Nucleolus as an emerging hub in maintenance of genome stability and cancer pathogenesis

The nucleolus is the major site for synthesis of ribosomes, complex molecular machines that are responsible for protein synthesis. A wealth of research over the past 20 years has clearly indicated that both quantitative and qualitative alterations in ribosome biogenesis can drive the malignant phenotype via dysregulation of protein synthesis. However, numerous recent proteomic, genomic, and functional studies have implicated the nucleolus in the regulation of processes that are unrelated to ribosome biogenesis, including DNA-damage response, maintenance of genome stability and its spatial organization, epigenetic regulation, cell-cycle control, stress responses, senescence, global gene expression, as well as assembly or maturation of various ribonucleoprotein particles. In this review, the focus will be on features of rDNA genes, which make them highly vulnerable to DNA damage and intra- and interchromosomal recombination as well as built-in mechanisms that prevent and repair rDNA damage, and how dysregulation of this interplay affects genome-wide DNA stability, gene expression and the balance between euchromatin and heterochromatin. We will also present the most recent insights into how malfunction of these cellular processes may be a central driving force of human malignancies, and propose a promising new therapeutic approach for the treatment of cancer

THE ROLE OF p53 TUMOR SUPPRESSOR IN PROTEIN HOMEOSTASIS REGULATION IN CELLS HETEROZYGOUS FOR RIBOSOMAL PROTEIN GENE L24

Cilj istraživanja: Heterozigotne mutacije RP u sisavaca uzrokuju razvojne anomalije i zloćudne tumore. Inaktivacija supresora tumora p53 u tim uvjetima sprječava nastanak razvojnih anomalija i potiče razvoj zloćudnih tumora. Međutim, molekularni mehanizmi putem kojih smanjeni izražaj RP uzrokuje promjene u stanicama i uloga p53 u tom kontekstu nepoznati su. Ključna pretpostavka ovog istraživanja je da heterozigotna inaktivacija RPL24 uzrokuje poremećaj homeostaze proteina te da p53 umanjuje negativne učinke tih promjena putem regulacije proteostatskih mehanizama. Ciljevi istraživanja su: 1. Izolirati fibroblaste iz wt, RPL24+/-, p53-/-, RPL24+/-:p53-/- embrija miševa (MEF, od engl. mouse embryonic fibroblasts); 2. Odrediti posljedice heterozigotnosti za RPL24 u MEF-ovima; 3. Odrediti ulogu p53 u RPL24+/- MEF-ovima. Materijal i metode: Istraživanja su provedena na MEF-ovima izoliranima iz wt, RPL24+/-, p53-/- i RPL24+/-:p53-/- embrija. Za određivanje posljedica heterozigotnosti za RPL24 u MEF-ovima i uloge p53 u tim procesima korištene su metode za analizu diobe stanica, sinteze proteina, signalnog puta mTORC1, proteasoma, autofagije, reaktivnih kisikovih radikala (ROS), agregata proteina te morfologije i funkcije mitohondrija. Rezultati: U RPL24+/- MEF-ovima smanjena je sinteza proteina ovisna o signalnom putu mTORC1, a povećana je aktivnost proteasoma i mTORC1-ovisne autofagije. Ti mehanizmi umanjuju proteotoksični stres u RPL24+/- MEF-ovima, ali nisu dostatni za njegovo potpuno