PeerJ:Medical Geneticshttps://peerj.com/articles/index.atom?journal=peerj&subject=5250Medical Genetics articles published in PeerJResting heart rate and risk of dementia: a Mendelian randomization study in the international genomics of Alzheimer’s Project and UK Biobankhttps://peerj.com/articles/170732024-03-152024-03-15Xingxing ChenYi ZhengJun WangBlake YueXian ZhangKenta NakaiLijing L. Yan
Background
Observational studies have demonstrated that a higher resting heart rate (RHR) is associated with an increased risk of dementia. However, it is not clear whether the association is causal. This study aimed to determine the causal effects of higher genetically predicted RHR on the risk of dementia.
Methods
We performed a two-sample Mendelian randomization analysis to investigate the causal effect of higher genetically predicted RHR on Alzheimer’s disease (AD) using summary statistics from genome-wide association studies. The generalized summary Mendelian randomization (GSMR) analysis was used to analyze the corresponding effects of RHR on following different outcomes: 1) diagnosis of AD (International Genomics of Alzheimer’s Project), 2) family history (maternal and paternal) of AD from UK Biobank, 3) combined meta-analysis including these three GWAS results. Further analyses were conducted to determine the possibility of reverse causal association by adjusting for RHR modifying medication.
Results
The results of GSMR showed no significant causal effect of higher genetically predicted RHR on the risk of AD (βGSMR = 0.12, P = 0.30). GSMR applied to the maternal family history of AD (βGSMR = −0.18, P = 0.13) and to the paternal family history of AD (βGSMR = −0.14, P = 0.39) showed the same results. Furthermore, the results were robust after adjusting for RHR modifying drugs (βGSMR = −0.03, P = 0.72).
Conclusion
Our study did not find any evidence that supports a causal effect of RHR on dementia. Previous observational associations between RHR and dementia are likely attributed to the correlation between RHR and other cardiovascular diseases.
Background
Observational studies have demonstrated that a higher resting heart rate (RHR) is associated with an increased risk of dementia. However, it is not clear whether the association is causal. This study aimed to determine the causal effects of higher genetically predicted RHR on the risk of dementia.
Methods
We performed a two-sample Mendelian randomization analysis to investigate the causal effect of higher genetically predicted RHR on Alzheimer’s disease (AD) using summary statistics from genome-wide association studies. The generalized summary Mendelian randomization (GSMR) analysis was used to analyze the corresponding effects of RHR on following different outcomes: 1) diagnosis of AD (International Genomics of Alzheimer’s Project), 2) family history (maternal and paternal) of AD from UK Biobank, 3) combined meta-analysis including these three GWAS results. Further analyses were conducted to determine the possibility of reverse causal association by adjusting for RHR modifying medication.
Results
The results of GSMR showed no significant causal effect of higher genetically predicted RHR on the risk of AD (βGSMR = 0.12, P = 0.30). GSMR applied to the maternal family history of AD (βGSMR = −0.18, P = 0.13) and to the paternal family history of AD (βGSMR = −0.14, P = 0.39) showed the same results. Furthermore, the results were robust after adjusting for RHR modifying drugs (βGSMR = −0.03, P = 0.72).
Conclusion
Our study did not find any evidence that supports a causal effect of RHR on dementia. Previous observational associations between RHR and dementia are likely attributed to the correlation between RHR and other cardiovascular diseases.Prognostic value of RNA methylation-related genes in gastric adenocarcinoma based on bioinformaticshttps://peerj.com/articles/169512024-02-292024-02-29Xionghui HeXiang ChenChangcheng YangWei WangHening SunJunjie WangJincheng FuHuaying Dong
Background
Gastric cancer (GC) is a malignant tumor that originates from the epithelium of the gastric mucosa and has a poor prognosis. Stomach adenocarcinoma (STAD) covers 95% of total gastric cancer. This study aimed to identify the prognostic value of RNA methylation-related genes in gastric cancer.
