Base Excision Repair Mechanism Research Articles

D239Y germline variant of NTHL1 glycosylase increases susceptibility to colorectal cancer in mice

Introduction: Persistent genotoxic stress leads to spontaneous DNA damage, which occurs on the order of 104−105 events per cell per day. The base excision repair is the first responder in the repair mechanisms after DNA damage, with DNA glycosylase being the first step in the repair process by binding to the DNA, cleaving the N-glycosidic bond and removing the oxidized pyrimidine DNA lesions. NTHL1 is a pivotal bifunctional DNA glycosylase enzyme involved in base excision repair mechanism. NTHL1 tumor syndrome is characterized by an increased lifetime risk for colorectal cancer (CRC), breast cancer, and colorectal polyposis. A rare rs3087468 polymorphism (D239Y) exhibits no glycosylase activity and may act as a dominant-negative mutation. Hypothesis: NTHL1-D239Y variant conforms susceptibility to inflammation-associated colorectal cancer. Methods: 6-8 weeks/old male and female C57BL/6 wild-type (WT, NTHL1WT/WT), heterozygous (NTHL1WT/D239Y), or homozygous (NTHL1D239Y/D239Y) knock-in mice were injected with 7.5mg/kg azoxymethane (AOM) followed by three cycles of alternating 2.5% dextran sulfate sodium (DSS, 5 days) and normal drinking water (14 days). We monitored body weight, collected fecal samples for microbial 16S rRNA amplicon sequencing, and analyzed colon length and number/size of polyps at euthanasia. The histology score was assessed by an unbiased pathologist to evaluate inflammation and tumor development. Blood samples were used to evaluate micronuclei formation. Results: NTHL1WT/D239Y and NTHL1D239Y/D239Y mice showed more pronounced weight loss starting from the 2nd DSS cycle. The number and size of polyps in the distal colon of NTHL1WT/D239Y and NTHL1D239Y/D239Y male mice were increased compared to WT littermates. NTHL1D239Y/D239Y females, but not males, showed increased polyp number compared to NTHL1WT/D239Y mice. No statistical difference was observed in the polyps’ size. Tumors extending into the proximal colon were observed uniquely in NTHL1D239Y/D239Y females. On the other hand, only NTHL1WT/D239Y males developed high adenomas in the distal colon compared to WT males. Interestingly, only NTHL1D239Y/D239Y males showed statistical difference in micronucleated normochromatic erythrocytes compared to WT mice. NTHL1 genotype did not significantly affect fecal microbial α- or β-diversity or colitis score and colon length in either gender. Conclusion: Our data suggest that NTHL1-D239Y variant confers a complex, zygosity- and sex-dependent susceptibility risk for inflammation-associated colorectal cancer that may be intrinsic and independent of changes in the gut microbiota. In females, it promotes more proximal tumor location, while in males, it promotes the size and tumor progression. 5P30CA023074 (JBS), Phoenix Women's Board of the Steele Children's Research Center (FKG). This is the full abstract presented at the American Physiology Summit 2024 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

Transcriptomic Evidence of Base and Nucleotide Excision Repair Mechanisms in Response to UV-B Radiation in an Arctic Fungus Pseudogymnoascus australis Strain HNDR4

Polar micro-fungi are known to have developed protective mechanisms and responses against the harmful effects of UV radiation. In this study, physiological, cellular, and transcriptomic responses of an Arctic fungal strain of Pseudogymnoascus australis towards UV-B radiation were examined. Fungal isolate was cultured on 0.45μm nylon membranes overlayed on Czapex-Dox agar (CDA) at 15ºC for 10 d in dark condition to reach the mid-log phase. To assess DNA damage and recovery, the isolates were exposed to UV-B radiation (UV dosage of 6.1 kj m-2 d-1) for 130 min, followed by 0, 2 and 6 hr incubation under light condition. Differential gene expression in DNA repair after UV-B treatment at these time points was analysed based on RNA-Seq data output of 40 million reads per sample from an Illumina NovaSeq 6000 system platform. The results revealed that radiation-repair (RAD) genes were upregulated and the photoreactivation (PHR1) gene was downregulated after UV-B exposure in light condition. Downregulation of oxidoreductase activity was observed from the GO enrichment analysis. The KEGG pathway enrichment analysis exhibited upregulation of base excision repair (BER) genes and nucleotide excision repair (NER) genes upon UV-B exposure. This is the fi rst RNASeq transcriptomic study on the DNA repair mechanisms employed by a polar fungus to mitigate UV-induced DNA damage.

