Biology subjects

van Putten, M.

Publications and source records attributed to van Putten, M..

9 recordsLinked to original sources

bioRxiv2026

Spatial transcriptomics maps region and isoform specific brain alterations in mdx and mdx4cv models of Duchenne muscular dystrophy

Duchenne muscular dystrophy (DMD) is accompanied by cognitive and neurodevelopmental difficulties. To investigate how the loss of different dystrophin isoforms affects gene expression across brain regions, we performed spatial transcriptomics on brains from mdx and mdx4cv mouse models (lacking Dp427 or Dp427+Dp140 respectively) and healthy controls aged 2 weeks. Both dystrophic models showed transcriptional changes converging on myelin and oligodendrocyte biology and oxidative phosphorylation, but with distinct regional patterns. In mdx mice, myelin genes were upregulated in the amygdala and hippocampus and downregulated in fiber tract regions, while mitochondrial genes were upregulated in most regions but downregulated in the thalamus and isocortex. In mdx4cv mice, myelin genes were broadly upregulated and mitochondrial genes downregulated across almost all regions. Direct comparison between mdx and mdx4cv mice demonstrated that the additional loss of Dp140 expanded localized myelin upregulation across the brain and shifts the mitochondrial response toward widespread downregulation. These differences in regional changes between the mouse models is in line with their dystrophin isoform(s) loss. Our findings provide a molecular basis for the brain-related impairments of DMD and a foundation for future therapeutic studies.

neuroscience↗

bioRxiv2026

The D2-mdx mouse as a preclinical model for Duchenne muscular dystrophy: a natural history study across two independent sites

IntroductionThe quality of preclinical studies for rare diseases, such as Duchenne muscular dystrophy (DMD), relies on the availability of comprehensive natural disease history data. In addition to the classic BL10-mdx mouse, in recent years, the D2-mdx model has increasingly been used as an alternative model due to its reportedly more severely impaired phenotype. To improve our understanding of disease progression in these two DMD models, we conducted a comprehensive natural history study. Materials and MethodsThis involved a cross-sectional analysis of key in vivo and ex vivo outcome measures performed in two independent laboratories, using the same study setup in compliance with TREAT-NMD Standard Operating Procedures (SOPs), while also taking advantage of site-specific expertise. Globally, largely comparable results were obtained across the two study sites. ResultsBody composition showed pronounced differences between the strains, with BL10-mdx mice displaying a hypertrophic and D2-mdx mice displaying an atrophic phenotype. Dystrophic mice of each strain exhibited significant alterations of disease-relevant indices related to muscle functionality and integrity, mostly worsening with age, in comparison to their wildtypes. Cardiac function was affected earlier and more severely in D2-mdx mice. DiscussionNotably, for some parameters, genetic-background related differences were observed, emphasizing the need to include control groups with matching genetic backgrounds in experimental designs. ConclusionsCollectively, our natural history study provides benchmark data for these two mdx mouse strains to guide model selection for preclinical DMD studies, allowing accurate data interpretation. HighlightsO_LIDistinct body composition phenotypes: BL10-mdx mice exhibit pseudohypertrophy while D2-mdx mice display pronounced atrophy. C_LIO_LIEarlier cardiac dysfunction in D2-mdx: D2-mdx mice develop reduced ejection fraction and stroke volume from 28 weeks, while BL10-mdx only at 52 weeks. C_LIO_LIGenetic background-dependent variations: Intrinsic deficits in wildtype D2 mice demonstrate that genetic background influences outcome measures independent of dystrophic pathology. C_LIO_LIComparable ex vivo muscle physiology: Despite divergent in vivo phenotypes, isolated muscle contractile parameters show similar impairment in both dystrophic models. C_LIO_LIMulti-site standardized validation: Cross-sectional study at two independent laboratories following harmonized TREAT-NMD Standard Operating Procedures. C_LI

pharmacology and toxicology↗

bioRxiv2025

Four new Duchenne muscular dystrophy mouse models with clinically relevant exon deletions in the human DMD gene

