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Baptista A, Brière G, Baudot A. Random walk with restart on multilayer networks: from node prioritisation to supervised link prediction and beyond. BMC Bioinformatics 2024; 25:70. [PMID: 38355439 PMCID: PMC10865648 DOI: 10.1186/s12859-024-05683-z] [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: 10/18/2023] [Accepted: 01/29/2024] [Indexed: 02/16/2024] Open
Abstract
BACKGROUND Biological networks have proven invaluable ability for representing biological knowledge. Multilayer networks, which gather different types of nodes and edges in multiplex, heterogeneous and bipartite networks, provide a natural way to integrate diverse and multi-scale data sources into a common framework. Recently, we developed MultiXrank, a Random Walk with Restart algorithm able to explore such multilayer networks. MultiXrank outputs scores reflecting the proximity between an initial set of seed node(s) and all the other nodes in the multilayer network. We illustrate here the versatility of bioinformatics tasks that can be performed using MultiXrank. RESULTS We first show that MultiXrank can be used to prioritise genes and drugs of interest by exploring multilayer networks containing interactions between genes, drugs, and diseases. In a second study, we illustrate how MultiXrank scores can also be used in a supervised strategy to train a binary classifier to predict gene-disease associations. The classifier performance are validated using outdated and novel gene-disease association for training and evaluation, respectively. Finally, we show that MultiXrank scores can be used to compute diffusion profiles and use them as disease signatures. We computed the diffusion profiles of more than 100 immune diseases using a multilayer network that includes cell-type specific genomic information. The clustering of the immune disease diffusion profiles reveals shared shared phenotypic characteristics. CONCLUSION Overall, we illustrate here diverse applications of MultiXrank to showcase its versatility. We expect that this can lead to further and broader bioinformatics applications.
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Affiliation(s)
- Anthony Baptista
- School of Mathematical Sciences, Queen Mary University of London, London, UK.
- The Alan Turing Institute, London, UK.
| | | | - Anaïs Baudot
- INSERM, MMG, Turing Center for Living Systems, Aix-Marseille Univ, Marseille, France.
- Barcelona Supercomputing Center, Barcelona, Spain.
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Sachdeva S, Raina A, Sardana K, Malhotra P. A case of orofacial granulomatosis evolving into Melkersson Rosenthal syndrome in a child treated with a steroid free regimen of Clofazimine and Minocycline. Dermatol Ther 2021; 34:e15009. [PMID: 34043275 DOI: 10.1111/dth.15009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/21/2021] [Accepted: 05/22/2021] [Indexed: 11/30/2022]
Abstract
Orofacial granulomatosis (OFG) is a rare disorder with varied etiological, immunological and infectious mechanisms implicated and is believed to be a umbrella term which includes Melkersson Rosethal syndrome (MRS). We describe a 17 year old female who was diagnosed with OFG and was successfully treated with a combination of minocycline and clofazimine without oral steroids with significant improvement within 1 month of therapy.
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Affiliation(s)
- Soumya Sachdeva
- Department of Dermatology, Venereology, and Leprosy, Dr Ram Manohar Lohia Hospital and ABVIMS, New Delhi, India
| | - Alok Raina
- Department of Dermatology, Venereology, and Leprosy, Dr Ram Manohar Lohia Hospital and ABVIMS, New Delhi, India
| | - Kabir Sardana
- Department of Dermatology, Venereology, and Leprosy, Dr Ram Manohar Lohia Hospital and ABVIMS, New Delhi, India
| | - Purnima Malhotra
- Department of Pathology, Dr Ram Manohar Lohia Hospital and ABVIMS, New Delhi, India
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Zewde YZ. Melkersson-Rosenthal syndrome misdiagnosed as recurrent Bell's palsy: a case report and review of literature. Allergy Asthma Clin Immunol 2021; 17:8. [PMID: 33422123 PMCID: PMC7796637 DOI: 10.1186/s13223-020-00508-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 12/21/2020] [Indexed: 11/24/2022] Open
Abstract
Background Melkersson–Rosenthal syndrome (MRS) is a rare neuro-mucocutaneous disorder of unknown cause, clinically characterized by a triad of recurrent facial palsy, orofacial swelling, and fissured tongue. It is frequently seen in females in their second and third decades of life. MRS is diagnosed based on clinical features and it is rarely possible to observe all the classical triad symptoms at the same time. The disorder may cause recurring peripheral facial palsy that is wrongly diagnosed as recurrent Bell’s palsy Case presentation A 25-year-old female patient was presented to the neurology clinic of Tikur Anbessa Specialized Hospital in Addis Ababa complaining of recurrent left-side peripheral facial weakness, facial swelling and fissured tongue of 5 days duration. Her past medical history was positive for similar symptoms, for which she was diagnosed with Bell’s palsy and received oral corticosteroid treatment. On examination left side lower facial swelling with flat naso-labial fold and fissured tongue were identified. After excluding other mimickers, she was diagnosed with Melkersson–Rosenthal syndrome and completely recovered with high dose of corticosteroid treatment. Conclusion Melkersson–Rosenthal syndrome may present with the classic triads of symptoms, but mostly it shows an incomplete clinical pattern. Therefore, when clinicians including allergists encountered patients with facial swelling and facial palsy, they should have to consider MRS in their differential diagnosis and specifically assess for recurrent facial palsy and fissured tongue. Unlike true angioedema, the facial swelling in MRS often develops gradually and it might cause permanent swelling with cosmetic disfigurement from multiple relapses, which can be prevented by early detection and timely initiation of treatment.