Investigation of APE1 and OGG1 expression in chronic hemodialysis patients.

The role of DNA repair mechanisms is of significant importance in diseases characterized by elevated oxidative DNA damage, such as chronic kidney disease. It is imperative to thoroughly understand the functions of molecules associated with DNA repair mechanisms, not only for assessing susceptibility to diseases but also for monitoring disease progression. In this research, we investigated the APE1 and OGG1 gene expression levels, both of which are involved in the base excision repair (BER) mechanism in chronic hemodialysis patients with malignancy (HPM; n = 8) and without malignancy (HP; n = 36) in pre- and post-dialysis period and 37 healty persons. We also assessed how these values correlate with the clinical profiles of the patients. We conducted gene expression analysis using real-time polymerase chain reaction (qRT-PCR). No significant differences in APE1 gene expression levels were observed in pre-dialysis when comparing the HP and HPM groups to the control group. The expression levels of the OGG1 gene were significantly lower in both the HP and HPM groups in pre- and post-dialysis periods compared to the control group. Dialysis procedures led to a reduction in APE1 and OGG1 gene expression levels in both HP and HPM groups. The findings of our study elucidate the impact of alterations in the base excision repair (BER) mechanism, including the hemodialysis process, in end-stage renal disease (ESRD).

MRC-5 Human Lung Fibroblasts Alleviate the Genotoxic Effect of Fe-N Co-Doped Titanium Dioxide Nanoparticles through an OGG1/2-Dependent Reparatory Mechanism

The current study was focused on the potential of pure P25 TiO2 nanoparticles (NPs) and Fe(1%)-N co-doped P25 TiO2 NPs to induce cyto- and genotoxic effects in MRC-5 human pulmonary fibroblasts. The oxidative lesions of P25 NPs were reflected in the amount of 8-hydroxydeoxyguanosine accumulated in DNA and the lysosomal damage produced, but iron-doping partially suppressed these effects. However, neither P25 nor Fe(1%)-N co-doped P25 NPs had such a serious effect of inducing DNA fragmentation or activating apoptosis signaling. Moreover, oxo-guanine glycosylase 1/2, a key enzyme of the base excision repair mechanism, was overexpressed in response to the oxidative DNA deterioration induced by P25 and P25-Fe(1%)-N NPs.

Increased oxidative DNA damage and altered base excision repair mechanisms in bipolar disorder and individuals at risk for bipolar disorder

Increased oxidative DNA damage and altered base excision repair mechanisms in bipolar disorder and individuals at risk for bipolar disorder

Active DNA demethylation in plants: 20 years of discovery and beyond.

Maintaining proper DNA methylation levels in the genome requires active demethylation of DNA. However, removing the methyl group from a modified cytosine is chemically difficult and therefore, the underlying mechanism of demethylation had remained unclear for many years. The discovery of the first eukaryotic DNA demethylase, Arabidopsis thaliana REPRESSOR OF SILENCING 1 (ROS1), led to elucidation of the 5-methylcytosine base excision repair mechanism of active DNA demethylation. In the 20 years since ROS1 was discovered, our understanding of this active DNA demethylation pathway, as well as its regulation and biological functions in plants, has greatly expanded. These exciting developments have laid the groundwork for further dissecting the regulatory mechanisms of active DNA demethylation, with potential applications in epigenome editing to facilitate crop breeding and gene therapy.

Development of QM/MM (ABEEM polarizable force field) method to simulate the excision reaction mechanism of damaged cytosine.

