Human topoisomerases and their roles in genome stability and organization

Highly-sensitive and logic platform based on spatially-constrained T7 transcription enhanced Cas13a for DNA repair enzyme detection and intracellular imaging

The activity of DNA repair enzymes, particularly Flap endonuclease 1 (FEN1) and apurinic/apyrimidinic endonuclease 1 (APE1), plays a critical role in disease prevention, diagnosis, and prognosis. Accurate detection of these enzymes is therefore essential. Recent advancements in CRISPR-Cas technology, particularly its programmable and trans-cleavage activity, have paved the way for the development of innovative detection methods. However, there is a need for a simple, low-background, highly sensitive detection platform with logical capabilities for FEN1 and APE1. In this study, we present a novel detection platform that integrates spatially constrained T7 transcription with the CRISPR-Cas13a system. This biosensor minimizes background interference and achieves high sensitivity, with limits of detection as low as 5 × 10-7 U/μL for FEN1 and 2 × 10-8 U/μL for APE1, making it one of the most sensitive methods available for detecting these enzymes. The platform supports both OR and logic detection, offering enhanced versatility. It demonstrates robustness by detecting FEN1 activity at concentrations as low as 1 cell/μL and screening enzyme inhibitors. Additionally, the system was successfully used for intracellular imaging of FEN1 activity in cells and reliably measured APE1 activity in ovarian tissue samples, confirming its clinical applicability. This biosensor represents a promising tool for detecting FEN1 and APE1, further expanding the potential of CRISPR-Cas13a in diagnostic applications.

Mitotic genome folding

Mitotic genome folding, or mitotic chromosome assembly, is essential for the faithful segregation of genetic information into daughter cells. While this process was once thought to be highly complex, requiring a myriad of protein components, recent studies have begun to revise this conventional view. An emerging view is that the core reaction of mitotic genome folding is mediated by a dynamic interplay of a limited number of structural components, namely, condensins, topoisomerase II (topo II), and histones. Condensins and topo II are two distinct classes of ATPases that cooperate to actively form and manipulate DNA loops, both accumulating at the central axial regions of the resulting chromosomes. In contrast, nucleosomes and linker histones help to compact DNA loops by cooperating and competing with the action of these ATPases. In this review, I will focus on the recent advances in the field, with an emphasis on the mechanistic aspects of mitotic genome folding.

Exploration of histone protein γ-H2AX as a prognostic factor in soft tissue sarcomas and its association with biological behavior, immune cell environment and survival in leiomyosarcoma

This study evaluates the H2AX/γ-H2AX expression in soft tissue sarcomas (STS), its implications for biological behavior and immune environment, and its potential as a prognostic biomarker. RNA-Seq data from 237 STS were obtained from The Cancer Genome Atlas project. Patients were stratified by H2AX mRNA expression using a survival-associated cutoff. Differentially expressed genes and pathways as well as immune signatures between H2AXhigh- and H2AXlow tumors were identified with DESeq2 analysis, gene set enrichment analyses (GSEA), Enrichr pathway analysis and CIBERSORTx. Tissue microarrays of a different cohort of 291 STS were generated for immunohistochemical staining to assess γ-H2AX protein expression, followed by statistical evaluation. High H2AX mRNA expression was associated with shorter overall survival (OS) in STS (p = 0.02), particularly in leiomyosarcomas (LMS) (p < 0.001), and was a negative prognostic factor in LMS (HR 11.15, p < 0.001). H2AXhigh LMS tumors showed upregulation of cell cycle-related pathways, while H2AXlow LMS exhibited increased inflammatory activity, including elevated M1 macrophage signatures and resting mast cell signatures (both p < 0.001). High γ-H2AX protein levels were an independent negative prognostic factor in the total LMS cohort (HR 12.12, p = 0.025) and in the subgroup of non-uterine LMS (HR 153.80, p = 0.013). Consistent with CIBERSORTx analysis, γ-H2AXlow LMS showed higher mast cell infiltration than γ-H2AXhigh LMS (p = 0.038). In conclusion, H2AX mRNA and γ-H2AX protein expression are associated with distinct biological behavior, differences in the immune cell environment, and might serve as useful prognostic biomarkers in LMS.

Disparity landscapes of viral-induced structural variations in HCC: Mechanistic characterization and functional implications

BACKGROUND AND AIMS

HCC is the most common type of primary liver cancer and is a common malignancy worldwide. About half of all new liver cancers worldwide each year occur in China, including Hong Kong, due to a high prevalence of HBV infection. HBV DNA integrates into the human genome, disrupting the endogenous tumor suppressors/regulatory genes or enhancing the activity of proto-oncogenes. It would be useful to examine the different NGS-based databases to provide a more unbiased and comprehensive survey of HBV integration.

APPROACH AND RESULTS

We aimed to take advantage of publicly available data sets of different regional cohorts to determine the disparity landscapes of integration events among sample cohorts, tissue types, chromosomal positions, individual host, and viral genes, as well as genic locations. By comparing HCC tumors with non tumorous livers, the landscape of HBV integration was delineated in gene-independent and gene-dependent manners. Moreover, we performed mechanistic investigations on how HBV-TERT integration led to TERT activation and derived a score to predict patients' prognostication according to their clonal disparity landscape of HBV integration.

CONCLUSIONS

Our study uncovered the different levels of clonal enrichment of HBV integration and identified mechanistic insights and prognostic biomarkers. This strengthens our understanding of HBV-associated hepatocarcinogenesis.

Topobexin targets the Topoisomerase II ATPase domain for beta isoform-selective inhibition and anthracycline cardioprotection

Topoisomerase II alpha and beta (TOP2A and TOP2B) isoenzymes perform essential and non-redundant cellular functions. Anthracyclines induce their potent anti-cancer effects primarily via TOP2A, but at the same time they induce a dose limiting cardiotoxicity through TOP2B. Here we describe the development of the obex class of TOP2 inhibitors that bind to a previously unidentified druggable pocket in the TOP2 ATPase domain to act as allosteric catalytic inhibitors by locking the ATPase domain conformation with the capability of isoform-selective inhibition. Through rational drug design we have developed topobexin, which interacts with residues that differ between TOP2A and TOP2B to provide inhibition that is both selective for TOP2B and superior to dexrazoxane. Topobexin is a potent protectant against chronic anthracycline cardiotoxicity in an animal model. This demonstration of TOP2 isoform-specific inhibition underscores the broader potential to improve drug specificity and minimize adverse effects in various medical treatments.

Furanoheliangolides from Centratherum punctatum and a General Approach for Stereochemical Assignment of Flexible Chiral Side Chains

Human topoisomerase 3β (TOP3B) is a potential molecular therapeutic target for cancer and viral infections. A high-throughput differential cell viability assay using colon cancer cell lines was developed to identify natural product modulators of TOP3B-associated cancer cell viability. The assay identified an organic extract of the plant Centratherum punctatum as having cytotoxic activity. Seven new furanoheliangolides, centratherolides A-G (1-7), along with two known analogues (2,3-epoxybutyryloxy)-goyazensolanolide (8) and goyazensolide (9), were isolated. Compounds 1, 8, and 9 exhibited selective cytotoxic activities against the TOP3B-knockout (TOP3B-KO) human colon carcinoma HCT116 cells compared with the wild-type HCT116 cells (TOP3B-WT). The challenging absolute configuration determination of the flexible chiral side chains in selected analogues (1-4 and 8) was resolved by combined approaches, including synthesis of chemical standards, DFT ECD calculation, and chiral HPLC analysis. Application of this elucidation methodology to a commercial sesquiterpene lactone clarified a contradiction in the stereochemical assignments reported for centaurepensin/chlorohyssopifolin A and 17-epi-chlorohyssopifolin A.