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Affiliation(s)
- Yared Zenebe Zewde
- Department of Neurology, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box 41690, Addis Ababa, Ethiopia.
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Wang S, Wang H, Shi X, Wu F, Lv L, Hu M, Sun W, Wu L, Zhou H. A case of Melkersson-Rosenthal syndrome with endocrine disorders: Extraordinary efficiency of hydroxychloroquine and mechanism hypothesis. Eur J Neurol 2020; 28:928-933. [PMID: 33270950 DOI: 10.1111/ene.14615] [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: 07/17/2020] [Revised: 09/17/2020] [Accepted: 10/22/2020] [Indexed: 02/05/2023]
Abstract
BACKGROUND AND PURPOSE Melkersson-Rosenthal syndrome (MRS) is a rare neuro-mucocutaneous disease. In addition to the traditional clinical triad, there is also a diversity of clinical signs, and it may be related to other systemic diseases. METHODS In the present study, we report a case of MRS with endocrine disorders that exhibits extraordinary therapeutic efficiency by using hydroxychloroquine (HCQ), explore whether there is an internal connection between MRS and endocrine disorders, and discuss the mechanism of the therapeutic efficiency of using HCQ. The hypothesis proposed for the first time is that MRS may essentially be a systemic granulomatous disease. RESULTS The physical examination revealed orofacial swelling and fissured tongue. The histopathologic examination showed epithelioid granulomas. Combined with the other examination, this case was diagnosed as incomplete MRS. HCQ and local drugs were introduced. The patient achieved clinical recovery and psychological cure by the 18-week follow-up, and the 1-year follow-up found no reactivation of MRS. Moreover, the levels of cortisol and adrenocorticotropic were within normal ranges. CONCLUSIONS After the drug therapy was targeted at granuloma, not only did all of the symptoms related to MRS disappear, but the endocrine system also returned to normal. It is speculated that the endocrine disorder in this patient may be related to MRS. We further propose the first-time hypothesis that MRS may essentially be a systemic granulomatous disease. It provides a new medication method with high-level efficiency.
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Affiliation(s)
- Shimeng Wang
- State Key Laboratory of Oral Diseases, Department of Oral Medicine, West China Hospital of Stomatology, National Clinical Research Center for Oral Diseases, Sichuan University, Chengdu, China
| | - Hongmei Wang
- State Key Laboratory of Oral Diseases, Department of Oral Medicine, West China Hospital of Stomatology, National Clinical Research Center for Oral Diseases, Sichuan University, Chengdu, China.,Mianyang Stomatological Hospital, Mianyang, China
| | - Xueke Shi
- State Key Laboratory of Oral Diseases, Department of Oral Medicine, West China Hospital of Stomatology, National Clinical Research Center for Oral Diseases, Sichuan University, Chengdu, China
| | - Fanglong Wu
- State Key Laboratory of Oral Diseases, Department of Oral Medicine, West China Hospital of Stomatology, National Clinical Research Center for Oral Diseases, Sichuan University, Chengdu, China
| | - Ling Lv
- State Key Laboratory of Oral Diseases, Department of Oral Medicine, West China Hospital of Stomatology, National Clinical Research Center for Oral Diseases, Sichuan University, Chengdu, China
| | - Mingjia Hu
- State Key Laboratory of Oral Diseases, Department of Oral Medicine, West China Hospital of Stomatology, National Clinical Research Center for Oral Diseases, Sichuan University, Chengdu, China
| | - Wanxin Sun
- State Key Laboratory of Oral Diseases, Department of Oral Medicine, West China Hospital of Stomatology, National Clinical Research Center for Oral Diseases, Sichuan University, Chengdu, China
| | - Lanyan Wu
- Department of Oral Pathology, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Hongmei Zhou
- State Key Laboratory of Oral Diseases, Department of Oral Medicine, West China Hospital of Stomatology, National Clinical Research Center for Oral Diseases, Sichuan University, Chengdu, China