DNA damages are regarded as having harmful effects on cell. The base excision repair mechanism combats these effects by removing damaged bases. The deglycosylation mechanism of excising damaged bases by DNA glycosylase and the state of the leaving base have been controversial. The enzymatic reaction of DNA glycosylase to remove the damaged bases involves not only the formation and breaking of chemical bonds, but also complex polarization effect and charge transfer, which cannot be accurately simulated by the QM/MM method combined with the fixed charge force field. This work has developed the ABEEM fluctuating polarizable force field combining with the QM method, that is (QM/MM[ABEEM]), to accurately simulate the proton transfer, charge transfer and the charge distribution. The piecewise function is used as the valence-state electronegativity in the QM/MM (ABEEM) to realize the accurate fitting of the charge distribution in reaction. And the charge transfer is accurately simulated by the local charge conservation conditions. Four deglycosylation mechanisms including the monofunctional and difunctional mechanisms of four neutral and protonated cytosine derivatives are explored. It is confirmed that the monofunctional mechanism of Asp-activated nucleophile water is a better deglycosylation mechanism and the base is protonated before the reaction occurs. Protonization of the base reduced the activation energy by 10.00-17.00 kcal/mol. Asp provides the necessary charge for the reaction, and DNA glycosylase preferentially cleaves ɛC. This work provides a theoretical basis for the research of excising damaged bases by DNA glycosylase.

Experience with olaparib in a patient with luminal HER2-positive metastatic breast cancer

Hereditary breast cancer (BC) accounts for about 5-10% of cases. BRCA-associated tumors have been identified as a separate group of malignant neoplasms with distinctive clinical manifestations and specific treatment features. Understanding of biological mechanisms leading to cancer in BRCA1/2 mutation carriers and discovery of potential molecular targets, such as poly (ADP-ribose) polymerase (PARP), involved in base excision repair mechanisms, led to the development of a new class of targeted drugs belonging to the PARP inhibitors group. PARP inhibition leads to the preservation of single-stranded DNA breaks, the arrest of the replication fork, and the realization of the “synthetic lethality” phenomenon due to the inability to repair double-stranded DNA breaks by homologous recombination in cells with mutations in the BRCA1/2 genes. Two randomized trials OlympiAD and EMBRACA evaluated and proved the effectiveness of PARP inhibitors in patients with metastatic BRCA-mutated HER2-negative breast cancer in comparison with standard chemotherapy. At the same time, data on the potential use of PARP inhibitors for the treatment of BRCA-mutated HER2-positive breast cancer patients are extremely limited. This article presents a clinical example of the use of olaparib in a patient with BRCA-mutated HER2-positive metastatic breast cancer.

Transcriptome and protein networks to elucidate the mechanism underlying nitrite degradation by Lactiplantibacillus plantarum

Excessive nitrite residue is one of the bottlenecks in the production of many fermented foods. Lactiplantibacillus plantarum PK25 obtained from traditional Chinese pickles exhibited excellent nitrite degradation ability. Here, transcriptome, protein-protein interaction networks, and phenotype were performed to evaluate systematically the mechanism of nitrite degradation of L. plantarum PK25. The results demonstrated that genes expression varied considerably at key time points for nitrite degradation. 553 (upregulated: 366, downregulated: 187) and 767 (upregulated: 425, downregulated: 342) differentially expressed genes were identified at 6 h and 24 h, respectively. The hub genes were mainly enriched in carbohydrate metabolism, energy metabolism, and nucleotide synthesis. PK25 expanded its carbon source utilizing profile and improved glycolysis to produce more ATP to counteract environmental stress. The related enzymes including glycoside hydrolase, sugar ABC transporter protein, and PTS sugar transporter were 5.714, 5.885, and 3.578-fold upregulated at the transcriptional level. For strain to sustain energy levels and acid generation, pyruvate metabolism was critical, with the result that phosphoenolpyruvate synthase and pyruvate oxidase were up-regulated to accelerate the pyruvate transition. To repair DNA lesions induced by nitrite, both base excision repair mechanism and recombinational DNA repair pathway were exploited, such as endodeoxyribonuclease upregulated 5.314 and 19.687-fold at the two moments. The results provided a theoretical reference and practical possibility to reduce nitrite residue and improve safety during food fermented products.

