Two novel mutations in TTN of a patient with congenital myopathy: A case report

Next Generation Sequencing and Electromyography Reveal the Involvement of the P2RX6 Gene in Myopathy

Ion channelopathies result from impaired ion channel protein function, due to mutations affecting ion transport across cell membranes. Over 40 diseases, including neuropathy, pain, migraine, epilepsy, and ataxia, are associated with ion channelopathies, impacting electrically excitable tissues and significantly affecting skeletal muscle. Gene mutations affecting transmembrane ionic flow are strongly linked to skeletal muscle disorders, particularly myopathies, disrupting muscle excitability and contraction. Electromyography (EMG) analysis performed on a patient who complained of weakness and fatigue revealed the presence of primary muscular damage, suggesting an early-stage myopathy. Whole exome sequencing (WES) did not detect potentially causative variants in known myopathy-associated genes but revealed a novel homozygous deletion of the P2RX6 gene likely disrupting protein function. The P2RX6 gene, predominantly expressed in skeletal muscle, is an ATP-gated ion channel receptor belonging to the purinergic receptors (P2RX) family. In addition, STRING pathways suggested a correlation with more proteins having a plausible role in myopathy. No previous studies have reported the implication of this gene in myopathy. Further studies are needed on patients with a defective ion channel pathway, and the use of in vitro functional assays in suppressing P2RX6 gene expression will be required to validate its functional role.

Two decades of advances in muscle imaging in children: from pattern recognition of muscle diseases to quantification and machine learning approaches

Muscle imaging has progressively gained popularity in the neuromuscular field. Together with detailed clinical examination and muscle biopsy, it has become one of the main tools for deep phenotyping and orientation of etiological diagnosis. Even in the current era of powerful new generation sequencing, muscle MRI has arisen as a tool for prioritization of certain genetic entities, supporting the pathogenicity of variants of unknown significance and facilitating diagnosis in cases with an initially inconclusive genetic study. Although the utility of muscle imaging is increasingly clear, it has not reached its full potential in clinical practice. Pattern recognition is known for a number of diseases and will certainly be enhanced by the use of machine learning approaches. For instance, MRI heatmap representations might be confronted with molecular results by obtaining a probabilistic diagnosis based in each disease "MRI fingerprints". Muscle ultrasound as a screening tool and quantified techniques such as Dixon MRI seem still underdeveloped. In this paper, we aim to appraise the advances in recent years in pediatric muscle imaging and try to define areas of uncertainty and potential advances that might become standardized to be widely used in the future.

Centronuclear myopathy due to a de novo nonsense variant and a maternally inherited splice-site variant in TTN: A case report

Next-generation sequencing has resulted in an explosion of rare de novo TTN variants. The clinical interpretation of these de novo variants in patients with recessive titinopathy is very difficult. Here, we provided a useful way to identify compound heterozygous mutations with a de novo one.

The constantly evolving spectrum of phenotypes in titinopathies - will it ever stop?

PURPOSE OF REVIEW

The last few years have confirmed previous assumptions of an enormous impact of the titin gene (TTN) on the occurrence of muscle disease, cardiomyopathy, or both together. The reason for this rather late understanding of its importance is because of the huge size which prevented sequencing of the whole gene by the previous Sanger technique in the individual cases. An update of the advances in diagnosing titinopathies is the main focus of this review.

RECENT FINDINGS

High throughput methods are now widely available for TTN sequencing and a corresponding explosion of different types of identified titinopathies is observed and published in the literature, although final confirmation is lacking in many cases with recessive missense variants.

SUMMARY

The implications of these findings for clinical practice are easy to understand: patients with previously undiagnosed muscle disease can now have a correct diagnosis and subsequently receive a likely prognosis, can have accurate genetic counseling for the whole family and early treatment for predictable complications from the heart and respiratory muscles. In addition not to forget, they can avoid wrong diagnoses leading to wrong treatments.

Identifying multi-hit carcinogenic gene combinations: Scaling up a weighted set cover algorithm using compressed binary matrix representation on a GPU

Despite decades of research, effective treatments for most cancers remain elusive. One reason is that different instances of cancer result from different combinations of multiple genetic mutations (hits). Therefore, treatments that may be effective in some cases are not effective in others. We previously developed an algorithm for identifying combinations of carcinogenic genes with mutations (multi-hit combinations), which could suggest a likely cause for individual instances of cancer. Most cancers are estimated to require three or more hits. However, the computational complexity of the algorithm scales exponentially with the number of hits, making it impractical for identifying combinations of more than two hits. To identify combinations of greater than two hits, we used a compressed binary matrix representation, and optimized the algorithm for parallel execution on an NVIDIA V100 graphics processing unit (GPU). With these enhancements, the optimized GPU implementation was on average an estimated 12,144 times faster than the original integer matrix based CPU implementation, for the 3-hit algorithm, allowing us to identify 3-hit combinations. The 3-hit combinations identified using a training set were able to differentiate between tumor and normal samples in a separate test set with 90% overall sensitivity and 93% overall specificity. We illustrate how the distribution of mutations in tumor and normal samples in the multi-hit gene combinations can suggest potential driver mutations for further investigation. With experimental validation, these combinations may provide insight into the etiology of cancer and a rational basis for targeted combination therapy.

Two novel mutations in TTN of a patient with congenital myopathy: A case report

Background

Early‐onset myopathies show a wide spectrum of phenotypes and are composed of various types of inherited neuromuscular diseases, making it difficult to diagnose. TTN mutation‐related myopathy is a known cause of early‐onset myopathy. Since a next‐generation sequencing (NGS) has enabled sequencing of the vast amount of DNA, TTN, which is the longest coding sequence of any human gene, mutations can now be revealed. We report a 10‐year‐old female with severe congenital muscular weakness and delayed motor development since birth.

Methods

Next‐generation sequencing as well as electromyography and muscle biopsy were performed.

Results

To date, she is incapable of walking alone. Her younger sister had similar but more severe symptoms with respiratory failure. In electromyography, short‐duration, small‐amplitude motor unit action potential, and early recruitment patterns were observed in the involved proximal muscles, suggesting myopathy. Muscle histopathology showed a specific atrophy of increased fiber size variability, frequent nuclear internalization, as well as degeneration and regeneration of fibers with type I fiber predominance, consistent with the findings of a previous report about congenital titinopathy. A NGS study revealed two different possible pathogenic variants in TTN: (a) canonical splicing mutation in the intron 105 (c. 29963‐1G>C) and (b) frameshift and truncating mutation in the exon 339 (c.92812dup/p.Arg30938LysfsTer15). All variants were confirmed by conventional Sanger sequencing.

Conclusion

We propose that unbiased genomic sequencing can be helpful in screening patients with early‐onset myopathy.