XRN2 interactome reveals its synthetic lethal relationship with PARP1 inhibition

Persistent R-loops (RNA–DNA hybrids with a displaced single-stranded DNA) create DNA damage and lead to genomic instability. The 5′-3′-exoribonuclease 2 (XRN2) degrades RNA to resolve R-loops and promotes transcription termination. Previously, XRN2 was implicated in DNA double strand break (DSB) repair and in resolving replication stress. Here, using tandem affinity purification-mass spectrometry, bioinformatics, and biochemical approaches, we found that XRN2 associates with proteins involved in DNA repair/replication (Ku70-Ku80, DNA-PKcs, PARP1, MCM2-7, PCNA, RPA1) and RNA metabolism (RNA helicases, PRP19, p54(nrb), splicing factors). Novel major pathways linked to XRN2 include cell cycle control of chromosomal replication and DSB repair by non-homologous end joining. Investigating the biological implications of these interactions led us to discover that XRN2 depletion compromised cell survival after additional knockdown of specific DNA repair proteins, including PARP1. XRN2-deficient cells also showed enhanced PARP1 activity. Consistent with concurrent depletion of XRN2 and PARP1 promoting cell death, XRN2-deficient fibroblast and lung cancer cells also demonstrated sensitivity to PARP1 inhibition. XRN2 alterations (mutations, copy number/expression changes) are frequent in cancers. Thus, PARP1 inhibition could target cancers exhibiting XRN2 functional loss. Collectively, our data suggest XRN2’s association with novel protein partners and unravel synthetic lethality between XRN2 depletion and PARP1 inhibition

Ku Regulates the Non-Homologous End Joining Pathway Choice of DNA Double-Strand Break Repair in Human Somatic Cells

The repair of DNA double-strand breaks (DSBs) is critical for the maintenance of genomic integrity and viability for all organisms. Mammals have evolved at least two genetically discrete ways to mediate DNA DSB repair: homologous recombination (HR) and non-homologous end joining (NHEJ). In mammalian cells, most DSBs are preferentially repaired by NHEJ. Recent work has demonstrated that NHEJ consists of at least two sub-pathways—the main Ku heterodimer-dependent or “classic” NHEJ (C-NHEJ) pathway and an “alternative” NHEJ (A-NHEJ) pathway, which usually generates microhomology-mediated signatures at repair junctions. In our study, recombinant adeno-associated virus knockout vectors were utilized to construct a series of isogenic human somatic cell lines deficient in the core C-NHEJ factors (Ku, DNA-PKcs, XLF, and LIGIV), and the resulting cell lines were characterized for their ability to carry out DNA DSB repair. The absence of DNA-PKcs, XLF, or LIGIV resulted in cell lines that were profoundly impaired in DNA DSB repair activity. Unexpectedly, Ku86-null cells showed wild-type levels of DNA DSB repair activity that was dominated by microhomology joining events indicative of A-NHEJ. Importantly, A-NHEJ DNA DSB repair activity could also be efficiently de-repressed in LIGIV-null and DNA-PKcs-null cells by subsequently reducing the level of Ku70. These studies demonstrate that in human cells C-NHEJ is the major DNA DSB repair pathway and they show that Ku is the critical C-NHEJ factor that regulates DNA NHEJ DSB pathway choice

Highly variable timing renders immunotherapy efficacy and toxicity impractical biomarkers of one another in clinical practice