Mutation specific therapeutic approaches, like exon skipping or gene-editing, hold promise for the treatment of Duchenne muscular dystrophy (DMD). Translatability of preclinical studies investigating these approaches could greatly be improved through the use of humanized mouse models, as these allow preclinical testing of human specific sequences. We developed four novel humanized DMD mouse models with either a deletion of exon 44, 45, 51 or 53 in the human DMD gene, in a mouse dystrophin negative background (mdx mouse; exon 23 nonsense mutation). Our optimized prescreening pipeline allowed us to do so very efficiently with the CRISPR-Cas9 technology. We confirmed either complete lack of dystrophin, or expression of trace levels, which led to development of muscle pathology consisting of muscle fiber de-, and regeneration, inflammation and fibrosis in young adult mice. Intramuscular treatment with vivo-morpholinos targeting a flanking exon induced exon skipping in the DMD strains, which restored the disrupted open reading frame and subsequently dystrophin expression. This validates these models as valuable tools for preclinical studies investigating human sequence specific therapeutic approaches for DMD. Summary statementHumanized Duchenne muscular dystrophy mouse models were created with deletions of exon 44, 45, 51 or 53 in the human DMD gene. These dystrophic models allow preclinical testing of human-specific dystrophin restoring approaches.

neuroscience↗

bioRxiv2025

Evaluating exon-skipping therapies targeting the central nervous system in Duchenne muscular dystrophy using high-resolution spatial transcriptomics

Duchenne muscular dystrophy (DMD) is marked by progressive muscle degeneration due to dystrophin deficiency. Despite cognitive impairments in up to one-third of patients, central nervous system (CNS)-targeted dystrophin restoration remains relatively underexplored compared to muscle-focused therapies. Since dystrophin is expressed in the brain during development and postnatally, it is important to assess which aspects of CNS pathology could be rescued. However, studying Dmd is difficult due to its size, low-abundance transcripts, and with multiple isoforms, limiting the sensitivity and isoform resolution of standard sequencing methods. To overcome these limitations, we applied Xenium spatial transcriptomics to target splice junctions, enabling isoform-specific and exon 51 skipping events detection across brain regions and cell types. Using this approach, we analyzed mdx52 mice lacking the full-length and Dp140 isoforms, treated with two exon 51 skipping therapies (antisense oligonucleotides or AAV-U7ex51). We observed distinct spatial expression patterns in the wild type brain between the full-length isoforms (Dp427c/m/p1) and shorter isoforms (Dp71 and Dp40). The full-length isoforms were predominantly expressed in cortex layers 2/3-6b and the CA1 region, while the shorter isoforms were localized to cortex layer 1 and the dentate gyrus. Among the exon skipping therapies tested, U7ex51 delivered neonatally induced broad exon skipping in neurons and effectively restored full-length isoforms in the targeted cells. This study introduces the first subcellular-resolution spatial transcriptomic atlas of dystrophin presence and rescue in the CNS and demonstrates a framework for evaluating gene therapies in spatially and transcriptionally complex tissues such as the brain.

neuroscience↗

bioRxiv2025

Myonuclear domain-associated and central nucleation-dependent spatial restriction of dystrophin protein expression in a novel DMD mouse model

The restoration of uniformly-distributed dystrophin protein expression is an important consideration for the development of advanced therapeutics for Duchenne muscular dystrophy (DMD). To explore this concept, we generated a novel genetic mouse model (mdx52-Xist{Delta}hs) that expresses variable, and non-uniformly distributed, dystrophin protein from birth as a consequence of skewed X-chromosome inactivation. mdx52-Xist{Delta}hs myofibers are heterokaryons containing a mixture of myonuclei expressing either wild-type or mutant dystrophin alleles in a mutually exclusive manner, resulting in dystrophin protein being spatially restricted to corresponding dystrophin-expressing myonuclear domains. This phenotype models the situation in female DMD carriers, and dystrophic muscle in which dystrophin has been incompletely restored by partially-effective experimental therapeutics. Total dystrophin expression increased in aged (60-week-old) mdx52-Xist{Delta}hs mice relative to 6-week-old adults, suggestive of an accumulation of dystrophin-expressing myonuclei through positive selection, although this was insufficient to resolve sarcolemmal dystrophin patchiness. Nevertheless, compared to mice expressing no dystrophin, non-uniformly-distributed dystrophin was protective against pathology-related muscle turnover in an expression-level-dependent manner in both adult and aged mdx52-Xist{Delta}hs mice. Systematic classification of isolated mdx52-Xist{Delta}hs myofibers revealed profound differences associated with central nucleation, with dystrophin found to be translationally repressed in centrally-nucleated myofibers and myofiber segments. These findings have important implications for the development of dystrophin restoration therapies.

cell biology↗

bioRxiv2024

Investigating the effects of prednisolone on behavior in mouse models of Duchenne muscular dystrophy

