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 geno...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.展开更多
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 challen...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.展开更多
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 du...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.展开更多
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...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.展开更多
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 chrom...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.展开更多
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 evalua...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 (r<sub>s</sub> = -0.47, p = 0.00, n = 50), follicle-stimulating hormone (r<sub>s</sub> = -0.41, p = 0.00, n = 50) and progesterone (r<sub>s</sub> = -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 (r<sub>s</sub> = 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.展开更多
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 m...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.展开更多
<strong>Background: </strong>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 w...<strong>Background: </strong>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. <strong>Methods: </strong>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. <strong>Results: </strong>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.展开更多
Mantle cell lymphoma(MCL)is recognized as one of the most genetically heterogeneous diseases,with high instability at the genomic level.MCL is common in males with a male-to-female ratio of about 2:1,and its incidence...Mantle cell lymphoma(MCL)is recognized as one of the most genetically heterogeneous diseases,with high instability at the genomic level.MCL is common in males with a male-to-female ratio of about 2:1,and its incidence accounts for 3%e10%of adult non-Hodgkin lymphoma cases.The evolutionary dynamics of MCL clones at the single-cell level remain largely unclear.Our research suggests that MCL may arise from multiple cells within the abnormal microenvironment of the entire hematopoietic lineage,particularly from initiating cells.These initiating cells predominantly consist of CD19^(-)/IgM^(-) subclones and exhibit a disrupted malignant clonal differentiation of pre-B cells along the tumor immunity evolution tree.展开更多
R-loops,three-strand nucleic acid structures,have emerged as crucial players in various physiological processes,including the regulation of gene expression,DNA replication,and class switch recombination.However,their ...R-loops,three-strand nucleic acid structures,have emerged as crucial players in various physiological processes,including the regulation of gene expression,DNA replication,and class switch recombination.However,their presence also poses a significant threat to genome stability.A particularly challenging aspect is understanding the dynamic balance between R-loops’“light”and“dark”sites,especially concerning maintaining genome integrity.The complex and multifaceted roles of R-loops in genome stability necessitate a deeper understanding.This review offers a comprehensive exploration of the formation,resolution,and implications of R-loops,particularly in the context of DNA damage and human disease.We delve into the dualistic nature of R-loops,highlighting their role in DNA damage response and repair,and discuss the therapeutic potential arising from our evolving understanding of these enigmatic entities.Emphasizing recent advancements and unresolved questions,this review aims to provide a cohesive overview of R-loops,inviting further inquiry and investigation into their complex biological significance.展开更多
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 cisplat...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.展开更多
Multiple lines of evidence indicate that Wnt/β-catenin signaling plays a fundamental role in colorectal cancer (CRC) initiation and progression. Recent genome-wide data have confirmed that in CRC this path...Multiple lines of evidence indicate that Wnt/β-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/β-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 γ (PPARγ) 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/β-catenin pathway. Based on these results, the identification of new selective PPARγ modulators with inhibitory effects on the Wnt/β-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/β-catenin and PPARγ 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 PPARγ agonists endowed with Wnt/β-catenin inhibitory effects to be used as therapeutic and/or preventive agents.展开更多
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 ...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.展开更多
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, ubiquityla...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.展开更多
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 Rec...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.展开更多
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...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.展开更多
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 fractio...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 “missing heritability” 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 “missing heritability” 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.展开更多
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 re...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.展开更多