BackgroundA useful clinical biomarker requires not only association but also a consistent temporal relationship. For instance, chemotherapy-induced neutropenia and epidermal growth-factor inhibitor-related acneiform rash both occur within weeks of treatment initiation, thereby providing information prior to efficacy assessment. Although immune checkpoint inhibitor (ICI)-associated immune-related adverse events (irAE) have been associated with therapeutic benefit, irAE may have delayed and highly variable onset. To determine whether ICI efficacy and irAE could serve as clinically useful biomarkers for predicting each other, we determined the temporal relationship between initial efficacy assessment and irAE onset in a diverse population treated with ICI.MethodsUsing two-sided Fisher exact and Cochran-Armitage tests, we determined the relative timing of initial efficacy assessment and irAE occurrence in a cohort of 155 ICI-treated patients (median age 68 years, 40% women).ResultsInitial efficacy assessment was performed a median of 50 days [interquartile range (IQR) 39-59 days] after ICI initiation; median time to any irAE was 77 days (IQR 28-145 days) after ICI initiation. Median time to first irAE was 42 days (IQR 20-88 days). Overall, 58% of any irAE and 47% of first irAE occurred after initial efficacy assessment. For clinically significant (grade ≥2) irAE, 60% of any and 53% of first occurred after initial efficacy assessment. The likelihood of any future irAE did not differ according to response (45% for complete or partial response vs. 47% for other cases; P=1). In landmark analyses controlling for clinical and toxicity follow-up, patients demonstrating greater tumor shrinkage at initial efficacy assessment were more likely to develop future grade ≥2 (P=0.05) and multi-organ (P=0.02) irAE.ConclusionsIn contrast to that seen with chemotherapy and molecularly targeted therapies, the temporal relationship between ICI efficacy and toxicity is complex and bidirectional. In practice, neither parameter can be routinely relied on as a clinical biomarker to predict the other

The impact of loss of function mutations of NHEJ genes on gene targeting and DNA DSB repair in human somatic cells.

University of Minnesota Ph.D. dissertation. April 2009. Major: Biochemistry, Molecular Biology, and Biophysics. Advisor: Eric A Hendrickson, PhD. 1 computer file (PDF); x, 201 pages.Non-homologous end-joining (NHEJ) is the predominant repair pathway for DNA double-strand breaks (DSBs) in human cells. The core NHEJ pathway is composed of seven factors: Ku70, Ku86, DNA-PKcs, Artemis, XRCC4, XLF and LIGIV. Mutation of any one of these NHEJ genes leads either to death, profound immune deficiencies, ionizing radiation sensitivity and/or cancer predisposition in human patients. We attempted to generate Ku70-null human somatic cells using a rAAV-based gene knockout strategy. Our data demonstrated that Ku70 is an essential gene in human somatic cells. More importantly, however, in Ku70+/- cells, the frequency of gene targeting was 5- to 10-fold higher than in wild type cells. RNA interference and short-hairpinned RNA strategies to deplete Ku70 phenocopied these results in wild-type cells and greatly accentuated them in Ku70+/- cell lines. Thus, Ku70 protein levels significantly influenced the frequency of rAAV-mediated gene targeting in human somatic cells. XLF is the newly identified core factor for NHEJ. To characterize XLF function in human cells, we knocked out XLF gene in HCT116 cells. XLF deficient cells are highly sensitive to ionizing radiation and DNA damaging agent, and have intrinsic DNA DSB repair defects. In V(D)J recombination assay, we find that XLF deficient cells have dramatic defect to form both V(D)J coding and signal joints. The phenotypes of XLF deficiency were rescued by a WT XLF cDNA over-expression. We conclude that, in humans, XLF is essential for C-NHEJ mediated repair of DNA-DSBs. Biochemical and genetic studies in mouse and hamster cells showed that DNA ends can also be joined via a backup pathway, especially when proteins responsible for NHEJ, are reduced or absent. In order to get insights in to backup NHEJ mechanism, we employed a reporter system based on the in vivo rejoining of cohesive and incompatible ends. We report here more than 10 to 20 fold reduction in NHEJ proficiency in DNA-PKcs, XLF and LIGIV null human cells, which is characterized by an increase in microhomology use. Strikingly, conditional knock-out of Ku86 did not result in defect in end-joining, while having an impact on repair fidelity

Regulation of Telomere Length and Suppression of Genomic Instability in Human Somatic Cells by Ku86