Exploring the Anti-Leukemic Effect of the Synthetic Retinoid ST1926 on Malignant T Cells: A Comprehensive Proteomics Approach

T-cell malignancies represent a group of complex cancers arising from T cells and include aggressive subtypes such as Adult T-cell Leukemia/Lymphoma (ATL) and T-cell Acute Lymphoblastic Leukemia (T-ALL). Patients with these aggressive subtypes still represent an unmet medical condition. The synthetic adamantyl retinoid ST1926, a potent DNA polymerase-α inhibitor, proved a promising potency in preclinical models of ATL and peripheral T-cell lymphoma. Using advanced liquid chromatography-mass spectrometry (LC-MS/MS) techniques, we explored the effects of ST1926 on global protein expression in ATL (HuT-102) and T-ALL (MOLT-4) cells. We demonstrate that ST1926 triggers differentiation and apoptosis in malignant T-cells while halting tumor progression. Evidence at the proteomics level reveals the impact of ST1926 on crucial DNA replication enzymes and cell cycle regulation, highlighting its potential to reduce leukemogenesis and promote apoptosis. Our findings underscore the potential of ST1926 as an innovative therapeutic approach to address these aggressive T-cell malignancies, providing valuable insights into developing new targeted therapies and improving the outcomes and prognosis of patients with these challenging diseases.

Molecular basis of cell fate plasticity - insights from the privileged cells

In the post-Yamanaka era, the rolling balls on Waddington's hilly landscape not only roll downward, but also go upward or sideways. This new-found mobility implies that the tantalizing somatic cell plasticity fueling regeneration, once only known to planarians and newts, might be sparking in the cells of mice and humans, if only we knew how to fully unlock it. The hope for ultimate regeneration was made even more tangible by the observations that partial reprogramming by the Yamanaka factors reverses many hallmarks of aging [76], even though the underlying mechanism remains unclear. We intend to revisit the milestones in the evolving understanding of cell fate plasticity and glean molecular insights from an unusual somatic cell state, the privileged cell state that reprograms in a manner defying the stochastic model. We synthesize our view of the molecular underpinning of cell fate plasticity, from which we speculate how to harness it for regeneration and rejuvenation. We propose that senescence, aging and malignancy represent distinct cell states with definable biochemical and biophysical parameters.

Joining of DNA breaks- interplay between DNA ligases and poly (ADP-ribose) polymerases

The joining of DNA single- and double-strand breaks (SSB and DSB) is essential for maintaining genome stability and integrity. While this is ultimately accomplished in human cells by the DNA ligases encoded by the LIG1, LIG3 and LIG4 genes, these enzymes are recruited to DNA breaks through specific interactions with proteins involved in break sensing and recognition and/or break processing. In this review, we focus on the interplay between the DNA break-activated poly (ADP-ribose) polymerases, PARP1 and PARP2, poly (ADP-ribose) (PAR) and the DNA ligases in DNA replication and repair. The most extensively studied example of this interplay is the recruitment of DNA ligase IIIα (LigIIIα) and other repair proteins to SSBs through an interaction between XRCC1, a scaffold protein and partner protein of nuclear LigIIIα, and PAR synthesized by PARP1 and to a lesser extent PARP2. Recently, these proteins have been implicated in a back-up pathway for joining Okazaki fragments that appears to have a critical function even in cells with no defect in the major LigI-dependent pathway. Finally, we discuss the effects of FDA-approved PARP1/2 inhibitors on DNA replication and repair in cancer and non-malignant cells and the potential utility of DNA ligase inhibitors as cancer therapeutics.

Patulin and Xestoquinol are inhibitors of DNA topoisomerase 1

DNA topoisomerase 1 (TOP1) is essential for transcription, replication, and repair. Its function relies on two catalytic steps, DNA breakage and rejoining. Inhibitors of the second step prevent DNA rejoining and lead to persistent DNA breaks, acting as topoisomerase poisons, used as anticancer drugs. However, reliable inhibitors of the first step are not available. Here, we provide genetic and molecular evidence supporting that Patulin and, to a lesser extent, Xestoquinol inhibit the first catalytic step of TOP1 in vitro, in yeast and in human cells. Particularly, Patulin prevents the accumulation of TOP1 cleavage complexes caused by the TOP1 poison camptothecin (CPT) in human cells. Moreover, Patulin pretreatment of human or yeast cells reduces DNA damage and the accumulation of DNA breaks upon CPT exposure. Consistent with the protective role of TOP1 against harmful R-loops, Patulin treatment increases R-loops and R-loop-associated cytotoxicity, mimicking the effect of TOP1 silencing. Altogether our findings indicate that Patulin and Xestoquinol are nonpoisoning inhibitors of TOP1, which should potentiate new research approaches in molecular biology and medicine.

Extrachromosomal DNA replication and maintenance couple with DNA damage pathway in tumors

Extrachromosomal DNA (ecDNA) drives the evolution of cancer cells. However, the functional significance of ecDNA and the molecular components involved in its replication and maintenance remain largely unknown. Here, using CRISPR-C technology, we generated ecDNA-carrying (ecDNA+) cell models. By leveraging these models alongside other well-established systems, we demonstrated that ecDNA can replicate and be maintained in ecDNA+ cells. The replication of ecDNA activates the ataxia telangiectasia mutated (ATM)-mediated DNA damage response (DDR) pathway. Topoisomerases, such as TOP1 and TOP2B, play a role in ecDNA replication-induced DNA double-strand breaks (DSBs). A subset of these elevated DSBs persists into the mitotic phase and is primarily repaired by the alternative non-homologous end joining (alt-NHEJ) pathway, which involves POLθ and LIG3. Correspondingly, ecDNA maintenance requires DDR, and inhibiting DDR impairs the circularization of ecDNA. In summary, we demonstrate reciprocal interactions between ecDNA maintenance and DDR, providing new insights into the detection and treatment of ecDNA+ tumors.

Deciphering the human TopIIIα activity modulated by Rmi1 using magnetic tweezers

Topoisomerases IA (TopoIAs) are universal and essential enzymes present in the three domains of life. Most of the Metazoa exhibit two TopoIAs-TopIIIα and TopIIIβ-assuming different roles in the cell. TopIIIα is essential for genome stability by disentangling precatenanes and hemicatenanes during DNA replication or dissolving the double Holliday junctions in recombination, with the help of several partners, such as Rmi1. However, the detail of the TopIIIα enzymatic cycle and the precise role of Rmi1 remain essentially unknown. The single-molecule approach allows to deconvolute the different early reaction steps and distinguish between intrinsic catalytic characteristics of human TopIIIα that are invariable and those that can be modulated by Rmi1. We determined that the limiting step is the TopIIIα-DNA binding, which requires a small single-stranded region. TopIIIα punctuates its catalytic cycle with long pause times to stabilize the open cleaved complex. Rmi1 helps TopIIIα trap the single-stranded DNA and therefore greatly increases the efficiency of the binding step. Rmi1 also enhances the stabilization of the open cleaved complex to favour intermolecular reactions with improved discrimination of DNA substrates. Rmi1 is therefore a crucial partner for TopIIIα in ensuring that the DNA transaction processes run smoothly in vivo.

Machine Learning Approach and Bioinformatics Analysis Discovered Key Genomic Signatures for Hepatitis B Virus-Associated Hepatocyte Remodeling and Hepatocellular Carcinoma

Hepatitis B virus (HBV) causes liver cancer, which is the third most common cause of cancer-related death worldwide. Chronic inflammation via HBV in the host hepatocytes causes hepatocyte remodeling (hepatocyte transformation and immortalization) and hepatocellular carcinoma (HCC). Recognizing cancer stages accurately to optimize early screening and diagnosis is a primary concern in the outlook of HBV-induced hepatocyte remodeling and liver cancer. Genomic signatures play important roles in addressing this issue. Recently, machine learning (ML) models and bioinformatics analysis have become very important in discovering novel genomic signatures for the early diagnosis, treatment, and prognosis of HBV-induced hepatic cell remodeling and HCC. We discuss the recent literature on the ML approach and bioinformatics analysis revealed novel genomic signatures for diagnosing and forecasting HBV-associated hepatocyte remodeling and HCC. Various genomic signatures, including various microRNAs and their associated genes, long noncoding RNAs (lncRNAs), and small nucleolar RNAs (snoRNAs), have been discovered to be involved in the upregulation and downregulation of HBV-HCC. Moreover, these genetic biomarkers also affect different biological processes, such as proliferation, migration, circulation, assault, dissemination, antiapoptosis, mitogenesis, transformation, and angiogenesis in HBV-infected hepatocytes.

