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Ibáñez Cabellos, José Santiago
García Giménez, José Luis (dir.); Pérez Machado, Gisselle (dir.); Tabarés Seisdedos, Rafael (dir.) Departament de Fisiologia |
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Aquest document és un/a tesi, creat/da en: 2018 | |
La pérdida de la función de la Disquerina (DKC1), NOP10 y TIN2, son responsables de diferentes patrones de herencia de Disqueratosis congénita (DC; ORPHA1775). Son componentes clave de la telomerasa (DKC1 y NOP10) y telosoma (TIN2), y juegan un papel importante en la homeostasis de los telómeros. Estos genes participan en varios procesos celulares fundamentales para la célula y contribuyen al fenotipo observado en la Disqueratosis Congénita, a través de mecanismos que no se comprenden por completo. La presencia de estrés oxidativo se postuló como resultado de la disfunción de la telomerasa. Sin embargo, el estado redox alterado resultante puede promover el desgaste de los telómeros al generar un círculo vicioso, que promueve la senescencia celular. Este hecho nos llevó a estudiar si la pérdida de DKC1, NOP10 y TINF2, puede promover el desequilibrio redox como un evento temprano cuando e...
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La pérdida de la función de la Disquerina (DKC1), NOP10 y TIN2, son responsables de diferentes patrones de herencia de Disqueratosis congénita (DC; ORPHA1775). Son componentes clave de la telomerasa (DKC1 y NOP10) y telosoma (TIN2), y juegan un papel importante en la homeostasis de los telómeros. Estos genes participan en varios procesos celulares fundamentales para la célula y contribuyen al fenotipo observado en la Disqueratosis Congénita, a través de mecanismos que no se comprenden por completo. La presencia de estrés oxidativo se postuló como resultado de la disfunción de la telomerasa. Sin embargo, el estado redox alterado resultante puede promover el desgaste de los telómeros al generar un círculo vicioso, que promueve la senescencia celular. Este hecho nos llevó a estudiar si la pérdida de DKC1, NOP10 y TINF2, puede promover el desequilibrio redox como un evento temprano cuando el acortamiento de los telómeros aún no ha tenido lugar. El análisis transcriptómico constituye una buena herramienta para analizar estos modelos celulares, con el fin de observar qué genes y rutas se ven afectados en los diferentes modelos de células silenciadas. Se generaron líneas celulares mediadas por interferencia de ARN (DKC1, NOP10 y TINF2), que se confirmaron mediante análisis de expresión génica y proteica. No se produjo acortamiento de los telómeros en ninguna línea celular silenciada. La depleción de las ribonucleoproteínas Disquerina y NOP10 H/ACA disminuyó la actividad de la telomerasa, a través de la regulación a la baja de TERC, y produjo alteraciones en la pseudouridilación y la biogénesis ribosomal. Una vez caracterizados los modelos, analizamos su transcriptoma mediante matrices de expresión génica. Observamos un total de 1951 genes alterados en siNOP10, un total de 217 genes alterados en siDKC1, y un total de 216 genes alterados en siTINF2. Después de la identificación de genes con expresión diferencial, se procedió a estudiar el número significativo de vías metabólicas KEGG para cada modelo, obteniendo 22 rutas para siNOP10, 9 vías para siTINF2 y 6 vías para siDKC1. Las vías obtenidas en cada modelo se compararon entre ellas para identificar rutas similares. Los resultados muestran que los modelos siDKC1 y siNOP10 tenían en común la vía de señalización de p53, que implica los genes comunes SESN3 y ZMAT3. Por otro lado, siNOP10 y siTINF2 tenían en común la vía de las uniones adherentes, con los genes YES1 y TGFBR1. Se observó un aumento en la relación GSSG/GSH, proteínas carboniladas y peroxirredoxina-6 oxidada, en los modelos de siDKC1 y siNOP10, indicativo de un estrés oxidativo. Además, se observó una sobreexpresión de MnSOD y TRX1 en las células de siNOP10. Del mismo modo, se detectaron altos niveles de PARsilación y mayor expresión génica de PARP1 en condiciones de estímulo, lo que sugiere una mayor susceptibilidad al daño en los modelos de siDKC1 y siNOP10. Por el contrario, las células TINF2 silenciadas no alteraron ningún marcador de estrés oxidativo evaluado. En conjunto, estos hallazgos conducen a la conclusión de que las funciones DKC1 y NOP10 inducen el estrés oxidativo en los primeros estadios y de forma totalmente independiente a un acortamiento de los telómeros.Telomeres are special structures located at the end of chromosomes in eukaryotic cells. The main function of telomeres involve regulation of the structure of chromosomes, control of cell division, and regulation of cellular life through cellular senescence. Length and structure of telomeres depend on action of multiprotein complexes that compose the telosome and telomerase complexes. Telosome is formed by telomere binding proteins, which bind to the terminal end of telomeric DNA. The structural unit consists of six protein subunit: POT1, TRF1, TRF2, TIN2, ACD, and RAP1, that provide structural support. The function of telosome is to protect and to maintain the structure of telomeres, in addition to regulating telomerase activity. Telomerase is an enzymatic complex formed by a set of ribonucleoproteins with polymerase activity. The proteins involved are TERT, with reverse transcriptase activity; TERC, ribonucleotide complex; Disquerin, NOP10, NHP2, GAR1, and TCAB1.