Ku86 plays a key role in nonhomologous end joining in organisms as evolutionarily disparate as bacteria and humans. In eukaryotic cells, Ku86 has also been implicated in the regulation of telomere length although the effect of Ku86 mutations varies considerably between species. Indeed, telomeres either shorten significantly, shorten slightly, remain unchanged, or lengthen significantly in budding yeast, fission yeast, chicken cells, or plants, respectively, that are null for Ku86 expression. Thus, it has been unclear which model system is most relevant for humans. We demonstrate here that the functional inactivation of even a single allele of Ku86 in human somatic cells results in profound telomere loss, which is accompanied by an increase in chromosomal fusions, translocations, and genomic instability. Together, these experiments demonstrate that Ku86, separate from its role in nonhomologous end joining, performs the additional function in human somatic cells of suppressing genomic instability through the regulation of telomere length

The Transcription Factor TFII-I Promotes DNA Translesion Synthesis and Genomic Stability

<div><p>Translesion synthesis (TLS) enables DNA replication through damaged bases, increases cellular DNA damage tolerance, and maintains genomic stability. The sliding clamp PCNA and the adaptor polymerase Rev1 coordinate polymerase switching during TLS. The polymerases Pol η, ι, and κ insert nucleotides opposite damaged bases. Pol ζ, consisting of the catalytic subunit Rev3 and the regulatory subunit Rev7, then extends DNA synthesis past the lesion. Here, we show that Rev7 binds to the transcription factor TFII-I in human cells. TFII-I is required for TLS and DNA damage tolerance. The TLS function of TFII-I appears to be independent of its role in transcription, but requires homodimerization and binding to PCNA. We propose that TFII-I bridges PCNA and Pol ζ to promote TLS. Our findings extend the general principle of component sharing among divergent nuclear processes and implicate TLS deficiency as a possible contributing factor in Williams-Beuren syndrome.</p></div

TFII-I is required for DNA translesion synthesis (TLS) in human cells.

<p>(A) The mutation frequency of UV-treated <i>SupF</i> plasmid in 293T cells transfected with the indicated siRNAs. The mean and SD of three experiments are shown. (B) The mutation frequency of UV-treated <i>SupF</i> plasmid in 293T cells transfected with the indicated siRNAs. The mean and SD of two experiments are shown. (C) The mutation spectra of the UV-irradiated <i>SupF</i> gene recovered from 293T cells transfected with the indicated siRNAs. The number of clones sequenced for each group is shown in parentheses.</p

TFII-I depletion in human cells causes UV and cisplatin sensitivity.

<p>(A) Lysates of 293T cells transfected with the indicated siRNAs were blotted with indicated antibodies. (B) Quantitative PCR analysis of the Rev3L mRNA levels in mock or siRev3L transfected 293T cells. (C) Colony survival curves of 293T cells that were transfected with the indicated siRNAs and irradiated with increasing doses of UV. The mean and standard deviation (SD) of three independent experiments are shown. (D) Colony survival curves of 293T cells that were transfected with the indicated siRNAs and increasing doses of cisplatin. The mean and standard deviation (SD) of three independent experiments are shown. (E) Colony survival curves of U2OS cells that were transfected with the indicated siRNAs and irradiated with increasing doses of UV. The mean and standard deviation (SD) of three independent experiments are shown. (F) Colony survival curves of U2OS cells that were transfected with the indicated siRNAs and increasing doses of cisplatin. The mean and standard deviation (SD) of three independent experiments are shown.</p

The TFII-I dimer bridges PCNA and Rev7.

<p>(A) The monomeric TFII-I fragment (residues 330–667) does not form a ternary complex with PCNA and Rev7. The indicated combinations of recombinant purified Rev7 R124A, PCNA, and TFII-I (residues 330–667) proteins were fractionated on a Superdex 200 gel filtration column. Selected fractions were separated by SDS-PAGE followed by Coomassie staining. The positions of native molecular mass standards are indicated by arrowheads. (B) Purified TFII-I^1–667 and TFII-I^270–667 fragments were fractionated on a Superdex 200 gel filtration column. (C) HeLa Tet-On cells were transfected with the indicated plasmids. Lysates, IgG IP, and anti-Myc IP of these cells were blotted with the indicated antibodies. (D) Model for TFII-I-dependent recruitment of Pol ζ (Rev3L–Rev7) to PCNA at DNA damage sites during translesion synthesis. Ub, ubiquitin. CTD, C-terminal domain.</p