Transcription-Coupled Repair and R-Loop Crosstalk in Genome Stability

Transcription-coupled repair (TCR) and R-loops are two interrelated processes critical to the maintenance of genome stability during transcription. TCR, a specialized sub-pathway of nucleotide excision repair, rapidly removes transcription-blocking lesions from the transcribed strand of active genes, thereby safeguarding transcription fidelity and cellular homeostasis. In contrast, R-loops, RNA-DNA hybrid structures formed co-transcriptionally, play not only regulatory roles in gene expression and replication but can also contribute to genome instability when persistently accumulated. Recent experimental evidence has revealed dynamic crosstalk between TCR and R-loop resolution pathways. This review highlights current molecular and cellular insights into TCR and R-loop biology, discusses the impact of their crosstalk, and explores emerging therapeutic strategies aimed at optimizing DNA repair and reducing disease risk in conditions such as cancer and neurodegenerative disorders.

In Vivo and In Vitro Pharmacokinetic Studies of a Dual Topoisomerase I/II Inhibitor

Due to high mortality rates, new and more effective drugs are urgently needed in cancer therapy. The novel dual topoisomerase inhibitor P8-D6, a dimethylaminoethyl-substituted pyridophenanthroline, showed in vitro impressive induction of apoptosis in tumors such as ovarian cancer or multiple myeloma compared to the current standard therapy. The purpose of this study was to investigate its in vitro and in vivo pharmacokinetics and to discover further potential drug candidates. Samples of plasma, various tissues, urine, feces, and cell culture supernatants were examined by HPLC. In addition, the efficacy of the metabolites against ovarian cancer was determined in vitro. Three phase I metabolites were identified in vitro and in vivo, and one phase II metabolite was identified in vivo. Among the metabolites, N-dealkylated P8-D6 (P8-D6 mono) achieved efficacy similar to that of P8-D6 in ovarian cancer. P8-D6 showed a relevant inhibitory effect on the efflux pumps P-GP (IC50 = 20.63 μM) and BCRP (16.32 μM). The calculated oral bioavailability in Sprague-Dawley rats was 21.5%, while P8-D6 had a high plasma protein binding of 99% and an extensive tissue distribution with an apparent volume of distribution between 57.69 (i.v.) and 82.92 (p.o.) L/m2. Both P8-D6 and its metabolites were detected in urine and feces. This study provides a basis for the clinical application of P8-D6 and has also identified P8-D6 mono as a very potent and metabolically stable drug candidate.

An autism spectrum disorder mutation in Topoisomerase 3β causes accumulation of covalent mRNA intermediates by disrupting metal binding within the zinc finger domain

The loss and mutation of Topoisomerase 3β (TOP3B), the only known eukaryotic topoisomerase with the ability to catalyze RNA strand passage reactions, is linked to schizophrenia, autism, and intellectual disability. Uniquely, TOP3B primarily localizes to the cytoplasm and has been shown to regulate translation and stability of a subset of mRNA transcripts. Three neurological disease-linked de novo TOP3B point mutations outside of the active site have been identified but their impact on TOP3B activity in cells remains poorly understood. Upon establishing a new Neuro2A cell-based TOP3B activity assay, we provide genetic and biochemical evidence that the autism-linked C666R mutation causes accumulation of unresolved TOP3B•mRNA covalent intermediates by directly disrupting metal coordination via an atypical D1C3-type metal binding motif within the zinc finger domain. Furthermore, we show that primary neurons are sensitive to high levels of TOP3B•mRNA covalent intermediates and that such adducts are capable of causing ribosome collisions. Together, these data identify a previously underappreciated role of the zinc finger domain and how non-active site disease-linked mutations affect TOP3B activity.

Real-time imaging of rotation during synthesis by the replisome

During chromosome replication, unwinding by the helicase and synthesis by the polymerases can lead to overwinding and supercoiling of DNA. The mechanical consequences of these events and resulting local dynamics at the replication fork are not well understood. To address these issues, we developed a transverse DNA flow-stretching approach to spatially resolve the parental, leading and lagging strands in real-time. Using bacteriophage T7 as a model system, this approach revealed bursts of high-speed replisome rotation that support continuous DNA synthesis. Surprisingly, excessive rotation does not reduce replisome speed, but increases pausing, reduces processivity, and increases polymerase exchange. Taken together, our observations reveal intrinsic pathways to overcome challenges posed by unfavorable DNA topologies during DNA replication.

Spo11: from topoisomerase VI to meiotic recombination initiator

Meiotic recombination is required to break up gene linkage and facilitate faithful chromosome segregation during gamete formation. By inducing DNA double-strand breaks, Spo11, a protein that is conserved in all meiotic organisms, initiates the process of recombination. Here, we chart the evolutionary history of Spo11 and compare the protein to its ancestors. Evolving from the A subunit of archaeal topoisomerase VI (Topo VI), a heterotetrameric type II topoisomerase, Spo11 appears to have evolved alongside meiosis and been present in the last eukaryotic common ancestor. There are many differences between Spo11 and TopVIA, particularly in regulation, despite similarities in structure and mechanism of action. Critical to its function as an inducer of recombination, Spo11 has an apparently amputated activity that, unlike topoisomerases, does not re-seal the DNA breaks it creates. We discuss how and why Spo11 has taken its path down the tree of life, considering its regulation and its roles compared with those of its progenitor Topo VI, in both meiotic and non-meiotic species. We find some commonality between different forms and orthologs of Spo11 in different species and touch upon how recent biochemical advances are beginning to finally unlock the molecular secrets hidden within this fundamental yet enigmatic protein.

ATM and IRAK1 orchestrate two distinct mechanisms of NF-κB activation in response to DNA damage

DNA damage in cells induces the expression of inflammatory genes. However, the mechanism by which cells initiate an innate immune response in the presence of DNA lesions blocking transcription remains unknown. Here we find that genotoxic stresses lead to an acute activation of the transcription factor NF-κB through two distinct pathways, each triggered by different types of DNA lesions and coordinated by either ataxia-telangiectasia mutated (ATM) or IRAK1 kinases. ATM stimulates NF-κB in cells with DNA double-strand breaks. By contrast, IRAK1-induced NF-κB signaling occurs in neighboring cells through IL-1α secretion from transcriptionally stressed cells caused by DNA lesions blocking RNA polymerases. Subsequently, both pathways stimulate TRAF6 and the IKK complex to promote NF-κB-mediated inflammatory gene expression. These findings provide an alternative mechanism for damaged cells with impaired transcription to initiate an inflammatory response without relying on their own gene expression, a necessary step that injured cells depend on during canonical innate immune responses.

