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Wang Y, Song J, Dai Q, Duan X. Hierarchical Negative Sampling Based Graph Contrastive Learning Approach for Drug-Disease Association Prediction. IEEE J Biomed Health Inform 2024; 28:3146-3157. [PMID: 38294927 DOI: 10.1109/jbhi.2024.3360437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
Predicting potential drug-disease associations (RDAs) plays a pivotal role in elucidating therapeutic strategies for diseases and facilitating drug repositioning, making it of paramount importance. However, existing methods are constrained and rely heavily on limited domain-specific knowledge, impeding their ability to effectively predict candidate associations between drugs and diseases. Moreover, the simplistic definition of unknown information pertaining to drug-disease relationships as negative samples presents inherent limitations. To overcome these challenges, we introduce a novel hierarchical negative sampling-based graph contrastive model, termed HSGCLRDA, which aims to forecast latent associations between drugs and diseases. In this study, HSGCLRDA integrates the association information as well as similarity between drugs, diseases and proteins. Meanwhile, the model constructs a drug-disease-protein heterogeneous network. Subsequently, employing a hierarchical structural sampling technique, we establish reliable negative drug-disease samples utilizing PageRank algorithms. Utilizing meta-path aggregation within the heterogeneous network, we derive low-dimensional representations for drugs and diseases, thereby constructing global and local feature graphs that capture their interactions comprehensively. To obtain representation information, we adopt a self-supervised graph contrastive approach that leverages graph convolutional networks (GCNs) and second-order GCNs to extract feature graph information. Furthermore, we integrate a contrastive cost function derived from the cross-entropy cost function, facilitating holistic model optimization. Experimental results obtained from benchmark datasets not only showcase the superior performance of HSGCLRDA compared to various baseline methods in predicting RDAs but also emphasize its practical utility in identifying novel potential diseases associated with existing drugs through meticulous case studies.
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Gong Y, Liu Z, Zhang X, Shen S, Xu Q, Zhao H, Shang J, Li W, Wang Y, Chen J, Liu X, Zheng QY. Endolymphatic Hydrop Phenotype in Familial Norrie Disease Caused by Large Fragment Deletion of NDP. Front Aging Neurosci 2022; 14:771328. [PMID: 35517050 PMCID: PMC9062296 DOI: 10.3389/fnagi.2022.771328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 03/14/2022] [Indexed: 11/13/2022] Open
Abstract
Norrie disease (ND; OMIM 310600), a rare X-linked recessive genetic disorder, is characterized by congenital blindness and occasionally, sensorineural hearing loss, and developmental delay. The congenital blindness of ND patients is almost untreatable; thus, hearing is particularly important for them. However, the mechanism of hearing loss of ND patients is unclear, and no good treatment is available except wearing hearing-aid. Therefore, revealing the mechanism of hearing loss in ND patients and exploring effective treatment methods are greatly important. In addition, as a serious monogenic genetic disease, convenient gene identification method is important for ND patients and their family members, as well as prenatal diagnosis and preimplantation genetic diagnosis to block intergenerational transmission of pathogenic genes. In this study, a Norrie family with two male patients was reported. This pedigree was ND caused by large fragment deletion of NDP (norrin cystine knot growth factor NDP) gene. In addition to typical severe ophthalmologic and audiologic defects, the patients showed new pathological features of endolymphatic hydrops (EH), and they also showed acoustic nerves abnormal as described in a very recent report. PCR methods were developed to analyze and diagnose the variation of the family members. This study expands the understanding of the clinical manifestation and pathogenesis of ND and provides a new idea for the treatment of patients in this family and a convenient method for the genetic screen for this ND family.
