Biology subjects

Burn, J.

Publications and source records attributed to Burn, J..

4 recordsLinked to original sources

bioRxiv2025

A Slc5a6 Deficient Mouse Model Reveals a Metabolically Driven Dilated Cardiomyopathy with Therapeutic Potential for Vitamin-Based Intervention

Background and AimsThe sodium-dependent multivitamin transporter, encoded by SLC5A6, mediates cellular uptake of the vitamins, biotin and pantothenic acid, both of which are essential cofactors for energy metabolism. Here, we report two families with SLC5A6 mutations presenting with early-onset dilated cardiomyopathy (DCM). To investigate the link between vitamin deficiency and DCM, we generated a novel cardiac-specific Slc5a6 knockout (Slc5a6cKO) mouse model and tested the therapeutic potential of vitamin supplementation. MethodsCardiac function in Slc5a6cKO mice was assessed by cardiac magnetic resonance imaging and ECG measurements. Histological, biochemical, and proteomic analyses were conducted to identify structural and metabolic changes. The impact of dietary biotin and pantothenic acid supplementation on disease progression was evaluated. ResultsSlc5a6cKO mice developed progressive cardiac dysfunction, manifesting as DCM with cardiac dilation, cardiomyocyte hypertrophy, fibrosis, impaired Coenzyme A synthesis, and metabolic imbalance, culminating in premature death by 26 weeks. Proteomic analysis revealed early mitochondrial metabolic disruption and extracellular matrix protein upregulation at 8 weeks, preceding overt cardiac dysfunction. Strikingly, vitamin supplementation from preconception onwards, prevented the cardiac phenotype, preserving cardiac structure, function, morphology and survival. This parallels the clinical outcome in one patient who received early vitamin treatment, compared to another who required a heart transplant following delayed vitamin treatment. ConclusionsThis study establishes a direct link between SLC5A6-mediated vitamin transport, mitochondrial function, and cardiac health. It highlights how vitamin deficiency contributes to DCM pathogenesis and supports early vitamin supplementation as a potential therapeutic strategy for metabolic cardiomyopathies. Translational perspectiveThis study highlights the therapeutic potential of vitamin supplementation in treating dilated cardiomyopathy (DCM) caused by mitochondrial abnormalities. Using a cardiac-specific Slc5a6 knockout mouse model, we demonstrated that deficiencies in key vitamins, biotin and pantothenic acid, impair mitochondrial energy metabolism, leading to DCM progression. Remarkably, vitamin supplementation preserved cardiac function, morphology, and survival, suggesting that restoring vitamin levels could be a promising therapeutic strategy for DCM and other cardiomyopathies linked to metabolic deficiencies. These findings could inform newborn screening programmes and clinical approaches for treating mitochondrial-related cardiac diseases by targeting specific vitamin deficiencies. Key QuestionWhat is the underlying molecular cause of early-onset dilated cardiomyopathy in patients with SLC5A6 mutations, and can insights from a cardiac-specific knockout mouse model reveal potential metabolic mechanisms and therapeutic strategies involving vitamin supplementation? Key FindingCardiac-specific deletion of Slc5a6 in mice caused early mitochondrial dysfunction, metabolic derangement, and progressive dilated cardiomyopathy. Strikingly, early and continuous supplementation with biotin and pantothenic acid completely preserved cardiac structure, function, and survival, paralleling successful outcomes in patients treated early. Take Home MessageThis study establishes a mechanistic link between SLC5A6 mutations, vitamin deficiency and mitochondrial abnormalities as a cause of dilated cardiomyopathy. Early vitamin supplementation prevents disease onset, highlighting the potential of targeted vitamin therapy in metabolic cardiomyopathies. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=115 SRC="FIGDIR/small/658273v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@cf8e8corg.highwire.dtl.DTLVardef@97c74borg.highwire.dtl.DTLVardef@9d0e41org.highwire.dtl.DTLVardef@112eb77_HPS_FORMAT_FIGEXP M_FIG C_FIG

genetics↗

bioRxiv2023

The influence of marker number and sequencing depth on the ability to identify mismatch repair deficient tumours.