Causes and consequences of DNA double-stranded breaks in cardiovascular disease

The genome, whose stability is essential for survival, is incessantly exposed to internal and external stressors, which introduce an estimated 104 to 105 lesions, such as oxidation, in the nuclear genome of each mammalian cell each day. A delicate homeostatic balance between the generation and repair of DNA lesions maintains genomic stability. To initiate transcription, DNA strands unwind to form a transcription bubble and provide a template for the RNA polymerase II (RNAPII) complex to synthesize nascent RNA. The process generates DNA supercoils and introduces torsional stress. To enable RNAPII processing, the supercoils are released by topoisomerases by introducing strand breaks, including double-stranded breaks (DSBs). Thus, DSBs are intrinsic genomic features of gene expression. The breaks are quickly repaired upon processing of the transcription. DNA lesions and damaged proteins involved in transcription could impede the integrity and efficiency of RNAPII processing. The impediment, which is referred to as transcription stress, not only could lead to the generation of aberrant RNA species but also the accumulation of DSBs. The latter is particularly the case when topoisomerase processing and/or the repair mechanisms are compromised. The DSBs activate the DNA damage response (DDR) pathways to repair the damaged DNA and/or impose cell cycle arrest and cell death. In addition, the release of DSBs into the cytosol activates the cytosolic DNA-sensing proteins (CDSPs), which along with the nuclear DDR pathways induce the expression of senescence-associated secretory phenotype (SASP), cell cycle arrest, senescence, cell death, inflammation, and aging. The primary stimulus in hereditary cardiomyopathies is a mutation(s) in genes encoding the protein constituents of cardiac myocytes; however, the phenotype is the consequence of intertwined complex interactions among numerous stressors and the causal mutation(s). Increased internal DNA stressors, such as oxidation, alkylation, and cross-linking, are expected to be common in pathological conditions, including in hereditary cardiomyopathies. In addition, dysregulation of gene expression also imposes transcriptional stress and collectively with other stressors provokes the generation of DSBs. In addition, the depletion of nicotinamide adenine dinucleotide (NAD), which occurs in pathological conditions, impairs the repair mechanism and further facilitates the accumulation of DSBs. Because DSBs activate the DDR pathways, they are expected to contribute to the pathogenesis of cardiomyopathies. Thus, interventions to reduce the generation of DSBs, enhance their repair, and block the deleterious DDR pathways would be expected to impart salubrious effects not only in pathological states, as in hereditary cardiomyopathies but also aging.

Substrate binding of human and bacterial type IA topoisomerase: An experimentation with AlphaFold 3.0

Advancements in biophysical techniques such as X-ray crystallography and Cryo-EM have allowed the determination of three-dimensional structures of many proteins and nucleic acids. There, however, is still a lack of 3D structures of proteins that are difficult to crystallize or proteins in complex with other macromolecules. With the advent of deep learning applications such as AlphaFold and RoseTTAFold, it is becoming possible to obtain 3D structures of proteins from their 1D sequences while also generating models of protein-nucleic acid complexes that have been difficult to capture through traditional methods. In this project, we utilized AlphaFold3 (AF3) to create a large number of predicted complexes of two type IA topoisomerases: human topoisomerase 3 beta (hTOP3B) and Mycobacterium tuberculosis topoisomerase I bound to a single-stranded DNA (ssDNA). Topoisomerases are enzymes responsible for resolving topological barriers that arise during regular cellular activity. Obtaining structures of topoisomerase complexed with a ssDNA will allow us to discover possible sequence preferences of this enzyme and obtain structures that can be used to screen potential inhibitors. Our analysis showed that AF3 can predict the structure of the enzymes, especially the N-terminal domain, with high confidence. However, predicted protein-DNA complexes, especially with longer (> 25-mer) oligos, are unreliable. The models generated with shorter (9-mer) oligos are obtained with improved confidence and the substrates are placed similarly to crystal structures, but they do not reliably replicate the sequence specificity of the DNA binding of topoisomerase observed in biochemical assays and crystal structures.

How do neurons live long and healthy? The mechanism of neuronal genome integrity

Genome DNA of neurons in the brain is unstable, and mutations caused by inaccurate repair can lead to neurodevelopmental and neurodegenerative disorders. Damage to the neuronal genome is induced both exogenously and endogenously. Rapid cell proliferation of neural stem cells during embryonic brain development can lead to errors in genome duplication. Electrical excitations and drastic changes in gene expression in functional neurons cause risks of damaging genomic DNA. The precise repair of DNA damages caused by events making genomic DNA unstable maintains neuronal functions. The maintenance of the DNA sequence and structure of the genome is known as genomic integrity. Molecular mechanisms that maintain genomic integrity are critical for healthy neuronal function. In this review, we describe recent progress in understanding the genome integrity in functional neurons referring to their disruptions reported in neurological diseases.

Comprehensive genomic dependency landscape of a human colon cancer organoid

Identifying genetic dependencies in human colon cancer could help identify effective treatment strategies. Genome-wide CRISPR-Cas9 dropout screens have the potential to reveal genetic dependencies, some of which could be exploited as therapeutic targets using existing drugs. In this study, we comprehensively characterized genetic dependencies present in a colon cancer organoid avatar, and validated tumor-specific selectivity of select pharmacologic agents. We conducted a genome-wide CRISPR dropout screen to elucidate the genetic dependencies that interacted with select driver somatic mutations. We found distinct genetic dependencies that interacted with WNT, MAPK, PI3K, TP53, and mismatch repair pathways and validated targets that could be exploited as treatments for this specific subtype of colon cancer. These findings demonstrate the utility of functional genomic screening in the context of personalized medicine.

Preclinical evaluation of a novel antibody-drug conjugate OBI-992 for Cancer therapy

Trophoblast cell surface antigen 2 (TROP2), a transmembrane glycoprotein highly expressed in a variety of epithelial cancers, has been considered as a primary therapeutic target for the development of antibody-drug conjugates (ADCs). OBI-992, an investigational TROP2-targeted ADC, is composed of a novel TROP2 antibody (R4702) conjugated to the topoisomerase I (TOP1) inhibitor exatecan through a hydrophilic enzyme-cleavable linker. This study aimed to characterize R4702 and OBI-992 in vitro. TROP2-targeted antibodies sacituzumab and datopotamab were employed as the comparators for R4702. ADCs sacituzumab govitecan (SG) and datopotamab deruxtecan (Dato-DXd) were used as benchmarks for OBI-992. Results revealed that R4702 binds to an epitope that is distinct from sacituzumab and datopotamab. The cytotoxicity of the OBI-992, SG, and Dato-DXd against different cancer cells is comparable despite they have different internalization profile. Upregulation of breast cancer resistance protein (BCRP) was observed in SG-resistant and Dato-DXd-resistant cells, but not in OBI-992-resistant cells. In addition, significant downregulation of TROP2 expression was detected with Dato-DXd-resistant cells and only slightly downregulation with SG- and OBI-992-resistant cells was observed. Moreover, substantial enhancement of cytotoxicity and DNA damage was found in the combination of OBI-992 with a poly (ADP-ribose) polymerase (PARP) inhibitor (talazoparib). Taken together, the findings in this study support further clinical development of OBI-992.

Recurrent patterns of widespread neuronal genomic damage shared by major neurodegenerative disorders

Amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), and Alzheimer's disease (AD) are common neurodegenerative disorders for which the mechanisms driving neuronal death remain unclear. Single-cell whole-genome sequencing of 429 neurons from three C9ORF72 ALS, six C9ORF72 FTD, seven AD, and twenty-three neurotypical control brains revealed significantly increased burdens in somatic single nucleotide variant (sSNV) and insertion/deletion (sIndel) in all three disease conditions. Mutational signature analysis identified a disease-associated sSNV signature suggestive of oxidative damage and an sIndel process, affecting 28% of ALS, 79% of FTD, and 65% of AD neurons but only 5% of control neurons (diseased vs. control: OR=31.20, p = 2.35×10-10). Disease-associated sIndels were primarily two-basepair deletions resembling signature ID4, which was previously linked to topoisomerase 1 (TOP1)-mediated mutagenesis. Duplex sequencing confirmed the presence of sIndels and identified similar single-strand events as potential precursor lesions. TOP1-associated sIndel mutagenesis and resulting genome instability may thus represent a common mechanism of neurodegeneration.

