Requirements for PARP-1 covalent crosslinking to DNA (PARP-1 DPC)

Cancer prognosis using base excision repair genes

The base excision repair (BER) pathway is a critical mechanism in genomic stability. This review investigates the role of the BER pathway in advanced cancer therapies considering the pivotal role of genetic factors in cancer patient responses and prognosis. BER factors significantly influence genetic instability and cancer prognosis, as well as the effectiveness of chemotherapy and radiation therapy. In various cancers such as breast, colon, lung, and bladder, BER factors have shown potential as critical biological markers for predicting cancer outcomes. This study focuses on the polymorphisms and expression levels of key BER genes, including OGG1, XRCC1, APE1, and Polβ. Our findings demonstrate that the expression levels of BER genes and proteins are closely associated with the risk, progression, treatment response, and prognosis of various cancers. These insights could improve cancer treatments and aid in the development of drugs targeting BER proteins. Ongoing research in this field requires extensive statistical analyses and large-scale prospective studies to effectively utilize BER protein levels. Ultimately, these results suggest that the BER pathway represents a potential target for cancer diagnosis, prognostic prediction, and the development of personalized therapeutic strategies. This paves the way for effective cancer treatment in the future.

Cdc48/p97 segregase: Spotlight on DNA-protein crosslinks

The ATP-dependent molecular chaperone Cdc48 (in yeast) and its human counterpart p97 (also known as VCP), are essential for a variety of cellular processes, including the removal of DNA-protein crosslinks (DPCs) from the DNA. Growing evidence demonstrates in the last years that Cdc48/p97 is pivotal in targeting ubiquitinated and SUMOylated substrates on chromatin, thereby supporting the DNA damage response. Along with its cofactors, notably Ufd1-Npl4, Cdc48/p97 has emerged as a central player in the unfolding and processing of DPCs. This review introduces the detailed structure, mechanism and cellular functions of Cdc48/p97 with an emphasis on the current knowledge of DNA-protein crosslink repair pathways across several organisms. The review concludes by discussing the potential therapeutic relevance of targeting p97 in DPC repair.

Isolation and detection of DNA-protein crosslinks in mammalian cells

DNA-protein crosslinks (DPCs) are toxic DNA lesions wherein a protein is covalently attached to DNA. If not rapidly repaired, DPCs create obstacles that disturb DNA replication, transcription and DNA damage repair, ultimately leading to genome instability. The persistence of DPCs is associated with premature ageing, cancer and neurodegeneration. In mammalian cells, the repair of DPCs mainly relies on the proteolytic activities of SPRTN and the 26S proteasome, complemented by other enzymes including TDP1/2 and the MRN complex, and many of the activities involved are essential, restricting genetic approaches. For many years, the study of DPC repair in mammalian cells was hindered by the lack of standardised assays, most notably assays that reliably quantified the proteins or proteolytic fragments covalently bound to DNA. Recent interest in the field has spurred the development of several biochemical methods for DPC analysis. Here, we critically analyse the latest techniques for DPC isolation and the benefits and drawbacks of each. We aim to assist researchers in selecting the most suitable isolation method for their experimental requirements and questions, and to facilitate the comparison of results across different laboratories using different approaches.

Enzymatic Processing of DNA-Protein Crosslinks

DNA-protein crosslinks (DPCs) represent a unique and complex form of DNA damage formed by covalent attachment of proteins to DNA. DPCs are formed through a variety of mechanisms and can significantly impede essential cellular processes such as transcription and replication. For this reason, anti-cancer drugs that form DPCs have proven effective in cancer therapy. While cells rely on numerous different processes to remove DPCs, the molecular mechanisms responsible for orchestrating these processes remain obscure. Having this insight could potentially be harnessed therapeutically to improve clinical outcomes in the battle against cancer. In this review, we describe the ways cells enzymatically process DPCs. These processing events include direct reversal of the DPC via hydrolysis, nuclease digestion of the DNA backbone to delete the DPC and surrounding DNA, proteolytic processing of the crosslinked protein, as well as covalent modification of the DNA-crosslinked proteins with ubiquitin, SUMO, and Poly(ADP) Ribose (PAR).

