Genome-wide direct quantification of in vivo mutagenesis using high-accuracy paired-end and complementary consensus sequencing.

Error-corrected next-generation sequencing (ecNGS) is an emerging technology for accurately measuring somatic mutations. Here, we report paired-end and complementary consensus sequencing (PECC-Seq), a high-accuracy ecNGS approach for genome-wide somatic mutation detection. We characterize a novel 2-aminoimidazolone lesion besides 7,8-dihydro-8-oxoguanine and the resulting end-repair artifacts originating from NGS library preparation that obscure the sequencing accuracy of NGS. We modify library preparation protocol for the enzymatic removal of end-repair artifacts and improve the accuracy of our previously developed duplex consensus sequencing method. Optimized PECC-Seq shows an error rate of <5 × 10-8 with consensus bases compressed from approximately 25 Gb of raw sequencing data, enabling the accurate detection of low-abundance somatic mutations. We apply PECC-Seq to the quantification of in vivo mutagenesis. Compared with the classic gpt gene mutation assay using gpt delta transgenic mice, PECC-Seq exhibits high sensitivity in quantitatively measuring dose-dependent mutagenesis induced by Aristolochic acid I (AAI). Moreover, PECC-Seq specifically characterizes the distinct genome-wide mutational signatures of AAI, Benzo[a]pyrene, N-Nitroso-N-ethylurea and N-nitrosodiethylamine and reveals the mutational signature of Quinoline in common mouse models. Overall, our findings demonstrate that high-accuracy PECC-Seq is a promising tool for genome-wide somatic mutagenesis quantification and for in vivo mutagenicity testing.

Maternal pre-pregnancy overweight or obesity and risk of birth defects in offspring: Population-based cohort study.

INTRODUCTION: Maternal obesity, a health condition increasingly prevalent worldwide, has been suggested to be associated with a higher risk of birth defects in offspring, whereas evidence from population-based data from China was largely lacking. Additionally, the role of gestational diabetes in the association between maternal obesity and birth defects remains unclear. We aimed to investigate the association of maternal pre-pregnancy overweight or obesity with any and different types of birth defects in offspring and the interaction between pre-pregnancy overweight or obesity and gestational diabetes. MATERIAL AND METHODS: We conducted a population-based cohort study including 257 107 singletons born between 2015 and 2021 in Longgang District, Shenzhen, China, using data from the Shenzhen Maternal and Child Health Management System. Poisson regression was conducted to estimate the associations of maternal pre-pregnancy overweight or obesity, as well as the interaction between pre-pregnancy overweight or obesity and gestational diabetes, with the risk of birth defects. Models were adjusted for maternal age at delivery, educational level, type of household registration, and gravidity. RESULTS: Maternal pre-pregnancy overweight was associated with a higher risk of any birth defect (risk ratio [RR] 1.21, 95% confidence interval [CI] 1.12 to 1.31) as well as of congenital malformations of the circulatory system (RR 1.26, 95% CI 1.12 to 1.41), eye/ear/face/neck (RR 1.42, 95% CI 1.04 to 1.94), and musculoskeletal system (RR 1.21, 95% CI 1.01 to 1.44). Maternal pre-pregnancy obesity was associated with a higher risk of any birth defect (RR 1.38, 95% CI 1.18 to 1.63) and congenital malformations of the circulatory system (RR 1.61, 95% CI 1.30 to 1.98). Infants born to overweight or obese mothers with gestational diabetes had a higher risk of congenital malformations of the circulatory system than infants born to overweight or obese mothers without gestational diabetes. CONCLUSIONS: Maternal pre-pregnancy overweight or obesity was associated with a higher risk of birth defects, particularly congenital malformations of the circulatory system, in offspring. Gestational diabetes interacts additively with pre-pregnancy overweight or obesity on modifying the risk of congenital malformations of the circulatory system. The importance of improving weight management and assessment of glucose and metabolic functions was emphasized among women planning for pregnancy who are overweight or obese.

