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Sexual reproduction and DNA repair mechanisms are processes that shape the evolution of eukaryotic species’ genomes. There appears to be a paradox in sexual reproduction because it has no evident direct benefits while it is almost universal among eukaryotes. DNA repair mechanisms are also crucial for reproduction as they ensure genome integrity across generations while simultaneously generating errors, thereby fostering genetic diversity.Understanding how these processes shape genetic diversity and genomes is of significant interest in biology. One approach to gain insights into their evolutionary impact is by studying species with alternative modes of reproduction while showing a high tolerance to DNA damage.One of the most notorious animal model system, reproducing asexually through a modified meiosis and exhibiting exceptional resilience to DNA-damaging conditions like desiccation and radiation, is the bdelloid rotifer species Adineta vaga, which is the primary focus of this PhD. More specifically, this PhD research investigates the genome dynamics, DNA repair mechanisms, and the consequences of asexual reproduction on genetic diversity in Adineta vaga.The work presented in this thesis begins by comparing genome assembly methods to prevent haplotig contamination in haploid assemblies, as well as obtaining chromosome-scale assemblies to study the genome evolution of A. vaga. Subsequently, using the best strategies we determined, it describes the genome structure of A. vaga, providing evidence for pairs of homologous chromosomes and recombination. Furthermore, it unveils the first description of a trans-generational DNA repair mechanism in an animal species, providing new insights onA. vaga's survival mechanisms in harsh environmental conditions. The thesis also explores how long-term asexuality, coupled with intra-individual homologous recombination, impacts the transposable element dynamics, the genome heterozygosity, and allele-specific expression. Lastly, this, Doctorat en Sciences, info:eu-repo/semantics/nonPublished

Human Immunodeficiency Virus type 1 (HIV-1) infection can be managed but not cured by the current combinatory antiretroviral therapy (cART). The replication rate of HIV-1, which is directly correlated to the rate of disease progression to Acquired Immunodeficiency Syndrome (AIDS), is controlled primarily at the transcription level of viral genes, which is not targeted by cART. The arrest of the cART is associated with a rapid viremia rebound due to the persistence of long-term reservoirs of virally infected cells, which cannot be eliminated by cART corresponding to cell types or tissue compartments where virally infected cells are maintained. These reservoirs are heterogeneous and principally composed of CD4+ T cells and myeloid cells, the latter understudied and poorly represented in cure-based efforts. Importantly, each reservoir harbors a unique regulation of HIV-1 gene expression. Even though most transcriptional studies on HIV-1 have only focused on the viral promoter 5’long terminal repeat (5’LTR), our laboratory has previously reported an intragenic cis-regulatory region (IRR), which the complete functional unit forming the HIV-1 IRR is composed, from 5’ to 3’, of three subdomains: the 5103 fragment, the hypersensitive site 7 (HS7), and the 5105 fragment. In this context, further deciphering the specific molecular mechanisms underlying HIV-1 gene expression in all host cell types (including myeloid cells) and from each transcriptional regulatory element (including the IRR) is crucial for a deeper understanding of HIV-1 biology and pathogenesis.In the first part of my PhD thesis, we determined the in vivo epigenetic landscape of the IRR in latent and reactivated conditions and in both T-lymphoid and myeloid-infected cells, representing the two major cellular contexts of HIV-1 infection. We demonstrated that the IRR harbored the characteristic features of an enhancer in these two physiological contexts. Second, we explored the contribution of the intragenic lin, Doctorat en Sciences, info:eu-repo/semantics/nonPublished

A novel pillar of epigenetics has recently gained the attention of the scientific community: mRNA modifications. This new field, commonly referred to as “epitranscriptomics”, has emerged as a crucial regulatory level of gene expression. Yet, the study of these modifications is still in its early days and has definitely not reached its full potential.The presence of modifications in mitochondrial mRNAs has emerged very recently, and is suggested to play a role in fine-tuning mitochondrial gene expression and function. However, the epitranscriptomic landscape of mitochondrial mRNA remains very poorly explored. The aim of this thesis was to investigate a novel mitochondrial mRNA modification: the N3- methylcytosine (m3C), from its physiological to its pathological relevance.In the first part of this thesis, we show that METTL8 catalyzes m3C on mitochondrial mRNA, specifically on complex I subunits transcripts of the electron transport chain (ETC). Furthermore, we report that METTL8 influences the protein level of its modified targets, and therefore regulates the complex I activity. Finally, we confirm the complex I deficiency in a Mettl8-knockout mouse model, that we established.In the second part of this thesis, we aimed to tackle the pathological impact of this modification. In regard to the emerging crosstalk between cervical cancer and mitochondria, we decided to investigate for the first time, the potential pathological role of m3C in cervical cancer. First, we confirmed that METTL8 expression is higher in patient’s biopsies compared to normal cervical tissues, and correlates with the disease progression. We then showed that METTL8-dependent m3C promotes cell proliferation and migration; and tumor growth in a xenografts model. Furthermore, we decipher that METTL8-driven signature is enriched for mitochondrial functions and complex I activity.In conclusion, our findings improve our understanding of this emerging epitranscriptomic field, and specifically unravel the, Doctorat en Sciences biomédicales et pharmaceutiques (Médecine), info:eu-repo/semantics/nonPublished

Nowadays, life expectancy is increasing but is not systematically accompanied by a decent quality of life during aging. With the overall aging of the population, it is urgent to highlight strategies to promote the maintenance of autonomy at old age. While the effects of exercise training on limiting the loss of functional autonomy in the elderly are well-established, the molecular mechanisms by which it may slowdown the hallmarks of skeletal muscle aging, notably through the regulation of telomere health and cellular senescence, need to be further investigated. In this thesis, we found that even if endurance training did not effectively reduce senescence, the training status might attenuate the senescence-associated secretory phenotype in human skeletal muscle. Moreover, the age-dependent increase in TERRA expression might represent a novel biological marker of aging which is alleviated by endurance training., (MOTR - Sciences de la motricité) -- UCL, 2022

