Publications de l'unité - UMR9187 / U1196 - Chimie et Modélisation pour la Biologie du Cancer (CMBC) - Institut Curie
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Publications de l’unité
UMR9187 / U1196 – Chimie et Modélisation pour la Biologie du Cancer
(CMBC)
Année de publication : 2020
Paudel B.P., Moye A.L., Assi H.A., El-Khoury R., Cohen S.B., Birrento M.L., Samosorn S.,
Intharapichai K., Tomlinson C.G., Teulade-Fichou M.P., Gonz'alez C., Beck J.L., Damha M.J., van
Oijen A.M., Bryan T.M. (2020 Feb 27)
A mechanism for the extension and unfolding of parallel telomeric G-
quadruplexes by human telomerase at single-molecule resolution
bioRxiv : DOI : 10.1101/2020.02.26.965269
Résumé
Telomeric G-quadruplexes (G4) were long believed to form a protective structure at
telomeres, preventing their extension by the ribonucleoprotein telomerase. Contrary to this
belief, we have previously demonstrated that parallel-stranded conformations of telomeric
G4 can be extended by human and ciliate telomerase. However, a mechanistic
understanding of the interaction of telomerase with structured DNA remained elusive. Here,
we use single-molecule fluorescence resonance energy transfer (smFRET) microscopy and
bulk-phase enzymology to propose a mechanism for the resolution and extension of parallel
G4 by telomerase. Binding is initiated by the RNA template of telomerase interacting with
the G-quadruplex; nucleotide addition then proceeds to the end of the RNA template. It is
only through the large conformational change of translocation following synthesis that the G-
quadruplex structure is completely unfolded to a linear product. Surprisingly, parallel G4
stabilization with either small molecule ligands or by chemical modification does not always
inhibit G4 unfolding and extension by telomerase. These data reveal that telomerase is a
parallel G-quadruplex resolvase.
Marie-Ming Aynaud, Olivier Mirabeau, Nadege Gruel, Sandrine Grossetête, Valentina Boeva,
Simon Durand, Didier Surdez, Olivier Saulnier, Sakina Zaïdi, Svetlana Gribkova, Aziz Fouché,
Ulykbek Kairov, Virginie Raynal, Franck Tirode, Thomas G P Grünewald, Mylene Bohec, Sylvain
Baulande, Isabelle Janoueix-Lerosey, Jean-Philippe Vert, Emmanuel Barillot, Olivier Delattre,
Andrei Zinovyev (2020 Feb 13)
Transcriptional Programs Define Intratumoral Heterogeneity of Ewing Sarcoma
at Single-Cell Resolution.
Cell reports : 1767-1779.e6 : DOI : S2211-1247(20)30074-7
Résumé
EWSR1-FLI1, the chimeric oncogene specific for Ewing sarcoma (EwS), induces a cascade of
signaling events leading to cell transformation. However, it remains elusive how genetically
homogeneous EwS cells can drive the heterogeneity of transcriptional programs. Here, we
combine independent component analysis of single-cell RNA sequencing data from diverse
cell types and model systems with time-resolved mapping of EWSR1-FLI1 binding sites and
of open chromatin regions to characterize dynamic cellular processes associated with
EWSR1-FLI1 activity. We thus define an exquisitely specific and direct enhancer-driven
INSTITUT CURIE, 20 rue d’Ulm, 75248 Paris Cedex 05, France | 1Publications de l’unité
UMR9187 / U1196 – Chimie et Modélisation pour la Biologie du Cancer
(CMBC)
EWSR1-FLI1 program. In EwS tumors, cell proliferation and strong oxidative phosphorylation
metabolism are associated with a well-defined range of EWSR1-FLI1 activity. In contrast, a
subpopulation of cells from below and above the intermediary EWSR1-FLI1 activity is
characterized by increased hypoxia. Overall, our study reveals sources of intratumoral
heterogeneity within EwS tumors.