BackgroundNext to progressive muscle loss, Duchenne muscular dystrophy patients suffer from behavioral and cognitive problems. This is due to mutations in the DMD gene, that result in the lack of dystrophin in both the muscles and brain. As part of the standards of care, patients receive corticosteroids (prednisolone or deflazacort) to slow down muscle degeneration. The precise consequences of chronic corticosteroid usage on the behavior of DMD patients remain unclear, mainly due to challenges of recruiting corticosteroid naive patients into clinical studies. ObjectiveThis study used DMD mouse models, representing mutations resulting in lack of one or more dystrophin isoforms, to analyze the effects of corticosteroid treatment on different behavioral domains. MethodsPrednisolone (PDN) or placebo was administered via a subcutaneous 60-day slow release pellet (66 {micro}g/day) and mice were subjected to several behavioral tests. ResultsUnfortunately, the pellet only exposed mice to PDN for half of the intended duration. During the time of PDN exposure, we found a small amelioration in anxiety but were unable to find any differences in social interaction and spatial learning and memory. ConclusionsShort term exposure to PDN via a slow release pellet does not seem to negatively affect anxiety, social interaction or spatial learning and memory. We cannot rule out that a longer treatment period than 4 weeks would affect behavior in DMD mice.

animal behavior and cognition↗

bioRxiv2023

Not one size fits all: influence of EEG type when training a deep neural network for interictal epileptiform discharge detection

ObjectiveDeep learning methods have shown potential in automating interictal epileptiform discharge (IED) detection in electroencephalograms (EEGs). While it is known that these algorithms are dependent on the type of data used for training, this has not been explored in EEG analysis applications. We study the difference in performance of deep learning algorithms on routine and ambulatory EEG data. MethodsWe trained the same neural network on three datasets: 166 routine EEGs (VGGC-R), 75 ambulatory EEGs (VGGC-A) and a combination of the two data types (VGGC-C, 241 EEGs total). Networks were tested on 34 routine EEGs and 33 ambulatory recordings, where all 2 s non-overlapping epochs were labeled with a probability that expressed the likelihood of containing an epileptiform discharge. Performance was quantified as sensitivity, specificity and the rate of false detections (FPR). ResultsThe VGGC-R led to 84% sensitivity at 99% specificity on the routine EEGs, but its sensitivity was only 53% on ambulatory EEGs, with a FPR > 3 FP/min. The VGGC-C and VGGC-A yielded sensitivities of 79% and 60%, respectively, at 99% specificity on ambulatory data, but their sensitivity was less than 60% for routine EEGs. ConclusionWe show that performance of deep nets for IED detection depends critically on the type of recording. The VGGC-R should be used for routine recordings and the VGGC-C should be used for ambulatory recordings for IED detection. SignificanceThe type of data used to train algorithms should be optimized according to their application, as this has a significant impact on algorithm performance.

neuroscience↗

bioRxiv2022

Spatial transcriptomics reveal markers of histopathological changes in Duchenne muscular dystrophy mouse models

Duchenne muscular dystrophy (DMD) is caused by mutations in the DMD gene, leading to lack of dystrophin. Chronic muscle damage eventually leads to histological alterations in skeletal muscles. The identification of genes and cell types driving tissue remodeling is a key step to develop effective therapies. Here we use spatial transcriptomics in two DMD mouse models differing in disease severity to identify gene expression signatures underlying skeletal muscle pathologies and directly link this to the muscle histology. Deconvolution analysis allowed the identification of cell types contributing to histological alterations. We show how the expression of specific genes is enriched in areas of muscle regeneration (Myl4, Sparc, Hspg2), fibrosis (Vim, Fn1, Thbs4) and calcification (Bgn, Ctsk, Spp1). Finally, our analysis of differentiation dynamics in the severely affected D2-mdx muscle shows a subset of the muscle fibers are predicted to become affected in its future state. Genes associated with tissue remodeling could enable to design new diagnostic and therapeutic strategies for DMD.

genomics↗

bioRxiv2018

High-throughput data-driven analysis of myofiber composition reveals muscle-specific disease and age-associated patterns

Contractile properties of myofibers are dictated by the abundance of myosin heavy chain (MyHC) isoforms. MyHC composition designates muscle function and its alterations could unravel differential muscle involvement in muscular dystrophies and aging. Current analyses are limited to visual assessments in which myofibers expressing multiple MyHC isoforms are prone to misclassifications. As a result, complex patterns and subtle alterations are unidentified. We developed a high-throughput data-driven myofiber analysis to quantitatively describe the variations in myofibers across the muscle. We investigated alterations in myofiber composition between genotypes, two muscles and two age groups. We show that this analysis facilitates the discovery of complex myofiber compositions and its dependency on age, muscle type and genetic conditions.\n\nNonstandard abbreviations

bioinformatics↗