New framework for recombination and adaptive evolution analysis with application to the novel coronavirus SARS-CoV-2.

The 2019 novel coronavirus (SARS-CoV-2) has spread rapidly worldwide and was declared a pandemic by the WHO in March 2020. The evolution of SARS-CoV-2, either in its natural reservoir or in the human population, is still unclear, but this knowledge is essential for effective prevention and control. We propose a new framework to systematically identify recombination events, excluding those due to noise and convergent evolution. We found that several recombination events occurred for SARS-CoV-2 before its transfer to humans, including a more recent recombination event in the receptor-binding domain. We also constructed a probabilistic mutation network to explore the diversity and evolution of SARS-CoV-2 after human infection. Clustering results show that the novel coronavirus has diverged into several clusters that cocirculate over time in various regions and that several mutations across the genome are fixed during transmission throughout the human population, including D614G in the S gene and two accompanied mutations in ORF1ab. Together, these findings suggest that SARS-CoV-2 experienced a complicated evolution process in the natural environment and point to its continuous adaptation to humans. The new framework proposed in this study can help our understanding of and response to other emerging pathogens.

Regulatory mechanism of downregulation of SOD1 expression on cardiomyocyte function.

BACKGROUND: Many diseases are clinically related to oxidative stress. Obstructive sleep apnea (OSA) is a common disease with oxidative stress in clinical practice, which is mostly associated with cardio-cerebrovascular diseases. It has been shown that the level of oxidative stress increases and the level of antioxidant copper zinc superoxide dismutase (SOD1) decreases in intermittent hypoxia (IH). SOD1 is one of the key antioxidant enzymes in organisms, and it can also be used as a signal transmission controller. Its abnormal expression further affects organ functions, but the specific mechanism is not yet fully clear. METHODS: We downregulated the SOD1 gene in H9C2 cell line, using high-throughput RNA sequencing (RNA-seq) to find differentially expressed genes (DEGs) related to cardiomyocyte function by using GO and KEGG databases to annotate, enrich and analyze the metabolic pathways of DEGs. RESULTS: Through the analysis of these functional gene changes, we can understand the regulation of SOD1 downregulation on cardiomyocyte function. The results found 213 DEGs, of which 135 genes were upregulated and 78 genes were downregulated. The upregulated DEGs were mainly enriched in biological processes such as transcriptional regulation and metabolism. The expression levels of EGR1 and NR1D1 exceeded 1 in the samples. EGR1 was reported to be involved in oxidative stress and cardiac hypertrophy, and NR1D1 played an important regulatory role in regulating inflammatory responses and reducing ROS production. The biological processes involved in downregulated DEGs mainly involve metabolism and redox processes. Among them, SCD1 and CCL2 genes were highly expressed among the genes involved in the redox process involved in SOD1. SCD1 is an important player in the regulation of cardiometabolic processes; downregulation of CCL2 reduces atherosclerosis. We found that the TNF signaling pathway, NOD-like receptor signaling pathway, and chemokine signaling pathway, which were enriched in KEGG analysis, were all associated with inflammation, and the CXCL1 and CCL7 genes are all related to inflammation. CONCLUSION: The gene and signaling pathways involved in oxidative stress and inflammatory response process regulated by SOD1 were demonstrated. SOD1 may affect the function of the heart by affecting myocardial contraction, inflammation, lipid metabolism, and other pathways. It is inferred that they may also play a role in the process of OSA-related myocardial injury, which is worthy of attention and further study.

Effects of CPAP and Mandibular Advancement Devices on depressive symptoms in patients with obstructive sleep apnea: a meta-analysis of randomized controlled trials.

