Intronic small nucleolar RNAs regulate host gene splicing through base pairing with their adjacent intronic sequences

Background Small nucleolar RNAs (snoRNAs) are abundant noncoding RNAs best known for their involvement in ribosomal RNA maturation. In mammals, most expressed snoRNAs are embedded in introns of longer genes and produced through transcription and splicing of their host. Intronic snoRNAs were long viewed as inert passengers with little effect on host expression. However, a recent study reported a snoRNA influencing the splicing and ultimate output of its host gene. Overall, the general contribution of intronic snoRNAs to host expression remains unclear. Results Computational analysis of large-scale human RNA-RNA interaction datasets indicates that 30% of detected snoRNAs interact with their host transcripts. Many snoRNA-host duplexes are located near alternatively spliced exons and display high sequence conservation suggesting a possible role in splicing regulation. The study of the model SNORD2-EIF4A2 duplex indicates that the snoRNA interaction with the host intronic sequence conceals the branch point leading to decreased inclusion of the adjacent alternative exon. Extended SNORD2 sequence containing the interacting intronic region accumulates in sequencing datasets in a cell-type-specific manner. Antisense oligonucleotides and mutations that disrupt the formation of the snoRNA-intron structure promote the splicing of the alternative exon, shifting the EIF4A2 transcript ratio away from nonsense-mediated decay. Conclusions Many snoRNAs form RNA duplexes near alternative exons of their host transcripts, placing them in optimal positions to control host output as shown for the SNORD2-EIF4A2 model system. Overall, our study supports a more widespread role for intronic snoRNAs in the regulation of their host transcript maturation

Recessive mutations in the kinase ZAK cause a congenital myopathy with fibre type disproportion

Congenital myopathies define a heterogeneous group of neuromuscular diseases with neonatal or childhood hypotonia and muscle weakness. The genetic cause is still unknown in many patients, precluding genetic counselling and better understanding of the physiopathology. To identify novel genetic causes of congenital myopathies, exome sequencing was performed in three consanguineous families. We identified two homozygous frameshift mutations and a homozygous nonsense mutation in the mitogen-activated protein triple kinase ZAK. In total, six affected patients carry these mutations. Reverse transcription polymerase chain reaction and transcriptome analyses suggested nonsense mRNA decay as a main impact of mutations. The patients demonstrated a generalized slowly progressive muscle weakness accompanied by decreased vital capacities. A combination of proximal contractures with distal joint hyperlaxity is a distinct feature in one family. The low endurance and compound muscle action potential amplitude were strongly ameliorated on treatment with anticholinesterase inhibitor in another patient. Common histopathological features encompassed fibre size variation, predominance of type 1 fibre and centralized nuclei. A peculiar subsarcolemmal accumulation of mitochondria pointing towards the centre of the fibre was a novel histological hallmark in one family. These findings will improve the molecular diagnosis of congenital myopathies and implicate the mitogen-activated protein kinase (MAPK) signalling as a novel pathway altered in these rare myopathies

Suivi par IRM de l'évolution des propriétés mécaniques des tissus lors des ablations thermiques par ultrasons focalisés

High Intensity Focused Ultrasound (HIFU) thermal ablation is an innovative and promising therapy relying on the unique ability of HIFU to deliver localized treatment in a non-invasive and non-ionizing manner. In order to be safe and effective, HIFU therapy requires precise monitoring of the tissue destruction. One of the most accurate monitoring methods is Magnetic Resonance (MR) thermometry, which provides real-time mapping of tissue temperature variation. However, the limitations of MR thermometry, including its relative nature, its sensitivity to multiple sources of error, and the fact that temperature is an instantaneous indicator of ablation, call for the development of complementary biomarkers. Thermal ablations are also associated with variations in the mechanical properties of the tissues, and can therefore be considered as biomarkers of permanent thermal damage. In this thesis work, we developed a method based on the acoustic radiation force and the encoding of the shear wave propagating from the ultrasound focus in the MR phase images. This approach provides the estimation of the mean elasticity along radii of the focal spot, taking into account the viscosity estimated at the focus, without compromising the monitoring with temperature maps during the HIFU treatment. This method was characterized on calibrated phantoms and was subsequently used to monitor HIFU ablations in vitro and in vivo. The evolution of the local elasticity was monitored in anisotropic tissue, while the viscosity of tissue was found to also vary as a consequence of HIFU ablation.Les ablations thermiques par ultrasons focalisés de haute intensité (HIFU en anglais, pour High Intensity Focused Ultrasound) représentent des techniques thérapeutiques innovantes et prometteuses du fait de leur capacité unique à délivrer un traitement localisé de manière non invasive et non ionisante. Afin d’évaluer l’efficacité du traitement en temps réel tout en garantissant la sécurité de la procédure, la thérapie HIFU nécessite un monitoring précis de la destruction tissulaire. L’une des méthodes les plus précises pour assurer ce suivi est la thermométrie IRM, permettant d’obtenir une cartographie en temps réel de la variation de température des tissus. Cependant, les limitations de la thermométrie IRM, notamment son caractère relatif, sa sensibilité à de multiples sources d’erreur ainsi que le fait que la température soit un indicateur instantané de l’ablation, appellent au développement de biomarqueurs complémentaires. Les ablations thermiques étant également associées aux variations des propriétés mécaniques des tissus, celles-ci peuvent à ce titre être considérées comme de tels biomarqueurs, témoignant des dommages thermiques permanents subis au cours de la procédure. Lors de ce travail de thèse, nous avons développé une méthode s’appuyant sur la force de radiation ultrasonore et l’encodage par IRM de l’onde de cisaillement se propageant à partir du foyer ultrasonore. Cette approche permet l’estimation de l’élasticité moyenne le long de rayons dans la tache ARFI, en prenant en compte la viscosité estimée au point focal, sans compromettre l’obtention des cartes de température pendant le traitement HIFU. Cette méthode a été caractérisée sur des fantômes calibrés et a été par la suite utilisée pour le suivi d’ablations in vitro et in vivo. Elle a permis de suivre l’évolution de l’élasticité locale dans des tissus anisotropes, et pose la question du suivi de l’évolution de la viscosité des tissus pendant les ablations HIFU