Methods
In this study, The Cancer Genome Atlas (TCGA)-STAD and GSE84426 cohorts were downloaded from public databases. Patients were classified by consistent cluster analysis based on prognosis-related differentially expressed RNA methylation genes Prognostic genes were obtained by differential expression, univariate Cox and least absolute shrinkage and selection operator (LASSO) analyses. The prognostic model was established and validated in the training set, test set and validation set respectively. Independent prognostic analysis was implemented. Finally, the expression of prognostic genes was affirmed by reverse transcription quantitative PCR (RT-qPCR).
Results
In total, four prognostic genes (ACTA2, SAPCD2, PDK4 and APOD) related to RNA methylation were identified and enrolled into the risk signature. The STAD patients were divided into high- and low-risk groups based on the medium value of the risk score, and patients in the high-risk group had a poor prognosis. In addition, the RNA methylation-relevant risk signature was validated in the test and validation sets, and was authenticated as a reliable independent prognostic predictor. The nomogram was constructed based on the independent predictors to predict the 1/3/5-year survival probability of STAD patients. The gene set enrichment analysis (GSEA) result suggested that the poor prognosis in the high-risk subgroup may be related to immune-related pathways. Finally, the experimental results indicated that the expression trends of RNA methylation-relevant prognostic genes in gastric cancer cells were in agreement with the result of bioinformatics.
Conclusion
Our study established a novel RNA methylation-related risk signature for STAD, which was of considerable significance for improving prognosis of STAD patients and offering theoretical support for clinical therapy.
Background
Gastric cancer (GC) is a malignant tumor that originates from the epithelium of the gastric mucosa and has a poor prognosis. Stomach adenocarcinoma (STAD) covers 95% of total gastric cancer. This study aimed to identify the prognostic value of RNA methylation-related genes in gastric cancer.
Methods
In this study, The Cancer Genome Atlas (TCGA)-STAD and GSE84426 cohorts were downloaded from public databases. Patients were classified by consistent cluster analysis based on prognosis-related differentially expressed RNA methylation genes Prognostic genes were obtained by differential expression, univariate Cox and least absolute shrinkage and selection operator (LASSO) analyses. The prognostic model was established and validated in the training set, test set and validation set respectively. Independent prognostic analysis was implemented. Finally, the expression of prognostic genes was affirmed by reverse transcription quantitative PCR (RT-qPCR).
Results
In total, four prognostic genes (ACTA2, SAPCD2, PDK4 and APOD) related to RNA methylation were identified and enrolled into the risk signature. The STAD patients were divided into high- and low-risk groups based on the medium value of the risk score, and patients in the high-risk group had a poor prognosis. In addition, the RNA methylation-relevant risk signature was validated in the test and validation sets, and was authenticated as a reliable independent prognostic predictor. The nomogram was constructed based on the independent predictors to predict the 1/3/5-year survival probability of STAD patients. The gene set enrichment analysis (GSEA) result suggested that the poor prognosis in the high-risk subgroup may be related to immune-related pathways. Finally, the experimental results indicated that the expression trends of RNA methylation-relevant prognostic genes in gastric cancer cells were in agreement with the result of bioinformatics.
Conclusion
Our study established a novel RNA methylation-related risk signature for STAD, which was of considerable significance for improving prognosis of STAD patients and offering theoretical support for clinical therapy.Identification of m6A-associated autophagy genes in non-alcoholic fatty liverhttps://peerj.com/articles/170112024-02-292024-02-29Ziqing HuangLinfei LuoZhengqiang WuZhihua XiaoZhili Wen
Background
Studies had shown that autophagy was closely related to nonalcoholic fat liver disease (NAFLD), while N6-methyladenosine (m6A) was involved in the regulation of autophagy. However, the mechanism of m6A related autophagy in NAFLD was unclear.