SART3 promotes homologous recombination repair by stimulating DNA-RNA hybrids removal and DNA end resection

DNA-RNA hybrids triggered by double-strand breaks (DSBs) are crucial intermediates during DSB repair, and their timely resolution requires numbers of RNA helicases, including DEAD box 1 (DDX1). However, how these helicases are recruited to DSB-induced hybrids in time remains largely unclear. Here, we revealed that squamous cell carcinoma antigen recognized by T cells 3 (SART3) promotes DDX1 binding to DNA-RNA hybrids at DSBs for optimal homologous recombination (HR) repair. SART3 itself associates with DNA-RNA hybrids and PAR chains and accumulates at DSBs in both PARylation- and DNA-RNA hybrids-dependent fashion. SART3 also associates with DDX1 and is necessary for DDX1 enrichment at DSBs. The defective SART3-DDX1 association observed in cells expressing the cancer-associated variant SART3-R836W impairs not only the accumulation of DDX1, but also hybrid removal and HR efficiency. Moreover, SART3 promotes DNA end resection through enhancing USP15-BARD1 association and BRCA1-BARD1 retention. Together, our study reveals an role of SART3 in DSB repair, rendering SART3 a promising target for cancer therapy.

CENPF (+) cancer cells promote malignant progression of early-stage TP53 mutant lung adenocarcinoma

The prevention and precise treatment of early-stage lung adenocarcinoma (LUAD) characterized by small nodules (stage IA) remains a significant challenge for clinicians, which is due largely to the limited understanding of the oncogenic mechanisms spanning from preneoplasia to invasive adenocarcinoma. Our study highlights the pivotal role of cancer cells exhibiting high expression of centromere protein F (CENPF), driven by TP53 mutations, which become increasingly prevalent during the transition from preneoplasia to invasive LUAD. Biologically, cancer cells (CENPF+) exhibited robust proliferative and stem-like capabilities, thereby propelling the malignant progression of early-stage LUAD. Clinically, autoantibodies against CENPF in the serum and elevated cancer cells (CENPF+) in tissue correlated positively with the progression of early-stage LUAD, especially those in stage IA. Our findings suggest that cancer cells (CENPF+) play a central role in orchestrating the malignant evolution of LUAD and hold potential as a novel biomarker for early-stage detection and management of the disease.

DNA Damage Response Pharmacogenomic (DDR_PGx) Score Predicts Response to Chemotherapy Consisting of Gemtuzumab Ozogamicin in Pediatric AML: A Report from the Children's Oncology Group

PURPOSE

Comprehensive pharmacogenomics (PGx) evaluation of calicheamicin pathway to identify predictive PGx markers of response to gemtuzumab ozogamicin (GO) treatment in acute myeloid leukemia (AML).

EXPERIMENTAL DESIGN

SNPs in DNA damage response (DDR) pathway genes were tested for association with event-free survival (EFS), overall survival (OS), and risk of relapse after induction 1 (RR1) in patients treated with standard chemotherapy consisting of Ara-C, daunorubicin, and etoposide (ADE) with or without addition of GO on COG-AAML03P1 and COGAAAML0531 trials (ADE+GO, n = 755; ADE n = 470). SNPs with significant association with any endpoint within ADE+GO arm but not in the ADE arm were tested using multi-SNP modeling to develop DDR_PGx7 score.

RESULTS

Patients with low DDR_PGx7 score (<0) had significantly worse EFS [HR = 1.51, 95% confidence interval (CI: 1.21-1.89), P < 0.001], worse OS [HR = 1.59, 95% CI (1.22-2.08), P < 0.001], and higher RR1 [HR = 1.87, 95% CI (1.41-2.47), P < 0.0001] compared with patients with highDDR_PGx7 score (≥0)when treated withGO (ADE+GO cohort). However, no difference between low and high DDR_PGx7 score groups was observed for EFS, OS, and RR1 (all P > 0.3) in patients treated on ADE arm.

CONCLUSIONS

Our results suggest that DDR pathway-based pharmacogenomic score holds potential to predict outcome in patients treated with GO which consists of DNA damaging cytotoxin, calicheamicin. The potential clinical relevance for this score to personalize GO in AML requires further validation in independent and expanded cohorts.

Multi-omics analysis reveals the panoramic picture of TOP2A in pan-cancer

Topoisomerases are critical nuclear enzymes that resolve DNA topological challenges during genetic processes. However, there is currently a lack of comprehensive multi-omics analysis of TOP2A from a pan-cancer perspective, despite its significance. A multiomics analysis was conducted to investigate TOP2A across various cancer types. This study involved the integration of over 10,000 multidimensional genomic datasets from 33 distinct cancer types, obtained from The Cancer Genome Atlas (TCGA). The analysis focused on evaluating the overall activity levels of TOP2A in pan-cancers, which encompassed differential expression, clinical significance, immune cell infiltration, and the regulation of pathways related to cancer. Aberrant epigenetic modifications and genomic alterations have been identified as being associated with the dysregulation of TOP2A expression levels. These molecular changes have substantial impacts on cancer progression, intratumoral heterogeneity, immunological status, and the regulation of pathways related to cancer biomarkers. Consequently, patient prognosis varies significantly based on the presence and specific nature of these alterations. The potential of TOP2A to serve as a novel biomarker for prognosis may offer valuable insights into the diagnosis and treatment of cancer.

SRBD1 facilitates chromosome segregation by promoting topoisomerase IIα localization to mitotic chromosomes

Accurate sister chromatid segregation requires remodeling chromosome architecture, decatenation, and attachment to the mitotic spindle. Some of these events are initiated during S-phase, but they accelerate and conclude during mitosis. Here we describe SRBD1 as a histone and nucleic acid binding protein that prevents DNA damage in interphase cells, localizes to nascent DNA during replication and the chromosome scaffold in mitosis, and is required for chromosome segregation. SRBD1 inactivation causes micronuclei, chromatin bridges, and cell death. Inactivating SRBD1 immediately prior to mitotic entry causes anaphase failure, with a reduction in topoisomerase IIα localization to mitotic chromosomes and defects in properly condensing and decatenating chromosomes. In contrast, SRBD1 is not required to complete cell division after chromosomes are condensed. Strikingly, depleting condensin II reduces the severity of the anaphase defects in SRBD1-deficient cells by restoring topoisomerase IIα localization. Thus, SRBD1 is an essential genome maintenance protein required for mitotic chromosome organization and segregation.

Synthesis, Structural Modification, and Antismall Cell Lung Cancer Activity of 3-Arylisoquinolines with Dual Inhibitory Activity on Topoisomerase I and II

To overcome the compensatory effect between Topo I and II, one of the reasons accounting for the resistance of SCLC patients, we are pioneering the use of 3-arylisoquinolines to develop dual inhibitors of Topo I/II for the management of SCLC. A total of 46 new compounds were synthesized. Compounds 3g (IC50 = 1.30 μM for NCI-H446 cells and 1.42 μM for NCI-H1048 cells) and 3x (IC50 = 1.32 μM for NCI-H446 cells and 2.45 μM for NCI-H1048 cells) were selected for detailed pharmacological investigation, due to their outstanding cytotoxicity and dual Topo I and II inhibitory activity. 3g and 3x effectively prevent SCLC cell proliferation, invasion, and migration in vitro, byinducing mitochondrial apoptosis and inhibiting the PI3K/Akt/mTOR pathway. Their in vivo tumor inhibition rate is comparable to etoposide with lower toxicity. These results indicated their potential therapeutic values as dual Topo I and II inhibitors for treating SCLC.

Design and Synthesis of Topoisomerases-Histone Deacetylase Dual Targeted Quinoline-Bridged Hydroxamates as Anticancer Agents

The multifactorial nature of cancer requires treatment that involves simultaneous targeting of associated overexpressed proteins and cell signaling pathways, possibly leading to synergistic effects. Herein, we present a systematic study that involves the simultaneous inhibition of human topoisomerases (hTopos) and histone deacetylases (HDACs) by multitargeted quinoline-bridged hydroxamic acid derivatives. These compounds were rationally designed considering pharmacophoric features and catalytic sites of the cross-talk proteins, synthesized, and assessed for their anticancer potential. Our findings revealed that the compound 5c significantly produced anticancer effects in vitro and in vivo by reducing the tumor growth and its size in the A549 cell-induced lung cancer xenograft model through multiple mechanisms, primarily by multi-inhibition of hTopoI/II and HDACs, especially HDAC1 via atypical binding. The present paper discusses detailed mechanistic biological investigations, structure-activity effects supported by computational docking studies, and DMPK studies and provides future scope for lead optimization and modification.