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Affiliation(s)
- Yuerong Gong
- Department of Ophthalmology, Binzhou Medical University Hospital, Binzhou, China
| | - Zhang Liu
- Department of Otolaryngology Head and Neck Surgery, Institute of Otolaryngology, Binzhou Medical University Hospital, Binzhou, China
| | - Xiaolin Zhang
- Department of Otolaryngology Head and Neck Surgery, Institute of Otolaryngology, Binzhou Medical University Hospital, Binzhou, China
| | - Shuang Shen
- Institute of Hearing and Speech Rehabilitation, College of Special Education, Binzhou Medical University, Yantai, China
| | - Qijun Xu
- Department of Otolaryngology Head and Neck Surgery, Institute of Otolaryngology, Binzhou Medical University Hospital, Binzhou, China
| | - Hongchun Zhao
- Department of Otolaryngology Head and Neck Surgery, Institute of Otolaryngology, Binzhou Medical University Hospital, Binzhou, China
| | - Jing Shang
- Department of Otolaryngology Head and Neck Surgery, Institute of Otolaryngology, Binzhou Medical University Hospital, Binzhou, China
| | - Weiguo Li
- Department of Ophthalmology, Binzhou Medical University Hospital, Binzhou, China
| | - Yanfei Wang
- Department of Otolaryngology Head and Neck Surgery, Institute of Otolaryngology, Binzhou Medical University Hospital, Binzhou, China
| | - Jun Chen
- Department of Otolaryngology Head and Neck Surgery, Institute of Otolaryngology, Binzhou Medical University Hospital, Binzhou, China
- *Correspondence: Jun Chen,
| | - Xiuzhen Liu
- Medical Research Center, Binzhou Medical University Hospital, Binzhou, China
- Xiuzhen Liu,
| | - Qing Yin Zheng
- Department of Otolaryngology Head and Neck Surgery, Case Western Reserve University, Cleveland, OH, United States
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Sowden JC, Kros CJ, Sirimanna T, Pagarkar W, Oluonye N, Henderson RH. Impact of sight and hearing loss in patients with Norrie disease: advantages of Dual Sensory clinics in patient care. BMJ Paediatr Open 2020; 4:e000781. [PMID: 33225082 PMCID: PMC7670942 DOI: 10.1136/bmjpo-2020-000781] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/30/2020] [Accepted: 10/05/2020] [Indexed: 11/17/2022] Open
Abstract
Norrie disease (ND) is a rare, X-linked condition of visual and auditory impairment, often presenting with additional neurological features and developmental delays of varying severity. While all affected patients are born blind, or lose their vision in infancy, progressive sensorineural hearing loss develops in the majority of cases and is typically detected in the second decade of life. A range of additional symptoms of ND, such as seizure disorders, typically appear from a young age, but it is difficult to predict the range of symptoms ND patients will experience. After growing up without vision, hearing loss represents the greatest worry for many patients with ND, as they may lose the ability to participate in previously enjoyed activities or to communicate with others. Dual sensory loss has a physical, psychosocial and financial impact on both patients with ND and their families. Routine monitoring of the condition is required in order to identify, treat and provide support for emerging health problems, leading to a large burden of medical appointments. Many patients need to travel long distances to meet with specialists, representing a further burden on time and finances. Additionally, the rare nature of dual sensory impairment in children means that few clinical environments are designed to meet their needs. Dual Sensory clinics are multidisciplinary environments designed for sensory-impaired children and have been suggested to alleviate the impact of diseases involving sensory loss such as ND. Here, we discuss the diagnosis, monitoring and management of ND and the impact it has on paediatric patients and their caregivers. We describe the potential for dual sensory clinics to reduce disease burden through providing an appropriate clinical environment, access to multiple clinical experts in one visit, and ease of monitoring for patients with ND.
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Affiliation(s)
- Jane C Sowden
- Developmental Biology and Cancer Department, UCL Great Ormond Street Institute of Child Health, London, London, UK
| | - Corné J Kros
- School of Life Sciences, University of Sussex, Brighton, Brighton and Hove, UK
| | - Tony Sirimanna
- Great Ormond Street Hospital for Children, London, London, UK
| | | | - Ngozi Oluonye
- Wolfson Neurodisability Service, Great Ormond Street Hospital for Children, London, London, UK
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Cação G, Garrido C, Miranda V, Pinto-Basto J, Chaves J, Chorão R. Refractory epilepsy in Norrie disease. Neurol Sci 2018; 39:1631-1633. [DOI: 10.1007/s10072-018-3428-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Accepted: 04/23/2018] [Indexed: 10/17/2022]
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Cho C, Smallwood PM, Nathans J. Reck and Gpr124 Are Essential Receptor Cofactors for Wnt7a/Wnt7b-Specific Signaling in Mammalian CNS Angiogenesis and Blood-Brain Barrier Regulation. Neuron 2017; 95:1056-1073.e5. [PMID: 28803732 PMCID: PMC5586543 DOI: 10.1016/j.neuron.2017.07.031] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 06/14/2017] [Accepted: 07/26/2017] [Indexed: 10/19/2022]
Abstract
Reck, a GPI-anchored membrane protein, and Gpr124, an orphan GPCR, have been implicated in Wnt7a/Wnt7b signaling in the CNS vasculature. We show here that vascular endothelial cell (EC)-specific reduction in Reck impairs CNS angiogenesis and that EC-specific postnatal loss of Reck, combined with loss of Norrin, impairs blood-brain barrier (BBB) maintenance. The most N-terminal domain of Reck binds to the leucine-rich repeat (LRR) and immunoglobulin (Ig) domains of Gpr124, and weakening this interaction by targeted mutagenesis reduces Reck/Gpr124 stimulation of Wnt7a signaling in cell culture and impairs CNS angiogenesis. Finally, a soluble Gpr124(LRR-Ig) probe binds to cells expressing Frizzled, Wnt7a or Wnt7b, and Reck, and a soluble Reck(CC1-5) probe binds to cells expressing Frizzled, Wnt7a or Wnt7b, and Gpr124. These experiments indicate that Reck and Gpr124 are part of the cell surface protein complex that transduces Wnt7a- and Wnt7b-specific signals in mammalian CNS ECs to promote angiogenesis and regulate the BBB.
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Affiliation(s)
- Chris Cho
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Philip M Smallwood
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jeremy Nathans
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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Clinical and genetic analysis of Indian patients with NDP-related retinopathies. Int Ophthalmol 2017; 38:1251-1260. [DOI: 10.1007/s10792-017-0589-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Accepted: 06/05/2017] [Indexed: 11/25/2022]
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