Model Construction and Identification of Genome Instability-Associated LncRNA Signature Markers in Bladder Cancer

Background: Studies have shown that long non-coding RNA (LncRNA) plays a critical role in maintaining genomic instability. The correlation between lncRNA and genomic instability is still worth exploring in bladder cancer as a new tumour marker. Methods: Therefore, combined with the lncRNA expression profile and somatic mutation profile of bladder cancer, we established a computing framework of lncRNA related to genomic instability and identified 58 new lncRNA related to genomic instability. Next, we identified a lncRNA signature (GILncSig), based on these 58 new genes, which divided patients into high-risk and low-risk groups. The clinical prognosis was significantly different and was further verified in an independent cohort of patients. Results: We confirmed that GILncSig is related to the genomic mutation rate of bladder cancer, suggesting that GILncSig can be used as an indicator of genomic instability. The results show that GILncSig has prognostic value independent of age, sex, grade, and stage and is vital in evaluating clinical prognosis. To sum up, this study provides a vital research basis and methods for further exploring the role of lncRNA in the genomic instability of bladder cancer and provides a theoretical basis for the identification of bladder cancer biomarkers related to genomic instability.

Impaired dNKAP function drives genome instability and tumorigenic growth in Drosophila epithelia

Mutations or dysregulated expression of NF-kappaB-activating protein(NKAP)family genes have been found in human cancers.How NKAP family gene mutations promote tumor initiation and progression remains to be determined.Here,we characterized dNKAP,the Drosophila homolog of NKAP,and showed that impaired dNKAP function causes genome instability and tumorigenic growth in a Drosophila epithelial tumor model.dNKAP-knockdown wing imaginal discs exhibit tumorigenic characteristics,including tissue overgrowth,cell-invasive behavior,abnormal cell polarity,and cell adhesion defects.dNKAP knockdown causes both R-loop accumulation and DNA damage,indicating the disruption of genome integrity.Further analysis showed that dNKAP knockdown induces c-Jun N-terminal kinase(JNK)-dependent apoptosis and causes aberrant cell proliferation in distinct cell populations.Activation of the Notch and JAK/STAT signaling pathways contributes to the tumorigenic growth of dNKAP-knockdown tissues.Furthermore,JNK signaling is essential for dNKAP depletion-mediated cell invasion.Transcriptome analysis of dNKAP-knockdown tissues confirmed the misregulation of signaling pathways involved in promoting tumorigenesis and revealed abnormal regulation of metabolic pathways.dNKAP knockdown and oncogenic Ras,Notch,or Yki mutations show synergies in driving tumorigenesis,further supporting the tumor-suppressive role of dNKAP.In summary,this study demonstrates that dNKAP plays a tumor-suppressive role by preventing genome instability in Drosophila epithelia and thus provides novel insights into the roles of human NKAP family genes in tumor initiation and progression.

Construction and validation of somatic mutation-derived long noncoding RNAs signatures of genomic instability to predict prognosis of hepatocellular carcinoma

BACKGROUND Long non-coding RNAs(LncRNAs)have been found to be a potential prognostic factor for cancers,including hepatocellular carcinoma(HCC).Some LncRNAs have been confirmed as potential indicators to quantify genomic instability(GI).Nevertheless,GI-LncRNAs remain largely unexplored.This study established a GI-derived LncRNA signature(GILncSig)that can predict the prognosis of HCC patients.AIM To establish a GILncSig that can predict the prognosis of HCC patients.METHODS Identification of GI-LncRNAs was conducted by combining LncRNA expression and somatic mutation profiles.The GI-LncRNAs were then analyzed for functional enrichment.The GILncSig was established in the training set by Cox regression analysis,and its predictive ability was verified in the testing set and TCGA set.In addition,we explored the effects of the GILncSig and TP53 on prognosis.RESULTS A total of 88 GI-LncRNAs were found,and functional enrichment analysis showed that their functions were mainly involved in small molecule metabolism and GI.The GILncSig was constructed by 5 LncRNAs(miR210HG,AC016735.1,AC116351.1,AC010643.1,LUCAT1).In the training set,the prognosis of high-risk patients was significantly worse than that of low-risk patients,and similar results were verified in the testing set and TCGA set.Multivariate Cox regression analysis and stratified analysis confirmed that the GILncSig could be used as an independent prognostic factor.Receiver operating characteristic curve analysis of the GILncSig showed that the area under the curve(0.773)was higher than the two LncRNA signatures published recently.Furthermore,the GILncSig may have a better predictive performance than TP53 mutation status alone.CONCLUSION We established a GILncSig that can predict the prognosis of HCC patients,which will help to guide prognostic evaluation and treatment decisions.