HOGG1 and APE1 Gene Polymorphism and Risk of Gastrointestinal Cancer in Rural Population of South-Western Maharashtra

The base excision repair (BER) mechanism plays a key role in repair of DNA modifications caused by oxidized or reduced bases which help in maintaining the genomic stability. Genetic variations in BER pathway genes are known to alter the DNA repair capacity, thereby appealing the susceptibility to various cancer risks. Present study was undertaken to evaluate an association between the polymorphisms in hOGG1 and APE1 genes and the susceptibility of gastrointestinal cancer in unexplored population of south-western Maharashtra. In this hospital-based case-control study, we used polymerase chain reaction- restriction fragment length polymorphism (PCR-RFLP) method to examine the genotype distribution of hOGG1 (rs1052133) and APE1 (rs1130409) genes in 200 GI cancer patients in comparison with 200 healthy controls. Results of our investigations revealed no direct significant association between the variant genotype of hOGG1 (OR: 0.99; CI: 0.55-1.78; p: 0.99) and GI cancer risk when compared with the wild type genotype while variant genotype of APE1 (OR: 0.31; CI: 0.12-0.82; p: 0.014) showed a decreased risk for susceptibility of GI cancer. Thus, our study indicated that the polymorphism in APE1gene may contribute to the protective effect of GI cancer development among rural population of the south-western Maharashtra.

Role of PPAR-γ in diabetes-induced testicular dysfunction, oxidative DNA damage and repair in leptin receptor-deficient obese type 2 diabetic mice

The testis expresses peroxisome proliferator-activated receptor-γ (PPAR-γ), but its involvement in regulating diabetes-induced testicular dysfunction and DNA damage repair is not known. Pioglitazone-induced activation of PPAR-γ for 12 weeks in db/db obese diabetic mice increases bodyweights and reduces blood glucose levels, but PPAR-γ inhibition by 2-chloro-5-nitro-N-phenylbenzamide does not alter these parameters; instead, improves testis and epididymis weights and sperm count. Neither activation nor inhibition of PPAR-γ normalizes the diabetes-induced seminiferous epithelial degeneration. The PPAR-γ activation normalizes testicular lipid peroxidation, but its inhibition reduces lipid peroxidation and oxidative DNA damage (8-oxo-dG) in diabetic mice. As a response to diabetes-induced oxidative DNA damage, the base-excision repair (BER) mechanism proteins- 8-oxoguanine DNA glycosylases (OGG1/2) and X-ray repair cross-complementing protein-1 (XRCC1) increase, whereas the redox-factor-1 (REF1), DNA polymerase (pol) δ and poly (ADP-ribose) polymerase-1 (PARP1) show a tendency to increase suggesting an attempt to repair the oxidative DNA damage. The PPAR-γ stimulation inhibits OGG2, DNA pol δ, and XRCC1 in diabetic mice testes, but PPAR-γ inhibition reduces oxidative DNA damage and normalizes BER protein levels. In conclusion, type 2 diabetes negatively affects testicular structure and function and increases oxidative DNA damage and BER protein levels due to increased DNA damage. The PPAR-γ modulation does not significantly affect the structural changes in the testis. The PPAR-γ stimulation aggravates diabetes-induced effects on testis, including oxidative DNA damage and BER proteins, but PPAR-γ inhibition marginally recovers these diabetic effects indicating the involvement of the receptor in the reproductive effects of diabetes.

MUTYH-associated tumor syndrome: The other face of MAP.

