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Wylezinski LS, Sesler CL, Shaginurova GI, Grigorenko EV, Wohlgemuth JG, Cockerill FR, Racke MK, Spurlock CF. Machine Learning Analysis Using RNA Sequencing to Distinguish Neuromyelitis Optica from Multiple Sclerosis and Identify Therapeutic Candidates. J Mol Diagn 2024; 26:520-529. [PMID: 38522839 PMCID: PMC11163981 DOI: 10.1016/j.jmoldx.2024.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 01/19/2024] [Accepted: 03/01/2024] [Indexed: 03/26/2024] Open
Abstract
This study aims to identify RNA biomarkers distinguishing neuromyelitis optica (NMO) from relapsing-remitting multiple sclerosis (RRMS) and explore potential therapeutic applications leveraging machine learning (ML). An ensemble approach was developed using differential gene expression analysis and competitive ML methods, interrogating total RNA-sequencing data sets from peripheral whole blood of treatment-naïve patients with RRMS and NMO and healthy individuals. Pathway analysis of candidate biomarkers informed the biological context of disease, transcription factor activity, and small-molecule therapeutic potential. ML models differentiated between patients with NMO and RRMS, with the performance of certain models exceeding 90% accuracy. RNA biomarkers driving model performance were associated with ribosomal dysfunction and viral infection. Regulatory networks of kinases and transcription factors identified biological associations and identified potential therapeutic targets. Small-molecule candidates capable of reversing perturbed gene expression were uncovered. Mitoxantrone and vorinostat-two identified small molecules with previously reported use in patients with NMO and experimental autoimmune encephalomyelitis-reinforced discovered expression signatures and highlighted the potential to identify new therapeutic candidates. Putative RNA biomarkers were identified that accurately distinguish NMO from RRMS and healthy individuals. The application of multivariate approaches in analysis of RNA-sequencing data further enhances the discovery of unique RNA biomarkers, accelerating the development of new methods for disease detection, monitoring, and therapeutics. Integrating biological understanding further enhances detection of disease-specific signatures and possible therapeutic targets.
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Affiliation(s)
- Lukasz S Wylezinski
- Decode Health, Inc., Nashville, Tennessee; Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee
| | | | | | | | - Jay G Wohlgemuth
- Quest Diagnostics, Secaucus, New Jersey; Trusted Health Advisors, San Juan Capistrano, California
| | - Franklin R Cockerill
- Decode Health, Inc., Nashville, Tennessee; Trusted Health Advisors, San Juan Capistrano, California; Department of Medicine, Rush University Medical Center, Chicago, Illinois
| | | | - Charles F Spurlock
- Decode Health, Inc., Nashville, Tennessee; Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee; Wagner School of Public Service, New York University, New York, New York.
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Rotstein DL, Freedman MS, Lee L, Marrie RA, Morrow SA, McCombe JA, Parks NE, Smyth P, Konig A, Vyas MV. Predicting time to serologic diagnosis of AQP4+ NMOSD based on clinical factors and social determinants of health. Mult Scler Relat Disord 2024; 83:105434. [PMID: 38242051 DOI: 10.1016/j.msard.2024.105434] [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: 09/03/2023] [Revised: 12/27/2023] [Accepted: 01/06/2024] [Indexed: 01/21/2024]
Abstract
BACKGROUND Early serologic diagnosis and initiation of targeted therapy are associated with better outcomes in aquaporin-4 IgG positive (AQP4+) neuromyelitis optica spectrum disorder (NMOSD). OBJECTIVE To determine predictors of time to serologic diagnosis of AQP4+ NMOSD. METHODS In CANOPTICS, a multi-centre, Canadian cohort study of NMOSD, we retrospectively evaluated time from the first clinical attack to first positive AQP4-IgG serology. We used a multivariable negative binomial regression model to evaluate possible predictors of time to diagnosis. RESULTS We identified 129 participants with AQP4+ NMOSD from 7 centres. Diagnostic delay of >1 month was observed in 82 (63.6 %). Asian compared to European (White) ethnicity (IRR:0.40, 95 % CI:0.21-0.78), female sex (IRR:0.56, 95 % CI:0.32-0.99), later calendar year (IRR:0.84, 95 % CI:0.81-0.86), and hospitalization for the first attack (IRR:0.35, 95 % CI:0.20-0.62) were associated with shorter times to serologic diagnosis. We did not observe any overall effect of Afro-Caribbean ethnicity, but in exploratory analyses, Afro-Caribbean individuals with low income had longer times to diagnosis. CONCLUSION More than 60 % of patients with NMOSD experienced delays to AQP4-IgG serologic diagnosis in this cohort. Given evidence of more adverse long-term outcomes in Afro-Caribbean individuals with NMOSD, intersectional effects of ethnicity and social determinants of health merit further study.