PARP1 Incises Abasic Sites and Covalently Cross-links to 3'-DNA Termini via Cysteine Addition Not Reductive Amination

Poly [ADP-ribose] polymerase 1 (PARP1) is a ubiquitous nuclear enzyme that plays multifaceted roles in the cellular response to DNA damage. Previous studies demonstrated that PARP1 incises the most frequently formed DNA lesion, the apurinic/apyrimidinic (AP) site, and in the process is trapped as a DNA-PARP1 cross-link at the 3'-terminus. The covalent linkage was proposed to be composed of a secondary amine resulting from formal reductive amination of an initially formed incision product. PARP1 cysteine residues were proposed to reduce the initially formed Schiff base. Here, we report evidence to support a different mechanism in which DNA-PARP1 cross-links result from cysteine addition to incised AP sites.

Targeting DNA-Protein Crosslinks via Post-Translational Modifications

Covalent binding of proteins to DNA forms DNA-protein crosslinks (DPCs), which represent cytotoxic DNA lesions that interfere with essential processes such as DNA replication and transcription. Cells possess different enzymatic activities to counteract DPCs. These include enzymes that degrade the adducted proteins, resolve the crosslinks, or incise the DNA to remove the crosslinked proteins. An important question is how DPCs are sensed and targeted for removal via the most suited pathway. Recent advances have shown the inherent role of DNA replication in triggering DPC removal by proteolysis. However, DPCs are also efficiently sensed and removed in the absence of DNA replication. In either scenario, post-translational modifications (PTMs) on DPCs play essential and versatile roles in orchestrating the repair routes. In this review, we summarize the current knowledge of the mechanisms that trigger DPC removal via PTMs, focusing on ubiquitylation, small ubiquitin-related modifier (SUMO) conjugation (SUMOylation), and poly (ADP-ribosyl)ation (PARylation). We also briefly discuss the current knowledge gaps and emerging hypotheses in the field.

Rucaparib and olaparib for the treatment of prostate cancer: A clinician's guide to choice of therapy

OBJECTIVE

This review will provide an overview of the use rucaparib and olaparib in patients with metastatic castration resistant prostate cancer (mCRPC) with the goal to assist the clinician's decision-making process when considering these agents for an individual patient.

DATA SOURCES

Searches were conducted in PubMed, relevant meeting abstracts, clinicaltrials.gov, and United States Food and Drug Administration (FDA) documents to identify literature published through July 1, 2021, related to use of rucaparib and olaparib for treatment of prostate cancer.

DATA SUMMARY

In May 2020, the FDA approved rucaparib and olaparib for treatment of mCRPC that is homologous recombination repair (HRR)-deficient. Both agents are approved for previously-treated patients, but there are notable differences in strength of evidence, outcomes studied, required HRR alteration, and required prior therapies. In patients who qualify for therapy, additional factors that may help guide choice of PARP inhibitor include baseline organ function, drug interaction potential, toxicity profiles, and financial factors.

CONCLUSIONS

Rucaparib and olaparib have the potential to improve outcomes for patients with HRR-deficient mCRPC. Differences in strength of evidence and patient- and drug-specific characteristics will assist the clinician when choosing between agents.

Lipopolysaccharide induces pyroptosis through regulation of autophagy in cardiomyocytes

Background

Autophagy, a stress response in eukaryotic cells, is closely related to cardiogenic diseases. Pyroptosis, a newly discovered way of programmed cell death, also plays an important role in cardiovascular disease. However, the role and relationship of autophagy and pyroptosis in lipopolysaccharide (LPS)-induced inflammatory response of cardiomyocytes were still unclear.

Methods

Western blot was performed to determine the expression of poly ADP-ribosepolmesera-1 (PARP-1), LC3B, NLRP3 and GSDMD in cardiomyocytes after the treatment of LPS. Transfection of si-LC3B, western blot and immunofluorescence (IF) staining were performed to investigate the role of autophagy in LPS-induced pyroptosis. Co-immunoprecipitation (Co-IP) assays and quantitative real-time PCR (qRT-PCR) were conducted to explore whether PARP-1 binding to LC3B and modulating its expression. Transfections of si-PARP-1, western blot and IF were carried out to confirm the role of PARP-1 in the regulation of LPS-induced pyroptosis by autophagy.

