UHRF1 is a genome caretaker that facilitates the DNA damage response to γ-irradiation

DNA damage evokes a complex and highly coordinated DNA damage response (DDR) that is integral to the suppression of genomic instability. Double-strand breaks (DSBs) are considered the most deleterious form damage. Evidence suggests that trimethylation of histone H3 lysine 9 (H3K9me3) presents a barrier to DSB repair. Also, global levels of histone methylation are clinically predictive for several tumor types. Therefore, demethylation of H3K9 may be an important step in the repair of DSBs. The KDM4 subfamily of demethylases removes H3K9 tri- and dimethylation and contributes to the regulation of cellular differentiation and proliferation; mutation or aberrant expression of KDM4 proteins has been identified in several human tumors. We hypothesize that members of the KDM4 subfamily may be components of the DDR. We found that Kdm4b-enhanced GFP (EGFP) and KDM4D-EGFP were recruited rapidly to DNA damage induced by laser micro-irradiation. Focusing on the clinically relevant Kdm4b, we found that recruitment was dependent on poly(ADP-ribose) polymerase 1 activity as well as Kdm4b demethylase activity. The Kdm4 proteins did not measurably accumulate at γ-irradiation-induced γH2AX foci. Nevertheless, increased levels of Kdm4b were associated with decreased numbers of γH2AX foci 6 h after irradiation as well as increased cell survival. Finally, we found that levels of H3K9me2 and H3K9me3 were decreased at early time points after 2 gray of γ-irradiation. Taken together, these data demonstrate that Kdm4b is a DDR protein and that overexpression of Kdm4b may contribute to the failure of anti-cancer therapy that relies on the induction of DNA damage.

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Impact of DNA Damage Response—Targeted Therapies on the Immune Response to Tumours

Cancers ◽

10.3390/cancers13236008 ◽

2021 ◽

Vol 13 (23) ◽

pp. 6008

Author(s):

Nura Lutfi ◽

Miguel Alejandro Galindo-Campos ◽

José Yélamos

Keyword(s):

Dna Damage ◽

Immune System ◽

Dna Damage Response ◽

Targeted Therapies ◽

Tumour Progression ◽

Tumour Cells ◽

Targeted Agents ◽

A Genome ◽

Damage Response ◽

The Stability

The DNA damage response (DDR) maintains the stability of a genome faced with genotoxic insults (exogenous or endogenous), and aberrations of the DDR are a hallmark of cancer cells. These cancer-specific DDR defects present new therapeutic opportunities, and different compounds that inhibit key components of DDR have been approved for clinical use or are in various stages of clinical trials. Although the therapeutic rationale of these DDR-targeted agents initially focused on their action against tumour cells themselves, these agents might also impact the crosstalk between tumour cells and the immune system, which can facilitate or impede tumour progression. In this review, we summarise recent data on how DDR-targeted agents can affect the interactions between tumour cells and the components of the immune system, both by acting directly on the immune cells themselves and by altering the expression of different molecules and pathways in tumour cells that are critical for their relationship with the immune system. Obtaining an in-depth understanding of the mechanisms behind how DDR-targeted therapies affect the immune system, and their crosstalk with tumour cells, may provide invaluable clues for the rational development of new therapeutic strategies in cancer.

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Genome-wide screening identifies cell cycle control as a synthetic lethal pathway with SRSF2P95H mutation

Blood Advances ◽

10.1182/bloodadvances.2021004571 ◽

2021 ◽

Author(s):

Jane Jialu Xu ◽

Alistair M Chalk ◽

Iva Nikolic ◽

Kaylene Simpson ◽

Monique F Smeets ◽

...

Keyword(s):

Cell Cycle ◽

Dna Damage ◽

Cell Lines ◽

Dna Damage Response ◽

Functional Screening ◽

Wild Type ◽

Synthetic Lethal ◽

Genome Wide ◽

A Genome ◽

Damage Response

Current strategies to target RNA splicing mutant myeloid cancers proposes targeting the remaining splicing apparatus. This approach has only been modestly sensitizing and is also toxic to non-mutant bearing wild-type cells. To explore potentially exploitable genetic interactions with spliceosome mutations, we combined data mining and functional screening for synthetic lethal interactions with an Srsf2P95H/+ mutation. Analysis of mis-splicing events in a series of both human and murine SRSF2P95H mutant samples across multiple myeloid diseases (AML, MDS, CMML) was performed to identify conserved mis-splicing events. From this analysis, we identified that the cell cycle and DNA repair pathways were overrepresented within the conserved mis-spliced transcript sets. In parallel, to functionally define pathways essential for survival and proliferation of Srsf2P95H/+ cells, we performed a genome-wide CRISPR loss of function screen using Hoxb8 immortalized R26-CreERki/+ Srsf2P95H/+ and R26-CreERki/+ Srsf2+/+ cell lines. We assessed loss of sgRNA representation at three timepoints: immediately after Srsf2P95H/+ activation, and at one week and two weeks post Srsf2P95H/+ mutation. Pathway analysis demonstrated that the cell cycle and DNA damage response pathways were amongst the top synthetic lethal pathways with Srsf2P95H/+ mutation. Based on the loss of guide RNAs targeting Cdk6, we identified that Palbociclib, a CDK6 inhibitor, showed preferential sensitivity in Srsf2P95H/+ cell lines and in primary non-immortalized lin-cKIT+Sca-1+ cells compared to wild type controls. Our data strongly suggest that the cell cycle and DNA damage response pathways are required for Srsf2P95H/+ cell survival, and that Palbociclib could be an alternative therapeutic option for targeting SRSF2 mutant cancers.