sprječavanje, što se očituje nakupljanjem agregata proteina i ROS-a. Inaktivacija p53 u RPL24+/- MEF-ovima sprječava inhibiciju Sesn2/mTORC1-ovisne sinteze proteina i inhibira mTORC1-ovisnu autofagiju, što rezultira dodatnim nakupljanjem agregata proteina. Povećana sinteza proteina, smanjena količina ROS-a i p21 uslijed inaktivacije p53 u RPL24+/- MEF-ovima omogućuju njihovu ubrzanu diobu. Inaktivacija p53 u RPL24+/- MEF-ovima remeti normalnu morfologiju i smještaj mitohondrija i uzrokuje energetski stres. Zaključak: Razjašnjenje mehanizama putem kojih RPL24+/- uzrokuje promjene u MEF- ovima te uloge p53 u njihovoj regulaciji važne su za razumijevanje patogeneze bolesti karakteriziranih smanjenim izražajem RP poput anemije Diamond i Blackfan i zloćudnih tumora te mogu doprinijeti identifikaciji ciljeva za njihovo liječenje.Aim of the study: Mutations of genes encoding RPs in mammals cause congenital malformations and malignant tumors. Inactivation of p53 tumor supressor under this conditions prevents congenital malformations and facilitates the development of malignant tumors. However, molecular mechanisms underlying these processes are unknown. I hypothesized that heterozygous inactivation of RPL24 leads to perturbation of cellular proteostasis and that p53 modulates the pathological phenotype by regulating proteostatic mechanisms. Specific aims of this research are: 1.To isolate fibroblasts from wt, RPL24+/- , p53-/-, RPL24+/-:p53-/- mouse embryos (MEFs), 2. To identify the consequences of RPL24 heterozygosity in MEFs, 3. To determine the role of p53 in RPL24+/- MEFs. Materials and methods: wt, RPL24+/-, p53-/-, RPL24+/-:p53-/- MEFs are used in this study. To determine the consequences of RPL24 heterozygosity on protein homeostatsis and the role of p53 in that processes, I used a number of methods to assess cell division, protein synthesis, reactive oxygen species (ROS), protein aggregates and mitochondria morfology and function as well as activity of mTORC1 signaling pathway, proteasomes and autophagy. Results: In RPL24+/- MEFs mTORC1-dependant protein synthesis is downregulated, whereas proteasomal and autophagosomal degradation are upregulated. However, activation of these proteostatic mechanisms are not sufficient to fully prevent formation of protein aggregates and ROS in these MEFs. Inactivation of p53 in RPL24+/- MEFs prevents Sesn2/mTORC1-dependant inhibition of protein synthesis and inhibits autophagy, which enhances the accumulation of protein aggregates. Despite the presence of protein aggregates, increased protein synthesis, reduced amount of ROS and p21 upon p53 inactivation in RPL24+/- MEFs enable accelaration of their proliferation. Finally, inactivation of p53 in RPL24+/- MEFs disrupts normal mitochondria morphology and cellular localization leading to the energetic stress. Conclusion: These results will enable better understanding of the molecular mechanisms by which perturbations in ribosome biogenesis lead to Diamond and Blackfan anemia and malignant tumors and they may reveal therapeutic liabilities in these diseases