PURPOSE: Studies show that patients with obstructive sleep apnea (OSA) are more likely than the general population to have psychological disorders such as depression. However, it is less clear how OSA treatment affects this association. This meta-analysis aimed to assess whether or not continuous positive airway pressure (CPAP) and mandibular advancement devices (MADs) reduce depression symptoms in patients with OSA. METHODS: We searched Pubmed, Embase, Web of Science, and Cochrane Library from creating the databases until November 2022. Our analysis included RCTs that examined CPAP and MAD treatment effectiveness for depression in patients with OSA. RESULTS: We identified 17 CPAP studies comprising 1,931 patients for inclusion in the meta-analysis. The results of the meta-analysis using a fixed effects model found that CPAP improved depressed mood in patients with OSA relative to controls (SMD = 0.27;95% CI:0.18,0.36), with small heterogeneity among trials (I2 = 8.1% < 50%, P = 0.359). We performed subgroup analyses on three factors: the length of trial follow-up, patient adherence data, and depression assessment scales. The meta-analysis also identified six MAD studies involving 315 patients. According to this analysis, there was no heterogeneity between studies (I2 = 0%, P = 0.748). MADs did not significantly improve depression symptoms compared to controls, indicating a combined effect of SMD = 0.07 (95% CI: - 0.15,0.29), P > 0.05. CONCLUSION: The present findings confirm that CPAP may improve depressive symptoms in patients with OSA. However, the review results suggest that MADs have no significant effect on depressive symptoms in patients with OSA, a finding that is different from the results of previous meta-analyses.

Correction to: miR-484 suppresses proliferation and epithelial-mesenchymal transition by targeting ZEB1 and SMAD2 in cervical cancer cells.

[This corrects the article DOI: 10.1186/s12935-017-0407-9.].

Edaravone Improves Intermittent Hypoxia-Induced Cognitive Impairment and Hippocampal Damage in Rats.

Oxidative stress plays an essential role in obstructive sleep apnea-hypopnea syndrome-induced cognitive dysfunction in children. This study investigated the effects of edaravone, a potent free radical scavenger, on intermittent hypoxia (IH)-induced oxidative damage and cognition impairment in a young rat model of IH. IH rats were treated with edaravone for 4 weeks. Behavioral testing was performed using the Morris water maze, and hippocampal tissues were harvested for further analyses. Edaravone attenuated IH-induced cognitive impairment, reduced morphological and structural abnormalities, and increased the number of mitochondria in the IH rats. Furthermore, edaravone significantly increased the inhibition of hydroxyl free radicals; reduced expressions of superoxide anion, malondialdehyde, and 8-hydroxy-2'-deoxyguanosine; and upregulated the expression of manganese superoxide dismutase, catalase, cAMP, protein kinase A, phosphorylated-cAMP response element-binding (p-CREB), B-cell lymphoma 2, and brain-derived neurotrophic factor in the hippocampal tissue of IH rats. Our findings suggest that edaravone attenuated IH-induced cognitive impairment and hippocampal damage by upregulating p-CREB in young rats.

Detection of genome-wide low-frequency mutations with Paired-End and Complementary Consensus Sequencing (PECC-Seq) revealed end-repair-derived artifacts as residual errors.

To improve the accuracy and the cost-efficiency of next-generation sequencing in ultralow-frequency mutation detection, we developed the Paired-End and Complementary Consensus Sequencing (PECC-Seq), a PCR-free duplex consensus sequencing approach. PECC-Seq employed shear points as endogenous barcodes to identify consensus sequences from the overlap in the shortened, complementary DNA strand-derived paired-end reads for sequencing error correction. With the high accuracy of PECC-Seq, we identified the characteristic base substitution errors introduced by the end-repair process of mechanical fragmentation-based library preparations, which were prominent at the terminal 7 bp of the library fragments in the 5'-NpCpA-3' and 5'-NpCpT-3' trinucleotide context. As demonstrated at the human genome scale (TK6 cells), after removing these potential end-repair artifacts from the terminal 7 bp, PECC-Seq could reduce the sequencing error frequency to mid-10-7 with a relatively low sequencing depth. For TA base pairs, the background error rate could be suppressed to mid-10-8. In mutagen-treated (6 µg/mL methyl methanesulfonate or 12 µg/mL N-nitroso-N-ethylurea) TK6, increases in mutagen treatment-related mutant frequencies could be detected, indicating the potential of PECC-Seq in detecting genome-wide ultra-rare mutations. In addition, our finding on the patterns of end-repair artifacts may provide new insights into further reducing technical errors not only for PECC-Seq, but also for other next-generation sequencing techniques.