The loss of plasma membrane from red blood cells (RBCs) through the budding and release of extracellular vesicles (EVs) affects their shape, deformability and functionality. Although oxidative stress appears as the main triggering factor for RBC vesiculation, the role of plasma membrane properties is largely overlooked. We here addressed if plasma membrane biophysical properties as well as lipid transversal and lateral distribution could contribute to the RBC vesiculation process upon RBC storage and in hereditary spherocytosis, a membrane fragility disease. Results indicate that, in contrast to spherocytosis, the release of EVs during hypothermic storage in blood tubes and in RBC concentrates is accompanied by the successive impairment of RBC membrane rigidity, lateral heterogeneity in lipid domains and transversal asymmetry. Our data open the way to use EVs or lipid domains for quality control in transfusion centers and to target domains to minimize vesiculation in RBC concentrates., (BIFA - Sciences biomédicales et pharmaceutiques) -- UCL, 2022

In this issue of Molecular Cell, Kaminski et al. and Yadav et al. demonstrate that RAD51AP1 and TERRA non-coding RNA positively regulate the alternative mechanism of telomere maintenance by promoting D-loop formation and chromatin-directed mechanisms to suppress transcription-collision events during ALT telomere synthesis.

Telomeres protect the ends of our chromosomes. The replicative immortality of cancer cells depends on the activation of a telomere maintenance mechanism: the telomerase or an alternative lengthening of telomeres (ALT) mechanism. ALT is activated in about 10% of tumors but this prevalence increases greatly in pediatric tumors. The latter are in need of targeted therapies but, to date, there is still no therapy targeting ALT. In this thesis, we identified TSPYL5 (testis-specific Y-encoded-like protein 5) as a critical protein for ALT+ cell viability, opening new perspectives for anti-ALT targeted therapies. We also established a mouse xenograft model with human ALT+ cancer cells to test the efficiency of future anti-ALT compounds. The lack of good tools for the diagnosis of ALT also led us to the development of a new robust test on tumor sections. Finally, we provided additional evidence that replicative stress induces some characteristics of ALT telomeres., (BIFA - Sciences biomédicales et pharmaceutiques) -- UCL, 2022

Habitat engineers make strong and far-reaching imprints on ecosystem processes. In intertidal mudflats, the dominant primary producer, microphytobenthos (MPB), often forms high biomass patches around oyster reefs. We evaluate multiple hypotheses linking MPB with oyster reefs, including oyster biodeposition, meiofaunal grazing, and abiotic factors, aiming to help predict effects of reef removal or proliferation. We quantify spatial patterns of an Atlantic mudflat community and its environment around two large Crassostrea reefs before experimentally sacrificing one reef via burning. MPB biomass was enriched surrounding living oyster reefs although infaunal biomass and individual sizes were low. Structural equation modelling best supported the hypothesis that crab predation intensity, which decayed with distance from the reefs, locally freed MPB from grazing. Our results suggest that Crassostrea reef expansion may enrich local MPB patches and redirect trophic energy flows away from mudflat infauna, with potential implications for the sustainability of local fisheries and bird conservation.

Habitat engineers make strong and far-reaching imprints on ecosystem processes. In intertidal mudflats, the dominant primary producer, microphytobenthos (MPB), often forms high biomass patches around oyster reefs. We evaluate multiple hypotheses linking MPB with oyster reefs, including oyster biodeposition, meiofaunal grazing, and abiotic factors, aiming to help predict effects of reef removal or proliferation. We quantify spatial patterns of an Atlantic mudflat community and its environment around two large Crassostrea reefs before experimentally sacrificing one reef via burning. MPB biomass was enriched surrounding living oyster reefs although infaunal biomass and individual sizes were low. Structural equation modelling best supported the hypothesis that crab predation intensity, which decayed with distance from the reefs, locally freed MPB from grazing. Our results suggest that Crassostrea reef expansion may enrich local MPB patches and redirect trophic energy flows away from mudflat infauna, with potential implications for the sustainability of local fisheries and bird conservation.

More than two decades ago, the G-rich sequences of telomeric DNA were proposed to be preferential targets of oxidative damage with potential detrimental impact on telomere length and integrity. If not breathing is not an option (Markkanen, 2017), understanding how cellular respiration impacts on telomere regulation remains a challenging question that has, so far, not been addressed in the context of naturally-induced oxidative stress. ATP production, through oxidative phosphorylation in mitochondria, is the major endogenous source of ROS in cells. Both oxygen consumption and the proton gradient strength across the inner mitochondrial membrane regulate ROS production. Here, using a transmitochondrial cybrid approach with mitochondria isolated from donors with either very long (>P90), average or short telomeres, we evaluated the impact of the mitochondrial genome on oxidative stress and telomere length in Rho0 recipient cells. Our data revealed that specific mtDNA-encoded mitochondrial protein variants regulate oxidative stress and telomere length. We will discuss how these variants may impact on ROS production and offer a maternal inheritance of telomere length.

