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- Beneventi, Giulia
(författare)
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RNA modifications and post-transcriptional control in cancer and stem cells
- 2021
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Splicing and translation are two of the key steps of post-transcriptional regulation of gene expression. Their tight regulation is essential for development, whereas their deregulation is involved in cancer pathogenesis. Nevertheless, many of the molecular mechanisms controlling these processes are still unknown. Hence, the main aim of this thesis is to elucidate novel regulatory mechanisms that affect splicing and translation in stem and cancer cells.An emerging layer of regulation is represented by RNA modifications, evolutionarily conserved hallmarks of coding and non-coding RNA. Indeed, small nuclear RNA (snRNA) and ribosomal RNA (rRNA), the RNA components of the spliceosome and ribosome, are decorated with pseudouridines (Ψ) and 2’-O-methyl groups (2’OMe) within key functional regions. These modifications are introduced by RNA-dependent small ribonucleoproteins (snoRNPs), guided by snoRNAs and scaRNAs. In Paper I I identified the role of the SCARNA15-guided U2 snRNA-Ψ in driving alternative splicing events affecting the pivotal tumor suppressor p53 and redox homeostasis in cancer cells. In Paper II I unraveled the importance of the rRNA pseudouridylation machinery for the homeostasis of the hematopoietic system and the reconstitution capacity of HSCs in vivo. In Paper III I discovered a developmentally regulated 28S rRNA-2’OMe guided by SNORD123. The loss of this modification affected hESCs differentiation and caused translation defects perturbing the resistance to A-site specific antibiotics in fibroblasts. In Paper IV I highlighted a novel interplay between splicing and translation. Here, I uncovered a translationally regulated splicing factor, SF3A3, upon oncogenic stress which affects splicing of genes contributing to mitochondrial homeostasis and metabolism and that influences tumorigenesis of MYC-driven breast cancer.In sum, this doctoral thesis explores novel post-transcriptional regulatory mechanisms, especially involving RNA modification modulation and dysregulation, with the aim to broaden the knowledge on stem and cancer cells functioning and to contribute to the discovery of future clinical implications.
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| 2. |
- Beneventi, Giulia, et al.
(författare)
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The small Cajal body-specific RNA 15 (SCARNA15) directs p53 and redox homeostasis via selective splicing in cancer cells
- 2021
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Ingår i: NAR Cancer. - : Oxford University Press (OUP). - 2632-8674. ; 3:3
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Tidskriftsartikel (refereegranskat)abstract
- Small Cajal body-specific RNAs (scaRNAs) guide post-transcriptional modification of spliceosomal RNA and, while commonly altered in cancer, have poorly defined roles in tumorigenesis. Here, we uncover that SCARNA15 directs alternative splicing (AS) and stress adaptation in cancer cells. Specifically, we find that SCARNA15 guides critical pseudouridylation (Ψ) of U2 spliceosomal RNA to fine-tune AS of distinct transcripts enriched for chromatin and transcriptional regulators in malignant cells. This critically impacts the expression and function of the key tumor suppressors ATRX and p53. Significantly, SCARNA15 loss impairs p53-mediated redox homeostasis and hampers cancer cell sur- vival, motility and anchorage-independent growth. In sum, these findings highlight an unanticipated role for SCARNA15 and Ψ in directing cancer-associated splicing programs.
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| 3. |
- Ciesla, Maciej, et al.
(författare)
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Oncogenic translation directs spliceosome dynamics revealing an integral role for SF3A3 in breast cancer
- 2021
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Ingår i: Molecular Cell. - : Elsevier BV. - 1097-2765. ; 81:7
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Tidskriftsartikel (refereegranskat)abstract
- Splicing is a central RNA-based process commonly altered in human cancers; however, how spliceosomal components are co-opted during tumorigenesis remains poorly defined. Here we unravel the core splice factor SF3A3 at the nexus of a translation-based program that rewires splicing during malignant transformation. Upon MYC hyperactivation, SF3A3 levels are modulated translationally through an RNA stem-loop in an eIF3D-dependent manner. This ensures accurate splicing of mRNAs enriched for mitochondrial regulators. Altered SF3A3 translation leads to metabolic reprogramming and stem-like properties that fuel MYC tumorigenic potential in vivo. Our analysis reveals that SF3A3 protein levels predict molecular and phenotypic features of aggressive human breast cancers. These findings unveil a post-transcriptional interplay between splicing and translation that governs critical facets of MYC-driven oncogenesis.
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| 4. |
- Phung, Bengt, et al.
(författare)
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The X-Linked DDX3X RNA Helicase Dictates Translation Reprogramming and Metastasis in Melanoma
- 2019
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Ingår i: Cell Reports. - : Elsevier BV. - 2211-1247. ; 27:12, s. 7-3586
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Tidskriftsartikel (refereegranskat)abstract
- The X-linked DDX3X gene encodes an ATP-dependent DEAD-box RNA helicase frequently altered in various human cancers, including melanomas. Despite its important roles in translation and splicing, how DDX3X dysfunction specifically rewires gene expression in melanoma remains completely unknown. Here, we uncover a DDX3X-driven post-transcriptional program that dictates melanoma phenotype and poor disease prognosis. Through an unbiased analysis of translating ribosomes, we identified the microphthalmia-associated transcription factor, MITF, as a key DDX3X translational target that directs a proliferative-to-metastatic phenotypic switch in melanoma cells. Mechanistically, DDX3X controls MITF mRNA translation via an internal ribosome entry site (IRES) embedded within the 5' UTR. Through this exquisite translation-based regulatory mechanism, DDX3X steers MITF protein levels dictating melanoma metastatic potential in vivo and response to targeted therapy. Together, these findings unravel a post-transcriptional layer of gene regulation that may provide a unique therapeutic vulnerability in aggressive male melanomas.
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| 5. |
- Vanhee, Stijn, et al.
(författare)
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Lin28b controls a neonatal to adult switch in B cell positive selection
- 2019
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Ingår i: Science immunology. - : AMER ASSOC ADVANCEMENT SCIENCE. - 2470-9468. ; 4:39
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Tidskriftsartikel (refereegranskat)abstract
- The ability of B-1 cells to become positively selected into the mature B cell pool, despite being weakly self-reactive, has puzzled the field since its initial discovery. Here, we explore changes in B cell positive selection as a function of developmental time by exploiting a link between CD5 surface levels and the natural occurrence of self-reactive B cell receptors (BCRs) in BCR wild-type mice. We show that the heterochronic RNA binding protein Lin28b potentiates a neonatal mode of B cell selection characterized by enhanced overall positive selection in general and the developmental progression of CD5(+) immature B cells in particular. Lin28b achieves this by amplifying the CD19/PI3K/c-Myc positive feedback loop, and ectopic Lin28b expression restores both positive selection and mature B cell numbers in CD19(-/-) adult mice. Thus, the temporally restricted expression of Lin28b relaxes the rules for B cell selection during ontogeny by modulating tonic signaling. We propose that this neonatal mode of B cell selection represents a cell-intrinsic cue to accelerate the de novo establishment of the adaptive immune system and incorporate a layer of natural antibody-mediated immunity throughout life.
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