Johnson Courtney R. , Steingesser Marc G., Khan Anum, Gladfelter Amy, Bertin Aurélie, McMurray
Michael A. (2020 Jan 28)
Guanidine hydrochloride reactivates an ancient septin hetero-oligomer
assembly pathway in budding yeast
eLife : eLife 2020;9:e54355 : DOI : DOI: 10.7554/eLife.54355
Résumé
Septin proteins evolved from ancestral GTPases and co-assemble into hetero-oligomers and
cytoskeletal filaments. In Saccharomyces cerevisiae, five septins comprise two species of
hetero-octamers, Cdc11/Shs1–Cdc12–Cdc3–Cdc10–Cdc10–Cdc3–Cdc12–Cdc11/Shs1. Slow
GTPase activity by Cdc12 directs the choice of incorporation of Cdc11 vs Shs1, but many
septins, including Cdc3, lack GTPase activity. We serendipitously discovered that guanidine
hydrochloride rescues septin function in cdc10 mutants by promoting assembly of non-native
Cdc11/Shs1–Cdc12–Cdc3–Cdc3–Cdc12–Cdc11/Shs1 hexamers. We provide evidence that in S.
cerevisiae Cdc3 guanidinium occupies the site of a ‘missing’ Arg side chain found in other
fungal species where (i) the Cdc3 subunit is an active GTPase and (ii) Cdc10-less hexamers
natively co-exist with octamers. We propose that guanidinium reactivates a latent septin
assembly pathway that was suppressed during fungal evolution in order to restrict assembly
to octamers. Since homodimerization by a GTPase-active human septin also creates
hexamers that exclude Cdc10-like central subunits, our new mechanistic insights likely apply
throughout phylogeny.
Nishit Srivastava, David Traynor, Matthieu Piel, Alexandre J Kabla, Robert R Kay (2020 Jan 23)
Pressure sensing through Piezo channels controls whether cells migrate with
blebs or pseudopods.
Proceedings of the National Academy of Sciences of the United States of America : DOI :
201905730
Résumé
Blebs and pseudopods can both power cell migration, with blebs often favored in tissues,
where cells encounter increased mechanical resistance. To investigate how migrating cells
detect and respond to mechanical forces, we used a « cell squasher » to apply uniaxial
pressure to cells chemotaxing under soft agarose. As little as 100 Pa causes a rapid (Publications de l’unité
UMR9187 / U1196 – Chimie et Modélisation pour la Biologie du Cancer
(CMBC)
motility requires extracellular calcium and is accompanied by increased cytosolic calcium. It
is largely abrogated in cells lacking the Piezo stretch-operated channel; under load, these
cells persist in using pseudopods and chemotax poorly. We propose that migrating cells
sense pressure through Piezo, which mediates calcium influx, directing movement with blebs
instead of pseudopods.
Xavier Sabaté-Cadenas, Alena Shkumatava (2020 Jan 18)
In-Cell Discovery of RNA-Protein Interactions.
Trends in biochemical sciences : DOI : S0968-0004(19)30264-6
Résumé
Jiawei Wang, Mingpan Cheng, Jielin Chen, Huangxian Ju, David Monchaud, Jean-Louis Mergny, Jun
Zhou (2020 Jan 18)
An oxidatively damaged G-quadruplex/hemin DNAzyme.
Chemical communications (Cambridge, England) : 56 : 1839-1842 : DOI : 10.1039/c9cc09237d
Résumé
Oxidative damage of guanine to 8-oxoguanine triggers a partial and variable loss of G-
quadruplex/hemin DNAzyme activity and provides clues to the mechanistic origins of
DNAzyme deactivation, which originates from an interplay between decreased G-quadruplex
stability, lower hemin affinity and a modification of the nature of hemin binding sites.
Decaudin Didier, Frisch Dit Leitz Estelle, Nemati Fariba, Tarin Malcy, Naguez Adnan, Zerara
Mohamed, Marande Benjamin, Vivet-Noguer Raquel, Halilovic Ensar, Fabre Claire, Jochemsen
Aart, Roman-Roman Sergio, Alsafadi Samar. (2020 Jan 9)
Preclinical evaluation of drug combinations identifies co-inhibition of Bcl-2/XL/W
and MDM2 as a potential therapy in uveal melanoma.
