ALC1 links chromatin accessibility to PARP inhibitor response in homologous recombination deficient cells
Posted on: 31 December 2020
Preprint posted on 16 December 2020
Article now published in Nature Cell Biology at http://dx.doi.org/10.1038/s41556-020-00624-3
The chromatin remodeler ALC1 contributes to PARPi toxicity in BRCA-deficient cancer cells.
Selected by Giuseppina D'AlessandroCategories: cancer biology, cell biology
Background
Everyday thousands of lesions challenge the stability of our DNA. To preserve genome integrity, our cells activate a number of dedicated DNA repair pathways. The poly(ADP-ribose) polymerase (PARP) enzymes, in particular PARP1 and PARP2, recognize single-strand DNA breaks (SSB) and other DNA lesions and deposit poly(ADP-ribose) (PAR) chains that modulate the DNA damage response and chromatin remodelling (Ray Chaudhuri and Nussenzweig, 2017). PARP inhibitors (PARPi) not only impair the enzymes catalytic activity but can also “trap” them on chromatin, thus leading to the generation of DNA lesions that require the homologous recombination (HR) proteins BRCA1 and BRCA2 for repair (Murai, 2012). This makes HR-deficient cancer cells specifically sensitive to PARPi.
Despite numerous studies investigated the impact of PARylation on chromatin accessibility, the contribution of chromatin remodelling to the toxicity of PARPi in HR deficient cells is less clear. In this preprint, the authors demonstrate that loss of the PAR-dependent chromatin remodeler ALC1 contributes to PARPi toxicity in BRCA-deficient cancer cells.
Figure 1: PARP-mediated PARylation induces chromatin de-condensation and mediates ALC1 recruitment, which, in turn, further increases chromatin accessibility. In the absence of ALC1 and PARP activities, recruitment of base damage repair factors to the chromatin is reduced. During S-phase, unrepaired lesions generate replication coupled single-strand gaps and DSBs that rely on BRCA-dependent HR repair (From this preprint under the CC-BY-NC-ND 4.0 International license).
Key findings:
- ALC1 loss is synthetically lethal with BRCA loss, hypersensitizes BRCA-deficient cells to PARPi, and overcomes known mechanisms of resistance to PARPi
By performing a CRISPR-screen, the authors identified the chromatin remodeler ALC1/CHD1L as a factor that further sensitized BRCA-mutant cancer cells to the PARPi, olaparib. PARPi hyper-sensitivity of ALC1 knockout cells was not due to defective SSB or DNA double-strand breaks (DSB) response, as demonstrated by additivity between loss of ALC1 and SSBR/HR proteins. The authors also demonstrated that ALC1 loss overcame known mechanisms of resistance to PARPi, such as 53BP1 loss, which removes the barrier to DNA end resection, thus partially restoring HR in BRCA1-deficient cells. ALC1 depletion was also able to overcome olaparib resistance due to PARP1 loss, thus suggesting a role for PARP2 in mediating PARPi toxicity in this context, likely caused by the increased PARP2 trapping observed in ALC1 deficient cells.
- ALC1 loss increases genomic instability and reliance on BRCA-dependent HR.
ALC1 loss in BRCA-mutant cells increased single-strand DNA (as monitored by non-denaturing CIdU immunofluorescence), DSBs in S-phase (as monitored by γH2AX immunofluorescence), and radial chromosomes. ALC1 deficiency hyper-sensitized cells to SSBs induced by the alkylating agent methyl methanesulfonate (MMS), but not by the topoisomerase I poison camptothecin. Based on these data, the authors argue that ALC1 remodels chromatin around complex lesions, as those generated by alkylating agents, rather than being generally required for SSB repair. ALC1-deficient cells accumulated replication-coupled single-strand gaps, as shown by the higher S1 nuclease sensitivity of nascent replication tracts, that require SSB and HR repair mechanisms.
- ALC1 localizes to chromatin via PARP1 and PARP2-dependent PARylation.
Immunofluorescence of undamaged cells revealed ALC1 localization on S-phase chromatin in the presence of PARG inhibitor, which enhances PARylation. Differently, ALC1 chromatinization was detected in both S- and non-S- phase cells upon treatment with MMS and was abolished in PARP1 and PARP2 knockout cells.