The emerging regulatory interface between DNA repair and steroid hormone receptors in cancer

Human cells potentiate highly diverse functions through tight transcriptional regulation and maintenance of genome integrity. While the DNA damage response (DDR) safeguards the genome, ligand-activated transcription factors, such as steroid hormone receptors (SHRs), provide complex transcriptional outputs. Interestingly, an increasing body of evidence reveals a direct biological and functional interplay between DDR factors and SHR cascades in cancer. SHRs can directly affect DDR gene expression, but DDR factors in turn act as transcriptional coregulators, enabling oncogenic SHR-mediated signaling, which has the potential for novel therapeutic interventions. With a focus on breast and prostate cancer, we describe in this review recent developments in, and insights into, the complex interplay between SHR signaling and the DDR, highlighting opportunities for future clinical interventions.

Comprehensive SUMO Proteomic Analyses Identify HIV Latency-Associated Proteins in Microglia

SUMOylation, the post-translational modification of proteins by small ubiquitin-like modifiers, plays a critical role in regulating various cellular processes, including innate immunity. This modification is essential for modulating immune responses and influencing signaling pathways that govern the activation and function of immune cells. Recent studies suggest that SUMOylation also contributes to the pathophysiology of central nervous system (CNS) viral infections, where it contributes to the host response and viral replication dynamics. Here, we explore the multifaceted role of SUMOylation in innate immune signaling and its implications for viral infections within the CNS. Notably, we present novel proteomic analyses aimed at elucidating the role of the small ubiquitin-related modifier (SUMO) in human immunodeficiency virus (HIV) latency in microglial cells. Our findings indicate that SUMOylation may regulate key proteins involved in maintaining viral latency, suggesting a potential mechanism by which HIV evades immune detection in the CNS. By integrating insights from proteomics with functional studies, we anticipate these findings to be the groundwork for future studies on HIV-host interactions and the mechanisms that underlie SUMOylation during latent and productive infection.

Identifying Safeguards Disabled by Epstein-Barr Virus Infections in Genomes From Patients With Breast Cancer: Chromosomal Bioinformatics Analysis

Background

The causes of breast cancer are poorly understood. A potential risk factor is Epstein-Barr virus (EBV), a lifelong infection nearly everyone acquires. EBV-transformed human mammary cells accelerate breast cancer when transplanted into immunosuppressed mice, but the virus can disappear as malignant cells reproduce. If this model applies to human breast cancers, then they should have genome damage characteristic of EBV infection.

Objective

This study tests the hypothesis that EBV infection predisposes one to breast cancer by causing permanent genome damage that compromises cancer safeguards.

Methods

Publicly available genome data from approximately 2100 breast cancers and 25 ovarian cancers were compared to cancers with proven associations to EBV, including 70 nasopharyngeal cancers, 90 Burkitt lymphomas, 88 diffuse large B-cell lymphomas, and 34 gastric cancers. Calculation algorithms to make these comparisons were developed.

Results

Chromosome breakpoints in breast and ovarian cancer clustered around breakpoints in EBV-associated cancers. Breakpoint distributions in breast and EBV-associated cancers on some chromosomes were not confidently distinguished (P>.05), but differed from controls unrelated to EBV infection. Viral breakpoint clusters occurred in high-risk, sporadic, and other breast cancer subgroups. Breakpoint clusters disrupted gene functions essential for cancer protection, which remain compromised even if EBV infection disappears. As CRISPR (clustered regularly interspaced short palindromic repeats)-like reminders of past infection during evolution, EBV genome fragments were found regularly interspaced between Piwi-interacting RNA (piRNA) genes on chromosome 6. Both breast and EBV-associated cancers had inactivated genes that guard piRNA defenses and the major histocompatibility complex (MHC) locus. Breast and EBV-associated cancer breakpoints and other variations converged around the highly polymorphic MHC. Not everyone develops cancer because MHC differences produce differing responses to EBV infection. Chromosome shattering and mutation hot spots in breast cancers preferentially occurred at incorporated viral sequences. On chromosome 17, breast cancer breakpoints that clustered around those in EBV-mediated cancers were linked to estrogen effects. Other breast cancer breaks affected sites where EBV inhibits JAK-STAT and SWI-SNF signaling pathways. A characteristic EBV-cancer gene deletion that shifts metabolism to favor tumors was also found in breast cancers. These changes push breast cancer into metastasis and then favor survival of metastatic cells.

Conclusions

EBV infection predisposes one to breast cancer and metastasis, even if the virus disappears. Identifying this pathogenic viral damage may improve screening, treatment, and prevention. Immunizing children against EBV may protect against breast, ovarian, other cancers, and potentially even chronic unexplained diseases.

Identification of a novel TOP2B::AFF2 fusion gene in B-cell acute lymphoblastic leukemia

Genetic alterations play a pivotal role in leukemic clonal transformation, significantly influencing disease pathogenesis and clinical outcomes. Here, we report a novel fusion gene and investigate its pathogenic role in acute lymphoblastic leukemia (ALL). We engineer a transposon transfection system expressing the TOP2B::AFF2 transcript and introduce it into Ba/F3 cells. Functional studies, including proliferation, cell cycle, and apoptosis assays, were conducted to assess the fusion gene's impact. In vitro assays reveal that the TOP2B::AFF2 fusion significantly enhances Ba/F3 cell proliferation and G1/S phase transition while suppressing differentiation and apoptosis. This study identifies TOP2B::AFF2 as a potential oncogenic driver. However, further validation through in vivo studies are warranted to fully elucidate the fusion gene's role in leukemogenesis.

Identification of MCM2-Interacting Proteins Associated with Replication Initiation Using APEX2-Based Proximity Labeling Technology

DNA replication is a crucial biological process that ensures the accurate transmission of genetic information, underpinning the growth, development, and reproduction of organisms. Abnormalities in DNA replication are a primary source of genomic instability and tumorigenesis. During DNA replication, the assembly of the pre-RC at the G1-G1/S transition is a crucial licensing step that ensures the successful initiation of replication. Although many pre-replication complex (pre-RC) proteins have been identified, technical limitations hinder the detection of transiently interacting proteins. The APEX system employs peroxidase-mediated rapid labeling with high catalytic efficiency, enabling protein labeling within one minute and detection of transient protein interactions. MCM2 is a key component of the eukaryotic replication initiation complex, which is essential for DNA replication. In this study, we fused MCM2 with enhanced APEX2 to perform in situ biotinylation. By combining this approach with mass spectrometry, we identified proteins proximal to the replication initiation complex in synchronized mouse ESCs and NIH/3T3. Through a comparison of the results from both cell types, we identified some candidate proteins. Interactions between MCM2 and the candidate proteins CD2BP2, VRK1, and GTSE1 were confirmed by bimolecular fluorescence complementation. This research establishes a basis for further study of the component proteins of the conserved DNA replication initiation complex and the transient regulatory network involving its proximal proteins.

The E2F4 transcriptional repressor is a key mechanistic regulator of colon cancer resistance to irinotecan (CPT-11)

Background

Colorectal carcinomas (CRCs) are seldom eradicated by cytotoxic chemotherapy. Cancer cells with stem-like functional properties, often referred to as "cancer stem cells" (CSCs), display preferential resistance to several anti-tumor agents used in cancer chemotherapy, but the molecular mechanisms underpinning their selective survival remain only partially understood.

Methods

In this study, we used Transcription Factor Target Genes (TFTG) enrichment analysis to identify transcriptional regulators (activators or repressors) that undergo preferential activation by chemotherapy in CRC cells with a "bottom-of-the-crypt" phenotype (EPCAM+/CD44+/CD166+; CSC-enriched) as compared to CRC cells with a "top-of-the-crypt" phenotype (EPCAM+/CD44neg/CD166neg; CSC-depleted). The two cell populations were purified in parallel by fluorescence-activated cell sorting (FACS) from a patient-derived xenograft (PDX) line representative of a moderately differentiated human CRC, following in vivo chemotherapy with irinotecan (CPT-11). The transcriptional regulators identified as differentially activated were tested for differential expression in normal vs. cancer tissues, and in cell populations enriched in stem/progenitor cell-types as compared to differentiated lineages (goblet cells, enterocytes) in the mouse colon epithelium. Finally, the top candidate was tested for mechanistic contribution to drug-resistance by selective down-regulation using short-hairpin RNAs (shRNAs).