European Journal of CancerEuropean Journal of Cancer : DOI : 10.1016/j.ejca.2019.12.012
Résumé
Allard A, Bouzid M, Betz T, Simon C, Abou-Ghali M, Lemière J, Valentino F, Manzi J, Brochard-
Wyart F, Guevorkian K, Plastino J, Lenz M, Campillo C*, Sykes C* (2020 Jan 1)
Actin modulates shape and mechanics of tubular membranes
bioRxiv : DOI : 10.1101/712505
Résumé
INSTITUT CURIE, 20 rue d’Ulm, 75248 Paris Cedex 05, France | 3Publications de l’unité
UMR9187 / U1196 – Chimie et Modélisation pour la Biologie du Cancer
(CMBC)
Davidson PM, Battistella A, Déjardin T, Betz T, Plastino J, Cadot B, Borghi N, Sykes C (2020 Jan 1)
Actin accumulates nesprin-2 at the front of the nucleus during confined cell
migration
bioRxiv : DOI : 10.1101/713982
Résumé
Zuffo M., Gandolfini A., Heddi B., Granzhan A. (2020 Jan 1)
Harnessing intrinsic fluorescence for typing of secondary structures of DNA
bioRxiv : DOI : 10.1101/2020.01.15.907501
Résumé
DNA is polymorphic since, despite its ubiquitous presence as a double-stranded helix, it is
able to fold into a plethora of other secondary structures both in vitro and in cells. Despite
the considerable advances that have been made in understanding this structural diversity,
its high-throughput investigation still faces severe limitations. This mainly stems from the
lack of suitable label-free methods, combining a fast and cheap experimental workflow with
high information content. Here, we explore the use of intrinsic fluorescence emitted by
nucleic acids for this scope. After a preliminary assessment of the suitability of this
phenomenon for tracking the conformational changes of DNA, we examined the intrinsic
steady-state emission spectra of an 89-membered set of synthetic oligonucleotides with
reported conformation (G-quadruplexes, i-motifs, single- and double stranded DNA) by
means of multivariate analysis. Specifically, principal component analysis of emission
spectra resulted in successful clustering of oligonucleotides into three corresponding
conformational groups, albeit without discrimination between single- and double-stranded
structures. Linear discriminant analysis of the same training set was exploited for the
assessment of new sequences, allowing the evaluation of their G4-forming propensity. Our
method does not require any labelling agent or dye, avoiding the related intrinsic bias, and
can be utilized to screen novel sequences of interest in a high-throughput and cost-effective
manner. In addition, we observed that left-handed (Z-) G4 structures were systematically
more fluorescent than most other G4 structures, almost reaching the quantum yield of 5′-
d[(G3T)3G3]-3′ (G3T), the most fluorescent G4 structure reported to date. This property is
likely to arise from the similar base-stacking geometry in both types of structures.
Année de publication : 2019
Stéphanie Lemaître, Florent Poyer, Paul Fréneaux, Sophie Leboucher, François Doz, Nathalie
Cassoux, Carole D Thomas (2019 Dec 25)
Low retinal toxicity of intravitreal carboplatin associated with good retinal
tumor control in transgenic murine retinoblastoma.
Clinical & experimental ophthalmology : DOI : 10.1111/ceo.13711
INSTITUT CURIE, 20 rue d’Ulm, 75248 Paris Cedex 05, France | 4Publications de l’unité
UMR9187 / U1196 – Chimie et Modélisation pour la Biologie du Cancer
(CMBC)
Résumé
Purpose
Retinoblastoma is a rare intraocular malignancy in children. Current treatments have many
adverse effects. New therapeutic approaches like intravitreal injections of chemotherapies
are currently being developed but their toxicities need to be evaluated on animal models.
This study compares the efficacy and toxicity of intravitreal melphalan, topotecan and
carboplatin, alone or in combination (sequential administration), in the LHBetaTag
retinoblastoma mice.