- ALC1 chromatin remodeling and PAR binding activities are essential to protect BRCA-mutant cells from PARPi and alkylation damage
As a member of the SNF2 superfamily, ALC1 uses its ATPase activity to remodel nucleosome in vitro and it also contains a PAR-binding macrodomain that controls its recruitment to chromatin and its allosteric activation (Ahel, 2009; Gottschalk, 2009). To study how each of these domains affected PARPi hypersensitivity of BRCA-mutant cells, the authors complemented ALC1 knockout cells with different ALC1 mutants. ALC1 mutants lacking nucleosome sliding activity (by either mutation within the ATPase domain or mutation of the residues responsible for the interaction with the basic histone H4) or mutants unable to bind PAR (by mutations within the macrodomain) did not rescue PARPi sensitivity of BRCA mutant cells, thus suggesting that both the nucleosome remodeling and PAR-binding activity are required to protect BRCA-mutant cells from PARPi.
- ALC1 and PARP activity cooperate to promote chromatin accessibility
ALC1 loss reduced overall chromatin accessibility, as monitored by ATAC-seq (Assay for Transpose-Accessible Chromatin), while not causing locus-specific changes or transcriptional changes. As a consequence, the chromatin association of base damage repair factors, including the apurinic/apyrimidinic endonuclease APE1 and XRCC1, was reduced. Reduced chromatin accessibility and recruitment of base damage repair protein were exacerbated by PARPi, thus suggesting that ALC1 and PARP cooperate to promote chromatin accessibility.
Future perspectives and questions for the authors
In summary, the authors demonstrated that ALC1 loss reduces the viability of BRCA-mutant cells and further sensitizes them to PARPi, thus revealing a new vulnerability in HR deficient cancers. Since loss of ALC1 ATPase activity phenocopies ALC1-loss, ALC1 inhibitors could represent a future opportunity to overcome acquired PARPi resistance in BRCA-deficient cells. The authors propose that ALC1 chromatin remodeling activity favors the processing of complex lesions and, together with PARP1 and PARP2 activity, enhances chromatin recruitment of base repair factors. PARP inhibition in ALC1 deficient cells causes accumulation of lesions that rely on BRCA-mediated HR during S-phase.
- ALC1 loss hyper-sensitizes BRCA-deficient cells to all the tested PARPi: veliparib, olaparib and talazoparib. Interestingly, a smaller sensitivity window is observed with the strongest PARP trapper talazoparib: could this suggest that PARP trapping is less crucial in the context of ALC1 loss?
- It is interesting that ALC1 loss increases PARP2 trapping, but does not seem to affect PARP1, as observed in chromatin fractionation experiment. It would be interesting to hear the author’s opinion on this, also in the light of the recent publication reporting a role for ALC1 in releasing PARP2 but not PARP1 from chromatin (Blessing, 2020).
- ALC1 loss is synthetically lethal with BRCA deficiency even in the absence of PARPi: could this suggest that ALC1 inhibitors would be effective in BRCA deficient tumors even as an alternative to PARPi? What could be the underlying mechanism responsible for this synthetic lethality?
doi: https://doi.org/10.1242/prelights.26696
Read preprintSign up to customise the site to your preferences and to receive alerts
Register hereAlso in the cancer biology category:
Mitochondria-derived nuclear ATP surge protects against confinement-induced proliferation defects
Teodora Piskova
Spatial transcriptomics elucidates medulla niche supporting germinal center response in myasthenia gravis thymoma
Jessica Chevallier
Invasion of glioma cells through confined space requires membrane tension regulation and mechano-electrical coupling via Plexin-B2
Jade Chan
Also in the cell biology category:
The RNA binding protein HNRNPA2B1 regulates RNA abundance and motor protein activity in neurites
Felipe Del Valle Batalla
Pharyngeal neuronal mechanisms governing sour taste perception in Drosophila melanogaster
Matthew Davies
Feedback regulation by the RhoA-specific GEF ARHGEF17 regulates actomyosin network disassembly
Vibha SINGH
preListscancer biology category:
in theBSCB-Biochemical Society 2024 Cell Migration meeting
This preList features preprints that were discussed and presented during the BSCB-Biochemical Society 2024 Cell Migration meeting in Birmingham, UK in April 2024. Kindly put together by Sara Morais da Silva, Reviews Editor at Journal of Cell Science.
