Telomere biology disorders (TBDs) are characterized by short telomeres, premature aging, bone marrow failure and cancer predisposition. Germline mutations in NHP2, encoding for one component of the telomerase cofactor H/ACA RNA binding complex together with Dyskerin, NOP10 and GAR1, have been previously reported in rare cases of TBDs. Here, we report two novel NHP2 variants (NHP2-A39T and NHP2-T44M) identified in a compound heterozygous patient affected by premature aging, bone marrow failure/myelodysplastic syndrome and gastric cancer. Although still able to support cell viability, both variants reduce the levels of hTR, the telomerase RNA component, and telomerase activity, expanding the panel of NHP2 pathological variants. Furthermore, both variants fail to be incorporated in the H/ACA RNA binding complex when in competition with wild-type endogenous NHP2, and the lack of incorporation causes their drastic proteasomal degradation. By RoseTTAFold prediction followed by molecular dynamics simulations, we reveal a dramatic distortion of residues 33-41, which normally position on top of the NHP2 core, as the main defect of NHP2-A39T, and high flexibility and the misplacement of the N-terminal region (residues 1-24) in NHP2-T44M and, to a lower degree, in NHP2-A39T. Because deletion of amino acids 2-24 causes a reduction in NHP2 levels only in the presence of wild-type NHP2, while deletion of amino acids 2-38 completely disrupts NHP2 stability, we propose that the two variants are mis-incorporated into the H/ACA binding complex due to the altered dynamics of the first 23 amino acids and/or the distortion of the residues 25-41 loop.

Cells are continuously exposed to DNA damaging agents that cause different types of lesions. Double strand breaks (DSBs), where both strands of DNA are broken, are the most toxic lesions. To repair DSBs and ensure genome stability and cell survival, mammalian cells evolved two main pathways, Homologous recombination (HR) and classical Nonhomologous end joining (c-NHEJ). Failure in these pathways triggers genome instability, which correlates with tumorigenesis and cancer progression, but can also contribute to cancer treatment when properly exploited. At the same time, the end of our chromosomes, the telomeres, should be protected from being sensed as DSBs and aberrantly repaired. In fact, failure in telomere protection due to short or dysfunctional telomeres can cause chromosome fusions, genome instability and, in some cases, contribute to tumorigenesis. To this end, telomeres are protected by the shelterin complex in all cell types and elongated by telomerase in germline and somatic stem cells. 

This thesis aims to find new factors involved in the DNA damage response (DDR) that could be used as markers for cancer diagnosis and/or targets in cancer therapy. 

In paper I, we explore the effect of two novel variants in the H/ACA RNA binding complex component NHP2 identified in a patient with Aplastic anemia, gastric cancer, and signs of premature aging. H/ACA RNA binding complex is essential for the stability and maturation of both ribosomal RNA and the telomerase RNA component hTR. By in silico and in cells analysis, we found that both mutations reduce the affinity of NHP2 for the other components of the H/ACA RNA binding complex due to the misplacement of the N-terminus, affecting protein stability. Furthermore, these variants cause reduced telomerase activity by failing to preserve hTR. However, they do not affect the DDR. 

In papers II and III, we investigated the role of chromatin mobility in the maintenance of genome stability. In fact, the mobility of DSBs can cause translocations, one of the main hallmarks of cancer initiation and progression, but is also one of the mechanisms responsible for the efficacy of therapies based on PARP inhibition against breast and ovarian cancer defective in HR. In paper II, we describe a method for consistent and unbiased quantification of DSB mobility and nuclear deformations in the presence of multiple DSBs by fluorescent live-cell imaging. This method can be used with any fluorescent-tagged proteins binding specific genome regions, such as telomeres. In paper III Section A, we analyzed DSB mobility and mis-repair in the context of nuclear envelope (NE) alterations as Lamin A/C deletion or reduction in sphingolipids synthesis. In fact, previous studies have shown that different components of the NE are involved in promoting and/or counteracting such mobility, but the role of the NE itself was not yet explored. By combining genetic modifications and/or chemical inhibition with microscopy techniques, we found that the presence of invaginations significantly increases DSB mobility and mis-repair after treatment with PARP inhibitor in the absence of BRCA1, suggesting that the visualization of the NE could be used as marker for predicting the cancer therapy outcome and that, in the long run, the NE structure could be used as target in cancer therapy. In paper III Section B, we demonstrated that cells subjected to mechanical shear stress and/or to an agonist of the mechanosensor channel Piezo1 reduced DSB mobility and mis-repair. This effect is associated with chromatin decompaction, as observed by electron microscopy and ATAC sequencing, and reduced telomere mobility, suggesting that the shear stress-mediated activation of Piezo1 promotes the chromatin opening and that chromatin compaction can influence DSB mobility and repair. Since cancer cells are exposed to mechanical stress during metastasis, our work suggests that cotreatment with drugs closing the chromatin and/or inhibiting Piezo1 could increase the sensitivity of cancer cells to chemotherapy. 

The proteasome is a validated target of cancer therapeutics. Inhibition of proteasome activity results in the activation of the unfolded protein response (UPR) characterized by phosphorylation of eukaryotic initiation factor 2α (eIF2α), global translational arrest, and increased expression of the proapoptotic CHOP (C/EBP homologous protein) protein. Defects in the UPR response has been reported to result in altered sensitivity of tumor cells to proteasome inhibitors. Here, we characterized the effects of the deubiquitinase (DUB) inhibitor VLX1570 on protein homeostasis, both at the level of the UPR and on protein translation, in acute lymphoblastic leukemia (ALL). Similar to the 20S inhibitor bortezomib, VLX1570 induced accumulation of polyubiquitinated proteins and increased expression of the chaperone Grp78/Bip in ALL cells. Both compounds induced cleavage of PARP (Poly (ADP-ribose) polymerase) in ALL cells, consistent with induction of apoptosis. However, and in contrast to bortezomib, VLX1570 treatment resulted in limited induction of the proapoptotic CHOP protein. Translational inhibition was observed by both bortezomib and VLX1570. We report that in distinction to bortezomib, suppression of translation by VXL1570 occurred at the level of elongation. Increased levels of Hsc70/Hsp70 proteins were observed on polysomes following exposure to VLX1570, possibly suggesting defects in nascent protein folding. Our findings demonstrate apoptosis induction in ALL cells that appears to be uncoupled from CHOP induction, and show that VLX1570 suppresses protein translation by a mechanism distinct from that of bortezomib.