About 10% of cancer cells employ the Alternative Lengthening of Telomeres (ALT) pathway instead of re-activating the hTERT subunit of telomerase. The hTR RNA subunit is also abnormally silenced in some ALT+ cells not expressing hTERT, suggesting a possible negative impact of hTR on ALT, independently of telomerase. Accordingly, ectopically-expressed hTR reduces p-RPAS33 levels at ALT telomeres by promoting the hnRNPA1- and DNA-PK-dependent depletion of telomere-bound RPA. The resulting defective ATR signaling at telomeres impairs the recruitment of homologous recombination protein, RAD51. This induces ALT telomere fragility, increases POLD3-dependent C-circle production and promotes the recruitment of 53BP1 DNA damage marker at telomeres. In ALT+ cells that naturally retain hTR expression, NHP2 H/ACA ribonucleoprotein levels are downregulated, likely to restrain DNA damage response (DDR) activation at telomeres through a reduced recruitment of 53BP1. This unexpected role of NHP2 is independent from hTR’s non-canonical function in modulating telomeric p-RPAS33. Collectively, our study shines new light on the interference between telomerase- and ALT-pathways and unravels a crucial role for hTR and NHP2 in regulating DDR at ALT telomeres.

Protein kinase RNA-activated (PKR) and Double-stranded RNA-specific adenosine deaminase (ADAR1) are two double stranded RNA binding proteins, respectively involved in the antiviral response to viruses and in the metabolism of dsRNA molecules. PKR is a cellular protein kinase, that in response to dsRNA molecules generated during viral infections, gets activated and phosphorylates the translation initiation factor, eIF2a, leading to translational shutoff and apoptosis. As PKR thereby acts as a potent antiviral effector, many viruses evolved mechanisms to counteract its antiviral response. Previous studies showed that Theiler’s murine encephalomyelitis virus (TMEV), a cardiovirus belonging to the Picornaviridae family, can block PKR activation through the activity of its Leader (L) protein, an accessory protein of the virus known to block IFN gene transcription and perturb nucleocytoplasmic trafficking. In the first part of this thesis I contributed to a work showing that the L protein likely renders PKR insensitive to dsRNA molecules, possibly through the activation of cellular kinases. Next, we analyzed PKR phosphorylation modifications in the hope to identify potential phosphorylation sites responsible for PKR inhibition by TMEV L. We observed that the Ser6 residue located 3aa before the first double-stranded RNA binding motif (DRBM1) of PKR could be phosphorylated. A phospho-mimetic mutation of this site was inhibiting PKR activation after poly(I:C) transfection or viral infection, especially when combined to a phospho-mimetic mutation of the Ser97 residue, located 3aa before the second double- stranded RNA binding motif (DRBM2). We propose a model according to which phosphorylation occurring upstream of DRBMs would tighten the interaction of the DRBMs with the catalytic domain, blocking PKR in a closed conformation, and making it unable to be activated. ADAR1 is an editing enzyme, causing deamination of adenosines into inosines in dsRNA molecules, thus destabilizi, (BIFA - Sciences biomédicales et pharmaceutiques) -- UCL, 2021

Both oxidative stress and telomere transcription are up-regulated by acute endurance exercise in human skeletal muscle. Whether and how life-long exercise training influences the antioxidant system response at transcriptional level and TERRA expression is unknown, especially during aging. Response to acute endurance exercise was investigated in muscle biopsies of 3 male subjects after 45 min of cycling. MCP-1 and SOD1 mRNA levels increased up to, 15-fold and 63%, respectively, after the cycling session while the mRNA levels of SOD2 were downregulated by 25%. The effects of chronic endurance exercise and aging were tested in the blood and muscle of 34 male subjects divided into four groups: young (YU) or old (OU) untrained, young (YT) or old (OT) trained cyclists. Long-term endurance training limited the age-dependent elevation in SOD1 (OT vs OU, -26%, P = 0.03) and the decline in SOD2 mRNA levels (OU vs YU, -41%, P = 0.04). A high endurance training status alleviated the age-related increase in the aging biological marker MCP-1 in plasma (OU vs YU, +48%, P = 0.005). Similar results were observed for telomeric transcription as the age-associated increase in 16p TERRA levels (OU vs YU, +39%, P = 0.001) was counteracted by a high endurance training status (OT vs OU, -63%, P = 0.0005). In conclusion, as MCP-1, we propose that the age-related TERRA accumulation might represent a novel biological marker of aging. Those aging-related increase expression might be alleviated by a high endurance training status. Whether those biological markers of aging are linked to an elevation of oxidative stress is still an open question. Therefore, whether the positive adaptations provided by endurance training indeed reduce oxidative stress, including at telomeres, and whether TERRA plays any role in this, need to be further investigated.

AMP-activated protein kinase (AMPK) is important for metabolic control in many tissues but its role in white adipose tissue (WAT) is controversial. AMPK activation has been reported to have both anti- and pro- lipolytic effects. Furthermore, AMPK activation has been proposed to have no effect or to inhibit glucose uptake. The main aim of this study was to investigate the mechanism by which AMPK activation regulates metabolism in WAT using a pharmacological activator combination. The first part of the thesis focused on insulin-stimulated lipogenesis and phosphorylation state of lipogenic enzymes in WAT. The second part deals with effects of AMPK activation on lipogenesis and lipolysis. In the last part, a MS-based phosphoproteomics strategy was set up with a view to searching for metabolic targets in WAT, (BIFA - Sciences biomédicales et pharmaceutiques) -- UCL, 2021

Human telomerase progressively emerged as a multifaceted ribonucleoprotein complex with additional functions beyond telomeric repeat synthesis. Both the hTERT catalytic subunit and the hTR long non-coding RNA (lncRNA) subunit are engaged in highly regulated cellular pathways that, together, contribute to cell fitness and protection against apoptosis. We recently described a new role for hTR in regulating the abundance of replication protein A at telomeres, adding to the growing repertoire of hTR's functions. Here, we focus on the non-canonical roles of hTR and discuss them in the context of the structural elements of the lncRNA. We propose that some functions of hTR may compete amongst each other through distinct interactions with its partners, proteins or mRNAs. We postulate that hTR's non-canonical functions may be highly relevant in the context of normal somatic cells that naturally silence hTERT gene, while keeping hTR expression.