Methods
The NAFLD related datasets were gained via the Gene Expression Omnibus (GEO) database, and we also extracted 232 autophagy-related genes (ARGs) and 37 m6A. First, differentially expressed ARGs (DE-ARGs) and differentially expressed m6A (DE-m6A) were screened out by differential expression analysis. DE-ARGs associated with m6A were sifted out by Pearson correlation analysis, and the m6A-ARGs relationship pairs were acquired. Then, autophagic genes in m6A-ARGs pairs were analyzed for machine learning algorithms to obtain feature genes. Further, we validated the relationship between feature genes and NAFLD through quantitative real-time polymerase chain reaction (qRT-PCR), Western blot (WB). Finally, the immuno-infiltration analysis was implement, and we also constructed the TF-mRNA and drug-gene networks.
Results
There were 19 DE-ARGs and four DE-m6A between NAFLD and normal samples. The three m6A genes and five AGRs formed the m6A-ARGs relationship pairs. Afterwards, genes obtained from machine learning algorithms were intersected to yield three feature genes (TBK1, RAB1A, and GOPC), which showed significant positive correlation with astrocytes, macrophages, smooth muscle, and showed significant negative correlation with epithelial cells, and endothelial cells. Besides, qRT-PCR and WB indicate that TBK1, RAB1A and GOPC significantly upregulated in NAFLD. Ultimately, we found that the TF-mRNA network included FOXP1-GOPC, ATF1-RAB1A and other relationship pairs, and eight therapeutic agents such as R-406 and adavosertib were predicted based on the TBK1.
Conclusion
The study investigated the potential molecular mechanisms of m6A related autophagy feature genes (TBK1, RAB1A, and GOPC) in NAFLD through bioinformatic analyses and animal model validation. However, it is critical to note that these findings, although consequential, demonstrate correlations rather than cause-and-effect relationships. As such, more research is required to fully elucidate the underlying mechanisms and validate the clinical relevance of these feature genes.
Background
Studies had shown that autophagy was closely related to nonalcoholic fat liver disease (NAFLD), while N6-methyladenosine (m6A) was involved in the regulation of autophagy. However, the mechanism of m6A related autophagy in NAFLD was unclear.
Methods
The NAFLD related datasets were gained via the Gene Expression Omnibus (GEO) database, and we also extracted 232 autophagy-related genes (ARGs) and 37 m6A. First, differentially expressed ARGs (DE-ARGs) and differentially expressed m6A (DE-m6A) were screened out by differential expression analysis. DE-ARGs associated with m6A were sifted out by Pearson correlation analysis, and the m6A-ARGs relationship pairs were acquired. Then, autophagic genes in m6A-ARGs pairs were analyzed for machine learning algorithms to obtain feature genes. Further, we validated the relationship between feature genes and NAFLD through quantitative real-time polymerase chain reaction (qRT-PCR), Western blot (WB). Finally, the immuno-infiltration analysis was implement, and we also constructed the TF-mRNA and drug-gene networks.
Results
There were 19 DE-ARGs and four DE-m6A between NAFLD and normal samples. The three m6A genes and five AGRs formed the m6A-ARGs relationship pairs. Afterwards, genes obtained from machine learning algorithms were intersected to yield three feature genes (TBK1, RAB1A, and GOPC), which showed significant positive correlation with astrocytes, macrophages, smooth muscle, and showed significant negative correlation with epithelial cells, and endothelial cells. Besides, qRT-PCR and WB indicate that TBK1, RAB1A and GOPC significantly upregulated in NAFLD. Ultimately, we found that the TF-mRNA network included FOXP1-GOPC, ATF1-RAB1A and other relationship pairs, and eight therapeutic agents such as R-406 and adavosertib were predicted based on the TBK1.
