1
|
van Cruchten RTP, van As D, Glennon JC, van Engelen BGM, 't Hoen PAC, Wenninger S, Daidj F, Cumming S, Littleford R, Monckton DG, Lochmüller H, Catt M, Faber CG, Hapca A, Donnan PT, Gorman G, Bassez G, Schoser B, Knoop H, Treweek S, Wansink DG, Impens F, Gabriels R, Claeys T, Ravel-Chapuis A, Jasmin BJ, Mahon N, Nieuwenhuis S, Martens L, Novak P, Furling D, Baak A, Gourdon G, MacKenzie A, Martinat C, Neault N, Roos A, Duchesne E, Salz R, Thompson R, Baghdoyan S, Varghese AM, Blom P, Spendiff S, Manta A. Clinical improvement of DM1 patients reflected by reversal of disease-induced gene expression in blood. BMC Med 2022; 20:395. [PMID: 36352383 PMCID: PMC9646470 DOI: 10.1186/s12916-022-02591-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 09/30/2022] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Myotonic dystrophy type 1 (DM1) is an incurable multisystem disease caused by a CTG-repeat expansion in the DM1 protein kinase (DMPK) gene. The OPTIMISTIC clinical trial demonstrated positive and heterogenous effects of cognitive behavioral therapy (CBT) on the capacity for activity and social participations in DM1 patients. Through a process of reverse engineering, this study aims to identify druggable molecular biomarkers associated with the clinical improvement in the OPTIMISTIC cohort. METHODS Based on full blood samples collected during OPTIMISTIC, we performed paired mRNA sequencing for 27 patients before and after the CBT intervention. Linear mixed effect models were used to identify biomarkers associated with the disease-causing CTG expansion and the mean clinical improvement across all clinical outcome measures. RESULTS We identified 608 genes for which their expression was significantly associated with the CTG-repeat expansion, as well as 1176 genes significantly associated with the average clinical response towards the intervention. Remarkably, all 97 genes associated with both returned to more normal levels in patients who benefited the most from CBT. This main finding has been replicated based on an external dataset of mRNA data of DM1 patients and controls, singling these genes out as candidate biomarkers for therapy response. Among these candidate genes were DNAJB12, HDAC5, and TRIM8, each belonging to a protein family that is being studied in the context of neurological disorders or muscular dystrophies. Across the different gene sets, gene pathway enrichment analysis revealed disease-relevant impaired signaling in, among others, insulin-, metabolism-, and immune-related pathways. Furthermore, evidence for shared dysregulations with another neuromuscular disease, Duchenne muscular dystrophy, was found, suggesting a partial overlap in blood-based gene dysregulation. CONCLUSIONS DM1-relevant disease signatures can be identified on a molecular level in peripheral blood, opening new avenues for drug discovery and therapy efficacy assessments.
Collapse
Affiliation(s)
- Remco T P van Cruchten
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Daniël van As
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jeffrey C Glennon
- Conway Institute of Biomolecular and Biomedical Research, School of Medicine, University College Dublin, Dublin, Ireland
| | - Baziel G M van Engelen
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Peter A C 't Hoen
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
2
|
Rahmadi R, Groot P, van Rijn MHC, van den Brand JAJG, Heins M, Knoop H, Heskes T. Causality on longitudinal data: Stable specification search in constrained structural equation modeling. Stat Methods Med Res 2018; 27:3814-3834. [PMID: 28657454 PMCID: PMC6249641 DOI: 10.1177/0962280217713347] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
A typical problem in causal modeling is the instability of model structure learning, i.e., small changes in finite data can result in completely different optimal models. The present work introduces a novel causal modeling algorithm for longitudinal data, that is robust for finite samples based on recent advances in stability selection using subsampling and selection algorithms. Our approach uses exploratory search but allows incorporation of prior knowledge, e.g., the absence of a particular causal relationship between two specific variables. We represent causal relationships using structural equation models. Models are scored along two objectives: the model fit and the model complexity. Since both objectives are often conflicting, we apply a multi-objective evolutionary algorithm to search for Pareto optimal models. To handle the instability of small finite data samples, we repeatedly subsample the data and select those substructures (from the optimal models) that are both stable and parsimonious. These substructures can be visualized through a causal graph. Our more exploratory approach achieves at least comparable performance as, but often a significant improvement over state-of-the-art alternative approaches on a simulated data set with a known ground truth. We also present the results of our method on three real-world longitudinal data sets on chronic fatigue syndrome, Alzheimer disease, and chronic kidney disease. The findings obtained with our approach are generally in line with results from more hypothesis-driven analyses in earlier studies and suggest some novel relationships that deserve further research.
Collapse
Affiliation(s)
- Ridho Rahmadi
- Department of Informatics, Universitas Islam Indonesia, Sleman, Indonesia
- Institute for Computing and Information Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Perry Groot
- Institute for Computing and Information Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Marieke HC van Rijn
- Department of Nephrology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jan AJG van den Brand
- Department of Nephrology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marianne Heins
- Netherlands Institute for Health Services Research, Utrecht, The Netherlands
| | - Hans Knoop
- Department of Medical Psychology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Tom Heskes
- Institute for Computing and Information Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands
| | | | | | | |
Collapse
|