To The Editor:1.INTRODUCTION Fanconi anemia(FA)is a hereditary disorder characterized by genomic instability and increased sensitivity to DNA cross-linking agents.FA is typically diagnosed in childhood,with an average...To The Editor:1.INTRODUCTION Fanconi anemia(FA)is a hereditary disorder characterized by genomic instability and increased sensitivity to DNA cross-linking agents.FA is typically diagnosed in childhood,with an average age at diagnosis of 7 years.Mutations in any of the 23 genes associated with the FA/BRCA pathway can lead to the onset of FA.The clinical manifestations of FA primar-ily include congenital abnormalities,progressive bone marrow failure,and heightened susceptibility to malignancies.展开更多
The intricate relationship between cancer,circadian rhythms,and aging is increasingly recognized as a critical factor in understanding the mechanisms underlying tumorigenesis and cancer progression.Aging is a well-est...The intricate relationship between cancer,circadian rhythms,and aging is increasingly recognized as a critical factor in understanding the mechanisms underlying tumorigenesis and cancer progression.Aging is a well-established primary risk factor for cancer,while disruptions in circadian rhythms are intricately associated with the tumorigenesis and progression of various tumors.Moreover,aging itself disrupts circadian rhythms,leading to physiological changes that may accelerate cancer development.Despite these connections,the specific interplay between these processes and their collective impact on cancer remains inadequately explored in the literature.In this review,we systematically explore the physiological mechanisms of circadian rhythms and their influence on cancer development.We discuss how core circadian genes impact tumor risk and prognosis,highlighting the shared hallmarks of cancer and aging such as genomic instability,cellular senescence,and chronic inflammation.Furthermore,we examine the interplay between circadian rhythms and aging,focusing on how this crosstalk contributes to tumorigenesis,tumor proliferation,and apoptosis,as well as the impact on cellular metabolism and genomic stability.By elucidating the common pathways linking aging,circadian rhythms,and cancer,this review provides new insights into the pathophysiology of cancer and identifies potential therapeutic strategies.We propose that targeting the circadian regulation of cancer hallmarks could pave the way for novel treatments,including chronotherapy and antiaging interventions,which may offer important benefits in the clinical management of cancer.展开更多
文摘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.
基金Supported by The European Union-Next Generation EU,through the National Recovery and Resilience Plan of the Republic of Bulgaria,No.BG-RRP-2.004-0008.
文摘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.
基金The National Key R&D Program of China(Key Special Project for Marine Environmental Security and Sustainable Development of Coral Reefs 2022-3.3),No.2022YFC3103-004001Scientific Research Foundation of Shanghai Municipal Health Commission of Changning District,No.20234Y038.
文摘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.
文摘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.
基金supported in part by the Intramural Research Program of the NIH,the National Cancer Institute and the National Institute of Allergy and Infectious Diseases
文摘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.
文摘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 (r<sub>s</sub> = -0.47, p = 0.00, n = 50), follicle-stimulating hormone (r<sub>s</sub> = -0.41, p = 0.00, n = 50) and progesterone (r<sub>s</sub> = -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 (r<sub>s</sub> = 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.
基金supported by the Shandong Provincial Natural Science Foundation (ZR2020QH140 to B.N.Z.)the National Natural Science Foundation of China (82101091 to B.N.Z.).
文摘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.
文摘<strong>Background: </strong>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. <strong>Methods: </strong>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. <strong>Results: </strong>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.
基金funded by the Chongqing Medical Scientific Research Project(Joint Project of Chongqing Health Commission and Science and Technology Bureau,China)(No.2023GGXM006,2024ZDXM026,2024MSXM115)the Key Research Project from Science and Technology Department of Sichuan Province,China(No.2019YFS0301)+3 种基金the Chongqing Key Municipal Public Health Specialty Construction Project(China)the Key Research Project from Chongqing Medical and Pharmaceutical Vocational Education Group(China)(No.CQZJ202329)the Incubation Project of the First Affiliated Hospital of Chongqing Medical and Pharmaceutical College(China)(No.2022-2023ZD04,2022-2023ZD03,2022-2023MS04,2022-2023MS03,2022-2023MS010)the Science and Technology Research Program of Chongqing Education Commission(China)(No.KJQN202302811).
文摘Mantle cell lymphoma(MCL)is recognized as one of the most genetically heterogeneous diseases,with high instability at the genomic level.MCL is common in males with a male-to-female ratio of about 2:1,and its incidence accounts for 3%e10%of adult non-Hodgkin lymphoma cases.The evolutionary dynamics of MCL clones at the single-cell level remain largely unclear.Our research suggests that MCL may arise from multiple cells within the abnormal microenvironment of the entire hematopoietic lineage,particularly from initiating cells.These initiating cells predominantly consist of CD19^(-)/IgM^(-) subclones and exhibit a disrupted malignant clonal differentiation of pre-B cells along the tumor immunity evolution tree.