An Adaption of Human-Induced Hepatocytes to In Vitro Genetic Toxicity Tests.

Metabolic activation is essential in standard in vitro genotoxicity test systems. At present, there is a lack of suitable cell models that can express the major characteristics of liver function for predicting substance toxicity in humans. Human-induced hepatocytes (hiHeps), which have been generated from fibroblasts by lentiviral expression of liver transcription factors, can express hepatic gene programs and can be expanded in vitro and display functional characteristics of mature hepatocytes, including cytochrome P450 enzyme activity and biliary drug clearance. Our purpose was to investigate whether hiHeps could be used as a more suitable model for genotoxicity evaluation of chemicals. Therefore, a direct mutagen, methylmethanesulfonate (MMS), and five promutagens [2-nitrofluorene (2-NF), benzo[a]pyrene (B[a]P), aflatoxin B1, cyclophosphamide and N-nitrosodiethylamine] were tested by the cytokinesis-block micronucleus test and the comet assay. Results from genotoxicity tests showed that the micronucleus frequencies were significantly increased by all of the six clastogens tested. Moreover, MMS, 2-NF and B[a]P induced significant increases in the % Tail DNA in the comet assay. In conclusion, our findings from the preliminary study demonstrated that hiHeps could detect the genotoxicity of indirect carcinogens, suggesting their potential to be applied as an effective tool for in vitro genotoxicity assessments.

miR-377-3p drives malignancy characteristics via upregulating GSK-3ß expression and activating NF-κB pathway in hCRC cells.

MicroRNA (miRNA) dysregulation has been associated with carcinogenesis in many cancers, including human colorectal cancer (hCRC). However, the effect and mechanism of miR-377-3p on CRC remains elusive. Herein, we first found that miR-377-3p was upregulated in CRC tissues and promoted tumorigenic activity by accelerating the G1 -S phase transition, promoting cell proliferation and epithelial-mesenchymal transition (EMT) while repressing apoptosis in CRC cells. Glycogen synthase kinase-3ß (GSK-3ß) was a direct target of miR-377-3p, and upregulated by miR-377-3p. Knockdown of GSK-3ß partly rescued miR-377-3p-mediated malignancy characteristics. Most importantly, we showed that miR-377-3p promoted carcinogenesis by activating NF-κB pathway. Taken together, our results first reported that miR-377-3p functions as an oncogene and promotes carcinogenesis via upregulating GSK-3ß expression and activating NF-κB pathway in hCRC cells.

DCLK1 promotes epithelial-mesenchymal transition via the PI3K/Akt/NF-κB pathway in colorectal cancer.

Double cortin-like kinase 1 (DCLK1) plays important roles during the epithelial-mesenchymal transition (EMT) process in human colorectal cancer (CRC). However, the role of DCLK1 in regulating the EMT of CRC is still poorly understood. In this study, we report evidence that DCLK1 acts as a potent oncogene to drive its extremely malignant character of EMT in an NF-κB-dependent manner in CRC cells. Mechanistic investigations showed that DCLK1 induced the NF-κBp65 subunit expression through the PI3K/Akt/Sp1 axis and activated NF-κBp65 through the PI3K/Akt/IκBα pathway during the EMT of CRC cells. Moreover, we found that silencing the expression of DCLK1 inhibited the invasion and metastasis of CRC cells in vivo. Collectively, our findings identify DCLK1 as a pivotal regulator of an EMT axis in CRC, thus implicating DCLK1 as a potential therapeutic target for CRC metastasis.

Gene mutation and micronucleus assays in gpt delta mice treated with 2,2',4,4'-tetrabromodiphenyl ether.