Results

Our analysis identified E2F4 and TFDP1, two core components of the DREAM transcriptional repression complex, as transcriptional modulators preferentially activated by irinotecan in EPCAM+/CD44+/CD166+ as compared to EPCAM+/CD44neg/CD166neg cancer cells. The expression levels of both genes (E2F4, TFDP1) were found up-regulated in CRCs as compared to human normal colon tissues, and in a sub-population of mouse colon epithelial cells enriched in stem/progenitor elements (Epcam+/Cd44+/Cd66alow/Kitneg) as compared to other sub-populations enriched in either goblet cells (Epcam+/Cd44+/Cd66alow/Kit+) or enterocytes (Epcam+/Cd44neg/Cd66ahigh). Most importantly, E2F4 down-regulation using shRNAs dramatically enhanced the sensitivity of human CRCs to in vivo treatment with irinotecan, across three independent PDX models.

Conclusions

Our data identified E2F4 and the DREAM repressor complex as critical regulators of human CRC resistance to irinotecan, and as candidate targets for the development of chemo-sensitizing agents.

Structural insights into human topoisomerase 3β DNA and RNA catalysis and nucleic acid gate dynamics

Type IA topoisomerases (TopoIAs) are present in all living organisms. They resolve DNA/RNA catenanes, knots and supercoils by breaking and rejoining single-stranded DNA/RNA segments and allowing the passage of another nucleic acid segment through the break. Topoisomerase III-β (TOP3B), the only RNA topoisomerase in metazoans, promotes R-loop disassembly and translation of mRNAs. Defects in TOP3B lead to severe neurological diseases. We present a series of cryo-EM structures of human TOP3B with its cofactor TDRD3 during cleavage and rejoining of DNA or RNA, thus elucidating the roles of divalent metal ions and key enzyme residues in each step of the catalytic cycle. We also obtained the structure of an open-gate configuration that addresses the long-standing question of the strand-passage mechanism. Our studies reveal how TOP3B catalyzes both DNA and RNA relaxation, while TOP3A acts only on DNA.

Flap endonuclease 1 repairs DNA-protein cross-links via ADP-ribosylation-dependent mechanisms

DNA-protein cross-links (DPCs) are among the most detrimental genomic lesions. They are ubiquitously produced by formaldehyde (FA), and failure to repair FA-induced DPCs blocks chromatin-based processes, leading to neurodegeneration and cancer. The type, structure, and repair of FA-induced DPCs remain largely unknown. Here, we profiled the proteome of FA-induced DPCs and found that flap endonuclease 1 (FEN1) resolves FA-induced DPCs. We revealed that FA also damages DNA bases adjoining the DPCs, leading to DPC-conjugated 5' flap structures via the base excision repair (BER) pathway. We also found that FEN1 repairs enzymatic topoisomerase II (TOP2)-DPCs. Furthermore, we report that both FA-induced and TOP2-DPCs are adenosine diphosphate (ADP) ribosylated by poly(ADP-ribose) polymerase 1 (PARP1). PARylation of the DPCs in association with FEN1 PARylation at residue E285 is required for the recruitment of FEN1. Our work unveils the identity of proteins forming FA-induced DPCs and a previously unrecognized PARP1-FEN1 nuclease pathway repairing both FA- and TOP2-DPCs.

Etoposide targets 2A protease to inhibit enterovirus 71 replication

Enterovirus 71 (EV71) is a major pathogen that causes hand, foot, and mouth disease (HFMD) in infants and children. Notably, no clinically approved drugs specifically target EV71. The EV71 2A protease (2Apro), a cysteine protease produced by the virus, is essential for the virus' replication and has a significant impact on the functioning of host cells. Thus, it presents a valuable target for the discovery of antiviral medications. In this study, based on the monomers and their derivatives in the Library of Traditional Chinese Medicine (TCM), we performed virtual screening and biological experiments. We identified a derivative of a traditional herbal monomer, Etoposide, commonly isolated from the roots and rhizomes of Podophyllum spp. Etoposide inhibited replication of EV71 A, B, C, and CVA16 viruses in a concentration-dependent manner in a variety of cell lines with minimal cytotoxicity. Furthermore, both molecular dynamics simulations and site-directed mutagenesis assays revealed that Etoposide inhibited the activity of the EV71 2A protease by mainly binding to two residues, Y89 and P107. The findings indicate that Etoposide serves as a promising inhibitor of the EV71 2Apro, demonstrating strong antiviral properties and positioning itself as a formidable candidate for clinical trials against EV71.IMPORTANCEWe first used a drug screening approach focused on monomeric compounds and their derivatives from traditional Chinese medicine to identify an EV71 2Apro inhibitor-Etoposide. We then performed biological experiments to validate that Etoposide suppresses the replication of the EV71 virus in a concentration-dependent manner with minimal cytotoxicity to various cell lines. Remarkably, it shows inhibitory activity against EV71 A, B, C, and CVA16, suggesting that Etoposide may be a potential broad-spectrum inhibitor. We revealed a novel mechanism that Etoposide inhibits EV71 proliferation by targeting 2Apro, and the interactions with Y89 and P107 are of great importance. The findings suggest that Etoposide serves as a promising inhibitor of EV71 2Apro, demonstrating significant antiviral properties. It stands out as a strong candidate for broad-spectrum applications in clinical research.

High-Resolution Genome-Wide Maps Reveal Widespread Presence of Torsional Insulation

Torsional stress in chromatin plays a fundamental role in cellular functions, influencing key processes such as transcription, replication, and chromatin organization. Transcription and other processes may generate and be regulated by torsional stress. In the genome, the interplay of these processes creates complicated patterns of both positive (+) and negative (-) torsion. However, a challenge in generating an accurate torsion map is determining the zero-torsion baseline signal, which is conflated with chromatin accessibility. Here, we introduce a high-resolution method based on the intercalator trimethylpsoralen (TMP) to address this challenge. We describe a method to establish the zero-torsion baseline while preserving the chromatin state of the genome of S. cerevisiae. This approach enables both high-resolution mapping of accessibility and torsional stress in chromatin in the cell. Our analysis shows transcription-generated torsional domains consistent with the twin-supercoiled-domain model of transcription and suggests a role for torsional stress in recruiting topoisomerases and in regulating 3D genome architecture via cohesin. Significantly, we reveal that insulator sequence-specific transcription factors decouple torsion between divergent promoters, whereas torsion spreads between divergent promoters lacking these factors, suggesting that torsion serves as a regulatory mechanism in these regions. Although insulators are known to decouple gene expression, our finding provides a physical explanation of how such decoupling may occur. This new method provides a potential path forward for using TMP to measure torsional stress in the genome without the confounding contribution of accessibility in chromatin.

Exploring the Potential of Malvidin and Echiodinin as Probable Antileishmanial Agents Through In Silico Analysis and In Vitro Efficacy

Leishmaniasis, a neglected tropical disease caused by Leishmania species, presents serious public health challenges due to limited treatment options, toxicity, high costs, and drug resistance. In this study, the in vitro potential of malvidin and echioidinin is examined as antileishmanial agents against L. amazonensis, L. braziliensis, and L. infantum, comparing their effects to amphotericin B (AmpB), a standard drug. Malvidin demonstrated greater potency than echioidinin across all parasite stages and species. Against L. amazonensis, malvidin's IC50 values were 197.71 ± 17.20 µM (stationary amastigotes) and 258.07 ± 17 µM (axenic amastigotes), compared to echioidinin's 272.99 ± 29.90 μM and 335.96 ± 19.35 μM. AmpB was more potent, with IC50 values of 0.06 ± 0.01 µM and 0.10 ± 0.03 µM. Malvidin exhibited lower cytotoxicity (CC50: 2920.31 ± 80.29 µM) than AmpB (1.06 ± 0.12 µM) and a favorable selectivity index. It reduced infection rates by 35.75% in L. amazonensis-infected macrophages. The in silico analysis revealed strong binding between malvidin and Leishmania arginase, with the residues HIS139 and PRO258 playing key roles. Gene expression analysis indicated malvidin's modulation of oxidative stress and DNA repair pathways, involving genes like GLO1 and APEX1. These findings suggest malvidin's potential as a safe, natural antileishmanial compound, warranting further in vivo studies to confirm its therapeutic efficacy and pharmacokinetics in animal models.

