Slinker: Visualising novel splicing events in RNA-Seq data

Visualisation of the transcriptome relative to a reference genome is fraught with sparsity. This is due to RNA sequencing (RNA-Seq) reads being predominantly mapped to exons that account for just under 3% of the human genome. Recently, we have used exon-only references, superTranscripts, to improve visualisation of aligned RNA-Seq data through the omission of supposedly unexpressed regions such as introns. However, variation within these regions can lead to novel splicing events that may drive a pathogenic phenotype. In these cases, the loss of information in only retaining annotated exons presents significant drawbacks. Here we present Slinker, a bioinformatics pipeline written in Python and Bpipe that uses a data-driven approach to assemble sample-specific superTranscripts. At its core, Slinker uses Stringtie2 to assemble transcripts with any sequence across any gene. This assembly is merged with reference transcripts, converted to a superTranscript, of which rich visualisations are made through Plotly with associated annotation and coverage information. Slinker was validated on five novel splicing events of rare disease samples from a cohort of primary muscular disorders. In addition, Slinker was shown to be effective in visualising deletion events within transcriptomes of tumour samples in the important leukemia gene, IKZF1. Slinker offers a succinct visualisation of RNA-Seq alignments across typically sparse regions and is freely available on Github.

Neurological and muscular disorders

This chapter describes the anaesthetic management of the patient with those neurological or muscular disorders which are relevant to anaesthetic practice, including malignant hyperthermia (MH). Other topics covered include epilepsy, cerebrovascular disease; Parkinson’s disease; spinal cord lesions; myasthenia gravis; multiple sclerosis; Guillain-Barré syndrome; motor neuron disease; dystrophia myotonica and the muscular dystrophies. For each topic, pre-operative investigation and optimisation, treatment, and anaesthetic management are described.

Inherited Muscle Disorders

Inherited muscular disorders can manifest at any age, from prenatal life to adulthood. The broad differential diagnosis includes muscular dystrophies, congenital myopathies, disorders of glycogen and lipid metabolism, channelopathies, and mitochondrial disorders. Muscular dystrophies may present at any age, are inherited, and involve progressive degeneration of muscle, which is often replaced by connective tissue. Muscular dystrophies result from defects in the sarcolemmal proteins of muscle, including dystrophin-associated muscle membrane protein complex, muscle intracellular proteins (eg, nuclear envelope proteins), and extracellular matrix proteins (eg, collagen VI).

Clinical efficacy and safety outcomes of bempedoic acid for LDL-C lowering therapy in patients at high cardiovascular risk: a systematic review and meta-analysis

Background Bempedoic acid (BA) is a novel oral low-density lipoprotein cholestrol (LDL-C) lowering drug. Its efficacy and safety for clinical outcomes in high cardiovascular risk patients remains unknown. Objectives and methods A systematic review was performed and randomized controlled trials (RCTs) of BA vs. placebo in high cardiovascular risk patients reporting clinical efficacy and safety outcomes were included in a meta-analysis. Cumulative odds ratios (OR) and mean differences with 95% confidence intervals (CI) were reported as summary statistics. Results Six RCTs with a total of 3,956 patients and follow-ups of four to 52 weeks were identified. There was no difference in MACE (OR 0.84; CI 0.61, 1.15), all-cause mortality (OR 2.37; CI 0.80, 6.99) and cardiovascular mortality (OR 1.66; CI 0.45, 6.04) for BA vs. placebo. BA showed beneficial trends for nonfatal myocardial infarction (OR 0.57; CI 0.32, 1.00) and was associated with a lower risk of new-onset or worsening of diabetes mellitus (OR 0.68; CI 0.49, 0.94) and non-coronary revascularization (OR 0.41; CI 0.18, 0.95), but higher risk of gout (OR 3.29; CI 1.28, 8.46) and a trend for worsening of renal function (OR 4.24; CI 0.98, 18.39) and muscular disorders (OR 2.60; CI 1.15, 5.91). Conclusion Bempedoic acid in high cardiovascular risk patients showed no significant effects on major cardiovascular outcomes in short-term follow-up. Unfavourable effects on muscular disorders, renal function and the incidence of gout sound a note of caution. Hence, further studies with longer-term follow-up are needed to clarify the risk/benefit ratio of this novel therapy. Funding Acknowledgement Type of funding sources: None.

Investigations on the occurrence of a muscular disorder in Austrian slaughter pigs

Background In slaughterhouse, veterinarians responsible for meat inspection are often confronted with abnormalities in carcasses, not only in pigs but in all livestock species. In 2017, a veterinarian responsible for meat inspection in a slaughterhouse in Styria, Austria, observed gluteal muscles infiltrated by fat and muscle tissue obviously being replaced by fat in two different slaughter pigs. These muscles were sent for further diagnostics to the University Clinic for Swine. Results The two muscle samples were investigated histopathologically and diagnosed with fatty muscular dystrophy. The results of routine histopathology were confirmed by dystrophin-specific immunohistochemistry. Sex of the two affected animals was determined retrospectively using a PCR-based protocol and resulted in one male and one female pig. A survey to determine the prevalence of fatty muscular disorders of pork revealed that this phenomenon gets frequently observed in Styria, but also occurs in Upper Austria and Lower Austria. Mostly gluteal and lumbal muscles were affected and approximately 20–40% of the affected muscles were replaced by fat. Conclusions Fatty muscular dystrophy or muscular steatosis, as it was sometimes called in early literature, seems not to be an uncommon and rare event and is known to have several different causes. As it was detected in both sexes, our observations are different to the described case in Japan, where only one male individual was affected. To avoid further increase of such cases (fatty muscular dystrophy), it would be useful to clarify the cause. First, whether the cause is environmental or genetic, and in case it is genetic it would be key to disentangle the underlying genomic architecture. Having causal variants described—one could think about integrating this information (depending on the mode of inheritance and the number of loci involved) in the breeding program of pigs. Furthermore, the proportion of non-Austrian pig genetics used for commercial pig production in Austria should be reviewed in order to be able to make reliable statements about the spread of the disease not only in Austrian pig breeds, but also in pig breeds worldwide.