Conclusion
The study investigated the potential molecular mechanisms of m6A related autophagy feature genes (TBK1, RAB1A, and GOPC) in NAFLD through bioinformatic analyses and animal model validation. However, it is critical to note that these findings, although consequential, demonstrate correlations rather than cause-and-effect relationships. As such, more research is required to fully elucidate the underlying mechanisms and validate the clinical relevance of these feature genes.Retrospective study and implementation of a low-cost LAMP-turbidimetric assay for screening α0-thalassemia (SEA deletion): preventing and controlling Hb Bart’s hydrops fetalis syndrome in Thailandhttps://peerj.com/articles/170542024-02-272024-02-27Wittaya JomouiKanokkorn SaknavaKanokpron PrechatrammaruchYanticha Ondee
Homozygous α0-thalassemia (SEA deletion) or Hb Bart’s hydrops fetalis syndrome is a significant public health issue in Thailand and Southeast Asia. A prevention and control program has been implemented in this region. This study focuses on retrospective laboratory data collected between January 2021 and April 2023 at a single center. Additionally, we developed a low-cost LAMP-turbidimetric assay to propose in the screening strategy. A total of 3,623 samples underwent screening tests (MCV, MCH, and DCIP), including 1,658 couple screenings (84.25%) and 310 single pregnant screenings (15.75%). Negative screenings, which did not require further investigation, were found in 75.51% for couple screenings and 46.58% for single pregnant screenings. At hemoglobin (Hb) analysis identified 129 couples which had fetuses at risk of severe thalassemia, whereas molecular analysis during the retrospective period revealed 210 samples with different genotypes. These remaining samples were validated using the low-cost LAMP-turbidimetric assay to detect α0-thalassemia (SEA deletion). The developed LAMP turbidimetric assay demonstrated a sensitivity and specificity of 100% (36/36 × 100) and 97.7% (170/174 × 100), respectively, when compared with gap-PCR. Furthermore, we propose a strategy involving the addition of the low-cost LAMP-turbidimetric assay before performing the gold standard. This strategy represents a cost-saving of USD 2,608 based on 210 samples that required DNA analysis. Finally, the developed LAMP turbidimetric assays offer advantages such as reduced time, workload, cost savings, no need for highly developed instruments, and a straightforward interpreting process. Therefore, implementation of LAMP assays into routine settings would be improve the efficiency of prevention and control program for severe thalassemia disease in this region.
Homozygous α0-thalassemia (SEA deletion) or Hb Bart’s hydrops fetalis syndrome is a significant public health issue in Thailand and Southeast Asia. A prevention and control program has been implemented in this region. This study focuses on retrospective laboratory data collected between January 2021 and April 2023 at a single center. Additionally, we developed a low-cost LAMP-turbidimetric assay to propose in the screening strategy. A total of 3,623 samples underwent screening tests (MCV, MCH, and DCIP), including 1,658 couple screenings (84.25%) and 310 single pregnant screenings (15.75%). Negative screenings, which did not require further investigation, were found in 75.51% for couple screenings and 46.58% for single pregnant screenings. At hemoglobin (Hb) analysis identified 129 couples which had fetuses at risk of severe thalassemia, whereas molecular analysis during the retrospective period revealed 210 samples with different genotypes. These remaining samples were validated using the low-cost LAMP-turbidimetric assay to detect α0-thalassemia (SEA deletion). The developed LAMP turbidimetric assay demonstrated a sensitivity and specificity of 100% (36/36 × 100) and 97.7% (170/174 × 100), respectively, when compared with gap-PCR. Furthermore, we propose a strategy involving the addition of the low-cost LAMP-turbidimetric assay before performing the gold standard. This strategy represents a cost-saving of USD 2,608 based on 210 samples that required DNA analysis. Finally, the developed LAMP turbidimetric assays offer advantages such as reduced time, workload, cost savings, no need for highly developed instruments, and a straightforward interpreting process. Therefore, implementation of LAMP assays into routine settings would be improve the efficiency of prevention and control program for severe thalassemia disease in this region.Effects of BRD4 inhibitor JQ1 on the expression profile of super-enhancer related lncRNAs and mRNAs in cervical cancer HeLa cellshttps://peerj.com/articles/170352024-02-232024-02-23Jianqing ZhengBifen HuangLihua XiaoMin Wu
Objective
To investigate the effects of bromine domain protein 4 (BRD4) inhibitor JQ1 on the expression profile of super-enhancer-related lncRNAs (SE-lncRNAs) and mRNAs in cervical cancer (CC) HeLa-cells.