There are a group of genetic diseases caused by alterations in telomeric maintenance, known as telomeropathies, which share clinical manifestations and molecular mechanisms. The first described telomeropathy was Dyskeratosis Congenita (DC). It is a rare multisystemic disease that presents premature aging. DC is characterized by a triad of mucocutaneous signs, consisting of nail dystrophy, abnormal pigmentation and oral leukoplakia. DC shows three types of inheritance: X-linked DC, where the mutated gene is DKC1; Autosomal Dominant DC, where can be TERC, TERT, TINF2, and ACD; and Autosomal Recessive DC, can be NOP10, NHP2, TCAB1, CTC1, and PARN.
In addition, molecular events that alter telomere length, due to genes mutations in telomerase and telosome complex, may not be the only molecular mechanism responsible for the phenotype associated with DC. Currently, there is a debate about which is the primary cause of the physiopathology of the disease. Telomerase deficiency and alterations in ribosome biogenesis have been proposed as primary causes in the etiopathogenesis of DC; besides, oxidative stress and alterations in the antioxidant response have been considered a secondary event to telomere dysfunction. It has also been observed that extra-telomeric functions could contribute to the pathophysiology of DC. For example DKC1, NOP10, and NHP2 are genes that code for small proteins present in the telomerase complex and H/ACA boxes. The H/ACA boxes are involved in the maturation of nucleolar, ribosomal and transfer RNA, by a pseudouridylation process. Other, such as TIN2, can migrate from the nucleus to mitochondria and regulate mitochondrial oxidative phosphorylation. Also TERT can migrate from the nucleus to mitochondria in order to reduce oxidative stress.
On the other hand, it has been described that DNA damage is a common feature of telomeropathies. Cells derived from DC patients have shown an increase in chromosomal fragmentation, an alteration in their ability to repair DNA.
In this thesis, we have designed a cellular model of acute silencing of DKC1, NOP10 and TINF2 genes. This allows the identification of gene expression profiles and the mechanisms altered as a consequence of the affectation of these genes. Moreover, the characterization of these models will contribute to distinguish molecular events that are affected before the telomeric shortening takes place. Transcriptomic analysis constitutes a good tool to analyse these cellular models, in order to observe which genes and routes are affected in the different silenced cell models.
The silencing for each cell model was confirmed by mRNA and protein expression of DKC1, NOP10, and TINF2 genes using RT-qPCR and Western blot. A decrease of 90% in gene expression and a decrease of 40% in protein expression were observed in silenced cells respect to siCONTROL. Moreover, cell viability and cell cycle were not affected by this silencing. Gene expression of TERC decreased in the siDKC1 and siNOP10 models, although the telomeric length was not affected in the cellular models, but a significant decrease in telomerase activity was observed for both the siDKC1 and siNOP10 models. Furthermore, a decrease in pseudouridylation and in 18S ribosomal subunit expression were observed by RT-qPCR when DKC1 and NOP10 were silenced. Consequently, the depletion of DKC1 and NOP10 caused a decrease in telomerase activity via TERC, in addition to altering pseudouridylation and ribosomal biogenesis.
Once characterized the models, we analysed their transcriptome by means of gene expression arrays. We observed a total of 1951 genes altered in siNOP10, a total of 217 genes altered in siDKC1, and a total 216 altered genes in siTINF2. Following identification of genes with differential expression, we proceeded to study the number of significant KEGG metabolic pathways for each model, obtaining 22 pathways for siNOP10, 9 pathways for siTINF2 and 6 pathways for siDKC1. The pathways obtained in each model were compared among them, to identify similar pathways. The results show that siDKC1 and siNOP10 models had in common the signalling pathway of p53, involving the common genes SESN3 and ZMAT3. On the other hand, siNOP10 and siTINF2 had in common the pathway of adherent junctions, with the genes YES1 and TGFBR1.