Role of DYSF Genetic Variant in Limb Girdle Muscular Dystrophy: A Case Report

Introduction: Muscular dystrophy is a hereditary degenerative muscle disease which progressively reduces the strength of the muscles that control movement. In this study, we tried to investigate genetic variants in muscular dystrophy using sequencing of whole exons. Case Presentation: A family with two affected patients with muscular dystrophy was referred for genetic counseling followed by exome sequencing testing on the proband. After filling out informed consent, blood samples were obtained from each available family member. Candidate genetic variant was confirmed using Sanger sequencing. Conclusions: Exome data analysis revealed a variant of c.2864 + 1G > A in the proband, which altered the exon-intron 26 splice site within the DYSF gene. Genetic changes in this gene are known to be associated with muscular disorders, such as limb-girdle muscular dystrophy and other dysferlinopathies. Assessment of this genetic variant in the patient's sister also showed homozygous variant. Since the patient's sister was married to her cousin, the same variant was tested in her husband, which was normal homozygous. NGS-based techniques, including whole-exome sequencing, can identify the molecular genetic basis of the disease in families with limb-girdle muscular dystrophy. The results can be helpful in identifying potential carriers in the family and in prenatal diagnosis to the families involved.

A Review on Neurotoxins from Clostridium botulinum against Neuro-muscular Disorders

Neuro-muscular disorders cause a series of serious complications in the human body, where some lead to considerable morbidity and mortality ocassionally. Neurological diseases result in dystrophy, inhibited growth, etc. This present review aimed to emphasize the employment of neurotoxins against neuro degenerative disorders. The source of neurotoxins includes botulinum (Clostridium botulinum), snakes like Vespa orientalis and some medically important arthropods like hornets and spiders. The review not only describes the potential of the neurotoxins in the treatment but also elucidates the mechanism of action of lethal toxins like botulinum. Safety and dosage regimens of various toxins with the help of proven study data would aid in endorsing researchers for further research on toxins making them more superior targeted drugs.

How Inflammation Pathways Contribute to Cell Death in Neuro-Muscular Disorders

Neuro-muscular disorders include a variety of diseases induced by genetic mutations resulting in muscle weakness and waste, swallowing and breathing difficulties. However, muscle alterations and nerve depletions involve specific molecular and cellular mechanisms which lead to the loss of motor-nerve or skeletal-muscle function, often due to an excessive cell death. Morphological and molecular studies demonstrated that a high number of these disorders seem characterized by an upregulated apoptosis which significantly contributes to the pathology. Cell death involvement is the consequence of some cellular processes that occur during diseases, including mitochondrial dysfunction, protein aggregation, free radical generation, excitotoxicity and inflammation. The latter represents an important mediator of disease progression, which, in the central nervous system, is known as neuroinflammation, characterized by reactive microglia and astroglia, as well the infiltration of peripheral monocytes and lymphocytes. Some of the mechanisms underlying inflammation have been linked to reactive oxygen species accumulation, which trigger mitochondrial genomic and respiratory chain instability, autophagy impairment and finally neuron or muscle cell death. This review discusses the main inflammatory pathways contributing to cell death in neuro-muscular disorders by highlighting the main mechanisms, the knowledge of which appears essential in developing therapeutic strategies to prevent the consequent neuron loss and muscle wasting.

Role of Immunoglobulins in Muscular Dystrophies and Inflammatory Myopathies

Muscular dystrophies and inflammatory myopathies are heterogeneous muscular disorders characterized by progressive muscle weakness and mass loss. Despite the high variability of etiology, inflammation and involvement of both innate and adaptive immune response are shared features. The best understood immune mechanisms involved in these pathologies include complement cascade activation, auto-antibodies directed against muscular proteins or de-novo expressed antigens in myofibers, MHC-I overexpression in myofibers, and lymphocytes-mediated cytotoxicity. Intravenous immunoglobulins (IVIGs) administration could represent a suitable immunomodulator with this respect. Here we focus on mechanisms of action of immunoglobulins in muscular dystrophies and inflammatory myopathies highlighting results of IVIGs from pre-clinical and case reports evidences.

Brain Computer Interface for Emergency Virtual Voice

Brain computer interface (BCI) is one of the thriving emergent technology which acts as an interface between a brain and an external device. BCI for speech communication is acquiring recognition in various fields. Speech is one of the most natural ways to express thoughts and feelings by articulate vocal sounds. The purpose of this study is to restore communication ability of the people suffering from severe muscular disorders like amyotrophic lateral sclerosis (ALS), stroke which causes paralysis, locked-in syndrome, tetraplegia and Myasthenia gravis. They cannot interact with their environment even though their intellectual capabilities are intact. Our work attempts to provide summary of the research articles being published in reputed journals which lead to the investigation of published BCI articles, BCI prototypes, Bio-Signals for BCI, intent of the articles, target applications, classification techniques, algorithms and methodologies, BCI system types. Thus, the result of detailed survey presents an outline of available studies, recent results and looks forward to future developments which provides a communication pathway for paralyzed patients to convey their needs.