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Cancian M, Giovannini S, Angelini A, Fedrigo M, Bendo R, Senter R, Sivolella S. Melkersson-Rosenthal syndrome: a case report of a rare disease with overlapping features. ALLERGY, ASTHMA, AND CLINICAL IMMUNOLOGY : OFFICIAL JOURNAL OF THE CANADIAN SOCIETY OF ALLERGY AND CLINICAL IMMUNOLOGY 2019; 15:1. [PMID: 30622569 PMCID: PMC6320604 DOI: 10.1186/s13223-018-0316-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Accepted: 12/24/2018] [Indexed: 01/27/2023]
Abstract
BACKGROUND Melkersson-Rosenthal syndrome (MRS) is a rare, neuro-mucocutaneous disease which presents as orofacial swelling, facial palsy and fissured tongue. These symptoms may occur simultaneously or, more frequently, with a oligosymptomatic or monosymptomatic pattern. Swelling, that is the most common initial finding, may mimic hereditary or acquired angioedema, a disorder caused by histamine or bradykinin-mediated plasma-leakage affecting subcutaneous and/or submucosal tissue. The differential diagnosis of MRS includes also chronic inflammatory and infective diseases characterized by granulomatous infiltration, as well as rosacea, contact dermatitis, allergic reactions and Bell's palsy. CASE PRESENTATION A 71-year old, non-allergic female patient with no familial and personal history of angioedema presented, a few days after a possible herpes simplex or varicella-zoster virus infection, with monolateral facial paraesthesia and lower lip edema. After temporary remission of symptoms on oral steroids and antihistamines, she showed swelling recurrence refractory to valaciclovir therapy and a subsequent course of antihistamines. The clinical picture and a previous history of non-Hodgkin lymphoma prompted us to rule out an acquired form of paraneoplastic, C1-inhibitor (C1-INH) deficiency: C1q and both antigen and functional C1-INH tested normal, whilst we found low plasma levels of C3 and C4 possibly related to the parallel detection of antiphospholipid antibodies. Thus, we hypothesized a non-histaminergic, idiopathic form of angioedema and planned further therapy with tranexamic acid and the leukotriene receptor antagonist montelukast. Treatment failure with both drugs finally suggested a Melkersson-Rosenthal syndrome, which was confirmed by histologic findings of non caseating granulomas on lip biopsy. CONCLUSION Melkersson-Rosenthal syndrome may occur with rather non-specific symptoms and overlap with alternative conditions, including recurrent angioedema. No specific biomarkers for MRS exist and clinical diagnosis is often of exclusion. The finding of complement or immune alterations, as in our patient, may be further confounding and justify the need for skin or mucosal biopsy to establish a correct diagnosis and prescribe targeted therapy.
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Affiliation(s)
- Mauro Cancian
- Department of Medicine, University of Padua, Padua, Italy
| | - Stefano Giovannini
- Department of Neuroscience, Division of Dentistry, University of Padua, Via Giustiniani 2, 35128 Padua, Italy
| | - Annalisa Angelini
- Department of Cardiac-Thoracic-Vascular Sciences and Public Health, University of Padua, Padua, Italy
| | - Marny Fedrigo
- Department of Cardiac-Thoracic-Vascular Sciences and Public Health, University of Padua, Padua, Italy
| | - Raffaele Bendo
- Department of Medicine, University of Padua, Padua, Italy
| | | | - Stefano Sivolella
- Department of Neuroscience, Division of Dentistry, University of Padua, Via Giustiniani 2, 35128 Padua, Italy
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Kirmani BH, Dobson CM, Zacharias J. Melkersson–Rosenthal syndrome: An unusual cause of intermittent raised hemidiaphragm? J Thorac Cardiovasc Surg 2011; 141:e27-8. [DOI: 10.1016/j.jtcvs.2011.01.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2010] [Revised: 12/08/2010] [Accepted: 12/08/2010] [Indexed: 10/18/2022]
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Abstract
Persistent lip swelling can be a diagnostic challenge. We report an unusual case of lip edema in the setting of lip surgery 30 years before presentation and because of retained foreign material. This case highlights the importance of accurate historical information and aggressive diagnostic methods in assessing persistent lip swelling.
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