Urgent need for prognostic markers for hepatocellular carcinoma in the light of genomic instability and non-coding RNA signatures

In this editorial,we comment on an original article by Duan et al.Despite ad-vancements in the diagnosis and treatment of hepatocellular carcinoma(HCC),the identification of suitable prognostic factors remains challenging.In their paper,Duan et al identified long non-coding RNAs(LncRNAs)to quantify ge-nomic instability(GI)by combining LncRNA expression and somatic mutation profiles.They confirmed that the GI-derived LncRNA signature(GI-LncSig)could be an independent prognostic factor with the area under the curve of 0.773.Fur-thermore,the authors stated that GI-LncSig may have a better predictive perfor-mance than TP53 mutation status alone.However,studies exploring genetic markers for predicting the prognosis of HCC are crucial for identifying thera-peutic targets and enhancing diagnostic and treatment strategies to mitigate the global burden of liver cancer.

Clinical application value of long non-coding RNAs signatures of genomic instability in predicting prognosis of hepatocellular carcinoma

Hepatocellular carcinoma(HCC)presents challenges due to its high recurrence and metastasis rates and poor prognosis.While current clinical diagnostic and prognostic indicators exist,their accuracy remains imperfect due to their biol-ogical complexity.Therefore,there is a quest to identify improved biomarkers for HCC diagnosis and prognosis.By combining long non-coding RNA(lncRNA)expression and somatic mutations,Duan et al identified five representative lncRNAs from 88 lncRNAs related to genomic instability(GI),forming a GI-derived lncRNA signature(LncSig).This signature outperforms previously re-ported LncSig and TP53 mutations in predicting HCC prognosis.In this editorial,we comprehensively evaluate the clinical application value of such prognostic evaluation model based on sequencing technology in terms of cost,time,and practicability.Additionally,we provide an overview of various prognostic models for HCC,aiding in a comprehensive understanding of research progress in pro-gnostic evaluation methods.

Advancing prognostic understanding in hepatocellular carcinoma through the integration of genomic instability and lncRNA signatures: GILncSig model

The recently published study by Duan et al introduces a promising method that combines genomic instability and long non-coding RNAs to improve the prognostic evaluation of hepatocellular carcinoma(HCC),a deadly cancer associated with considerable morbidity and mortality.This editorial aims to analyze the methodology,key findings,and broader implications of the study within the fields of gastroenterology and oncological surgery,highlighting the shift towards precision medicine in the management of HCC.

Genomic Instability Is a Mechanism for Diminished Male Fertility Following Chronic Dichlorvos Exposure

Background and Objectives: Chronic low-dose exposure to dichlorvos occurs in communities in Africa where the substance is used indiscriminately for a variety of purposes. This experiment used an animal model to evaluate genomic instability induced by this pattern of chronic exposure and its relationship with some measures of fertility in males. Methods: Seventy-five male Rattus norvegicus rats obtained for this experiment, were randomly allotted into five groups. Dichlorvos was given by oral gavage at doses of 0.28 mg/kg, 0.56 mg/kg and, 1.68 mg/kg, respectively, to three of the groups, on alternate days for 50 weeks. The remaining two groups received plain drinking water and cyclophosphamide as negative and positive controls, respectively. Samples were collected at 17, 34, and 50 weeks. Sperm count, sperm morphology and serum levels of follicle-stimulating hormone, luteinizing hormone, dihydrotestosterone, oestrogen and progesterone were determined. Furthermore, the frequency of micronucleated polychromatic erythrocytes was determined in bone marrow cells obtained from the femur. Results: The mean ranks of micronuclei frequency had an increasing trend. The frequency of micronucleated polychromatic erythrocytes (MnPCE) had a significant negative correlation with oestrogen (rs = -0.47, p = 0.00, n = 50), follicle-stimulating hormone (rs = -0.41, p = 0.00, n = 50) and progesterone (rs = -0.37, p = 0.01, n = 50) serum levels. A positive monotonic relationship also existed between micronuclei frequency and those of tubular necrosis, tubular vacuolation, and residual bodies. A positive significant moderate correlation was found between MnPCE and the proportion of immotile sperms (rs = 0.41, p = 0.00, n = 50). Conclusion: The nature of the correlations between micronuclei frequency and the proportion of immotile sperms, adverse histological changes and serum hormone levels found in this study suggest genomic instability as the possible mechanism for diminished fertility in males chronically exposed to dichlorvos.

