Gene expression profiling identifies molecular pathways associated with collagen VI deficiency and provides novel therapeutic targets

Ullrich congenital muscular dystrophy (UCMD), caused by collagen VI deficiency, is a common congenital muscular dystrophy. At present, the role of collagen VI in muscle and the mechanism of disease are not fully understood. To address this we have applied microarrays to analyse the transcriptome of UCMD muscle and compare it to healthy muscle and other muscular dystrophies. We identified 389 genes which are differentially regulated in UCMD relative to controls. In addition, there were 718 genes differentially expressed between UCMD and dystrophin deficient muscle. In contrast, only 29 genes were altered relative to other congenital muscular dystrophies. Changes in gene expression were confirmed by real-time PCR. The set of regulated genes was analysed by Gene Ontology, KEGG pathways and Ingenuity Pathway analysis to reveal the molecular functions and gene networks associated with collagen VI defects. The most significantly regulated pathways were those involved in muscle regeneration, extracellular matrix remodelling and inflammation. We characterised the immune response in UCMD biopsies as being mainly mediated via M2 macrophages and the complement pathway indicating that anti-inflammatory treatment may be beneficial to UCMD as for other dystrophies. We studied the immunolocalisation of ECM components and found that biglycan, a collagen VI interacting proteoglycan, was reduced in the basal lamina of UCMD patients. We propose that biglycan reduction is secondary to collagen VI loss and that it may be contributing towards UCMD pathophysiology. Consequently, strategies aimed at over-expressing biglycan and restore the link between the muscle cell surface and the extracellular matrix should be considered

Transcriptomic profiling of TK2 deficient human skeletal muscle suggests a role for the p53 signalling pathway and identifies growth and differentiation factor-15 as a potential novel biomarker for mitochondrial myopathies

BACKGROUND: Mutations in the gene encoding thymidine kinase 2 (TK2) result in the myopathic form of mitochondrial DNA depletion syndrome which is a mitochondrial encephalomyopathy presenting in children. In order to unveil some of the mechanisms involved in this pathology and to identify potential biomarkers and therapeutic targets we have investigated the gene expression profile of human skeletal muscle deficient for TK2 using cDNA microarrays. RESULTS: We have analysed the whole transcriptome of skeletal muscle from patients with TK2 mutations and compared it to normal muscle and to muscle from patients with other mitochondrial myopathies. We have identified a set of over 700 genes which are differentially expressed in TK2 deficient muscle. Bioinformatics analysis reveals important changes in muscle metabolism, in particular, in glucose and glycogen utilisation, and activation of the starvation response which affects aminoacid and lipid metabolism. We have identified those transcriptional regulators which are likely to be responsible for the observed changes in gene expression. CONCLUSION: Our data point towards the tumor suppressor p53 as the regulator at the centre of a network of genes which are responsible for a coordinated response to TK2 mutations which involves inflammation, activation of muscle cell death by apoptosis and induction of growth and differentiation factor 15 (GDF-15) in muscle and serum. We propose that GDF-15 may represent a potential novel biomarker for mitochondrial dysfunction although further studies are required

Determinacions del perfil genètic del càncer pediàtric

Oncologia; Perfil genètic; Càncer pediàtric; PrecisióOncología; Perfil genético; Cáncer pediátrico; PrecisiónOncology; Genetic profile; Pediatric cancer; AccuracyL'àmbit d'aquest grup de treball és la implementació de panels NGS per a diagnòstic / pronòstic / tractament de càncer en pacients menors de 18 anys (oncologia i hematologia). Els casos de predisposició genètica en pacients pediàtrics es tractaran en el grup de predisposició genètica. El càncer infantil comprèn més de 40 entitats entre leucèmies, limfomes, tumors cerebrals i sòlids extracranials; per la qual cosa no és possible tècnicament o operativament fer panels específics per a cada un d'aquests càncers. Serà necessari utilitzar panels comercials o acadèmics dissenyats específicament per a càncer infantil

Immune response generated with the administration of autologous dendritic cells pulsed with an allogenic tumoral cell lines lysate in patients with newly diagnosed DIPG