Flame retardant polybrominated diphenyl ethers (PBDEs) are a class of persistent organic pollutants (POPs). 2,2',4,4'-Tetrabromodiphenyl ether (BDE-47) is a representative PBDE congener with widespread distribution and relatively high toxicity potential. Although it has been reported that BDE-47 can cause DNA damage in various in vitro systems, few studies have provided in vivo genotoxicity information. The aim of the present study was to investigate the genotoxicity of BDE-47 in mice. Male gpt delta mice were administered BDE-47 by gavage at 0, 0.0015, 1.5, 10 and 30 mg/kg/day, and 6 days per week for six consecutive weeks. Before the first treatment, and at 2.5 and 5 weeks after the first treatment, peripheral blood was collected from tails and the micronucleus assay and the Pig-a gene mutation assay were performed. After the last treatment, the mutant frequencies of the gpt gene in the liver and the germ cells from seminiferous tubules were determined. All these assays failed to produce positive results, suggesting that BDE-47 was neither clastogenic nor mutagenic in both target and non-target tissues in gpt delta mice.

Genomic-driven discovery of an amidinohydrolase involved in the biosynthesis of mediomycin A.

Clethramycin (1) and mediomycin A (2) belong to the linear polyene polyketide (LPP) family of antibiotics that exhibit potent antifungal activity. Structural similarities exist between 1 and 2, except that 2 contains an amino moiety substituted for the guanidino moiety. Herein, the draft genome sequence of Streptomyces mediocidicus ATCC23936, a strain which produces both 1 and 2, was obtained through de novo sequencing. Bioinformatic analysis of the genome revealed a clethramycin (cle) gene cluster that contained 25 open reading frames (orfs). However, amidinohydrolase for 2 formation was not found in the cle gene cluster. Further genomic analysis revealed an amidinohydrolase MedX, which can hydrolyse the guanidino form (1) into the amino form (2) via heterologous co-expression of the cle cluster in Streptomyces lividans or by in vitro catalysis. These results also suggest the feasibility of engineering novel LPPs for drug discovery by manipulating the biosynthetic machinery of S. mediocidicus.

miR-484 suppresses proliferation and epithelial-mesenchymal transition by targeting ZEB1 and SMAD2 in cervical cancer cells.

BACKGROUND: MicroRNAs (miRNAs) play important roles in cancer initiation and development. Epithelial-mesenchymal transition (EMT) is a form of cellular plasticity that is critical for embryonic development and metastasis. The purpose of the study was to determine the function and mechanism of miR-484 in initiation and development of cervical cancer (CC). METHODS: We determined the expression levels of miR-484 in cervical cancer tissues and cell lines with RT-qPCR. Prediction algorithms and EGFP reporter assay were performed to evaluate the targets for miR-484. MTT assay, colony formation assay, flow cytometric analysis, transwell cell migration and invasion assays, and detection of EMT markers were employed to investigate the roles of miR-484 and the targets in regulation of cell proliferation and EMT process. We also used rescue experiments to confirm the effect of miR-484 on CC cells through directly regulating the expression of its targets. RESULTS: Firstly we found miR-484 was down-regulated in cervical cancer tissues and cell lines compared with their matched non-cancerous tissues or normal cervical keratinocytes cells. Further studies revealed that overexpression of miR-484 suppressed the cell proliferation, while exacerbates apoptosis. Besides, miR-484 suppressed cellular migration, invasion and EMT process of CC cells. EGFP reporter assay showed that miR-484 binds to ZEB1 and SMAD2 3'UTR region and reduced their expression. The expression of miR-484 had reverse correlation with SMAD2/ZEB1, and SMAD2/ZEB1 had positive correlation with each other in cervical cancer tissues and cell lines. Furthermore, the ectopic expression of ZEB1 or SMAD2 could rescue the malignancies suppressed by miR-484, suggesting that miR-484 down-regulates ZEB1 and SMAD2 to repress tumorigenic activities. CONCLUSION: We found miR-484 inhibits cell proliferation and the EMT process by targeting both ZEB1 and SMAD2 genes and functions as a tumor suppressor, which may served as potential biomarkers for cervical cancer.