MRI monitoring of mechanical properties of tissues during ablation therapies with focused ultrasound

Les ablations thermiques par ultrasons focalisés de haute intensité (HIFU en anglais, pour High Intensity Focused Ultrasound) représentent des techniques thérapeutiques innovantes et prometteuses du fait de leur capacité unique à délivrer un traitement localisé de manière non invasive et non ionisante. Afin d’évaluer l’efficacité du traitement en temps réel tout en garantissant la sécurité de la procédure, la thérapie HIFU nécessite un monitoring précis de la destruction tissulaire. L’une des méthodes les plus précises pour assurer ce suivi est la thermométrie IRM, permettant d’obtenir une cartographie en temps réel de la variation de température des tissus. Cependant, les limitations de la thermométrie IRM, notamment son caractère relatif, sa sensibilité à de multiples sources d’erreur ainsi que le fait que la température soit un indicateur instantané de l’ablation, appellent au développement de biomarqueurs complémentaires. Les ablations thermiques étant également associées aux variations des propriétés mécaniques des tissus, celles-ci peuvent à ce titre être considérées comme de tels biomarqueurs, témoignant des dommages thermiques permanents subis au cours de la procédure. Lors de ce travail de thèse, nous avons développé une méthode s’appuyant sur la force de radiation ultrasonore et l’encodage par IRM de l’onde de cisaillement se propageant à partir du foyer ultrasonore. Cette approche permet l’estimation de l’élasticité moyenne le long de rayons dans la tache ARFI, en prenant en compte la viscosité estimée au point focal, sans compromettre l’obtention des cartes de température pendant le traitement HIFU. Cette méthode a été caractérisée sur des fantômes calibrés et a été par la suite utilisée pour le suivi d’ablations in vitro et in vivo. Elle a permis de suivre l’évolution de l’élasticité locale dans des tissus anisotropes, et pose la question du suivi de l’évolution de la viscosité des tissus pendant les ablations HIFU.High Intensity Focused Ultrasound (HIFU) thermal ablation is an innovative and promising therapy relying on the unique ability of HIFU to deliver localized treatment in a non-invasive and non-ionizing manner. In order to be safe and effective, HIFU therapy requires precise monitoring of the tissue destruction. One of the most accurate monitoring methods is Magnetic Resonance (MR) thermometry, which provides real-time mapping of tissue temperature variation. However, the limitations of MR thermometry, including its relative nature, its sensitivity to multiple sources of error, and the fact that temperature is an instantaneous indicator of ablation, call for the development of complementary biomarkers. Thermal ablations are also associated with variations in the mechanical properties of the tissues, and can therefore be considered as biomarkers of permanent thermal damage. In this thesis work, we developed a method based on the acoustic radiation force and the encoding of the shear wave propagating from the ultrasound focus in the MR phase images. This approach provides the estimation of the mean elasticity along radii of the focal spot, taking into account the viscosity estimated at the focus, without compromising the monitoring with temperature maps during the HIFU treatment. This method was characterized on calibrated phantoms and was subsequently used to monitor HIFU ablations in vitro and in vivo. The evolution of the local elasticity was monitored in anisotropic tissue, while the viscosity of tissue was found to also vary as a consequence of HIFU ablation