Background and objective. Diffuse intrinsic pontine glioma (DIPG) is a lethal brainstem tumor in children. Dendritic cells (DCs) have T-cell stimulatory capacity and, therefore, potential antitumor activity for disease control. DCs vaccines have been shown to reactivate tumor-specific T cells in both clinical and pre-clinical settings. We designed a phase Ib immunotherapy (IT) clinical trial with the use of autologous dendritic cells (ADCs) pulsed with an allogeneic tumors cell-lines lysate (ATCL) in patients with newly diagnosed DIPG after irradiation (RT). Methods. Nine patients with newly diagnosed DIPG met enrollment criteria. Autologous dendritic cell vaccines (ADCV) were prepared from monocytes obtained by leukapheresis. Five ADCV doses were administered intradermally during induction phase. In the absence of tumor progression, patients received 3 boosts of tumor lysate every three months during the maintenance phase. Results. Vaccine fabrication was feasible in all patients included in the study. Non-specific KLH (9/9 patients) and specific (8/9 patients) antitumor response was identified by immunologic studies in peripheral blood mononuclear cells (PBMC). Immunological responses were also confirmed in the T lymphocytes isolated from the cerebrospinal fluid (CSF) of 2 patients. Vaccine administration resulted safe in all patients treated with this schema. Conclusions. These preliminary results demonstrate that ADCV preparation is feasible, safe and generate a DIPG-specific immune response detected in PBMC and CSF. This strategy shows a promising backbone for future schemas of combination immunotherapy

Mecanismes moleculars implicats en la secreció de pèptids en cèl•lules glials del sistema nerviós central

[cat] En els últims anys, diversos treballs han demostrat que els astròcits participen activament en el desenvolupament i la plasticitat del sistema nerviós central, així com en la modulació de la neurotransmissió. Característicament, la majoria de les accions descrites dels astròcits sobre la fisiologia i la patologia neuronal són mitjançades per secreció vesicular. En el aquest treball s’han identificat les molècules implicades en l’exocitosi de cèl•lules astroglials. Malgrat que alguns components són comuns amb les neurones, altres com sintaxina 4, VAMP3 i SNAP23 s’expressen de forma específica en les cèl•lules astroglials. Tractaments activadors o de maduració diferencialment regulen l’expressió de diferents isoformes de proteïnes exocítiques en cèl•lules glials in vitro. Així, l’activació amb citocines proinflamatòries augmenta l’expressió d’algunes SNAREs i els seus reguladors en glia, com sintaxina4 i munc18b. La correlació entre els nivells d’expressió d’aquestes proteïnes exocítiques i l’augment de la secreció de mediadors d’activació i inflamació suggereix un important paper d’aquestes molècules en la secreció de cèl•lules activades. Amb l’objectiu d’estudiar la secreció regulada per calci en astròcits madurs s’ha obtingut un fenotip madur glial in vitro mitjançant l’activació de la via del AMPc. L’anàlisi global amb "gene set enrichment analysis" del transcriptoma astrocitari ha demostrat que l’increment en els nivells intracel•lulars d’AMPc reprimeix la immaduresa i activació dels astròcits i promou la seva maduració. Aquesta maduració dependent de la via del AMPc augmenta l’expressió de proteïnes exocítiques, com per exemple VAMP2, així com la via de secreció regulada per calci dels pèptids ANP i SgII. Finalment, mitjançant assajos de pèrdua de funció, es demostra un paper d’aquestes proteïnes en la secreció de pèptids glials. Aquests resultats suggereixen que diferents molècules d’exocitosi mitjancen diferents processos de secreció glials. Per altra banda, en aquesta tesi s’ha identificat un nou component de la via de secreció astroglial, tant in vitro com in vivo, la SgIII. En cèl•lules neuroendocrines SgIII actua com un receptor de direccionament a grànuls secretors. En cèl•lules astroglials SgIII presenta una forma molecular i una dinàmica de secreció diferencial a cèl•lules neuroendocrines. A més, hem demostrat una notable sobreexpressió d’aquesta proteïna en astròcits reactius en lesions traumàtiques, la qual cosa suggereix una participació de SgIII en els mecanismes de protecció o dany cerebral en lesions del sistema nerviós central.[eng] In recent years, several studies have demonstrated that astrocytes influences neuronal development, function and plasticity through vesicular transmitter release. However, secretory pathways and the involved molecular mechanisms in astroglial cells are poorly known. In this study, we showed that a variety of SNARE and Munc18 isoforms were expressed by cultured astrocytes, with syntaxin-4, Munc18c, SNAP-23 and VAMP-3 being the most abundant variants. Exocytotic protein expression was differentially regulated by activating and differentiating agents. Specifically, proteins controlling Ca2+-dependent secretion in neuroendocrine cells were up-regulated after long-term 8Br-cAMP administration in astrocytes, but not by proinflammatory cytokines. We also analyzed the global transcriptome of cultured astroglial cells incubated with activators of cAMP pathways. cAMP analogs strongly upregulated genes involved in typical functions of mature astrocytes, whereas they downregulated a considerable number of proliferating and immaturity-related transcripts. Gene Set Enrichment Analysis and evaluation in situ of gene expression in astrocytes in different states showed that cAMP signaling conferred a mature and in vivo–like transcriptional profile to cultured astrocytes. Moreover, 8Br-cAMP treatment greatly increased the cellular content of exocytotic proteins such as VAMP-2 and stimulated Ca2+-dependent secretion of secretogranin-2 and ANP. Regulation of both exocytotic protein expression and Ca2+-dependent peptide secretion in astrocytes by differentiating and activating agents suggested that glial secretory pathways were adjusted in different physiological states. In this thesis, we showed the expression, transcriptional regulation, trafficking and release of the secretory pathway component SgIII in astroglial cells. In endocrine cells, SgIII is a key sorting receptor for peptide hormones while astrocytes produced and released a non-processed form. Moreover, SgIII expression was specifically upregulated in reactive astrocytes after perforating brain injury. These results showed that SgIII is a reliable component of the astrocyte secretory pathway and suggest important roles for glial SgIII in the glia–neuron communication