Methods
The CCK8 method was implemented to detect the inhibitory effect of JQ1 on HeLa cells and explore the best inhibitory concentration. Whole transcriptome sequencing was performed to detect the changes of lncRNAs and mRNAs expression profiles in cells of the JQ1 treatment group and control group, respectively. The differentially expressed SE-lncRNAs were obtained by matching, while the co-expressed mRNAs were obtained by Pearson correlation analysis.
Results
The inhibitory effect of JQ1 on HeLa cell proliferation increased significantly with increasing concentration and treatment time (P < 0.05). Under the experimental conditions of three concentrations of 0.01, 0.1 and 1 μmol/L of JQ1 on HeLa cells at 24, 48, 72 and 120 h, 1 μmol/L of JQ1 at 72 and 120 h had the same cell viability and the strongest cell proliferation inhibition. In order to understand the inhibitory mechanism of JQ1 on HeLa cells, this study analyzed the expression profile differences from the perspective of SE-lncRNAs and mRNAs. A total of 162 SE-lncRNAs were identified, of which 8 SE-lncRNAs were down-regulated and seven SE-lncRNAs were up-regulated. A total of 418 differentially expressed mRNAs related to SE-lncRNAs were identified, of which 395 mRNAs had positive correlation with 12 SE-lncRNAs and 408 mRNAs had negative correlation with 15 SE-lncRNAs.
Conclusion
JQ1 can significantly inhibit the proliferation of HeLa cells and affect the expression profile of SE-lncRNAs and mRNAs.
Objective
To investigate the effects of bromine domain protein 4 (BRD4) inhibitor JQ1 on the expression profile of super-enhancer-related lncRNAs (SE-lncRNAs) and mRNAs in cervical cancer (CC) HeLa-cells.
Methods
The CCK8 method was implemented to detect the inhibitory effect of JQ1 on HeLa cells and explore the best inhibitory concentration. Whole transcriptome sequencing was performed to detect the changes of lncRNAs and mRNAs expression profiles in cells of the JQ1 treatment group and control group, respectively. The differentially expressed SE-lncRNAs were obtained by matching, while the co-expressed mRNAs were obtained by Pearson correlation analysis.
Results
The inhibitory effect of JQ1 on HeLa cell proliferation increased significantly with increasing concentration and treatment time (P < 0.05). Under the experimental conditions of three concentrations of 0.01, 0.1 and 1 μmol/L of JQ1 on HeLa cells at 24, 48, 72 and 120 h, 1 μmol/L of JQ1 at 72 and 120 h had the same cell viability and the strongest cell proliferation inhibition. In order to understand the inhibitory mechanism of JQ1 on HeLa cells, this study analyzed the expression profile differences from the perspective of SE-lncRNAs and mRNAs. A total of 162 SE-lncRNAs were identified, of which 8 SE-lncRNAs were down-regulated and seven SE-lncRNAs were up-regulated. A total of 418 differentially expressed mRNAs related to SE-lncRNAs were identified, of which 395 mRNAs had positive correlation with 12 SE-lncRNAs and 408 mRNAs had negative correlation with 15 SE-lncRNAs.
Conclusion
JQ1 can significantly inhibit the proliferation of HeLa cells and affect the expression profile of SE-lncRNAs and mRNAs.Hormonal and psychological influences on performance anxiety in adolescent female volleyball players: a multi-approach studyhttps://peerj.com/articles/166172024-02-192024-02-19Carlo RossiAlessandra AmatoMarianna AlesiAnna AliotoGabriella SchieraPatrik DridGiulia MessinaAndrea PagliaroItalia Di LiegroPatrizia Proia
Background
The neuroendocrine system has important implications for affiliation behavior among humans and can be used to assess the correlation between social relationships, stress, and health. This can be influenced by social closeness; this aspect is the closeness towards another individual or a group of individuals such as a sports team. Sports performance anxiety is considered an unpleasant emotional reaction composed of physiological, cognitive, affective, and behavioral components. This motivates us to learn about the process that can influence the outcome of competition. Hormones and genetics would seem to influence outcome and performance. In this regard, many studies have focused on the exercise response as a function of ovarian hormones and it has been observed that progesterone is a hormone that plays a key role in reducing anxiety, and thus stress, in humans and other animals. On the other hand, high cortisol concentrations are known to contribute to increased anxiety levels. However, the salivary alpha-amylase (sAA) enzyme has been suggested as marker of acute stress than cortisol. Genetics also seem to influence anxiety and stress management as in the case of brain-derived neurotrophic factor (BDNF) and striatal dopamine transporter (DAT). Therefore, the study aims to investigate social closeness, as a measure of sports team cohesion that can influence athletes’ performance results, and its ability to influence the secretion of hormones, such as progesterone and cortisol, that affect the management of sports anxiety while also taking into account genetic background during a volleyball match.