List by | Reinier Prosee |
CSHL 87th Symposium: Stem Cells
Preprints mentioned by speakers at the #CSHLsymp23
List by | Alex Eve |
Journal of Cell Science meeting ‘Imaging Cell Dynamics’
This preList highlights the preprints discussed at the JCS meeting 'Imaging Cell Dynamics'. The meeting was held from 14 - 17 May 2023 in Lisbon, Portugal and was organised by Erika Holzbaur, Jennifer Lippincott-Schwartz, Rob Parton and Michael Way.
List by | Helen Zenner |
CellBio 2022 – An ASCB/EMBO Meeting
This preLists features preprints that were discussed and presented during the CellBio 2022 meeting in Washington, DC in December 2022.
List by | Nadja Hümpfer et al. |
Fibroblasts
The advances in fibroblast biology preList explores the recent discoveries and preprints of the fibroblast world. Get ready to immerse yourself with this list created for fibroblasts aficionados and lovers, and beyond. Here, my goal is to include preprints of fibroblast biology, heterogeneity, fate, extracellular matrix, behavior, topography, single-cell atlases, spatial transcriptomics, and their matrix!
List by | Osvaldo Contreras |
Single Cell Biology 2020
A list of preprints mentioned at the Wellcome Genome Campus Single Cell Biology 2020 meeting.
List by | Alex Eve |
ASCB EMBO Annual Meeting 2019
A collection of preprints presented at the 2019 ASCB EMBO Meeting in Washington, DC (December 7-11)
List by | Madhuja Samaddar et al. |
Lung Disease and Regeneration
This preprint list compiles highlights from the field of lung biology.
List by | Rob Hynds |
Anticancer agents: Discovery and clinical use
Preprints that describe the discovery of anticancer agents and their clinical use. Includes both small molecules and macromolecules like biologics.
List by | Zhang-He Goh |
Biophysical Society Annual Meeting 2019
Few of the preprints that were discussed in the recent BPS annual meeting at Baltimore, USA
List by | Joseph Jose Thottacherry |
Also in the cell biology category:
BSCB-Biochemical Society 2024 Cell Migration meeting
This preList features preprints that were discussed and presented during the BSCB-Biochemical Society 2024 Cell Migration meeting in Birmingham, UK in April 2024. Kindly put together by Sara Morais da Silva, Reviews Editor at Journal of Cell Science.
List by | Reinier Prosee |
‘In preprints’ from Development 2022-2023
A list of the preprints featured in Development's 'In preprints' articles between 2022-2023
List by | Alex Eve, Katherine Brown |
preLights peer support – preprints of interest
This is a preprint repository to organise the preprints and preLights covered through the 'preLights peer support' initiative.
List by | preLights peer support |
The Society for Developmental Biology 82nd Annual Meeting
This preList is made up of the preprints discussed during the Society for Developmental Biology 82nd Annual Meeting that took place in Chicago in July 2023.
List by | Joyce Yu, Katherine Brown |
CSHL 87th Symposium: Stem Cells
Preprints mentioned by speakers at the #CSHLsymp23
List by | Alex Eve |
Journal of Cell Science meeting ‘Imaging Cell Dynamics’
This preList highlights the preprints discussed at the JCS meeting 'Imaging Cell Dynamics'. The meeting was held from 14 - 17 May 2023 in Lisbon, Portugal and was organised by Erika Holzbaur, Jennifer Lippincott-Schwartz, Rob Parton and Michael Way.
List by | Helen Zenner |
9th International Symposium on the Biology of Vertebrate Sex Determination
This preList contains preprints discussed during the 9th International Symposium on the Biology of Vertebrate Sex Determination. This conference was held in Kona, Hawaii from April 17th to 21st 2023.