1.Analysis of somatic mutation patterns is widely used to infer exposure to exogenous and endogenous mutagenic influences. This raises the question of the amount of sequence data required to detect factors of interest. A common use of mutation pattern analysis is the identification of increased microsatellite instability to uncover mismatch repair (MMR) defects in tumours and normal tissues. Here we explore the effects of sequencing depth and the number of loci analysed on the ability to detect MMR deficiency using artificial neural networks and publicly available amplicon sequencing data from colorectal tumours on 24 short quasi monomorphic microsatellites (up to 12 bp in length, PMID 31471937) split in a training (99 samples) and a test set (95 samples). We show that, at a sequencing depth of 200, pairs mononucleotide repeats can achieve discrimination between MMR proficient and deficient colorectal tumours similar to that obtained with the full 24 marker panel, with accuracies above 97% and ROC AUCs in excess of 99% in the test set. Our results indicate that for short monomorphic microsatellites considering the length distribution of the different alleles at each locus, representing these distributions as two-dimensional structures and including convolutional layers in the network can facilitate discrimination between MMR deficient and proficient tumour material. They also indicate that, despite the limitations imposed by amplification, sequencing accuracy and the limited divergence time between the sequences from one locus, high depth sequencing can be used to identify MMR deficiency from a limited number of loci. However, they also suggest that, for a fixed total number of reads per sample, increasing sensitivity by increasing the number of targets is more efficient than by increasing per target sequencing depth. These results are of interest for screening large numbers of samples and for assessing the impact MMR deficiency in different areas of the genome.

genetics↗

bioRxiv2018

A molecular inversion probe and sequencing-based microsatellite instability assay for high throughput cancer diagnostics and Lynch syndrome screening

BackgroundClinical guidelines recommend microsatellite instability (MSI) and BRAF V600E testing of all colorectal cancers (CRCs) to screen for Lynch syndrome (LS), a hereditary predisposition to cancer. MSI is also associated with response to immunotherapy. However, uptake of MSI testing is poor and current assays are not suitable for high throughput diagnostics.\n\nWe aimed to develop a cheap and scalable sequencing assay for MSI classification, which is robust to variables in clinical samples and simultaneously tests for BRAF V600E to streamline the LS screening pipeline.\n\nMethods24 short (7-12bp) microsatellites and the BRAF V600E locus were amplified in multiplex using single molecule molecular inversion probes (smMIPs) and sequenced using the Illumina MiSeq platform. Reads were aligned to reference genome hg19. An MSI classifier was trained from 98 CRCs and validated in 99 independent CRCs collected in pathology laboratories in Edinburgh, Spain and Newcastle.\n\nResultsThe smMIP-based MSI assay has 100% accuracy for MSI status relative to MSI Analysis System (Promega). MSI classification is reproducible (100% concordance) and is robust to sample variables, detecting less than 5% MSI-high content in template DNA and giving reliable classification from sequencing only 75 DNA molecules per marker. BRAF V600E was detected with mutant allele frequencies down to 1.7%.\n\nConclusionsOur short microsatellite, smMIP-based, MSI assay provides a cheap and fully automatable assessment of MSI status and BRAF mutation. It is readily scalable to high throughput cancer diagnostics, and is suitable both as a companion diagnostic for immunotherapy and for streamlined LS screening.

cancer biology↗

bioRxiv2018

A novel panel of short mononucleotide repeats linked to informative polymorphisms enabling effective high volume low cost discrimination between mismatch repair deficient and proficient tumours

Somatic mutations in mononucleotide repeats are commonly used to assess the mismatch repair status of tumours. Current tests focus on repeats with a length above 15bp, which tend to be somatically more unstable than shorter ones. These longer repeats also have a substantially higher PCR error rate and tests that use capillary electrophoresis for fragment size analysis often require expert interpretation. In this communication, we present a panel of 17 short repeats (length 7-12bp) for sequence-based microsatellite instability (MSI) testing. Using a simple scoring procedure that incorporates the allelic distribution of the mutant repeats, and analysis of two cohort of tumours totalling 209 samples, we show that this panel is able to discriminate between MMR proficient and deficient tumours, even when constitutional DNA is not available. In the training cohort, the method achieved 100% concordance with fragment analysis, while in the testing cohort, 4 discordant samples were observed (corresponding to 97% concordance). Of these, 2 showed discrepancies between fragment analysis and immunohistochemistry and one was reclassified after re-testing using fragment analysis. These results indicate that our approach offers the option of a reliable, scalable routine test for MSI.

genomics↗