THE ROLE OF p53 TUMOR SUPPRESSOR IN PROTEIN HOMEOSTASIS REGULATION IN CELLS HETEROZYGOUS FOR RIBOSOMAL PROTEIN GENE L24

Cilj istraživanja: Heterozigotne mutacije RP u sisavaca uzrokuju razvojne anomalije i zloćudne tumore. Inaktivacija supresora tumora p53 u tim uvjetima sprječava nastanak razvojnih anomalija i potiče razvoj zloćudnih tumora. Međutim, molekularni mehanizmi putem kojih smanjeni izražaj RP uzrokuje promjene u stanicama i uloga p53 u tom kontekstu nepoznati su. Ključna pretpostavka ovog istraživanja je da heterozigotna inaktivacija RPL24 uzrokuje poremećaj homeostaze proteina te da p53 umanjuje negativne učinke tih promjena putem regulacije proteostatskih mehanizama. Ciljevi istraživanja su: 1. Izolirati fibroblaste iz wt, RPL24+/-, p53-/-, RPL24+/-:p53-/- embrija miševa (MEF, od engl. mouse embryonic fibroblasts); 2. Odrediti posljedice heterozigotnosti za RPL24 u MEF-ovima; 3. Odrediti ulogu p53 u RPL24+/- MEF-ovima. Materijal i metode: Istraživanja su provedena na MEF-ovima izoliranima iz wt, RPL24+/-, p53-/- i RPL24+/-:p53-/- embrija. Za određivanje posljedica heterozigotnosti za RPL24 u MEF-ovima i uloge p53 u tim procesima korištene su metode za analizu diobe stanica, sinteze proteina, signalnog puta mTORC1, proteasoma, autofagije, reaktivnih kisikovih radikala (ROS), agregata proteina te morfologije i funkcije mitohondrija. Rezultati: U RPL24+/- MEF-ovima smanjena je sinteza proteina ovisna o signalnom putu mTORC1, a povećana je aktivnost proteasoma i mTORC1-ovisne autofagije. Ti mehanizmi umanjuju proteotoksični stres u RPL24+/- MEF-ovima, ali nisu dostatni za njegovo potpuno sprječavanje, što se očituje nakupljanjem agregata proteina i ROS-a. Inaktivacija p53 u RPL24+/- MEF-ovima sprječava inhibiciju Sesn2/mTORC1-ovisne sinteze proteina i inhibira mTORC1-ovisnu autofagiju, što rezultira dodatnim nakupljanjem agregata proteina. Povećana sinteza proteina, smanjena količina ROS-a i p21 uslijed inaktivacije p53 u RPL24+/- MEF-ovima omogućuju njihovu ubrzanu diobu. Inaktivacija p53 u RPL24+/- MEF-ovima remeti normalnu morfologiju i smještaj mitohondrija i uzrokuje energetski stres. Zaključak: Razjašnjenje mehanizama putem kojih RPL24+/- uzrokuje promjene u MEF- ovima te uloge p53 u njihovoj regulaciji važne su za razumijevanje patogeneze bolesti karakteriziranih smanjenim izražajem RP poput anemije Diamond i Blackfan i zloćudnih tumora te mogu doprinijeti identifikaciji ciljeva za njihovo liječenje.Aim of the study: Mutations of genes encoding RPs in mammals cause congenital malformations and malignant tumors. Inactivation of p53 tumor supressor under this conditions prevents congenital malformations and facilitates the development of malignant tumors. However, molecular mechanisms underlying these processes are unknown. I hypothesized that heterozygous inactivation of RPL24 leads to perturbation of cellular proteostasis and that p53 modulates the pathological phenotype by regulating proteostatic mechanisms. Specific aims of this research are: 1.To isolate fibroblasts from wt, RPL24+/- , p53-/-, RPL24+/-:p53-/- mouse embryos (MEFs), 2. To identify the consequences of RPL24 heterozygosity in MEFs, 3. To determine the role of p53 in RPL24+/- MEFs. Materials and methods: wt, RPL24+/-, p53-/-, RPL24+/-:p53-/- MEFs are used in this study. To determine the consequences of RPL24 heterozygosity on protein homeostatsis and the role of p53 in that processes, I used a number of methods to assess cell division, protein synthesis, reactive oxygen species (ROS), protein aggregates and mitochondria morfology and function as well as activity of mTORC1 signaling pathway, proteasomes and autophagy. Results: In RPL24+/- MEFs mTORC1-dependant protein synthesis is downregulated, whereas proteasomal and autophagosomal degradation are upregulated. However, activation of these proteostatic mechanisms are not sufficient to fully prevent formation of protein aggregates and ROS in these MEFs. Inactivation of p53 in RPL24+/- MEFs prevents Sesn2/mTORC1-dependant inhibition of protein synthesis and inhibits autophagy, which enhances the accumulation of protein aggregates. Despite the presence of protein aggregates, increased protein synthesis, reduced amount of ROS and p21 upon p53 inactivation in RPL24+/- MEFs enable accelaration of their proliferation. Finally, inactivation of p53 in RPL24+/- MEFs disrupts normal mitochondria morphology and cellular localization leading to the energetic stress. Conclusion: These results will enable better understanding of the molecular mechanisms by which perturbations in ribosome biogenesis lead to Diamond and Blackfan anemia and malignant tumors and they may reveal therapeutic liabilities in these diseases