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Affiliation(s)
- Dalia L Rotstein
- St. Michael's Hospital, 30 Bond St., Toronto, Ontario M5B 1W8, Canada; Department of Medicine, University of Toronto, 6 Queen's Park Crescent West, 3rd floor, Toronto, Ontario M5S 3H2, Canada.
| | - Mark S Freedman
- Department of Medicine, University of Ottawa, Ottawa, Ontario, Canada; Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | - Liesly Lee
- Department of Medicine, University of Toronto, 6 Queen's Park Crescent West, 3rd floor, Toronto, Ontario M5S 3H2, Canada; Sunnybrook Health Sciences Centre, University of Toronto, 2075 Bayview Avenue, Toronto, Ontario, Canada
| | - Ruth Ann Marrie
- Departments of Medicine and Community Health Sciences, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Sarah A Morrow
- Western University, London, Ontario, Canada; London Health Sciences Centre, London, Ontario, Canada; University of Calgary, Calgary, Alberta, Canada
| | | | | | | | - Andrea Konig
- St. Michael's Hospital, 30 Bond St., Toronto, Ontario M5B 1W8, Canada
| | - Manav V Vyas
- St. Michael's Hospital, 30 Bond St., Toronto, Ontario M5B 1W8, Canada; Department of Medicine, University of Toronto, 6 Queen's Park Crescent West, 3rd floor, Toronto, Ontario M5S 3H2, Canada
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Okuda DT, Moog TM, McCreary M, Cook K, Burgess KW, Smith AD. Treatment transitions in neuromyelitis optica spectrum disorder increase risk for disease advancement. Mult Scler Relat Disord 2023; 79:105041. [PMID: 37804767 DOI: 10.1016/j.msard.2023.105041] [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: 07/06/2023] [Revised: 08/14/2023] [Accepted: 09/28/2023] [Indexed: 10/09/2023]
Abstract
BACKGROUND People with neuromyelitis optica spectrum disorder (PwNMOSD) commonly switch between disease modifying therapies, yet the consequence of transitions remains unknown. We aimed to understand if treatment transitions due to medical, non-medical, and tolerability reasons were related to disease progression. METHODS A retrospective study of medical records for PwNMOSD was performed between 2008 and 2022. A comprehensive clinical timeline was created for each person including details related to treatment history and associated clinical and radiological outcomes (i.e., hospital admission, relapses, and MRI advancement). If a transition occurred, the reason for the switch was categorized as being due to medical, non-medical, or tolerability issues. A proportional hazards model was created, and the assumptions were tested based on weighted residuals. RESULTS The cohort included 164 aquaporin-4 IgG positive NMOSD subjects with 89 (79 female; median disease duration (range) = 10.1 years (y) (1.7-32.8)) people switching therapies at least once (once: 42; twice: 26; three times: 12; four times: 6; 5 or more times: 3). A similar amount of higher efficacy therapies was used by PwNMOSD that switched due to a non-medical/tolerability or a medical-related reason. The results of the recurrent event survival analysis revealed that after an initial transition due to non-medical/tolerability reasons, the risk of a hospital admission, relapse, and MRI advancement decreases by 40.3 % (p = 0.005), 53.1 % (p = 0.002), and 65.9 % (p = 0.005), respectively. However, with each additional discontinuation due to non-medical/tolerability reasons, the risk of hospitalization increased by 25.2 % (p = 0.0003) and risk for MRI advancement increased by 41.9 % (p = 0.03). For transitions due to medical reasons, a significant increased risk of MRI advancement by 32.2 % (p = 0.005) for the first switch was identified with no associated observed risk with each additional discontinuation (p = 0.33). Within the first six months after stopping a medication due to non-medical/tolerability reasons, the rate of starting a new medication was less (p<0.0001) when compared to a discontinuation due to a medical-related event. CONCLUSIONS The risk associated with the time course of treatment transitions for people with NMOSD may assist in transforming the way healthcare providers bridge the gap between therapies and the approach to the timing of a switch. These data highlight additional factors that may be equatable to the efficacy of prescribed treatments in the prevention of acute neurological events.