Methods
Mice were divided into 9 groups: control, carboplatin 1.5 and 4μg, melphalan 0.1 and 1μg,
topotecan 0.1 and 1μg, carboplatin 4μg/ topotecan 0.1μg and melphalan 1μg/ topotecan
0.1μg. The follow‐up was performed using fundus imaging and optical coherence
tomography combined with histopathological analysis. Absence of tumor and presence of
calcified tumors were the criteria for therapeutic response assessment. Ocular complications
were assessed after 4 weekly injections. Retinal toxicity was defined by the decrease of
retinal thickness and of the number of retinal layers.
Results
Topotecan was inactive on retinal tumors. Melphalan (1μg) led to a complete tumor control
in 91.7% of eyes. Carboplatin strongly decreased the tumor burden (85.7‐93.8% of eyes
without retinal tumor). The intravitreal injection itself led to ocular complications (25% of
media opacities and 45.7% of retinal detachment). Only melphalan at 1μg showed a strong
retinal toxicity. The two combinations showed a good efficacy in reducing the number of
eyes with retinal tumors with a reduced retinal toxicity.
Conclusions
This preclinical study suggests that intravitreal injection of carboplatin has a low toxicity and
could be evaluated in clinical practice to treat patients suffering from retinoblastoma.
Mouawad L., Beswick V., Jamin N., Montigny C., Quiniou E., Barbot T. (2019 Dec 18)
Deciphering the mechanism of inhibition of SERCA1a by sarcolipin using
molecular simulations
bioRxiv : DOI : 10.1101/2019.12.17.879825
Résumé
SERCA1a is an ATPase calcium pump that transports Ca2+ from the cytoplasm to the
sarco/endoplasmic reticulum lumen. Sarcolipin (SLN), a transmembrane peptide, regulates
the activity of SERCA1a by decreasing its Ca2+ transport rate, but its mechanism of action is
INSTITUT CURIE, 20 rue d’Ulm, 75248 Paris Cedex 05, France | 5Publications de l’unité
UMR9187 / U1196 – Chimie et Modélisation pour la Biologie du Cancer
(CMBC)
still not well understood. To decipher this mechanism, we have performed normal modes
analysis in the all-atom model, with the SERCA1a-SLN complex or the isolated SERCA1a
embedded in an explicit membrane. The comparison of the results allowed us to provide an
explanation for the action of SLN that is in good agreement with experimental observations.
In our analyses, the presence of SLN locally perturbs the TM6 transmembrane helix and as a
consequence modifies the position of D800, one of the key metal-chelating residues.
Additionally, it reduces the flexibility of the gating residues, V304 and E309 in TM4, at the
entrance of the Ca2+ binding sites, which would decrease the affinity for Ca2+.
Unexpectedly, SLN has also an effect on the ATP binding site more than 35 r A away, due to
the straightening of TM5, a long helix considered as the spine of the protein. The
straightening of TM5 modifies the structure of the P-N linker that sits above it, and which
comprises the 351DKTG354 conserved motif, resulting in an increase of the distance
between ATP and the phosphorylation site. As a consequence, the turn-over rate could be
affected. All this gives SERCA1a the propensity to go toward a Ca2+-deprived E2-like state in
the presence of SLN and toward a Ca2+ high-affinity E1-like state in the absence of SLN,
although the SERCA1a-SLN complex was crystallized in an E1-like state. In addition to a
general mechanism of inhibition of SERCA1a regulatory peptides, this study also provides an
insight in the conformational transition between the E2 and E1 states.
Shensi Shen, Sara Faouzi, Amandine Bastide, Sylvain Martineau, Hélène Malka-Mahieu, Yu Fu,
Xiaoxiao Sun, Christine Mateus, Emilie Routier, Severine Roy, Laurent Desaubry, Fabrice André,
Alexander Eggermont, Alexandre David, Jean-Yves Scoazec, Stéphan Vagner, Caroline Robert
(2019 Dec 18)
An epitranscriptomic mechanism underlies selective mRNA translation
remodelling in melanoma persister cells.