The vast majority of adult cancer cells achieve cellular immortality by activating a telomere maintenance mechanism (TMM). While this is mostly achieved by the de-silencing of hTERT telomerase gene expression, an alternative homologous recombination-based and telomerase-independent mechanism, known as ALT (Alternative Lengthening of Telomeres), is frequently activated in a subset of tumors, including paediatric cancers. Being absent from normal cells, the ALT mechanism offers interesting perspectives for new targeted cancer therapies. To date, however, the development of better translationally applicable tools for ALT detection in tumor sections is still needed. Here, using a newly derived ALT-positive cancer cell mouse xenograft model, we extensively examined how the previously known ALT markers could be used as reliable tools for ALT diagnosis in tumor sections. We found that, together with the detection of ultra-bright telomeric signals (UBS), an ALT hallmark, native telomeric FISH, that detects single-stranded C-rich telomeric DNA, provides a very sensitive and robust tool for ALT diagnosis in tissues. We applied these assays to paediatric tumor samples and readily identified three ALT-positive tumors for which the TMM was confirmed by the gold-standard C-circle amplification assay. Although the latter offers a robust assay for ALT detection in the context of research laboratories, it is more difficult to set up in histopathological laboratories and could therefore be conveniently replaced by the combination of UBS detection and native telomeric FISH.

Mandibular hypoplasia, Deafness, Progeroid features, and Lipodystrophy (MDPL) syndrome is a rare autosomal dominant disorder caused by mutations in POLD1 gene and characterized by mandibular hypoplasia, deafness, progeroid features and lipodystrophy. One recurrent mutation p.(Ser605del) was reported in almost all affected patients. We report a novel de novo c.3214A>C p.(Thr1072Pro) variant in POLD1 in a 28-year-old male with MDPL syndrome. We provide a clinical description, molecular/immunohistological results, and literature review., SCOPUS: ar.j, info:eu-repo/semantics/published

The impact of a microplastic (MP) mixture composed of polyethylene (PE) and polypropylene (PP) plastic particles, prepared from commercially available products, was evaluated in blue mussels Mytilus spp. exposed to three environmentally relevant concentrations: 0.008 μg L−1 (low), 10 μg L−1 (medium), and 100 μg L−1 (high). Organisms were exposed for 10 days followed by 10 days of depuration in clean seawater under controlled laboratory conditions. The evaluation of MP effects on mussel clearance rate, tissue structure, antioxidant defenses, immune and digestive parameters, and DNA integrity were investigated while the identification of plastic particles in mussel tissues (gills, digestive gland, and remaining tissues), and biodeposits (feces and pseudofaeces) was performed using infrared microscopy (μFT-IR). Results showed the presence of MPs only in the digestive gland of mussels exposed to the highest tested concentration of MPs with a mean of 0.75 particle/mussel (after the 10 days of exposure). In biodeposits, PE and PP particles were detected following exposure to all tested concentrations confirming the ingestion of MPs by the organisms. A differential response of antioxidant enzyme activities between digestive gland and gills was observed. Significant increases in superoxide dismutase (SOD) and catalase (CAT) activities were measured in the digestive gland of mussels exposed to the low (0.008 μg L−1) and medium (10 μg L−1) concentrations of MPs and in the gills from mussels exposed to the highest concentration (100 μg L−1) of MPs that could be indicative of a change in the redox balance. Moreover, an increase in acid phosphatase activity was measured in hemolymph of mussels exposed to 0.008 and 10 μg L−1 concentrations. No significant difference was observed in the clearance rate, and histopathological parameters between control and exposed mussels. This study brings new insights on the potential sublethal impacts of MPs at environmentally relevant concentrat

Since the discovery of the anticancer properties of cisplatin, using new metals has progressively gained interest for the development of new therapeutic agents. Among them, polyazaaromatic complexes of Ru(II) have shown interesting photochemical and photophysical properties. Indeed, upon light irradiation, the oxidation and reduction potential of these compounds are enhanced and for some of them, photocleavage and/or photoadduct formation with DNA have been demonstrated [1]. In this context, we aim at designing new photo-oxidizing complexes of Ru(II) complexes for the targeting of G-quadruplex DNA. G-quadruplex (G4) consist in secondary structures adopted by guanines-rich nucleic acids. These structures are formed through the stacking of guanine tetrads (G-quartet), the latter resulting from the coplanar arrangement of four guanines. They have been found in the telomeres where they appear to play crucial biological roles [2]. Therefore, designing ligands able to selectively target G-quadruplex versus duplex DNA is of great interest. We report therein on the synthesis of new photo-oxidizing ruthenium(II) complexes (Figure 1). They are able to photo-induce oxidative damage to telomeric G-quadruplex DNA through photo-induced electron transfer (PET) with guanine. The affinity and selectivity for G-quadruplex DNA have been evidenced thanks to steady-state luminescence studies, BLI and molecular modelling. Finally, we demonstrated the cell internalization and the photo-cytotoxicity towards human osteosarcoma cells [3]. [1] B. Elias, A. Kirsch-De Mesmaeker, Coordination Chem. Review. 2006, 1627-1641. [2] H. Han, LH. Hurley, Trends in Pharmacological Sciences. 2000, 21, 136-142. [3] J. Weynand, A. Diman, M. Abraham, L. Marcélis, H. Jamet, A. Decottignies, J. Dejeu, E. Defrancq, B. Elias, Chem. Eur. J. 2018, 24, 19216-19227.