Cyclic AMP signaling restricts activation and promotes maturation and antioxidant defenses in astrocytes

Abstract Background: cAMP signaling produces dramatic changes in astrocyte morphology and physiology. However, its involvement in phenotype acquisition and the transcriptionally mediated mechanisms of action are largely unknown. Results: Here we analyzed the global transcriptome of cultured astroglial cells incubated with activators of cAMP pathways. A bulk of astroglial transcripts, 6221 annotated genes, were differentially regulated by cAMP signaling. cAMP analogs strongly upregulated genes involved in typical functions of mature astrocytes, such as homeostatic control, metabolic and structural support to neurons, antioxidant defense and communication, whereas they downregulated a considerable number of proliferating and immaturity-related transcripts. Moreover, numerous genes typically activated in reactive cells, such as scar components and immunological mediators, were repressed by cAMP. GSEA analysis contrasting gene expression profiles with transcriptome signatures of acutely isolated astrocytes and in situ evaluation of protein levels in these cells showed that cAMP signaling conferred mature and in vivo-like transcriptional features to cultured astrocytes. Conclusions: These results indicate that cAMP signaling is a key pathway promoting astrocyte maturation and restricting their developmental and activation features. Therefore, a positive modulation of cAMP signaling may promote the normal state of differentiated astrocytes and favor the protection and function of neuronal networks. Keywords: Antioxidant defense, Astrocytes, cAMP, Differentiation, Reactive glia, Transcriptomic, Brain, NR2

Gene expression profiling identifies molecular pathways associated with collagen VI deficiency and provides novel therapeutic targets