Nuclear pseudogenes of mitochondrial DNA as a variable part of the human genome

Novel pseudogenes homologous to the mitochondrial(mt) 16S rRNA gene were detected via different approaches. Eight pseudogenes were sequenced. Copynumber polymorphism of the mtDNA pseudogenes wasobserved among randomly chosen individuals, and evenamong siblings. A mtDNA pseudogene in the Ychromosome was observed in a YAC clone carrying onlyrepetitive sequence tag site (STS). PCR screening of human yeast artificial chromosome (YAC) libraries showedthat there were at least 5.7×105 hp of the mtDNA pseudogenes in each haploid nuclear genome. Possible involvement of the mtDNA pseudogenes in the variable part ofthe human nuclear genome is discussed.

Cellular exposure to muscle relaxants and propofol could lead to genomic instabilityin vitro

Anesthesia is widely used in several medical settings and accepted as safe. However, there is some evidence that anesthetic agents can induce genomic changes leading to neural degeneration or apoptosis. Although chromosomal changes have not been observed in vivo, this is most likely due to DNA repair mechanisms, apoptosis, or cellular senescence. Potential chromosomal alterations after exposure to common anesthetic agents may be relevant in patients with genomic instability syndromes or with aggressive treatment of malignancies. In this study, the P388 murine B cells were cultured in vitro, and spectral karyotyping （SKY） was utilized to uncover genomewide changes. Clinically relevant doses of cisatracurium and propofol increased structural and numerical chromosomal instability. These results may be relevant in patients with underlying chromosomal instability syndromes or concurrently being exposed to chemotherapeutic agents. Future studies may include utilization of stimulated peripheral blood lymphocytes to further confirm the significance of these results.

Effect of Recql5 deficiency on the intestinal tumor susceptibility of Apc^(min) mice

AIM:To investigate whether Recql5,a DNA helicase that plays an important role in the maintenance of genome integrity,is a tumor suppressor in the gastrointestinal tract in mice.METHODS:We generated cohorts of both Recql5-proficient and Recql5-deficient Apcmin/+mice and compared the tumor susceptibility in their gastrointestinal tracts.RESULTS:Recql5 deficiency in Apcmin/+mice resulted in a significant increase in the tumor incidence in both the colon(P=0.0162)and the small intestine(P<0.01).These findings have provided the first genetic evidence for a tumor suppression role of Recql5 in the gastrointestinal tract of mice.Importantly,since mouse Recql5 and human RECQL5 are highly conserved,these findings also suggest that RECQL5 may be a tu-mor suppressor for human colon cancer.CONCLUSION:Recql5 has a tumor suppression role in the mouse gastrointestinal tract.

Genetic variations in colorectal cancer risk and clinical outcome

Colorectal cancer (CRC) has an apparent hereditary component, as evidenced by the well-characterized genetic syndromes and family history associated with the increased risk of this disease. However, in a large fraction of CRC cases, no known genetic syndrome or family history can be identified, suggesting the presence of &#x0201c;missing heritability&#x0201d; in CRC etiology. The genome-wide association study (GWAS) platform has led to the identification of multiple replicable common genetic variants associated with CRC risk. These newly discovered genetic variations might account for a portion of the missing heritability. Here, we summarize the recent GWASs related to newly identified genetic variants associated with CRC risk and clinical outcome. The findings from these studies suggest that there is a lack of understanding of the mechanism of many single nucleotide polymorphisms (SNPs) that are associated with CRC. In addition, the utility of SNPs as prognostic markers of CRC in clinical settings remains to be further assessed. Finally, the currently validated SNPs explain only a small fraction of total heritability in complex-trait diseases like CRC. Thus, the &#x0201c;missing heritability&#x0201d; still needs to be explored further. Future epidemiological and functional investigations of these variants will add to our understanding of CRC pathogenesis, and may ultimately lead to individualized strategies for prevention and treatment of CRC.