Nature communications : 5713 : DOI : 10.1038/s41467-019-13360-6
Résumé
Cancer persister cells tolerate anticancer drugs and serve as the founders of acquired
resistance and cancer relapse. Here we show that a subpopulation of BRAF mutant
melanoma cells that tolerates exposure to BRAF and MEK inhibitors undergoes a reversible
remodelling of mRNA translation that evolves in parallel with drug sensitivity. Although this
process is associated with a global reduction in protein synthesis, a subset of mRNAs
undergoes an increased efficiency in translation. Inhibiting the eIF4A RNA helicase, a
component of the eIF4F translation initiation complex, abrogates this selectively increased
translation and is lethal to persister cells. Translation remodelling in persister cells coincides
with an increased N6-methyladenosine modification in the 5′-untranslated region of some
highly translated mRNAs. Combination of eIF4A inhibitor with BRAF and MEK inhibitors
effectively inhibits the emergence of persister cells and may represent a new therapeutic
strategy to prevent acquired drug resistance.
Olivier Brison, Sami El-Hilali, Dana Azar, Stéphane Koundrioukoff, Mélanie Schmidt, Viola Nähse,
Yan Jaszczyszyn, Anne-Marie Lachages, Bernard Dutrillaux, Claude Thermes, Michelle Debatisse,
INSTITUT CURIE, 20 rue d’Ulm, 75248 Paris Cedex 05, France | 6Publications de l’unité
UMR9187 / U1196 – Chimie et Modélisation pour la Biologie du Cancer
(CMBC)
Chun-Long Chen (2019 Dec 15)
Transcription-mediated organization of the replication initiation program across
large genes sets common fragile sites genome-wide.
Nature communications : 5693 : DOI : 10.1038/s41467-019-13674-5
Résumé
Common fragile sites (CFSs) are chromosome regions prone to breakage upon replication
stress known to drive chromosome rearrangements during oncogenesis. Most CFSs nest in
large expressed genes, suggesting that transcription could elicit their instability; however,
the underlying mechanisms remain elusive. Genome-wide replication timing analyses here
show that stress-induced delayed/under-replication is the hallmark of CFSs. Extensive
genome-wide analyses of nascent transcripts, replication origin positioning and fork
directionality reveal that 80% of CFSs nest in large transcribed domains poor in initiation
events, replicated by long-travelling forks. Forks that travel long in late S phase explains CFS
replication features, whereas formation of sequence-dependent fork barriers or head-on
transcription-replication conflicts do not. We further show that transcription inhibition during
S phase, which suppresses transcription-replication encounters and prevents origin resetting,
could not rescue CFS stability. Altogether, our results show that transcription-dependent
suppression of initiation events delays replication of large gene bodies, committing them to
instability.
Année de publication : 2020
Katerina Duskova, Pauline Lejault, Élie Benchimol, Régis Guillot, Sébastien Britton, Anton
Granzhan, David Monchaud (2019 Dec 13)
DNA junction ligands trigger DNA damage and are synthetic lethal with DNA
repair inhibitors in cancer cells
Journal of the American Chemical Society : 142 : 424-435 : DOI : 10.1021/jacs.9b11150
Résumé
INSTITUT CURIE, 20 rue d’Ulm, 75248 Paris Cedex 05, France | 7Publications de l’unité
UMR9187 / U1196 – Chimie et Modélisation pour la Biologie du Cancer
(CMBC)
Translocation of DNA and RNA polymerases along their duplex substrates results in DNA
supercoiling. This torsional stress promotes the formation of plectonemic structures,
including three-way DNA junction (TWJ), which can block DNA transactions and lead to DNA
damage. While cells have evolved multiple mechanisms to prevent the accumulation of such
structures, stabilizing TWJ through ad hoc ligands offer an opportunity to trigger DNA
damage in cells with high level of transcription and replication, such as cancer cells. Here,
we develop a series of azacryptand-based TWJ ligands, we thoroughly characterize their TWJ-
interacting properties in vitro and demonstrate their capacity to trigger DNA damage in
rapidly dividing human cancer cells. We also demonstrate that TWJ ligands are amenable to
chemically induced synthetic lethality strategies upon association with inhibitors of DNA
repair, thus paving the way towards innovative drug combinations to fight cancers.
INSTITUT CURIE, 20 rue d’Ulm, 75248 Paris Cedex 05, France | 8You can also read