Methods
Twenty-six female volleyball players who volunteered participated in this study (mean ± SD: age, 12.07 ± 0.7 years), and played in the final of the provincial volleyball championship in Palermo. All girls were during the ovarian cycle, in detail between the follicular and early ovulatory phases.
Results
The results showed a significant decrease in salivary cortisol only in the winning group (p < 0.039). In fact, whilst in the latter the pre-match level was 7.7 ng/ml and then decreased to 4.5 ng/ml after the match, in the losers group change was not statistically significant (7.8 ng/ml vs 6.6 ng/ml pre- and post-match). As to the sAA concentration, the winning team showed a statistically significant variation between pre- and post-match than the losers (166.01 ± 250 U/ml vs 291.59 ± 241 U/ml) (p = 0.01).
Conclusion
Analyzing the results of the SAS-2 psychological test it is highlighted that, on average, the loser group was more anxious than the winning group, and this contributed to the final result. In conclusion, there is strong evidence supporting the state of the art that many factors can affect performance anxiety and thus the performance itself.
Background
The neuroendocrine system has important implications for affiliation behavior among humans and can be used to assess the correlation between social relationships, stress, and health. This can be influenced by social closeness; this aspect is the closeness towards another individual or a group of individuals such as a sports team. Sports performance anxiety is considered an unpleasant emotional reaction composed of physiological, cognitive, affective, and behavioral components. This motivates us to learn about the process that can influence the outcome of competition. Hormones and genetics would seem to influence outcome and performance. In this regard, many studies have focused on the exercise response as a function of ovarian hormones and it has been observed that progesterone is a hormone that plays a key role in reducing anxiety, and thus stress, in humans and other animals. On the other hand, high cortisol concentrations are known to contribute to increased anxiety levels. However, the salivary alpha-amylase (sAA) enzyme has been suggested as marker of acute stress than cortisol. Genetics also seem to influence anxiety and stress management as in the case of brain-derived neurotrophic factor (BDNF) and striatal dopamine transporter (DAT). Therefore, the study aims to investigate social closeness, as a measure of sports team cohesion that can influence athletes’ performance results, and its ability to influence the secretion of hormones, such as progesterone and cortisol, that affect the management of sports anxiety while also taking into account genetic background during a volleyball match.
Methods
Twenty-six female volleyball players who volunteered participated in this study (mean ± SD: age, 12.07 ± 0.7 years), and played in the final of the provincial volleyball championship in Palermo. All girls were during the ovarian cycle, in detail between the follicular and early ovulatory phases.
Results
The results showed a significant decrease in salivary cortisol only in the winning group (p < 0.039). In fact, whilst in the latter the pre-match level was 7.7 ng/ml and then decreased to 4.5 ng/ml after the match, in the losers group change was not statistically significant (7.8 ng/ml vs 6.6 ng/ml pre- and post-match). As to the sAA concentration, the winning team showed a statistically significant variation between pre- and post-match than the losers (166.01 ± 250 U/ml vs 291.59 ± 241 U/ml) (p = 0.01).