List by | Martin Estermann |
Alumni picks – preLights 5th Birthday
This preList contains preprints that were picked and highlighted by preLights Alumni - an initiative that was set up to mark preLights 5th birthday. More entries will follow throughout February and March 2023.
List by | Sergio Menchero et al. |
CellBio 2022 – An ASCB/EMBO Meeting
This preLists features preprints that were discussed and presented during the CellBio 2022 meeting in Washington, DC in December 2022.
List by | Nadja Hümpfer et al. |
Fibroblasts
The advances in fibroblast biology preList explores the recent discoveries and preprints of the fibroblast world. Get ready to immerse yourself with this list created for fibroblasts aficionados and lovers, and beyond. Here, my goal is to include preprints of fibroblast biology, heterogeneity, fate, extracellular matrix, behavior, topography, single-cell atlases, spatial transcriptomics, and their matrix!
List by | Osvaldo Contreras |
EMBL Synthetic Morphogenesis: From Gene Circuits to Tissue Architecture (2021)
A list of preprints mentioned at the #EESmorphoG virtual meeting in 2021.
List by | Alex Eve |
FENS 2020
A collection of preprints presented during the virtual meeting of the Federation of European Neuroscience Societies (FENS) in 2020
List by | Ana Dorrego-Rivas |
Planar Cell Polarity – PCP
This preList contains preprints about the latest findings on Planar Cell Polarity (PCP) in various model organisms at the molecular, cellular and tissue levels.
List by | Ana Dorrego-Rivas |
BioMalPar XVI: Biology and Pathology of the Malaria Parasite
[under construction] Preprints presented at the (fully virtual) EMBL BioMalPar XVI, 17-18 May 2020 #emblmalaria
List by | Dey Lab, Samantha Seah |
1
Cell Polarity
Recent research from the field of cell polarity is summarized in this list of preprints. It comprises of studies focusing on various forms of cell polarity ranging from epithelial polarity, planar cell polarity to front-to-rear polarity.
List by | Yamini Ravichandran |
TAGC 2020
Preprints recently presented at the virtual Allied Genetics Conference, April 22-26, 2020. #TAGC20
List by | Maiko Kitaoka et al. |
3D Gastruloids
A curated list of preprints related to Gastruloids (in vitro models of early development obtained by 3D aggregation of embryonic cells). Updated until July 2021.
List by | Paul Gerald L. Sanchez and Stefano Vianello |
ECFG15 – Fungal biology
Preprints presented at 15th European Conference on Fungal Genetics 17-20 February 2020 Rome
List by | Hiral Shah |
ASCB EMBO Annual Meeting 2019
A collection of preprints presented at the 2019 ASCB EMBO Meeting in Washington, DC (December 7-11)
List by | Madhuja Samaddar et al. |
EMBL Seeing is Believing – Imaging the Molecular Processes of Life
Preprints discussed at the 2019 edition of Seeing is Believing, at EMBL Heidelberg from the 9th-12th October 2019
List by | Dey Lab |
Autophagy
Preprints on autophagy and lysosomal degradation and its role in neurodegeneration and disease. Includes molecular mechanisms, upstream signalling and regulation as well as studies on pharmaceutical interventions to upregulate the process.
List by | Sandra Malmgren Hill |
Lung Disease and Regeneration
This preprint list compiles highlights from the field of lung biology.
List by | Rob Hynds |
Cellular metabolism
A curated list of preprints related to cellular metabolism at Biorxiv by Pablo Ranea Robles from the Prelights community. Special interest on lipid metabolism, peroxisomes and mitochondria.
List by | Pablo Ranea Robles |
BSCB/BSDB Annual Meeting 2019
Preprints presented at the BSCB/BSDB Annual Meeting 2019
List by | Dey Lab |
MitoList
This list of preprints is focused on work expanding our knowledge on mitochondria in any organism, tissue or cell type, from the normal biology to the pathology.
List by | Sandra Franco Iborra |
ASCB/EMBO Annual Meeting 2018
This list relates to preprints that were discussed at the recent ASCB conference.
List by | Dey Lab, Amanda Haage |