Results

LPS induces autophagy and pyroptosis in cardiomyocytes, enhanced the level of autophagy and inhibited the level of pyroptosis in the concentration of 4 µg/mL. We further proved that autophagy inhibits LPS-induced pyroptosis in cardiomyocytes. In addition, PARP-1 binding to LC3B and regulate the expression of LC3B. Finally, we proved that knockdown of PARP-1 rescued the inhibition of autophagy on LPS-induced pyroptosis of cardiomyocytes.

Conclusions

LPS induces pyroptosis through regulation of autophagy via PARP-1 at a specific concentration, above which it causes deposition of autophagy flow to promote pyroptosis. Inhibiting LPS-induced pyroptosis could be a promising therapeutic target in treating cardiovascular diseases.

Replication-dependent cytotoxicity and Spartan-mediated repair of trapped PARP1-DNA complexes

The antitumor activity of poly(ADP-ribose) polymerase inhibitors (PARPis) has been ascribed to PARP trapping, which consists in tight DNA-protein complexes. Here we demonstrate that the cytotoxicity of talazoparib and olaparib results from DNA replication. To elucidate the repair of PARP1-DNA complexes associated with replication in human TK6 and chicken DT40 lymphoblastoid cells, we explored the role of Spartan (SPRTN), a metalloprotease associated with DNA replication, which removes proteins forming DPCs. We find that SPRTN-deficient cells are hypersensitive to talazoparib and olaparib, but not to veliparib, a weak PARP trapper. SPRTN-deficient cells exhibit delayed clearance of trapped PARP1 and increased replication fork stalling upon talazoparib and olaparib treatment. We also show that SPRTN interacts with PARP1 and forms nuclear foci that colocalize with the replicative cell division cycle 45 protein (CDC45) in response to talazoparib. Additionally, SPRTN is deubiquitinated and epistatic with translesion synthesis (TLS) in response to talazoparib. Our results demonstrate that SPRTN is recruited to trapped PARP1 in S-phase to assist in the excision and replication bypass of PARP1-DNA complexes.

DNA End Joining: G0-ing to the Core

Humans have evolved a series of DNA double-strand break (DSB) repair pathways to efficiently and accurately rejoin nascently formed pairs of double-stranded DNA ends (DSEs). In G0/G1-phase cells, non-homologous end joining (NHEJ) and alternative end joining (A-EJ) operate to support covalent rejoining of DSEs. While NHEJ is predominantly utilized and collaborates extensively with the DNA damage response (DDR) to support pairing of DSEs, much less is known about A-EJ collaboration with DDR factors when NHEJ is absent. Non-cycling lymphocyte progenitor cells use NHEJ to complete V(D)J recombination of antigen receptor genes, initiated by the RAG1/2 endonuclease which holds its pair of targeted DSBs in a synapse until each specified pair of DSEs is handed off to the NHEJ DSB sensor complex, Ku. Similar to designer endonuclease DSBs, the absence of Ku allows for A-EJ to access RAG1/2 DSEs but with random pairing to complete their repair. Here, we describe recent insights into the major phases of DSB end joining, with an emphasis on synapsis and tethering mechanisms, and bring together new and old concepts of NHEJ vs. A-EJ and on RAG2-mediated repair pathway choice.

The Role of Nucleotide Excision Repair in Cisplatin-Induced Peripheral Neuropathy: Mechanism, Prevention, and Treatment

Platinum-based chemotherapy-induced peripheral neuropathy (CIPN) is one of the most common dose-limiting effects of cancer treatment and results in dose reduction and discontinuation of life-saving chemotherapy. Its debilitating effects are often permanent and lead to lifelong impairment of quality of life in cancer patients. While the mechanisms underlying the toxicity are not yet fully defined, dorsal root ganglia sensory neurons play an integral role in symptom development. DNA-platinum adducts accumulate in these cells and inhibit normal cellular function. Nucleotide excision repair (NER) is integral to the repair of platinum adducts, and proteins involved in its mechanism serve as potential targets for future therapeutics. This review aims to highlight NER’s role in cisplatin-induced peripheral neuropathy, summarize current clinical approaches to the toxicity, and discuss future perspectives for the prevention and treatment of CIPN.