MUTYH gene is involved in the base excision repair (BER) mechanism and its pathogenic alterations are associated with colorectal polyposis and cancer. MUTYH-associated polyposis (MAP) is a condition which is inherited in an autosomal recessive manner. MAP patients, beyond colorectal cancer (CRC), may develop other types of tumors, including duodenal, breast, ovarian, pancreatic, bladder and skin cancers. Carriers of biallelic MUTYH likely pathogenic/pathogenic variants exhibit a high lifetime risk of CRC, though cancer risk evidence becomes less clear when monoallelic carriers and extraintestinal tumors are considered. However, several studies recently reported an increased genetic susceptibility to cancer also for carriers of germline monoallelic MUTYH mutations. Moreover, experimental evidence highlighted the MUTYH involvement in many other biological functions. In future, MUTYH mutation carriers might benefit from new target therapies involving the use of PD-1 or KRAS inhibitors. Therefore, "MUTYH-associated tumor syndrome" might be the most appropriate term, due to the multiplicity of tumors observed in MAP patients and different biological contexts in which MUTYH acts as a "playmaker". In this Review, we will investigate the impact of germline mono- and biallelic MUTYH mutations on cancer risk, providing a proposal for clinical surveillance of mutation carriers.

Role of PARP in TNBC: Mechanism of Inhibition, Clinical Applications, and Resistance.

Triple-negative breast cancer is a combative cancer type with a highly inflated histological grade that leads to poor theragnostic value. Gene, protein, and receptor-specific targets have shown effective clinical outcomes in patients with TNBC. Cells are frequently exposed to DNA-damaging agents. DNA damage is repaired by multiple pathways; accumulations of mutations occur due to damage to one or more pathways and lead to alterations in normal cellular mechanisms, which lead to development of tumors. Advances in target-specific cancer therapies have shown significant momentum; most treatment options cause off-target toxicity and side effects on healthy tissues. PARP (poly(ADP-ribose) polymerase) is a major protein and is involved in DNA repair pathways, base excision repair (BER) mechanisms, homologous recombination (HR), and nonhomologous end-joining (NEJ) deficiency-based repair mechanisms. DNA damage repair deficits cause an increased risk of tumor formation. Inhibitors of PARP favorably kill cancer cells in BRCA-mutations. For a few years, PARPi has shown promising activity as a chemotherapeutic agent in BRCA1- or BRCA2-associated breast cancers, and in combination with chemotherapy in triple-negative breast cancer. This review covers the current results of clinical trials testing and future directions for the field of PARP inhibitor development.

Genetic variants of APEX1 p.Asp148Glu and XRCC1 p.Gln399Arg with the susceptibility of hepatocellular carcinoma.

The DNA repair genes have a crucial function in the base excision repair (BER) mechanism among different cancerous disorders, particularly hepatocellular carcinoma (HCC). The foremost objective of this study is to explore the association of genetic variants of the APEX1 p.Asp148Glu and the XRCC1 p.Gln399Arg with the susceptibility of HCC and to identify the computational bioinformatics frameworks of these missense variants. A total of 250 participants were enrolled in this study, including 150 HCC patients and 100 cancer-free controls. The genomic DNA was characterized and genotyped by applying the PCR-CTPP method. The frequency of the APEX1 (rs1130409*Glu) allele was statistically significant with increased risk of HCC (OR = 1.66, 95% CI = 1.12-2.45), while the XRCC1 (rs25487*Gln) allele conferred a protection against the progression of HCC (OR = 0.64, 95% CI = 0.42-0.96). Furthermore, HCC patients carrying the APEX1 p.Asp148Glu and the XRCC1 p.Gln399Arg variants indicated no significant difference with the clinical, and laboratory parameters (p > .05). Our findings confirmed that the APEX1 p.Asp148Glu variant was associated with increased risk of HCC, while the XRCC1 p.Gln399Arg variant revealed protection against the development of HCC.

Ablation of SMUG1 Reduces Cell Viability and Increases UVC-Mediated Apoptosis in Hepatocarcinoma HepG2 Cells.