The envelope of Gram-negative bacteria is a complex compartment that is essential for viability. To ensure survival of the bacterial cells in fluctuating environments, several signal transduction systems, called envelope stress response systems (ESRSs), exist to monitor envelope biogenesis and homeostasis. We show that the Cpx two-component system, an extensively studied ESRS of E. coli, can monitor two essential envelope processes: cell wall synthesis and lipoprotein trafficking. We first show that Cpx is activated when peptidoglycan (PG) integrity is challenged and that this activation provides protection to cells exposed to antibiotics inhibiting PG synthesis. We also found evidence that an outer membrane lipoprotein, NlpE is used by Cpx to detect perturbations in lipoprotein trafficking. The activation of Cpx by NlpE improves fitness in these nefarious conditions., (BIFA - Sciences biomédicales et pharmaceutiques) -- UCL, 2019

PARN, poly(A)-specific ribonuclease, regulates the turnover of mRNAs and the maturation and stabilization of the hTR RNA component of telomerase. Biallelic PARN mutations were associated with Høyeraal–Hreidarsson (HH) syndrome, a rare telomere biology disorder that, because of its severity, is likely not exclusively due to hTR down-regulation. Whether PARN deficiency was affecting the expression of telomere-related genes was still unclear. Using cells from two unrelated HH individuals carrying novel PARN mutations and a human PARN knock-out (KO) cell line with inducible PARN complementation, we found that PARN deficiency affects both telomere length and stability and down-regulates the expression of TRF1, TRF2, TPP1, RAP1, and POT1 shelterin transcripts. Down-regulation of dyskerin-encoding DKC1 mRNA was also observed and found to result from p53 activation in PARN-deficient cells. We further showed that PARN deficiency compromises ribosomal RNA biogenesis in patients’ fibroblasts and cells from heterozygous Parn KO mice. Homozygous Parn KO however resulted in early embryonic lethality that was not overcome by p53 KO. Our results refine our knowledge on the pleiotropic cellular consequences of PARN deficiency

A significant fraction (~10%) of cancer cells maintain their telomere length via a telomerase-independent mechanism known as Alternative Lengthening of Telomeres (ALT). Currently, there are no known molecular, ALT-specific, therapeutic target. We have identified TSPYL5 (Testis Specific Y-encoded-Like Protein 5) as a PML body component, co-localizing with ALT telomeres and critical for ALT+ cell viability. TSPYL5 was described as an inhibitor of the USP7 deubiquitinase. We report that TSPYL5 prevents the poly-ubiquitination of POT1 – a shelterin component – and protects POT1 from proteasomal degradation, exclusively in ALT+ cells. USP7 depletion rescued POT1 poly-ubiquitination and loss, suggesting that the deubiquitinase activates POT1 E3 ubiquitin ligase(s). Similarly, PML depletion suppressed POT1 poly-ubiquitination, suggesting an interplay between USP7 and PML to trigger POT1 degradation in TSPYL5-depleted ALT+ cells. We demonstrate that ALT telomeres need to be protected from POT1 degradation in ALT-associated PML bodies, and identify TSPYL5 as a ALT+ cancer-specific therapeutic target.

A significant fraction (~10%) of cancer cells maintain their telomere length via a telomerase-independent mechanism known as Alternative Lengthening of Telomeres(ALT). Currently, there are no known molecular, ALT-specific, therapeutic target. We have identified TSPYL5 (Testis Specific Y-encoded-Like Protein 5) as a PML body component, co-localizing with ALT telomeres and critical for ALT+ cell viability. TSPYL5 was described as an inhibitor of the USP7 deubiquitinase. We report that TSPYL5 prevents the poly-ubiquitination of POT1 – a shelterin component – and protects POT1 from proteasomal degradation, exclusively in ALT+ cells. USP7 depletion rescued POT1 poly-ubiquitination and loss, suggesting that the deubiquitinase activates POT1 E3 ubiquitin ligase(s). Similarly, PML depletion suppressed POT1 poly-ubiquitination, suggesting an interplay between USP7 and PML to trigger POT1 degradation in TSPYL5-depleted ALT+ cells. We demonstrate that ALT telomeres need to be protected from POT1 degradation in ALT-associated PML bodies, and identify TSPYL5 as a ALT+ cancer-specific therapeutic target.

In photochemistry, the early 2000s have marked the beginning of the success story of iridium. Thanks to their exceptional optoelectronic properties and their great photostability, iridium(III)-based compounds have emerged as promising light-emitting and light-sensitive materials. Actually, iridium(III) is characterized by the unique capacity to accommodate up to three carbometalated bonds to give mono-, bis- or tris-cyclometalated complexes. Consequently, a wide variety of spectroelectrochemical properties are available, depending on the number of Ir-C bonds formed. Nevertheless, these properties may also be fine-tuned by modifying the chemical structure of the ligands chelated onto the metal center. Herein, we report on the synthesis of a novel family of trifluoromethyl-substituted bis-cyclometalated Ir(III) complexes with an increased photo-oxidizing power. Our goal was to develop type I sensitizers for oxygen-independent anticancer phototherapy. By modifying the diimine ligand, Ir(III)-based compounds with enhanced visible light absorption have also been obtained. They were studied in order to achieve photo-induced oxidation of halides upon solar excitation. Finally, more fundamental aspects, including the investigation of the primary light-induced processes leading to the final excited state of our complexes, have also been examined., (SC - Sciences) -- UCL, 2019