The Transcriptional Response of Arabidopsis thaliana L. Genes AtKu70, AtRAD51 and AtRadl to X-Ray Radiation

The study of influence of the fractionated and acute ionizing radiation on plants revealed that it is able to induce genomic instability. The hypothesis that transcription rate of several evolutionary conserved DNA repair genes AtKu 70, AtRAD51 and AtRadl, which keeps genome stability in cells of model plant Arabidopsis thaliana, changes differently depending on dose and mode of ionizing radiation exposure had been tested. Gel electrophoresis-based reverse transcription polymerase chain reaction （RT-PCR） method was used for quantifying mRNA transcription levels. The data demonstrated that mode and dose of irradiation affect transcription rate of the genes AtKuTO, AtRAD51 and AtRadI. The fractionated and acute X-ray irradiation may result in adaptive response through the induction of key DNA double-strand break （DSB） repair genes AtKu70 and AtRAD51, as well as in genome instability through transcriptional activation of error-prone AtRadl-mediated DNA DSB repair combined with decreased expression of AtRAD51. In plants at doses within the range of 3-9 Gy, an adaptive influence is prevailed, but at doses of 12-21 Gy an error-prone repair of double-strand DNA damage is activated. Fractionation of dose has a significant effect on the transcription of the genes AtKuTO, AtRAD51 and AtRadl only at doses of 15 Gy and 21 Gy. Acute dose of 15 Gy activates error-prone AtRadl-mediated DSB repair and repressed both AtRAD51-dependent and AtKu70-dependent repair pathways, while fractionated irradiation at the same total dose induces more accurate homologous recombination and canonical non-homologous end joining of the DNA strands. In case of A. thaliana exposed to X-rays at dose 21 Gy, the situation is going reversed because of strong induction of the all three genome caretaker genes in leaves of acutely irradiated plants in contrast to the plants under fractionated exposure.

emerging role of the β-catenin-PPARγ axis in the pathogenesis of colorectal cancer

Multiple lines of evidence indicate that Wnt/&#x003b2;-catenin signaling plays a fundamental role in colorectal cancer (CRC) initiation and progression. Recent genome-wide data have confirmed that in CRC this pathway is one of the most frequently modified by genetic or epigenetic alterations affecting almost 90% of Wnt/&#x003b2;-catenin gene members. A major challenge is thus learning how the corrupted coordination of this pathway is tied to other signalings to enhance cell growth. Peroxisome proliferator activated receptor &#x003b3; (PPAR&#x003b3;) is emerging as a growth-limiting and differentiation-promoting factor. In tumorigenesis it exerts a tumor suppressor role and is potentially linked with the Wnt/&#x003b2;-catenin pathway. Based on these results, the identification of new selective PPAR&#x003b3; modulators with inhibitory effects on the Wnt/&#x003b2;-catenin pathway is becoming an interesting perspective. Should, in fact, these molecules display such properties, new research avenues would be opened aimed at developing new molecular targeted drugs. Herein, we review the basic principles and present new hypotheses underlying the crosstalk between Wnt/&#x003b2;-catenin and PPAR&#x003b3; signaling. Furthermore, we discuss the advances in our understanding as to how their altered regulation can culminate in colon cancer and the efforts aimed at designing novel PPAR&#x003b3; agonists endowed with Wnt/&#x003b2;-catenin inhibitory effects to be used as therapeutic and/or preventive agents.

Evolving insights:how DNA repair pathways impact cancer evolution

Viewing cancer as a large,evolving population of heterogeneous cells is a common perspective.Because genomic instability is one of the fundamental features of cancer,this intrinsic tendency of genomic variation leads to striking intratumor heterogeneity and functions during the process of cancer formation,development,metastasis,and relapse.With the increased mutation rate and abundant diversity of the gene pool,this heterogeneity leads to cancer evolution,which is the major obstacle in the clinical treatment of cancer.Cells rely on the integrity of DNA repair machineries to maintain genomic stability,but these machineries often do not function properly in cancer cells.The deficiency of DNA repair could contribute to the generation of cancer genomic instability,and ultimately promote cancer evolution.With the rapid advance of new technologies,such as single-cell sequencing in recent years,we have the opportunity to better understand the specific processes and mechanisms of cancer evolution,and让s relationship with DNA repair.Here,we review recent findings on how DNA repair affects cancer evolution,and discuss how these mechanisms provide the basis for critical clinical challenges and therapeutic applications.