Uracil is an unavoidable aberrant base in DNA sequences, the repair of which takes place by a highly efficient base excision repair mechanism. The removal of uracil from the genome requires multiple biochemical steps with conformational changes of DNA that inhibit DNA replication and interfere with transcription. However, the relevance of uracil in DNA for cellular physiology and transcriptional regulation is not fully understood. We investigated the functional roles of SMUG1 using knock-down (KD) and knock-out (KO) models. The proliferation ratio of SMUG1 KD and KO cells was decreased compared to WT control cells, and the cell cycle was arrested in the G2/M phases before the transition to mitosis. The apoptotic cell death was increased in KD and KO cell lines through the increase of BAX and active caspase 3 expression. Phospho-gamma-H2AX expression, which reflected accumulated DNA damage, was also increased in KO cells. Moreover, the apoptotic cells by DNA damage accumulation were markedly increased in SMUG1 KD and KO cells after ultraviolet C irradiation. Transcriptomic analysis using RNA-seq revealed that SMUG1 was involved in gene sets expression including cell cycle transition and chromatin silencing. Together, the results implicate SMUG1 as a critical factor in cell cycle and transcriptional regulation.

MUTYH as an Emerging Predictive Biomarker in Ovarian Cancer.

Approximately 18% of ovarian cancers have an underlying genetic predisposition and many of the genetic alterations have become intervention and therapy targets. Although mutations in MutY homolog (MUTYH) are best known for MUTYH associated polyposis and colorectal cancer, it plays a role in the development of ovarian cancer. In this review, we discuss the function of the MUTYH gene, mutation epidemiology, and its mechanism for carcinogenesis. We additionally examine its emerging role in the development of ovarian cancer and how it may be used as a predictive and targetable biomarker. MUTYH mutations may confer the risk of ovarian cancer by the failure of its well-known base excision repair mechanism or by failure to induce cell death. Biallelic germline MUTYH mutations confer a 14% risk of ovarian cancer by age 70. A monoallelic germline mutation in conjunction with a somatic MUTYH mutation may also contribute to the development of ovarian cancer. Resistance to platinum-based chemotherapeutic agents may be seen in tumors with monoallelic mutations, but platinum sensitivity in the biallelic setting. As MUTYH is intimately associated with targetable molecular partners, therapeutic options for MUTYH driven ovarian cancers include programed-death 1/programed-death ligand-1 inhibitors and poly-adenosine diphosphate ribose polymerase inhibitors. Understanding the function of MUTYH and its associated partners is critical for determining screening, risk reduction, and therapeutic approaches for MUTYH-driven ovarian cancers.

Photon versus proton neurotoxicity: Impact on mitochondrial function and 8-OHdG base-excision repair mechanism in human astrocytes

This study assesses and compares the neurotoxic effects of proton and photon radiation on mitochondrial function and DNA repair capabilities of human astrocytes. Human astrocytes received either proton (0.5 Gy and 3 Gy), photon (0.5 Gy and 3 Gy), or sham-radiation treatment. The mRNA expression level of the DNA repair protein OGG1 was determined via RT-qPCR. The levels of 8-OHdG in the cell media were measured via ELISA. Real-time kinetic analysis of extracellular oxygen consumption rates was performed to assess mitochondrial function. Radiation-induced changes in mitochondrial mass and oxidative activity were assessed using fluorescent imaging with MitoTracker™ Green FM and MitoTracker™ Orange CM-H2TMRos dyes respectively. PCR was used to quantify the alteration in the mitochondrial DNA content, measured as the mitochondrial to nuclear DNA ratio. A significant increase in mitochondrial mass and levels of reactive oxygen species was observed after radiation treatment. Additionally, real-time PCR analysis indicated a significant depletion of mitochondrial DNA content in the irradiated cells when compared to the control. This was accompanied by a decreased gene expression of the DNA base-excision repair protein OGG1 and reduced clearance of 8-OHdG adducts from the genome. Photon radiation treatment was associated with a more detrimental cellular impact when compared to the same dose of proton radiation. These results are indicative of a radiation-induced dose-dependent decrease in mitochondrial function, an increase in senescence and astrogliosis, and impairment of the DNA repair capabilities in healthy glial cells. Photon irradiation was associated with a more significant disruption in mitochondrial function and base-excision repair mechanisms in vitro in comparison to proton treatment.