info:eu-repo/semantics/published

The slipper limpet Crepidula fornicata is an emblematic invasive species along the northeast Atlantic coast. This gregarious gastropod lives in stacks of several individuals and forms extended beds in shallow subtidal areas. The effects of this engineer species on the colonized habitat can be physical (e.g., presence of hard-shell substrates with uneven topography) or biological (e.g., nutrient enrichment by direct excretion or via biodeposition). We hypothesized that through biological activity, nutrient fluxes at the sediment-water interface are enhanced, leading to stimulated primary productivity by microphytobenthos (MPB) associated with Crepidula beds. To test this fertilization hypothesis, we conducted a 10-day mesocosm experiment using C. fornicata (live and dead) placed on top of sieved and homogenized sediment collected in situ. We used hyperspectral imaging to non-invasively map the development of MPB biomass, and to assess the potential influence of C. fornicata and its spatial extent. Our results showed that live C. fornicata significantly promote MPB growth through both physical and biological effects, with the biological effect dominating over the pure physical one. The highest stimulation was observed on the shells, suggesting that dissolved metabolic products excreted by C. fornicata were likely the main factor stimulating MPB growth in our short-term experiment. Our findings provide first direct evidence that stimulation of MPB growth by the biological activity of larger benthic epifauna occurs not only in intertidal but also in shallow subtidal habitats. More research is needed to assess the contribution of this fertilization effect to the trophic functioning of subtidal benthic systems.

Trophic ecology is the study of feeding interactions and food acquisition by organisms. It includes the causes and consequences of those behaviours at all levels of biological organisation. As a field of research, it crosses many disciplinary boundaries and provides knowledge that is pertinent to many other areas of ecology. Here we list and categorise the methods available to trophic ecologists whose toolbox has broadened considerably in recent years. They encompass empirical and numerical approaches with focus ranging from molecules to ecosystems. We further examine the relationship of each method to features such as the scale of observation (from microbes to largest organisms) and organisational level (from individuals to ecosystems) as well as the ecological question the method is capable of answering (from detecting predator-prey relationships to studying implications and consequences at different scales). Our survey reveals a very wide range of methodologies, each more-or-less appropriate for a particular line of research. It also identifies deficits, for example, trophic interactions at microscopic scales, for which empirical methods have hardly been used, as well as trophic models that have failed to consider fluxes at the ecosystem scale. Furthermore, we note that the combination of methodologies remains under-exploited despite great opportunities to solve complex ecological questions and to foster the emergence of new insights and hypotheses regarding organism, population and/or ecosystem properties.

The slipper limpet Crepidula fornicata is an emblematic invasive species along the northeast Atlantic coast. This gregarious gastropod lives in stacks of several individuals and forms extended beds in shallow subtidal areas. The effects of this engineer species on the colonized habitat can be physical (e.g., presence of hard-shell substrates with uneven topography) or biological (e.g., nutrient enrichment by direct excretion or via biodeposition). We hypothesized that through biological activity, nutrient fluxes at the sediment-water interface are enhanced, leading to stimulated primary productivity by microphytobenthos (MPB) associated with Crepidula beds. To test this fertilization hypothesis, we conducted a 10-day mesocosm experiment using C. fornicata (live and dead) placed on top of sieved and homogenized sediment collected in situ. We used hyperspectral imaging to non-invasively map the development of MPB biomass, and to assess the potential influence of C. fornicata and its spatial extent. Our results showed that live C. fornicata significantly promote MPB growth through both physical and biological effects, with the biological effect dominating over the pure physical one. The highest stimulation was observed on the shells, suggesting that dissolved metabolic products excreted by C. fornicata were likely the main factor stimulating MPB growth in our short-term experiment. Our findings provide first direct evidence that stimulation of MPB growth by the biological activity of larger benthic epifauna occurs not only in intertidal but also in shallow subtidal habitats. More research is needed to assess the contribution of this fertilization effect to the trophic functioning of subtidal benthic systems.

An estimated 10% of cancer cells maintain their telomeres with a telomerase-independent mechanism known as Alternative Lengthening of Telomeres, or ALT, for which no specific molecular target has been identified yet. Here, we unraveled novel roles for TSPYL5 (Testis Specific Y-encoded-Like Protein 5) in preventing proteasomal degradation of the shelterin component POT1 in ALT+ cells, but not in telomerase-expressing cells or normal fibroblasts. We found that TSPYL5 is a novel PML body component and protects ALT+ cells from telomere deprotection and cell death by titrating away the USP7 deubiquitinase, a TSPYL5-inhibited and PML body-associated protein, from the POT1 interaction partner, TPP1. Co-localization of ALT telomeres with PML bodies is responsible for the sensitivity to TSPYL5 depletion as PML depletion fully rescued POT1 loss. Our discovery that TSPYL5 is required for ALT+ cell viability by keeping POT1 offers novel therapeutic perspectives for ALT+ cancers.

An estimated 10% of cancer cells maintain their telomeres with a telomerase-independent mechanism known as Alternative Lengthening of Telomeres, or ALT, for which no specific molecular target has been identified yet. Here, we unraveled novel roles for TSPYL5 (Testis Specific Y-encoded-Like Protein 5) in preventing proteasomal degradation of the shelterin component POT1 in ALT+ cells, but not in telomerase-expressing cells or normal fibroblasts. We found that TSPYL5 is a novel PML body component and protects ALT+ cells from telomere deprotection and cell death by titrating away the USP7 deubiquitinase, a TSPYL5-inhibited and PML body-associated protein, from the POT1 interaction partner, TPP1. Co-localization of ALT telomeres with PML bodies is responsible for the sensitivity to TSPYL5 depletion as PML depletion fully rescued POT1 loss. Our discovery that TSPYL5 is required for ALT+ cell viability by keeping POT1 offers novel therapeutic perspectives for ALT+ cancers.

As the world demographic structure is getting older, highlighting strategies to counteract age-related diseases is a major public health concern. Telomeres are nucleoprotein structures that serve as guardians of genome stability by ensuring protection against both cell death and senescence. A hallmark of biological aging, telomere health is determined throughout the lifespan by a combination of both genetic and non-genetic influences. This review summarizes data from recently published studies looking at the effect of lifestyle variables such as nutrition and physical activity on telomere dynamics.