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Affiliation(s)
- Darin T Okuda
- Department of Neurology, Neuroinnovation Program, Multiple Sclerosis & Neuroimmunology Imaging Program, The University of Texas Southwestern Medical Center, Dallas, TX, USA; Revert Health Inc., Coppell, TX, USA.
| | - Tatum M Moog
- Department of Neurology, Neuroinnovation Program, Multiple Sclerosis & Neuroimmunology Imaging Program, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Morgan McCreary
- Department of Neurology, Neuroinnovation Program, Multiple Sclerosis & Neuroimmunology Imaging Program, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Karin Cook
- Department of Neurology, Neuroinnovation Program, Multiple Sclerosis & Neuroimmunology Imaging Program, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Katy W Burgess
- Department of Neurology, Neuroinnovation Program, Multiple Sclerosis & Neuroimmunology Imaging Program, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Alexander D Smith
- Department of Neurology, Neuroinnovation Program, Multiple Sclerosis & Neuroimmunology Imaging Program, The University of Texas Southwestern Medical Center, Dallas, TX, USA
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Zara P, Dinoto A, Carta S, Floris V, Turilli D, Budhram A, Ferrari S, Milia S, Solla P, Mariotto S, Flanagan EP, Chiriboga ASL, Sechi E. Non-demyelinating disorders mimicking and misdiagnosed as NMOSD: a literature review. Eur J Neurol 2023; 30:3367-3376. [PMID: 37433584 PMCID: PMC10530555 DOI: 10.1111/ene.15983] [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: 05/16/2023] [Revised: 06/30/2023] [Accepted: 07/06/2023] [Indexed: 07/13/2023]
Abstract
BACKGROUND Differentiating neuromyelitis optica spectrum disorder (NMOSD) from its mimics is crucial to avoid misdiagnosis, especially in the absence of aquaporin-4-IgG. While multiple sclerosis (MS) and myelin oligodendrocyte glycoprotein-IgG associated disease (MOGAD) represent major and well-defined differential diagnoses, non-demyelinating NMOSD mimics remain poorly characterized. METHODS We conducted a systematic review on PubMed/MEDLINE to identify reports of patients with non-demyelinating disorders that mimicked or were misdiagnosed as NMOSD. Three novel cases seen at the authors' institutions were also included. The characteristics of NMOSD mimics were analyzed and red flags associated with misdiagnosis identified. RESULTS A total of 68 patients were included; 35 (52%) were female. Median age at symptoms onset was 44 (range, 1-78) years. Fifty-six (82%) patients did not fulfil the 2015 NMOSD diagnostic criteria. The clinical syndromes misinterpreted for NMOSD were myelopathy (41%), myelopathy + optic neuropathy (41%), optic neuropathy (6%), or other (12%). Alternative etiologies included genetic/metabolic disorders, neoplasms, infections, vascular disorders, spondylosis, and other immune-mediated disorders. Common red flags associated with misdiagnosis were lack of cerebrospinal fluid (CSF) pleocytosis (57%), lack of response to immunotherapy (55%), progressive disease course (54%), and lack of magnetic resonance imaging gadolinium enhancement (31%). Aquaporin-4-IgG positivity was detected in five patients by enzyme-linked immunosorbent assay (n = 2), cell-based assay (n = 2: serum, 1; CSF, 1), and non-specified assay (n = 1). CONCLUSIONS The spectrum of NMOSD mimics is broad. Misdiagnosis frequently results from incorrect application of diagnostic criteria, in patients with multiple identifiable red flags. False aquaporin-4-IgG positivity, generally from nonspecific testing assays, may rarely contribute to misdiagnosis.