Association between POLG and XRCC1 gene polymorphisms and keratoconus occurrence among Egyptian patients

Abstract Background Keratoconus is a progressive disorder distinguished by thinning of the corneal tissue and bulging forward into a cone-shaped fashion. Yet its aetiology, which is multifactorial, despite intensive research remains elusive. Corneal exposure a reactive oxygen species causing oxidative DNA damage has been reported to be associated with QC and therefore suggesting that DNA base excision repair mechanism might lie behind the pathogenesis of the disease. Methods We studied the association of three variants in two REB genes (XRCC1 and POLG) and QC occurrence in a cohort of patients from Egypt. Genotyping of the three variants was performed using PCR and restriction enzymes analyses. Results We observed that A allele and A/A genotype of the c.1196A>G variant in the XRCC1 gene were significantly associated with increased QC occurrence while the G allele was associated with decreased QC occurrence. Similarly, the A/A genotype of the c.-1370T>A polymorphism in the POLG gene and the A allele were associated with increased occurrence of QC, while T/A genotype and the T allele were accompanied with decreased occurrence of QC. On the other hand, no association was observed between the c.580C>T variant in the XRCC1 gene and QC occurrence among the studied group of patients. Conclusion Our results suggest that c.1196A>G variant of the XRCC1 and c.-1370T>A variant of the POLG gene may be involved in QC pathogenesis and might be considered as a genetic risk factors of the disease among Egyptian population.

Decoding whole-genome mutational signatures in 37 human pan-cancers by denoising sparse autoencoder neural network.

Millions of somatic mutations have recently been discovered in cancer genomes. These mutations in cancer genomes occur due to internal and external mutagenesis forces. Decoding the mutational processes by examining their unique patterns has successfully revealed many known and novel signatures from whole exome data, but many still remain undiscovered. Here, we developed a deep learning approach, DeepMS, to decompose mutational signatures using 52,671,908 somatic mutations from 2780 highly curated cancer genomes with whole genome sequencing (WGS) in 37 cancer types/subtypes. With rigorous model training and comparison, we characterized 54 signatures for single base substitutions (SBSs), 11 for doublet base substitutions (DBSs) and 16 for small insertions and deletions (Indels). Compared to the previous methods, DeepMS could discover 37 SBS, 5 DBS and 9 Indel new signatures, many of which represent associations with DNA mismatch or base excision repair and cisplatin therapy mechanisms. We further developed a regression-based model to estimate the correlation between signatures and clinical and demographical phenotypes. The first deep learning model DeepMS on WGS somatic mutational profiles enable us identify more comprehensive context-based mutational signatures than traditional NMF approaches. Our work substantially expands the landscape of the naturally occurring mutational signatures in cancer genomes, and provides new insights into cancer biology.

Asociación entre polimorfismos de los genes POLG y XRCC1 y aparición de queratocono entre pacientes egipcios

BackgroundKeratoconus is a progressive disorder distinguished by thinning of the corneal tissue and bulging forward into a cone-shaped fashion. Yet its etiology, which is multifactorial, despite intensive research remains elusive. Corneal exposure a reactive oxygen species causing oxidative DNA damage has been reported to be associated with KC and therefore suggesting that DNA base excision repair mechanism might lie behind the pathogenesis of the disease. MethodsWe studied the association of three variants in two BER genes (XRCC1 and POLG) and QC occurrence in a cohort of patients from Egypt. Genotyping of the three variants was performed using PCR and restriction enzymes analysis. ResultsWe observed that A allele and A/A genotype of the c.1196A>G variant in the XRCC1 gene were significantly associated with increased KC occurrence while the G allele was associated with decreased KC occurrence. Similarly, the A/A genotype of the c.–1370T>A polymorphism in the POLG gene and the A allele were associated with increased occurrence of KC, while T/A genotype and the T allele were accompanied with decreased occurrence of KC. On the other hand, no association was observed between the c.580C>T variant in the XRCC1 gene and KC occurrence among the studied group of patients. ConclusionOur results suggest that c.1196A>G variant of the XRCC1 and c.–1370T>A variant of the POLG gene may be involved in KC pathogenesis and might be considered as a genetic risk factors of the disease among Egyptian population.