The design and characterization of new ruthenium(II) complexes aimed at targeting G-quadruplex DNA is reported. Importantly, these complexes are based on oxidizing 1,4,5,8-tetraazaphenanthrene (TAP) ancillary ligands known to favour photo-induced electron transfer (PET) with DNA. The photochemistry of complexes 1-4 has been studied by classical methods, which revealed two of them to be capable of photo-abstracting an electron from guanine. From studies of the interactions with DNA through luminescence, circular dichroism, bio-layer interferometry, and surface plasmon resonance experiments, we have demonstrated the selectivity of these complexes for telomeric G-quadruplex DNA over duplex DNA. Preliminary biological studies of these complexes have been performed: two of them showed remarkable photo-cytotoxicity towards telomerase-negative U2OS osteosarcoma cells, whereas very low mortality was observed in the dark at the same photo-drug concentration.

Among all small mols. that interfere with DNA replication, photodynamic therapeutic agents are of key interest in developing new strategies to design more specific and efficient anti-cancer treatments. Compared to classical chemotherapeutic agents, their activity can be finely controlled thanks to the light-triggering of their photoreactivity. Usually, the mechanism of photodynamic therapy relies on the generation of singlet oxygen by energy transfer from a photosensitizer. However, the activity of these type-II photosensitizers is significantly limited in hypoxic tumors. Therefore, the development of Type-I photosensitizing agents, which do not rely on the prodn. of ROS, is highly desirable. In this context, we developed new iridium(III) complexes which are able to photoreact with biomols.; namely, our Ir(III) complexes can oxidize guanine residues under visible light irradn. We report the synthesis and the extensive photophys. characterization of four new Ir(III) complexes. In addn. to an extensive exptl. and theor. study of the photophysics of these complexes, we characterize their photoreactivity towards model redox-active targets and the relevant biol. target, the guanine base. We demonstrate that photo-induced electron transfer takes place between the excited Ir(III) complex and guanine which leads to the formation of stable photoproducts, indicating that the targeted guanine is irreversibly damaged. These results pave the way to the elaboration of new Type-I photosensitizers for targeting cancerous cells.

Since the discovery of the anticancer properties of cisplatin, using new metals has progressively gained interest for the development of new therapeutic agents [1,2]. Among them, polyazaaromatic complexes of Ru(II) have shown interesting photochemical and photophysical properties. Indeed, upon light irradiation, the oxidation and reduction potential of these compounds are enhanced and for some of them, photocleavage and/or photoadduct formation with DNA have been demonstrated [3]. In this context, we aim at designing new photo-oxidizing complexes of Ru(II) complexes for the targeting of G-quadruplex DNA. G-quadruplex (G4) consist in secondary structures adopted by guanines-rich nucleic acids. These structures are formed through the stacking of guanine tetrads (G-quartet), the latter resulting from the coplanar arrangement of four guanines. They have been found in the telomeres where they appear to play crucial biological roles. Therefore, designing ligands able to selectively target G-quadruplex versus duplex DNA is of great interest. We report therein on the synthesis of new photo-oxidizing ruthenium(II) complexes [4]. They are able to photo-induce oxidative damage to telomeric G-quadruplex DNA through photo-induced electron transfer (PET) with guanine. The affinity and selectivity for G-quadruplex DNA have been evidenced thanks to steady-state luminescence studies, BLI and molecular modelling. Finally, we demonstrated the cell internalization and the photo-cytotoxicity towards human osteosarcoma cells. References [1] B. Rosenberg et al., Nature 2017, 222, 385-386. [2] MR. Gill et al., Chem. Soc. Rev. 2012, 41, 3179-3192. [3] B. Elias et al., Coordination Chem. Review. 2006, 1627-1641. [4] J. Weynand et al., Chem. Eur. J. 2018, in press.

The use of metal in medicine began with the serendipitous discovery of the anticancer properties of cisplatin.1 Since then, using new metals has progressively gained interest for the development of new therapeutic agents.2 Among them, polyazaaromatic complexes of Ru(II) have shown interesting photochemical and photophysical properties. Indeed, upon light irradiation, the oxidation and reduction potential of these compounds are enhanced and for some of them, photocleavage and/or photoadduct formation with DNA have been demonstrated.3 In this context, we aim at designing new photo-oxidizing complexes of Ru(II) complexes for the targeting of G-quadruplex DNA. G-quadruplex (G4) consist in particular secondary structures adopted by guanines-rich nucleic acids These structures are formed through the stacking of guanine tetrads (G-quartet), the latter resulting from the coplanar arrangement of four guanines.4 They have been found in the telomeres where they appear to play crucial biological roles. Therefore, designing ligands able to selectively target G-quadruplex versus duplex DNA is of great interest. We report therein on the synthesis of new photo-oxidizing ruthenium complexes. They are able to photo-induce oxidative damage to telomeric G-quadruplex DNA through photo-induced electron transfer (PET) with guanine. The affinity and selectivity for G-quadruplex DNA have been evidenced thanks to steady-state luminescence studies, BLI and molecular modelling. Finally, we demonstrated the cell internalization and the photo-cytotoxicity towards human osteosarcoma cells, which do not express telomerase.