DNA Cleavage Mediated by Bacterial Type II Topoisomerases

The maintenance of DNA topology is critical for cellular processes. Topoisomerases are a class of enzymes found in eukaryotic and prokaryotic organisms that modulate the topology of DNA during replication and transcription. Bacterial type II topoisomerases, DNA gyrase and topoisomerase IV, are essential for bacterial cell survival. These enzymes pass an intact double helix through a transient double-stranded break in a separate segment of DNA in order to carry out their specific functions. The DNA cleavage step is crucial for the activity of the type II enzymes. However, prolongation of this process, for example, with exposure to antibacterial agents, can lead to bacterial cell death. The DNA cleavage assay is an in vitro method used to study the effects of type II topoisomerase-targeting compounds on enzyme-mediated DNA cleavage. This chapter outlines a protocol for measuring DNA cleavage mediated by Escherichia coli gyrase in the presence or absence of antibacterial drugs.

Expression, Purification, and Measurement of DNA Supercoil Relaxation Activity by Eukaryotic Topoisomerase II

Topoisomerases play a critical role in safeguarding the genome by resolving topological challenges that both result from and interfere with transcription and replication. These enzymes have been the subject of research not only for understanding their complex mechanisms of action, but also because of their therapeutic utility as drug targets. To gain a better understanding of topoisomerases and how they function, in vitro assays are necessary to measure their activity under various conditions. In this chapter, we describe the expression and purification of a eukaryotic type II topoisomerase (human topo IIα) from budding yeast cells and a gel-based assay that permits measurement of its ability to relax supercoiled DNA.

Use of Xenopus Egg Extracts to Study the Effects of Topoisomerase Poisons During Vertebrate DNA Replication

Topoisomerases unlink chromosomes and relieve topological stress. Topoisomerase "poisons" are widely used chemotherapeutics that stabilize topoisomerase complexes on DNA, leading to cytotoxic DNA breaks and cancer cell killing. It is well established that topoisomerase poisons interfere with DNA replication, which is thought to be a major physiological target of these drugs. However, many questions remain about the mechanisms by which topoisomerase poisons impact DNA replication and the downstream consequences. Here, we describe assays to study topoisomerase poisons during vertebrate DNA replication using Xenopus egg extracts. These approaches allow for replication intermediates formed following poison treatment to be carefully monitored with high temporal resolution.

Topoisomerase II DNA Cleavage Assay Using Fluorescently Labelled Double-Stranded Oligonucleotides

DNA topoisomerase II (TOP2) regulates DNA topological states including supercoiling and knotting via a strand-passage reaction that involves transiently breaking and rejoining both strands of the DNA. These enzymes are the targets of a category of drugs termed topoisomerase poisons, which block the rejoining reaction, leading to DNA cleavage. In vitro DNA cleavage assays have been very useful in studying various properties of TOP2, including cleavage site preferences and the effects of TOP2 amino acid substitutions or reaction conditions on DNA cleavage. These assays employ purified or recombinant TOP2 in the presence or absence of TOP2 poisons, followed by electrophoretic separation of DNA cleavage products. The substrates for these assays have typically been radioactively end-labelled DNA fragments. Here, we describe an alternative method employing fluorescently labelled oligonucleotide substrates, combined with convenient mini-gel electrophoretic separation. This methodology combines stable, long-lived substrates with an easily used gel system and convenient imaging and quantification.

HBV-Induced Carcinogenesis: Mechanisms, Correlation With Viral Suppression, and Implications for Treatment

BACKGROUND

Chronic hepatitis B virus (HBV) infection is a common but underdiagnosed and undertreated health condition and is the leading cause of hepatocellular carcinoma (HCC) worldwide. HBV (rated a Grade 1 carcinogen by the International Agency for Research on Cancer) drives the transformation of hepatocytes in multiple ways by inducing viral DNA integrations, genetic dysregulation, chromosomal translocations, chronic inflammation, and oncogenic pathways facilitated by some HBV proteins. Importantly, these mechanisms are active throughout all phases of HBV infection. Nevertheless, most clinical guidelines for antiviral therapy recommend treatment based on a complex combination of HBV DNA levels, transaminasemia, liver histology, and demographic factors, rather than prompt treatment for all people with infection.

AIMS

To determine if current frameworks for antiviral treatment address the impacts of chronic HBV infection particularly preventing cancer development.

MATERIALS AND METHODS

We reviewed the recent data demonstrating pro-oncogenic factors acting throughout a chronic HBV infection can be inhibited by antiviral therapy.

RESULTS

We extensively reviewed Hepatitis B virology data and correlating clinical outcome data. From thi, we suggest that new findings support simplifying and expanding treatment initiation to reduce the incidence ofnew infections, progressive liver disease, and risk of hepatocellular carcinoma. We also consider lessons learned from other blood-borne pathogens, including the benefits of antiviral treatment in preventing transmission, reducing stigma, and reframing treatment as cancer prevention.

CONCLUSION

Incorporating these practice changes into treatment is likely to reduce the overall burden of chronic HBV infections and HCC. Through this, we may better achieve the World Health Organization's goal of eliminating viral hepatitis as a public health threat and minimise its impact on people's lives.

Topoisomerase-modulated genome-wide DNA supercoiling domains colocalize with nuclear compartments and regulate human gene expression

DNA supercoiling is a biophysical feature of the double helix with a pivotal role in biological processes. However, understanding of DNA supercoiling in the chromatin remains limited. Here, we developed azide-trimethylpsoralen sequencing (ATMP-seq), a DNA supercoiling assay offering quantitative accuracy while minimizing genomic bias and background noise. Using ATMP-seq, we directly visualized transcription-dependent negative and positive twin-supercoiled domains around genes and mapped kilobase-resolution DNA supercoiling throughout the human genome. Remarkably, we discovered megabase-scale supercoiling domains (SDs) across all chromosomes that are modulated mainly by topoisomerases I and IIβ. Transcription activities, but not the consequent supercoiling accumulation in the local region, contribute to SD formation, indicating the long-range propagation of transcription-generated supercoiling. Genome-wide SDs colocalize with A/B compartments in both human and Drosophila cells but are distinct from topologically associating domains (TADs), with negative supercoiling accumulation at TAD boundaries. Furthermore, genome-wide DNA supercoiling varies between cell states and types and regulates human gene expression, underscoring the importance of supercoiling dynamics in chromatin regulation and function.

Clues to transcription/replication collision-induced DNA damage: it was RNAP, in the chromosome, with the fork

DNA replication and RNA transcription processes compete for the same DNA template and, thus, frequently collide. These transcription-replication collisions are thought to lead to genomic instability, which places a selective pressure on organisms to avoid them. Here, we review the predisposing causes, molecular mechanisms, and downstream consequences of transcription-replication collisions (TRCs) with a strong emphasis on prokaryotic model systems, before contrasting prokaryotic findings with cases in eukaryotic systems. Current research points to genomic structure as the primary determinant of steady-state TRC levels and RNA polymerase regulation as the primary inducer of excess TRCs. We review the proposed mechanisms of TRC-induced DNA damage, attempting to clarify their mechanistic requirements. Finally, we discuss what drives genomes to select against TRCs.