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Affiliation(s)
- Pietro Zara
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Sassari, Italy
| | - Alessandro Dinoto
- Neurology Unit, Department of Neuroscience, Biomedicine and Movement Sciences, University of Verona, Italy
| | - Sara Carta
- Neurology Unit, Department of Neuroscience, Biomedicine and Movement Sciences, University of Verona, Italy
| | - Valentina Floris
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Sassari, Italy
| | - Davide Turilli
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Sassari, Italy
| | - Adrian Budhram
- Department of Clinical Neurological Sciences, Western University, London, Ontario, Canada
| | - Sergio Ferrari
- Neurology Unit, Department of Neuroscience, Biomedicine and Movement Sciences, University of Verona, Italy
| | - Stefania Milia
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Sassari, Italy
| | - Paolo Solla
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Sassari, Italy
| | - Sara Mariotto
- Neurology Unit, Department of Neuroscience, Biomedicine and Movement Sciences, University of Verona, Italy
| | - Eoin P. Flanagan
- Department of Neurology, Mayo Clinic, Rochester, MN, USA
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | | | - Elia Sechi
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Sassari, Italy
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Carnero Contentti E, Okuda DT, Rojas JI, Chien C, Paul F, Alonso R. MRI to differentiate multiple sclerosis, neuromyelitis optica, and myelin oligodendrocyte glycoprotein antibody disease. J Neuroimaging 2023; 33:688-702. [PMID: 37322542 DOI: 10.1111/jon.13137] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 05/31/2023] [Accepted: 06/05/2023] [Indexed: 06/17/2023] Open
Abstract
Differentiating multiple sclerosis (MS) from other relapsing inflammatory autoimmune diseases of the central nervous system such as neuromyelitis optica spectrum disorder (NMOSD) and myelin oligodendrocyte glycoprotein antibody-associated disease (MOGAD) is crucial in clinical practice. The differential diagnosis may be challenging but making the correct ultimate diagnosis is critical, since prognosis and treatments differ, and inappropriate therapy may promote disability. In the last two decades, significant advances have been made in MS, NMOSD, and MOGAD including new diagnostic criteria with better characterization of typical clinical symptoms and suggestive imaging (magnetic resonance imaging [MRI]) lesions. MRI is invaluable in making the ultimate diagnosis. An increasing amount of new evidence with respect to the specificity of observed lesions as well as the associated dynamic changes in the acute and follow-up phase in each condition has been reported in distinct studies recently published. Additionally, differences in brain (including the optic nerve) and spinal cord lesion patterns between MS, aquaporin4-antibody-positive NMOSD, and MOGAD have been described. We therefore present a narrative review on the most relevant findings in brain, spinal cord, and optic nerve lesions on conventional MRI for distinguishing adult patients with MS from NMOSD and MOGAD in clinical practice. In this context, cortical and central vein sign lesions, brain and spinal cord lesions characteristic of MS, NMOSD, and MOGAD, optic nerve involvement, role of MRI at follow-up, and new proposed diagnostic criteria to differentiate MS from NMOSD and MOGAD were discussed.