Ullrich congenital muscular dystrophy (UCMD), caused by collagen VI deficiency, is a common congenital muscular dystrophy. At present, the role of collagen VI in muscle and the mechanism of disease are not fully understood. To address this we have applied microarrays to analyse the transcriptome of UCMD muscle and compare it to healthy muscle and other muscular dystrophies. We identified 389 genes which are differentially regulated in UCMD relative to controls. In addition, there were 718 genes differentially expressed between UCMD and dystrophin deficient muscle. In contrast, only 29 genes were altered relative to other congenital muscular dystrophies. Changes in gene expression were confirmed by real-time PCR. The set of regulated genes was analysed by Gene Ontology, KEGG pathways and Ingenuity Pathway analysis to reveal the molecular functions and gene networks associated with collagen VI defects. The most significantly regulated pathways were those involved in muscle regeneration, extracellular matrix remodelling and inflammation. We characterised the immune response in UCMD biopsies as being mainly mediated via M2 macrophages and the complement pathway indicating that anti-inflammatory treatment may be beneficial to UCMD as for other dystrophies. We studied the immunolocalisation of ECM components and found that biglycan, a collagen VI interacting proteoglycan, was reduced in the basal lamina of UCMD patients. We propose that biglycan reduction is secondary to collagen VI loss and that it may be contributing towards UCMD pathophysiology. Consequently, strategies aimed at over-expressing biglycan and restore the link between the muscle cell surface and the extracellular matrix should be considered

Transcriptomic profiling of TK2 deficient human skeletal muscle suggests a role for the p53 signalling pathway and identifies growth and differentiation factor-15 as a potential novel biomarker for mitochondrial myopathies

BACKGROUND: Mutations in the gene encoding thymidine kinase 2 (TK2) result in the myopathic form of mitochondrial DNA depletion syndrome which is a mitochondrial encephalomyopathy presenting in children. In order to unveil some of the mechanisms involved in this pathology and to identify potential biomarkers and therapeutic targets we have investigated the gene expression profile of human skeletal muscle deficient for TK2 using cDNA microarrays. RESULTS: We have analysed the whole transcriptome of skeletal muscle from patients with TK2 mutations and compared it to normal muscle and to muscle from patients with other mitochondrial myopathies. We have identified a set of over 700 genes which are differentially expressed in TK2 deficient muscle. Bioinformatics analysis reveals important changes in muscle metabolism, in particular, in glucose and glycogen utilisation, and activation of the starvation response which affects aminoacid and lipid metabolism. We have identified those transcriptional regulators which are likely to be responsible for the observed changes in gene expression. CONCLUSION: Our data point towards the tumor suppressor p53 as the regulator at the centre of a network of genes which are responsible for a coordinated response to TK2 mutations which involves inflammation, activation of muscle cell death by apoptosis and induction of growth and differentiation factor 15 (GDF-15) in muscle and serum. We propose that GDF-15 may represent a potential novel biomarker for mitochondrial dysfunction although further studies are required

Transcriptomic profiling of TK2 deficient human skeletal muscle suggests a role for the p53 signalling pathway and identifies growth and differentiation factor-15 as a potential novel biomarker for mitochondrial myopathies

BACKGROUND: Mutations in the gene encoding thymidine kinase 2 (TK2) result in the myopathic form of mitochondrial DNA depletion syndrome which is a mitochondrial encephalomyopathy presenting in children. In order to unveil some of the mechanisms involved in this pathology and to identify potential biomarkers and therapeutic targets we have investigated the gene expression profile of human skeletal muscle deficient for TK2 using cDNA microarrays. RESULTS: We have analysed the whole transcriptome of skeletal muscle from patients with TK2 mutations and compared it to normal muscle and to muscle from patients with other mitochondrial myopathies. We have identified a set of over 700 genes which are differentially expressed in TK2 deficient muscle. Bioinformatics analysis reveals important changes in muscle metabolism, in particular, in glucose and glycogen utilisation, and activation of the starvation response which affects aminoacid and lipid metabolism. We have identified those transcriptional regulators which are likely to be responsible for the observed changes in gene expression. CONCLUSION: Our data point towards the tumor suppressor p53 as the regulator at the centre of a network of genes which are responsible for a coordinated response to TK2 mutations which involves inflammation, activation of muscle cell death by apoptosis and induction of growth and differentiation factor 15 (GDF-15) in muscle and serum. We propose that GDF-15 may represent a potential novel biomarker for mitochondrial dysfunction although further studies are required