-00003. [PMID: 34257233 DOI: 10.2106/jbjs.rvw.20.00245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
» Inborn errors of metabolism are disorders of carbohydrate, amino acid, organic acid, or purine and pyrimidine metabolism; disorders of fatty acid oxidation; disorders of metal metabolism; and lysosomal storage defects that can cause metabolic derangements that have secondary musculoskeletal effects. » Orthopaedic surgeons should be aware that patients with inborn errors of metabolism may be at high risk for spasticity, which may cause joint subluxations, scoliosis, and contractures, as well as poor bone quality, which is caused by malnutrition or disordered bone growth. » Multidisciplinary care and follow-up are important to identify musculoskeletal problems in a timely manner in order to provide effective treatment.
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Affiliation(s)
- Niyathi Prasad
- Departments of Orthopaedic Surgery and Genetic Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland
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Bjørklund G, Pivina L, Dadar M, Semenova Y, Chirumbolo S, Aaseth J. Long-Term Accumulation of Metals in the Skeleton as Related to Osteoporotic Derangements. Curr Med Chem 2021; 27:6837-6848. [PMID: 31333081 DOI: 10.2174/0929867326666190722153305] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 07/01/2019] [Accepted: 07/09/2019] [Indexed: 11/22/2022]
Abstract
The concentrations of metals in the environment are still not within the recommended limits as set by the regulatory authorities in various countries because of human activities. They can enter the food chain and bioaccumulate in soft and hard tissues/organs, often with a long half-life of the metal in the body. Metal exposure has a negative impact on bone health and may result in osteoporosis and increased fracture risk depending on concentration and duration of metal exposure and metal species. Bones are a long-term repository for lead and some other metals, and may approximately contain 90% of the total body burden in birds and mammals. The present review focuses on the most common metals found in contaminated areas (mercury, cadmium, lead, nickel, chromium, iron, and aluminum) and their effects on bone tissue, considering the possibility of the long-term bone accumulation, and also some differences that might exist between different age groups in the whole population.
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Affiliation(s)
- Geir Bjørklund
- Council for Nutritional and Environmental Medicine (CONEM), Toften 24, 8610 Mo i Rana, Norway
| | - Lyudmila Pivina
- Department of Internal Medicine, Semey Medical University, Semey, Kazakhstan,CONEM Kazakhstan Environmental Health and Safety Research Group, Semey Medical University, Semey, Kazakhstan
| | - Maryam Dadar
- Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Yuliya Semenova
- Department of Internal Medicine, Semey Medical University, Semey, Kazakhstan,CONEM Kazakhstan Environmental Health and Safety Research Group, Semey Medical University, Semey, Kazakhstan
| | - Salvatore Chirumbolo
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Italy,CONEM Scientific Secretary, Verona, Italy
| | - Jan Aaseth
- Research Department, Innlandet Hospital Trust, Brumunddal, Norway,Faculty of Health and Social Science, Inland Norway University of Applied Sciences,
Elverum, Norway
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Diaz J, Fonseca AG, Arboleda R, Frade A, Gennaro MP, Jayakar P, Schleifer P, Hernandez E. Case Report: The Association of Wilson Disease in a Patient With Ataxia and GLUT-1 Deficiency. Front Pediatr 2021; 9:750593. [PMID: 34676189 PMCID: PMC8524673 DOI: 10.3389/fped.2021.750593] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 09/07/2021] [Indexed: 11/16/2022] Open
Abstract
Background: Wilson disease (WD) and glucose transporter type 1 (GLUT1) deficiency syndrome are two syndromes with different modes of inheritance but share certain similarities on neurological presentation. To date we have not found previous reports of an association between these two disorders. Case Presentation: Here we describe a 9-year-old male with global developmental delay that presented with intermittent and sudden onset weakness that first occurred at age 3. He was diagnosed with a mutation in the SLC2A1 (Solute Carrier Family 2 Member 1) gene, which results in GLUT1 deficiency. A ketogenic diet could not be started because of unexplained elevated liver enzymes. Due to his liver enzymes' persistent elevation, further investigations demonstrated mildly decreased ceruloplasmin levels, high basal 24-h urinary copper excretion, and an elevated hepatic parenchymal copper concentration on liver biopsy, consistent with WD. Genetic testing revealed two separate mutations in the ATP7B (ATPase Copper Transporting Beta) gene, consistent with WD. The patient was treated with a low copper diet, zinc acetate, and trientine hydrochloride. When liver enzymes normalized, he was subsequently started on a ketogenic diet with improvement in neurological symptoms. His neurological symptoms were most likely secondary to GLUT1 deficiency syndrome, as WD's neurological symptoms are primarily observed in the second decade of life. Conclusion: Recent studies have demonstrated the importance of genetic testing upon unexplained persistent elevation of liver enzymes. This case highlights the importance of carefully evaluating a patient with an unexplained liver disorder, even in the presence of primary neurological disease, as it can have significant therapeutic implications.