The DNA damage response pathways： at the crossroad of protein modifications

Post-translational modifications play a crucial role in coordinating cellular response to DNA damage. Recent evidence suggests an interplay between multiple protein modifications, including phosphorylation, ubiquitylation, acetylation and sumoylation, that combine to propagate the DNA damage signal to elicit cell cycle arrest, DNA repair, apoptosis and senescence. Utility of specific post-translational modifiers allows temporal and spatial control over protein relo-calization and interactions, and may represent a means for trans-regulatory activation of protein activities. The ability to recognize these specific modifiers also underscores the capacity for signal amplification, a crucial step for the maintenance of genomic stability and tumor prevention. Here we have summarized recent findings that highlight the complexity of post-translational modifications in coordinating the DNA damage response, with emphasis on the DNA damage signaling cascade.

Genomic instability and eye diseases

Background:Genetic information is stored in the bases of double-stranded DNA.However,the integrity of DNA molecules is constantly threatened by various mutagenic agents,including pollutants,ultraviolet light(UV),and medications.To counteract these environmental damages,cells have established multiple mechanisms,such as producing molecules to identify and eliminate damaged DNA,as well as reconstruct the original DNA structures.Failure or insufficiency of these mechanisms can cause genetic instability.However,the role of genome stability in eye diseases is still under-researched,despite extensive study in cancer biology.Main text:As the eye is directly exposed to the external environment,the genetic materials of ocular cells are constantly under threat.Some of the proteins essential for DNA damage repair,such as pRb,p53,and RAD21,are also key during the ocular disease development.In this review,we discuss five ocular diseases that are associated with genomic instability.Retinoblastoma and pterygium are linked to abnormal cell cycles.Fuchs’corneal endothelial dystrophy and age-related macular degeneration are related to the accumulation of DNA damage caused by oxidative damage and UV.The mutation of the subunit of the cohesin complex during eye development is linked to sclerocornea.Conclusions:Failure of DNA damage detection or repair leads to increased genomic instability.Deciphering the role of genomic instability in ocular diseases can lead to the development of new treatments and strategies,such as protecting vulnerable cells from risk factors or intensifying damage to unwanted cells.

More efficient induction of genotoxicity by high-LET Fe-particle radiation than low-LET X-ray radiation at low doses

Objective:To understand differential effects on induction of genotoxicity and genomic instability(GI)by high-LET particle radiation and low-LET photon radiation,based on ground-based experiments using total body irradiation(TBI)of mice with Fe-particle radiation and X-ray radiation.Methods:TBI was delivered to C57BL/6J Jms strain female mice of 8 weeks old at a dose ranging from 0.1 to 3.0 Gy of Fe-particle radiation or at a dose ranging from 0.1 to 5.0 Gy of X-ray radiation.Induction of genotoxicity and GI by TBI was determined respectively at 1 and 2 months after exposure using frequency of micronuclei in bone marrow erythrocytes as the endpoint.Inhibition of bone marrow cell proliferation by TBI was measured as reduced erythropoiesis.Physiological conditions were also investigated.Results:TBI,regardless of the type of radiation,caused statistically significant increase in genotoxicity at 1 month after exposure,but did not induce GI at 2 months after exposure even at higher doses(>1.0 Gy).The doseresponse curve for the frequency of micronucleated polychromatic erythrocytes induced by Fe-particle radiation and X-ray radiation was y=0.7798 t 1.7889x–0.5978x^(2)(R^(2)=0.8109)and y=0.7421 t 1.3792x–0.2588 x^(2)(R^(2)=0.8081),respectively.The dose-response curve for the frequency of micronucleated normochromatic erythrocytes induced by Fe-particle radiation and X-ray radiation was y=0.7191 t 1.4545x–0.4978x^(2)(R^(2)=0.7047)and y=0.658 t 1.344x–0.2531x^(2)(R^(2)=0.7853),respectively.In general,high-LET Fe-particle radiation was more efficient in inducing genotoxicity than low-LET X-ray radiation at lower doses(<0.5 Gy).Conclusions:These results further confirm that exposure to TBI,even at higher doses and regardless the type of radiation,does not induce GI in C57BL/6J strain mice measured as increased micronuclei in bone marrow erythrocytes.These findings indicate that radiation-induced GI is mouse strain dependent and suggest that more comprehensive studies should be done to explore the late health consequences from exposure to high-LET radiation at low doses.