THE ROLE OF p53 TUMOR SUPPRESSOR IN PROTEIN HOMEOSTASIS REGULATION IN CELLS HETEROZYGOUS FOR RIBOSOMAL PROTEIN GENE L24

Cilj istraživanja: Heterozigotne mutacije RP u sisavaca uzrokuju razvojne anomalije i zloćudne tumore. Inaktivacija supresora tumora p53 u tim uvjetima sprječava nastanak razvojnih anomalija i potiče razvoj zloćudnih tumora. Međutim, molekularni mehanizmi putem kojih smanjeni izražaj RP uzrokuje promjene u stanicama i uloga p53 u tom kontekstu nepoznati su. Ključna pretpostavka ovog istraživanja je da heterozigotna inaktivacija RPL24 uzrokuje poremećaj homeostaze proteina te da p53 umanjuje negativne učinke tih promjena putem regulacije proteostatskih mehanizama. Ciljevi istraživanja su: 1. Izolirati fibroblaste iz wt, RPL24+/-, p53-/-, RPL24+/-:p53-/- embrija miševa (MEF, od engl. mouse embryonic fibroblasts); 2. Odrediti posljedice heterozigotnosti za RPL24 u MEF-ovima; 3. Odrediti ulogu p53 u RPL24+/- MEF-ovima. Materijal i metode: Istraživanja su provedena na MEF-ovima izoliranima iz wt, RPL24+/-, p53-/- i RPL24+/-:p53-/- embrija. Za određivanje posljedica heterozigotnosti za RPL24 u MEF-ovima i uloge p53 u tim procesima korištene su metode za analizu diobe stanica, sinteze proteina, signalnog puta mTORC1, proteasoma, autofagije, reaktivnih kisikovih radikala (ROS), agregata proteina te morfologije i funkcije mitohondrija. Rezultati: U RPL24+/- MEF-ovima smanjena je sinteza proteina ovisna o signalnom putu mTORC1, a povećana je aktivnost proteasoma i mTORC1-ovisne autofagije. Ti mehanizmi umanjuju proteotoksični stres u RPL24+/- MEF-ovima, ali nisu dostatni za njegovo potpuno sprječavanje, što se očituje nakupljanjem agregata proteina i ROS-a. Inaktivacija p53 u RPL24+/- MEF-ovima sprječava inhibiciju Sesn2/mTORC1-ovisne sinteze proteina i inhibira mTORC1-ovisnu autofagiju, što rezultira dodatnim nakupljanjem agregata proteina. Povećana sinteza proteina, smanjena količina ROS-a i p21 uslijed inaktivacije p53 u RPL24+/- MEF-ovima omogućuju njihovu ubrzanu diobu. Inaktivacija p53 u RPL24+/- MEF-ovima remeti normalnu morfologiju i smještaj mitohondrija i uzrokuje energetski stres. Zaključak: Razjašnjenje mehanizama putem kojih RPL24+/- uzrokuje promjene u MEF- ovima te uloge p53 u njihovoj regulaciji važne su za razumijevanje patogeneze bolesti karakteriziranih smanjenim izražajem RP poput anemije Diamond i Blackfan i zloćudnih tumora te mogu doprinijeti identifikaciji ciljeva za njihovo liječenje.Aim of the study: Mutations of genes encoding RPs in mammals cause congenital malformations and malignant tumors. Inactivation of p53 tumor supressor under this conditions prevents congenital malformations and facilitates the development of malignant tumors. However, molecular mechanisms underlying these processes are unknown. I hypothesized that heterozygous inactivation of RPL24 leads to perturbation of cellular proteostasis and that p53 modulates the pathological phenotype by regulating proteostatic mechanisms. Specific aims of this research are: 1.To isolate fibroblasts from wt, RPL24+/- , p53-/-, RPL24+/-:p53-/- mouse embryos (MEFs), 2. To identify the consequences of RPL24 heterozygosity in MEFs, 3. To determine the role of p53 in RPL24+/- MEFs. Materials and methods: wt, RPL24+/-, p53-/-, RPL24+/-:p53-/- MEFs are used in this study. To determine the consequences of RPL24 heterozygosity on protein homeostatsis and the role of p53 in that processes, I used a number of methods to assess cell division, protein synthesis, reactive oxygen species (ROS), protein aggregates and mitochondria morfology and function as well as activity of mTORC1 signaling pathway, proteasomes and autophagy. Results: In RPL24+/- MEFs mTORC1-dependant protein synthesis is downregulated, whereas proteasomal and autophagosomal degradation are upregulated. However, activation of these proteostatic mechanisms are not sufficient to fully prevent formation of protein aggregates and ROS in these MEFs. Inactivation of p53 in RPL24+/- MEFs prevents Sesn2/mTORC1-dependant inhibition of protein synthesis and inhibits autophagy, which enhances the accumulation of protein aggregates. Despite the presence of protein aggregates, increased protein synthesis, reduced amount of ROS and p21 upon p53 inactivation in RPL24+/- MEFs enable accelaration of their proliferation. Finally, inactivation of p53 in RPL24+/- MEFs disrupts normal mitochondria morphology and cellular localization leading to the energetic stress. Conclusion: These results will enable better understanding of the molecular mechanisms by which perturbations in ribosome biogenesis lead to Diamond and Blackfan anemia and malignant tumors and they may reveal therapeutic liabilities in these diseases