C14orf28 downregulated by miR-519d contributes to oncogenicity and regulates apoptosis and EMT in colorectal cancer.

C14orf28 [alias dopamine receptor-interacting protein (DRIP1)] is belonging to the family of DRIPs. However, the function of C14orf28 in cancer remains unclear. Herein, we found that C14orf28 was upregulated in colorectal cancer tissues compared to the adjacent non-tumor tissues. Overexpression of C14orf28 promoted the cellular proliferation, migration, invasion of colorectal cancer cells. In addition, C14orf28 inhibited apoptosis and promoted the EMT process. To explore the mechanism of dysregulation, C14orf28 was identified to be a target of miR-519d by targeting its 3'UTR. Furthermore, in agreement, C14orf28 overexpression counteracted the inhibitory effect of miR-519d. Together, these results evidenced that C14orf28 downregulated by miR-519d contributes to tumorigenesis and might provide new potential targets for colorectal cancer therapy.

miR-23a promotes IKKα expression but suppresses ST7L expression to contribute to the malignancy of epithelial ovarian cancer cells.

BACKGROUND: Dysregulation of microRNAs (miRNAs) has been found in human epithelial ovarian cancer (EOC). However, the role and mechanism of action of miR-23a in EOC remain unclear. METHODS: The roles of miR-23a, IKKα, and ST7L in EOC were determined by MTT, colony formation, wounding healing, transwell, flow cytometry, immunofluorescence, RT-qPCR, and western blotting experiments. miR-23a target genes were validated by EGFP reporter assays, RT-qPCR, and western blotting analysis. RESULTS: miR-23a is upregulated and promotes tumorigenic activity by facilitating the progress of cell cycle and EMT and repressing apoptosis in EOC cells. miR-23a enhances the expression of IKKα but suppresses the expression of ST7L by binding the 3'UTR of each transcript in EOC cells. The proliferation, migration, and invasion of EOC cells are increased by IKKα and inhibited by ST7L. Furthermore, miR-23a activates NF-κB by upregulating IKKα and WNT/MAPK pathway by downregulating ST7L. CONCLUSIONS: miR-23a functions as an oncogene by targeting IKKα and ST7L, thus contributing to the malignancy of EOC cells.

Computed tomography imaging-guided percutaneous argon-helium cryoablation of muscle-invasive bladder cancer: initial experience in 32 patients.

PURPOSE: To evaluate the initial clinical experience of computed tomography (CT) imaging-guided percutaneous cryotherapy of bladder cancer. PATIENTS AND METHODS: This study was approved by the human subjects committee. Written informed consent was obtained from all patients. Thirty-two patients (22 males and 10 females; mean age, 62.7 years) with muscle-invasive bladder cancer were treated with CT imaging-guided percutaneous cryoablation. By using CT imaging system and local anesthesia in patients, a single or multiple 1.47 mm cryoprobes were used to freeze the target bladder tumor (mean tumor size, 2.8 cm; range, 1.3-4.5 cm) with a dual freeze-thaw cycle. Follow-up was performed to assess the clinical and technical outcome of patients treated with cryoablation for a minimum of 6 months (mean, 33 months; range, 6-48 months). Tumors were considered completely ablated if there was no evidence to suggest tumor enhancement at follow-up CT images. RESULTS: Bladder cryoablation was clinically and technically successful in all 32 cases, 30 of which required only one treatment session. Bladder integrity was maintained in all patients. Major complications were not observed in any patient. CONCLUSION: Our initial experience of a minimally invasive method for ablating bladder tumors with CT imaging-guided percutaneous argon-helium cryoablation appears to be favorable, with acceptable operative and short-term clinical outcomes. The technique is safe and effective for the treatment of patients with muscle-invasive bladder cancer; however, long-term follow-up is needed.