More forks on the road to replication stress recovery

High-fidelity replication of DNA,and its accurate segregation to daughter cells,is critical for maintaining genome stability and suppressing cancer.DNA replication forks are stalled by many DNA lesions,activating checkpoint proteins that stabilize stalled forks.Stalled forks may eventually collapse,producing a broken DNA end.Fork restart is typically mediated by proteins initially identified by their roles in homologous recombination repair of DNA double-strand breaks(DSBs).In recent years,several proteins involved in DSB repair by non-homologous end joining(NHEJ)have been implicated in the replication stress response,including DNA-PKcs,Ku,DNA Ligase IV-XRCC4,Artemis,XLF and Metnase.It is currently unclear whether NHEJ proteins are involved in the replication stress response through indirect(signaling)roles,and/or direct roles involving DNA end joining.Additional complexity in the replication stress response centers around RPA,which undergoes significant post-translational modification after stress,and RAD52,a conserved HR protein whose role in DSB repair may have shifted to another protein in higher eukaryotes,such as BRCA2,but retained its role in fork restart.Most cancer therapeutic strategies create DNA replication stress.Thus,it is imperative to gain a better under-standing of replication stress response proteins and pathways to improve cancer therapy.

Alterations of DNA damage response pathway:Biomarker and therapeutic strategy for cancer immunotherapy

Genomic instability remains an enabling feature of cancer and promotes malignant transformation.Alterations of DNA damage response(DDR)pathways allow genomic instability,generate neoantigens,upregulate the expression of programmed death ligand 1(PD-L1)and interact with signaling such as cyclic GMPe AMP synthase-stimulator of interferon genes(cGASe STING)signaling.Here,we review the basic knowledge of DDR pathways,mechanisms of genomic instability induced by DDR alterations,impacts of DDR alterations on immune system,and the potential applications of DDR alterations as biomarkers and therapeutic targets in cancer immunotherapy.

Phyllanthus emblica Linn.fruit extract potentiates the anticancer efficacy of mitomycin C and cisplatin and reduces their genotoxicity to normal cells in vitro

Objective： Fruit of Phyllanthus emblica Linn. （PE） is widely consumed as a functional food and used as a folk medicine due to its remarkable nutritional and pharmacological effects. Mitomycin C （MMC） and cisplatin （cDDP） are the most widely used forms of chemotherapeutic drug, but their clinical use is limited by their genotoxicity to normal cells. We aimed to determine whether PE has potential to reduce the genotoxicity, while improving the anticancer effect, of MMC and cDDP. Methods： Cell proliferation was evaluated using the trypan blue exclusion assay and colony-forming assay. Genomic instability （GIN） was measured using the cytokinesis-block micronucieus assay. Results： Co-treatment （72 h） with PE at 20-320 μg/ml significantly enhanced the efficacy of MMC （0.05 μg/ml） and cDDP （1 μg/ml） against Colo205 colorectal cancer cells （P〈0.05）, and at 80-320 μg/ml significantly decreased MMC- and cDDP-induced GIN and multinucleation in normal colonic NCM460 cells （P〈0.05）. PE significantly decreased the mitotic index （P〈0.01）, blocked mitotic progression （P〈0.05）, and promoted apoptosis （P〈0.01） in MMC- and cDDP-treated NCM460 cells, suggesting that PE-mediated inhibition of mitosis and induction of apoptosis may limit the division and survival of highly damaged cells. Also, PE was found to inhibit the clonal expansion of MMC- and cDDP-treated NCM460 cells （P〈0.05） and decrease the heterogeneity of the surviving clones. Conclusions： PE potentiates the anticancer efficacy of MMC and cDDP, while preventing their genotoxicity and inhibiting clonal expansions of unstable genomes in normal cells. These data suggest that PE has the potential to reduce the risk of secondary cancers induced by chemotherapeutics.