基金supported by research funding from the National Natural Science Foundation of China(No.32201061)the Natural Science Foundation of Shandong,China(No.ZR2021QC083).
文摘R-loops,three-strand nucleic acid structures,have emerged as crucial players in various physiological processes,including the regulation of gene expression,DNA replication,and class switch recombination.However,their presence also poses a significant threat to genome stability.A particularly challenging aspect is understanding the dynamic balance between R-loops’“light”and“dark”sites,especially concerning maintaining genome integrity.The complex and multifaceted roles of R-loops in genome stability necessitate a deeper understanding.This review offers a comprehensive exploration of the formation,resolution,and implications of R-loops,particularly in the context of DNA damage and human disease.We delve into the dualistic nature of R-loops,highlighting their role in DNA damage response and repair,and discuss the therapeutic potential arising from our evolving understanding of these enigmatic entities.Emphasizing recent advancements and unresolved questions,this review aims to provide a cohesive overview of R-loops,inviting further inquiry and investigation into their complex biological significance.
基金Project supported by the National Natural Science Foundation of China(Nos.31260268 and 31560307)
文摘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.
基金Supported by Ministero dell’Istruzione,Università e Ricerca,MIUR-PRIN 2010-2011,No.prot.2010W7YRLZ_003
文摘Multiple lines of evidence indicate that Wnt/β-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/β-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 γ (PPARγ) 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/β-catenin pathway. Based on these results, the identification of new selective PPARγ modulators with inhibitory effects on the Wnt/β-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/β-catenin and PPARγ 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 PPARγ agonists endowed with Wnt/β-catenin inhibitory effects to be used as therapeutic and/or preventive agents.
基金supported by the National Natural Science Foundation of China(Grant Nos.81672981 and 81972240).
文摘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.
文摘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.
基金Supported by Grants RO1 CA88939,P20 CA103736 from the US National Institutes of HealthSearle Scholar Award 01-E-109 from the Searle Scholar Program
文摘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.
文摘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.
基金Supported by A start-up grant from Thomas Jefferson Universityand National Cancer Institute Grant,CA162201
文摘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 “missing heritability” 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 “missing heritability” 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.
文摘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.
文摘To The Editor:1.INTRODUCTION Fanconi anemia(FA)is a hereditary disorder characterized by genomic instability and increased sensitivity to DNA cross-linking agents.FA is typically diagnosed in childhood,with an average age at diagnosis of 7 years.Mutations in any of the 23 genes associated with the FA/BRCA pathway can lead to the onset of FA.The clinical manifestations of FA primar-ily include congenital abnormalities,progressive bone marrow failure,and heightened susceptibility to malignancies.
基金supported by the Chinese Scholarship Council(grant no.202206240086)a regional innovation cooperation project of Sichuan Province(grant no.23QYCX0136)。
文摘The intricate relationship between cancer,circadian rhythms,and aging is increasingly recognized as a critical factor in understanding the mechanisms underlying tumorigenesis and cancer progression.Aging is a well-established primary risk factor for cancer,while disruptions in circadian rhythms are intricately associated with the tumorigenesis and progression of various tumors.Moreover,aging itself disrupts circadian rhythms,leading to physiological changes that may accelerate cancer development.Despite these connections,the specific interplay between these processes and their collective impact on cancer remains inadequately explored in the literature.In this review,we systematically explore the physiological mechanisms of circadian rhythms and their influence on cancer development.We discuss how core circadian genes impact tumor risk and prognosis,highlighting the shared hallmarks of cancer and aging such as genomic instability,cellular senescence,and chronic inflammation.Furthermore,we examine the interplay between circadian rhythms and aging,focusing on how this crosstalk contributes to tumorigenesis,tumor proliferation,and apoptosis,as well as the impact on cellular metabolism and genomic stability.By elucidating the common pathways linking aging,circadian rhythms,and cancer,this review provides new insights into the pathophysiology of cancer and identifies potential therapeutic strategies.We propose that targeting the circadian regulation of cancer hallmarks could pave the way for novel treatments,including chronotherapy and antiaging interventions,which may offer important benefits in the clinical management of cancer.