New insights into HEATR1 functions

Human HEAT repeat containing 1 protein (HEATR1) is the structural and functional homolog of yeast U3 small nucleolar RNA-associated protein 10 (UTP 10). Human HEATR1 is a nucleolar protein that plays a prominent positive role in regulation of rRNA synthesis. Depletion of HEATR1 cause disruption of nucleolar structure and activate the ribosomal biogenesis stress pathway – RPL5 / RPL11 dependent stabilization and activation of the tumor suppressor protein p53

New insights into HEATR1 functions

Human HEAT repeat containing 1 protein (HEATR1) is the structural and functional homolog of yeast U3 small nucleolar RNA-associated protein 10 (UTP 10). Human HEATR1 is a nucleolar protein that plays a prominent positive role in regulation of rRNA synthesis. Depletion of HEATR1 cause disruption of nucleolar structure and activate the ribosomal biogenesis stress pathway – RPL5 / RPL11 dependent stabilization and activation of the tumor suppressor protein p53

The relationship between the nucleolus and cancer: Current evidence and emerging paradigms

The nucleolus is the most prominent nuclear substructure assigned to produce ribosomes ; molecular machines that are responsible for carrying out protein synthesis. To meet the increased demand for proteins during cell growth and proliferation the cell must increase protein synthetic capacity by upregulating ribosome biogenesis. While larger nucleolar size and number have been recognized as hallmark features of many tumor types, recent evidence has suggested that, in addition to overproduction of ribosomes, decreased ribosome biogenesis as well as qualitative changes in this process could also contribute to tumor initiation and cancer progression. Furthermore, the nucleolus has become the focus of intense attention for its involvement in processes that are clearly unrelated to ribosome biogenesis such as sensing and responding to endogenous and exogenous stressors, maintenance of genome stability, regulation of cell-cycle progression, cellular senescence, telomere function, chromatin structure, establishment of nuclear architecture, global regulation of gene expression and biogenesis of multiple ribonucleoprotein particles. The fact that dysregulation of many of these fundamental cellular processes may contribute to the malignant phenotype suggests that normal functioning of the nucleolus safeguards against the development of cancer and indicates its potential as a therapeutic approach. Here we review the recent advances made toward understanding these newly-recognized nucleolar functions and their roles in normal and cancer cells, and discuss possible future research directions

Cancer-associated mutations in the ribosomal protein L5 gene dysregulate the HDM2/p53-mediated ribosome biogenesis checkpoint

Perturbations in ribosome biogenesis have been associated with cancer. Such aberrations activate p53 through the RPL5/RPL11/5S rRNA complex-mediated inhibition of HDM2. Studies using animal models have suggested that this signaling pathway might constitute an important anticancer barrier. To gain a deeper insight into this issue in humans, here we analyze somatic mutations in RPL5 and RPL11 coding regions, reported in The Cancer Genome Atlas and International Cancer Genome Consortium databases. Using a combined computational and statistical approach, complemented by a range of biochemical and functional analyses in human cancer cell models, we demonstrate the existence of several mechanisms by which RPL5 mutations may impair wild-type p53 upregulation and ribosome biogenesis. Unexpectedly, the same approach provides only modest evidence for a similar role of RPL11, suggesting that RPL5 represents a preferred target during human tumorigenesis in cancers with wild-type p53. Furthermore, we find that several functional cancer-associated RPL5 somatic mutations occur as rare germline variants in general population. Our results shed light on the so-far enigmatic role of cancer-associated mutations in genes encoding ribosomal proteins, with implications for our understanding of the tumor suppressive role of the RPL5/RPL11/5S rRNA complex in human malignancies