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Affiliation(s)
| | - Darin T Okuda
- Department of Neurology, Neuroinnovation Program, Multiple Sclerosis & Neuroimmunology Imaging Program, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Juan I Rojas
- Centro de esclerosis múltiple de Buenos Aires, Buenos Aires, Argentina
| | - Claudia Chien
- NeuroCure Clinical Research Center, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Experimental and Clinical Research Center, Max Delbrueck Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Friedemman Paul
- NeuroCure Clinical Research Center, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Experimental and Clinical Research Center, Max Delbrueck Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Ricardo Alonso
- Centro Universitario de Esclerosis Múltiple (CUEM), Hospital Ramos Mejía, Buenos Aires, Argentina
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Moog TM, Smith AD, Burgess KW, McCreary M, Okuda DT. High-efficacy therapies reduce clinical and radiological events more effectively than traditional treatments in neuromyelitis optica spectrum disorder. J Neurol 2023:10.1007/s00415-023-11710-5. [PMID: 37052668 DOI: 10.1007/s00415-023-11710-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/04/2023] [Accepted: 04/05/2023] [Indexed: 04/14/2023]
Abstract
BACKGROUND People with neuromyelitis optica spectrum disorder (pwNMOSD) experience debilitating neurological attacks, resulting in permanent disability. OBJECTIVE To evaluate if high-efficacy treatment was better than traditional agents at preventing disease advancement in pwNMOSD. METHODS A retrospective study of pwNMOSD at one academic center was performed. Timelines were created for treatments subjects were exposed to along with clinical/radiological events related to disease worsening. High-efficacy treatments included eculizumab, inebilizumab, satralizumab, rituximab, ocrelizumab, tocilizumab, and sarilumab while therapies such as azathioprine, methotrexate, cyclophosphamide, and mycophenolate mofetil were classified as traditional agents. Poisson regression and mixed effects logistics models were constructed, and a subject-specific random intercept was used for intrasubject correlation. RESULTS Of 189 pwNMOSD identified, 161 were aquaporin-4 IgG positive (AQP4 +) with 92 (77 female; median disease duration (MDD) (range) of 6.6 years (y) (1.2-18.6)) exposed only to high-efficacy therapy, 33 (28 female; 10.4 y (0.8-32.7)) only to traditional therapy, and 64 (54 female; 10.8 y (0.7-20.2)) to both. High-efficacy treatments reduced the rate of MRI advancement by 62.4% (95% CrI = [- 86.9%, - 16.8%]), relapses by 99.8% (95% CrI = [- 99.9%, - 99.6%]), and hospitalizations by 99.3% (95% CrI = [- 99.6%, - 98.8%]) when compared to traditional treatments. For AQP4 + subjects, a 655.7-fold increase in the odds of new spinal cord lesion development (95% CrI = [+ 37.4-fold, + 3239.5-fold]) was observed with traditional agents (p < 0.0001). CONCLUSION High-efficacy treatments maximize opportunity for preventing disease advancement in newly diagnosed and established pwNMOSD.
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Affiliation(s)
- Tatum M Moog
- Department of Neurology, Neuroinnovation Program, Multiple Sclerosis and Neuroimmunology Imaging Program, The University of Texas Southwestern Medical Center, 5303 Harry Hines Blvd., Dallas, TX, 75390-8806, USA
| | - Alexander D Smith
- Department of Neurology, Neuroinnovation Program, Multiple Sclerosis and Neuroimmunology Imaging Program, The University of Texas Southwestern Medical Center, 5303 Harry Hines Blvd., Dallas, TX, 75390-8806, USA
| | - Katy W Burgess
- Department of Neurology, Neuroinnovation Program, Multiple Sclerosis and Neuroimmunology Imaging Program, The University of Texas Southwestern Medical Center, 5303 Harry Hines Blvd., Dallas, TX, 75390-8806, USA
| | - Morgan McCreary
- Department of Neurology, Neuroinnovation Program, Multiple Sclerosis and Neuroimmunology Imaging Program, The University of Texas Southwestern Medical Center, 5303 Harry Hines Blvd., Dallas, TX, 75390-8806, USA
| | - Darin T Okuda
- Department of Neurology, Neuroinnovation Program, Multiple Sclerosis and Neuroimmunology Imaging Program, The University of Texas Southwestern Medical Center, 5303 Harry Hines Blvd., Dallas, TX, 75390-8806, USA.
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