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A genome-wide homologous recombination screen identifies the RNA-binding protein RBMX as a component of the DNA-damage response

Nature Cell Biology ◽

10.1038/ncb2426 ◽

2012 ◽

Vol 14 (3) ◽

pp. 318-328 ◽

Cited By ~ 245

Author(s):

Britt Adamson ◽

Agata Smogorzewska ◽

Frederic D. Sigoillot ◽

Randall W. King ◽

Stephen J. Elledge

Keyword(s):

Dna Damage ◽

Homologous Recombination ◽

Dna Damage Response ◽

Rna Binding ◽

Binding Protein ◽

Rna Binding Protein ◽

Genome Wide ◽

A Genome ◽

Damage Response

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The histone demethylase LSD1/KDM1A promotes the DNA damage response

The Journal of Cell Biology ◽

10.1083/jcb.201302092 ◽

2013 ◽

Vol 203 (3) ◽

pp. 457-470 ◽

Cited By ~ 61

Author(s):

Nima Mosammaparast ◽

Haeyoung Kim ◽

Benoit Laurent ◽

Yu Zhao ◽

Hui Jun Lim ◽

...

Keyword(s):

Dna Damage ◽

Dna Damage Response ◽

Ubiquitin Ligase ◽

Histone Demethylase ◽

Dependent Manner ◽

Γ Irradiation ◽

Histone Demethylation ◽

Direct Role ◽

Damage Response ◽

Histone Ubiquitylation

Histone demethylation is known to regulate transcription, but its role in other processes is largely unknown. We report a role for the histone demethylase LSD1/KDM1A in the DNA damage response (DDR). We show that LSD1 is recruited directly to sites of DNA damage. H3K4 dimethylation, a major substrate for LSD1, is reduced at sites of DNA damage in an LSD1-dependent manner. The E3 ubiquitin ligase RNF168 physically interacts with LSD1 and we find this interaction to be important for LSD1 recruitment to DNA damage sites. Although loss of LSD1 did not affect the initial formation of pH2A.X foci, 53BP1 and BRCA1 complex recruitment were reduced upon LSD1 knockdown. Mechanistically, this was likely a result of compromised histone ubiquitylation preferentially in late S/G2. Consistent with a role in the DDR, knockdown of LSD1 resulted in moderate hypersensitivity to γ-irradiation and increased homologous recombination. Our findings uncover a direct role for LSD1 in the DDR and place LSD1 downstream of RNF168 in the DDR pathway.

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An Integrated Bioinformatics and Computational Biology Approach Identifies New BH3-Only Protein Candidates

The Open Biology Journal ◽

10.2174/1874196701205010006 ◽

2012 ◽

Vol 5 (1) ◽

pp. 6-16 ◽

Cited By ~ 7

Author(s):

Robert G. Hawley ◽

Yuzhong Chen ◽

Irene Riz ◽

Chen Zeng

Keyword(s):

Dna Damage ◽

Computational Biology ◽

Dna Damage Response ◽

Stress Responses ◽

Response Regulator ◽

Specific Binding ◽

Family Members ◽

Bcl2 Family ◽

A Genome ◽

Damage Response

In this study, we utilized an integrated bioinformatics and computational biology approach in search of new BH3-only proteins belonging to the BCL2 family of apoptotic regulators. The BH3 (BCL2 homology 3) domain mediates specific binding interactions among various BCL2 family members. It is composed of an amphipathic α-helical region of approximately 13 residues that has only a few amino acids that are highly conserved across all members. Using a generalized motif, we performed a genome-wide search for novel BH3-containing proteins in the NCBI Consensus Coding Sequence (CCDS) database. In addition to known pro-apoptotic BH3-only proteins, 197 proteins were recovered that satisfied the search criteria. These were categorized according to α-helical content and predictive binding to BCL-xL (encoded by BCL2L1) and MCL-1, two representative anti-apoptotic BCL2 family members, using position-specific scoring matrix models. Notably, the list is enriched for proteins associated with autophagy as well as a broad spectrum of cellular stress responses such as endoplasmic reticulum stress, oxidative stress, antiviral defense, and the DNA damage response. Several potential novel BH3-containing proteins are highlighted. In particular, the analysis strongly suggests that the apoptosis inhibitor and DNA damage response regulator, AVEN, which was originally isolated as a BCL-xLinteracting protein, is a functional BH3-only protein representing a distinct subclass of BCL2 family members.

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