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Affiliation(s)
- Jenna Diaz
- Department of Medical Education, Nicklaus Children's Hospital, Miami, FL, United States
| | - Ashley G Fonseca
- Department of Medical Education, Nicklaus Children's Hospital, Miami, FL, United States
| | - Richard Arboleda
- Department of Pediatric Gastroenterology, Hepatology, and Nutrition, Nicklaus Children's Hospital, Miami, FL, United States
| | - Alejandro Frade
- Department of Medical Education, Nicklaus Children's Hospital, Miami, FL, United States
| | - Maria Pilar Gennaro
- Department of Neurogenetics, Nicklaus Children's Hospital, Miami, FL, United States
| | - Parul Jayakar
- Department of Neurogenetics, Nicklaus Children's Hospital, Miami, FL, United States
| | - Paula Schleifer
- Department of Neurogenetics, Nicklaus Children's Hospital, Miami, FL, United States
| | - Erick Hernandez
- Department of Pediatric Gastroenterology, Hepatology, and Nutrition, Nicklaus Children's Hospital, Miami, FL, United States
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Ji JH, Hwang WH, Lee YS, Kim JO. A rare case of multiple and huge simple bone cysts in Wilson's disease. J Orthop Surg (Hong Kong) 2020; 27:2309499019843141. [PMID: 31035865 DOI: 10.1177/2309499019843141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
A simple bone cyst is a tumor-like lesion that is not a true neoplasm. It usually presents as a solitary lesion within the proximal humerus and proximal femur. The etiology of simple bone cysts is still to be elucidated. We describe our experience in the successful surgical management of a rare case of two, large-sized, simple bone cysts involving the entire left humerus and right femoral head, respectively, in a 34-year-old male patient with Wilson's disease and concomitant hepatic cirrhosis. We theorized that Wilson's disease could be the cause of the delay or blockage of the natural healing process of the simple long-bone cysts, leading to their abnormal growth and development. To our knowledge, such a combined occurrence of multiple, simple long-bone cysts and Wilson's disease has not been reported in the literature to date.
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Affiliation(s)
- Jong-Hun Ji
- 1 Department of Orthopaedic Surgery, Daejeon St Mary's Hospital, College of Medicine, The Catholic University of Korea, Jung-gu, Daejeon, Republic of Korea
| | - Won-Ha Hwang
- 1 Department of Orthopaedic Surgery, Daejeon St Mary's Hospital, College of Medicine, The Catholic University of Korea, Jung-gu, Daejeon, Republic of Korea
| | - Yeon Soo Lee
- 2 Department of Radiology, Daejeon St Mary's Hospital, College of Medicine, The Catholic University of Korea, Jung-gu, Daejeon, Republic of Korea
| | - Jong Ok Kim
- 3 Department of Pathology, Daejeon St Mary's Hospital, College of Medicine, The Catholic University of Korea, Jung-gu, Daejeon, Republic of Korea
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Rare Dementias. NEURODEGENER DIS 2018. [DOI: 10.1007/978-3-319-72938-1_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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