Among all small molecules that interfere with DNA replication, photodynamic therapeutic agents are of key interest in developing new strategies to design more specific and efficient anti-cancer treatments. Compared to classical chemotherapeutic agents, their activity can be finely controlled thanks to the light-triggering of their photoreactivity. Usually, the mechanism of photodynamic therapy relies on the generation of singlet oxygen by energy transfer from a photosensitizer. However, the activity of these type-II photosensitizers is significantly limited in hypoxic tumors. Therefore, the development of Type-I photosensitizing agents, which do not rely on the production of ROS, is highly desirable. In this context, we developed new iridium(III) complexes which are able to photoreact with biomolecules; namely, our Ir(III) complexes can oxidize guanine residues under visible light irradiation. We report the synthesis and the extensive photophysical characterization of four new Ir(III) complexes. In addition to an extensive experimental and theoretical study of the photophysics of these complexes, we characterize their photoreactivity towards model redox-active targets and the relevant biological target, the guanine base. We demonstrate that photo-induced electron transfer takes place between the excited Ir(III) complex and guanine which leads to the formation of stable photoproducts, indicating that the targeted guanine is irreversibly damaged. These results pave the way to the elaboration of new Type-I photosensitizers for targeting cancerous cells.

Trophic ecology is the study of feeding interactions and food acquisition by organisms. It includes the causes and consequences of those behaviours at all levels of biological organisation. As a field of research, it crosses many disciplinary boundaries and provides knowledge that is pertinent to many other areas of ecology. Here we list and categorise the methods available to trophic ecologists whose toolbox has broadened considerably in recent years. They encompass empirical and numerical approaches with focus ranging from molecules to ecosystems. We further examine the relationship of each method to features such as the scale of observation (from microbes to largest organisms) and organisational level (from individuals to ecosystems) as well as the ecological question the method is capable of answering (from detecting predator-prey relationships to studying implications and consequences at different scales). Our survey reveals a very wide range of methodologies, each more-or-less appropriate for a particular line of research. It also identifies deficits, for example, trophic interactions at microscopic scales, for which empirical methods have hardly been used, as well as trophic models that have failed to consider fluxes at the ecosystem scale. Furthermore, we note that the combination of methodologies remains under-exploited despite great opportunities to solve complex ecological questions and to foster the emergence of new insights and hypotheses regarding organism, population and/or ecosystem properties.

The slipper limpet Crepidula fornicata is an emblematic invasive species along the northeast Atlantic coast. This gregarious gastropod lives in stacks of several individuals and forms extended beds in shallow subtidal areas. The effects of this engineer species on the colonized habitat can be physical (e.g., presence of hard-shell substrates with uneven topography) or biological (e.g., nutrient enrichment by direct excretion or via biodeposition). We hypothesized that through biological activity, nutrient fluxes at the sediment-water interface are enhanced, leading to stimulated primary productivity by microphytobenthos (MPB) associated with Crepidula beds. To test this fertilization hypothesis, we conducted a 10-day mesocosm experiment using C. fornicata (live and dead) placed on top of sieved and homogenized sediment collected in situ. We used hyperspectral imaging to non-invasively map the development of MPB biomass, and to assess the potential influence of C. fornicata and its spatial extent. Our results showed that live C. fornicata significantly promote MPB growth through both physical and biological effects, with the biological effect dominating over the pure physical one. The highest stimulation was observed on the shells, suggesting that dissolved metabolic products excreted by C. fornicata were likely the main factor stimulating MPB growth in our short-term experiment. Our findings provide first direct evidence that stimulation of MPB growth by the biological activity of larger benthic epifauna occurs not only in intertidal but also in shallow subtidal habitats. More research is needed to assess the contribution of this fertilization effect to the trophic functioning of subtidal benthic systems.

Trophic ecology is the study of feeding interactions and food acquisition by organisms. It includes the causes and consequences of those behaviours at all levels of biological organisation. As a field of research, it crosses many disciplinary boundaries and provides knowledge that is pertinent to many other areas of ecology. Here we list and categorise the methods available to trophic ecologists whose toolbox has broadened considerably in recent years. They encompass empirical and numerical approaches with focus ranging from molecules to ecosystems. We further examine the relationship of each method to features such as the scale of observation (from microbes to largest organisms) and organisational level (from individuals to ecosystems) as well as the ecological question the method is capable of answering (from detecting predator-prey relationships to studying implications and consequences at different scales). Our survey reveals a very wide range of methodologies, each more-or-less appropriate for a particular line of research. It also identifies deficits, for example, trophic interactions at microscopic scales, for which empirical methods have hardly been used, as well as trophic models that have failed to consider fluxes at the ecosystem scale. Furthermore, we note that the combination of methodologies remains under-exploited despite great opportunities to solve complex ecological questions and to foster the emergence of new insights and hypotheses regarding organism, population and/or ecosystem properties.

The slipper limpet Crepidula fornicata is an emblematic invasive species along the northeast Atlantic coast. This gregarious gastropod lives in stacks of several individuals and forms extended beds in shallow subtidal areas. The effects of this engineer species on the colonized habitat can be physical (e.g., presence of hard-shell substrates with uneven topography) or biological (e.g., nutrient enrichment by direct excretion or via biodeposition). We hypothesized that through biological activity, nutrient fluxes at the sediment-water interface are enhanced, leading to stimulated primary productivity by microphytobenthos (MPB) associated with Crepidula beds. To test this fertilization hypothesis, we conducted a 10-day mesocosm experiment using C. fornicata (live and dead) placed on top of sieved and homogenized sediment collected in situ. We used hyperspectral imaging to non-invasively map the development of MPB biomass, and to assess the potential influence of C. fornicata and its spatial extent. Our results showed that live C. fornicata significantly promote MPB growth through both physical and biological effects, with the biological effect dominating over the pure physical one. The highest stimulation was observed on the shells, suggesting that dissolved metabolic products excreted by C. fornicata were likely the main factor stimulating MPB growth in our short-term experiment. Our findings provide first direct evidence that stimulation of MPB growth by the biological activity of larger benthic epifauna occurs not only in intertidal but also in shallow subtidal habitats. More research is needed to assess the contribution of this fertilization effect to the trophic functioning of subtidal benthic systems.

info:eu-repo/semantics/nonPublished

info:eu-repo/semantics/nonPublished