The results obtained from the expression matrices were validated by RT-qPCR. Regarding ZMAT3 gene expression, a decrease was observed for siDKC1 and an increase for siNOP10, while in SESN3, a decrease was observed in siDKC1 and siNOP10. The expression of YES1 was increased in all the silenced models, while for TGFBR1 an increase was observed in siNOP10 and siTINF2. The genes YES1 and TGFBR1 are involved in cell cycle and apoptosis; thus, it is possible that after longer silencing times the cell cycle will be affected and cells would enter apoptosis. Next, we proceeded to observe if p53 was activated. Our results showed an increased gene expression of p53 and higher phosphorylation levels in siDKC1 and siNOP10 models.
For characterization of oxidative stress, different parameters were evaluated, such as the levels of carbonylated proteins, the GSSG/GSH ratio and the oxidation of Peroxiredoxin 6 (PRDX6-SO3H). An increase of all these parameters was observed in siDKC1 and siNOP10 models. In addition, these results are in agreement with SESN3 gene expression, where a decrease in SESN3 was observed for siDKC1 and siNOP10. Sestrins are necessary to reduce oxidized peroxiredoxins. In siTINF2, no changes were observed, although these results are in agreement with other studies of acute silencing.
Next, we studied the main antioxidant enzymes. The ones responsible for detoxifying cellular superoxide showed a decrease in SOD1 gene expression for siNOP10, and an increase in SOD2 gene expression for siDKC1 and siNOP10. The results in protein expression of these genes, CuZnSOD and MnSOD proteins respectively, showed a significant increase in MnSOD when NOP10 was silenced. The enzymes responsible for detoxifying hydrogen peroxide were also studied, finding an increase in CAT expression in siNOP10, and an increase in GPX1 expression in siDKC1. The results obtained for Catalase and Glutathione peroxidase protein levels did not show significant differences in any of the cellular models. Also the enzymes responsible for reduction of disulphide bridges, thioredoxins, were studied. The results showed an increase in TRX1 gene expression in siDKC1 and siNOP10 models, whereas a decrease in TRX2 gene expression was observed in siTINF2, and an increase in siNOP10. The results for protein levels showed an increase in TRX1 when NOP10 was silenced, and a decrease in TRX2 when TINF2 was silenced. These results suggest the generation of a response in order to attenuate oxidative stress.
After confirming the presence of oxidative stress, we studied DNA damage. The levels of γ-H2A.X were analyzed in all cellular models, under basal conditions and after stimulation with H2O2. The results did not show significant differences for any models, in any conditions. Probably, because the number of double-strand breaks in DNA can be still very low after 48h of silencing. On the other hand, the levels of PARsylation were evaluated, in basal conditions and after stimulation with etoposide. The results did not show differences in basal levels, but showed an increase with etoposide in siDKC1 and siNOP10. These findings indicate that cells were more susceptible to single chain damage in DNA, results that agree with other studies of DC patient cells, were more susceptibility to damage with etoposide was found.
Finally, the profile of the main enzymes repairing DNA damage was studied. We focused in the enzyme oGG1, responsible for the repair of bases; the enzyme XPA, responsible for repair through the nucleotide excision repair mechanism; the enzymes RAD53 and RAD51, involved in the homologous recombination; and the enzymes WRN and PARP1, involved in non-homologous end joining. The results obtained for gene expression analysis of each of these enzymes, in basal conditions or after stimulation with etoposide, showed an increase in RAD53 gene expression under basal conditions and after stimulus in siNOP10, and an increase in PARP1 gene expression after stimulus in siDKC1 and siNOP10. These results correlate with those obtained in PARsylation levels after stimulation with etoposide.
In conclusion, the silencing of DKC1 and NOP10, but not of TINF2, affects the H/ACA boxes. This impairment affects the pseudouridylation processes, necessary for the maturation of ribosomal, nuclear and transfer RNA. In addition, oxidative stress is an early event for DKC1 and NOP10 depletion, but might be a secondary consequence of telomere shortening, for TINF2. The susceptibility to DNA damage is increased after DKC1 and NOP10 silencing, mainly through PARP1-related molecular pathways. Finally, the onset of oxidative stress and the increased susceptibility to DNA damage observed after DKC1 and NOP10 silencing is promoted by p53 activation.
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