Comprehensive analysis across SMN2 excludes DNA methylation as an epigenetic biomarker for spinal muscular atrophy
Maria M. Zwartkruis,
Joris V. Kortooms,
Demi Gommers,
Martin G. Elferink,
Ilaria Signoria,
Joyce van der Sel,
Paul J. Hop,
Ramona A.J. Zwamborn,
Robin Geene,
Jared W. Green,
Hanneke W.M. van Deutekom,
Wouter van Rheenen,
Jan H. Veldink,
Fay-Lynn Asselman,
Renske I. Wadman,
W. Ludo van der Pol,
Gijs W. van Haaften,
Ewout J.N. Groen
Affiliations
Maria M. Zwartkruis
Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands; Department of Genetics, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
Joris V. Kortooms
Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
Demi Gommers
Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands; Department of Genetics, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
Martin G. Elferink
Department of Genetics, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
Ilaria Signoria
Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
Joyce van der Sel
Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands; Department of Genetics, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
Paul J. Hop
Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands; Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
Ramona A.J. Zwamborn
Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
Robin Geene
Utrecht Sequencing Facility, Center for Molecular Medicine, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
Jared W. Green
Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
Hanneke W.M. van Deutekom
Department of Genetics, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
Wouter van Rheenen
Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
Jan H. Veldink
Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
Fay-Lynn Asselman
Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
Renske I. Wadman
Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
W. Ludo van der Pol
Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
Gijs W. van Haaften
Department of Genetics, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands; Corresponding author
Ewout J.N. Groen
Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands; Corresponding author
Summary: Spinal muscular atrophy (SMA) is a severe neurodegenerative disease caused by defects in the survival motor neuron 1 (SMN1) gene. Although disease severity partially correlates with SMN2 copy number, significant variability in disease severity and treatment response remains unexplained, prompting a search for additional biomarkers. Using native, long-read nanopore and targeted short-read bisulfite sequencing, we analyzed methylation patterns across the 30 kb SMN2 gene. Our long-read analysis of 29 SMA patients identified tissue-specific variation in SMN2 intronic regions and the 3′UTR. Further analysis of blood-derived DNA of 365 SMA patients identified no association between SMN2 methylation and disease severity or treatment response, excluding blood-derived DNA methylation as a predictive biomarker. However, we discovered significant age-associated variation in SMN2 methylation in intron 1 and the 3′UTR, suggesting a possible role in modifying SMN expression during development and aging. This study provides a framework for detailed methylation analysis in complex genetic regions.