Conclusion
Analyzing the results of the SAS-2 psychological test it is highlighted that, on average, the loser group was more anxious than the winning group, and this contributed to the final result. In conclusion, there is strong evidence supporting the state of the art that many factors can affect performance anxiety and thus the performance itself.Fine-scale mapping of chromosome 9q22.33 identifies candidate causal variant in ovarian cancerhttps://peerj.com/articles/169182024-02-142024-02-14Tongyu XingYanrui ZhaoLili WangWei GengWei LiuJingjing ZhouCaiyun HuangWei WangXinlei ChuBen LiuKexin ChenHong ZhengLian Li
Ovarian cancer is a complex polygenic disease in which genetic factors play a significant role in disease etiology. A genome-wide association study (GWAS) identified a novel variant on chromosome 9q22.33 as a susceptibility locus for epithelial ovarian cancer (EOC) in the Han Chinese population. However, the underlying mechanism of this genomic region remained unknown. In this study, we conducted a fine-mapping analysis of 130 kb regions, including 1,039 variants in 200 healthy women. Ten variants were selected to evaluate the association with EOC risk in 1,099 EOC cases and 1,591 controls. We identified two variants that were significantly associated with ovarian cancer risk (rs7027650, P = 1.91 × 10−7; rs1889268, P = 3.71 × 10−2). Expression quantitative trait locus (eQTL) analysis found that rs7027650 was significantly correlated with COL15A1 gene expression (P = 0.009). The Luciferase reporter gene assay confirmed that rs7027650 could interact with the promoter region of COL15A1, reducing its activity. An electrophoretic mobility shift assay (EMSA) showed the allele-specific binding capacity of rs7027650. These findings revealed that rs7027650 could be a potential causal variant at 9q22.33 region and may regulate the expression level of COL15A1. This study offered insight into the molecular mechanism behind a potential causal variant that affects the risk of ovarian cancer.
Ovarian cancer is a complex polygenic disease in which genetic factors play a significant role in disease etiology. A genome-wide association study (GWAS) identified a novel variant on chromosome 9q22.33 as a susceptibility locus for epithelial ovarian cancer (EOC) in the Han Chinese population. However, the underlying mechanism of this genomic region remained unknown. In this study, we conducted a fine-mapping analysis of 130 kb regions, including 1,039 variants in 200 healthy women. Ten variants were selected to evaluate the association with EOC risk in 1,099 EOC cases and 1,591 controls. We identified two variants that were significantly associated with ovarian cancer risk (rs7027650, P = 1.91 × 10−7; rs1889268, P = 3.71 × 10−2). Expression quantitative trait locus (eQTL) analysis found that rs7027650 was significantly correlated with COL15A1 gene expression (P = 0.009). The Luciferase reporter gene assay confirmed that rs7027650 could interact with the promoter region of COL15A1, reducing its activity. An electrophoretic mobility shift assay (EMSA) showed the allele-specific binding capacity of rs7027650. These findings revealed that rs7027650 could be a potential causal variant at 9q22.33 region and may regulate the expression level of COL15A1. This study offered insight into the molecular mechanism behind a potential causal variant that affects the risk of ovarian cancer.Retrospective study of BRAFV600E mutation and CT features of papillary thyroid carcinomahttps://peerj.com/articles/168102024-01-242024-01-24Xiaoquan HongJuxiang LiShaoyin DuanYoukuang You
Objective
This study aimed to examine the correlation between BRAFV600E status and computed tomography (CT) imaging characteristics in papillary thyroid carcinoma (PTC) and determine if suspicious CT imaging features could predict BRAFV600E status.
Methods
This retrospective study included patients with pathologically confirmed PTC at the Department of Thyroid Surgery of Zhongshan Hospital, Xiamen University, between July 2020 and June 2022. We compared the clinicopathologic factors and CT findings of nodules with and without the mutation, and the multiple logistical regression test was used to determine independent parameters of the BRAFV600E mutation.
Results
This study included 381 patients with PTC, among them, BRAFV600E mutation was detected in 314 patients (82.4%). Multivariate logistic regression analysis showed that gender (OR = 0.542, 95% CI [0.296–0.993], P = 0.047) and shape (OR = 0.510, 95% CI [0.275–0.944], P = 0.032) were associated with BRAFV600E mutation.
Conclusions
Compared to BRAFV600E mutation-negative, BRAFV600E-positive PTC lesions were more likely to be found in female patients and were characterized by irregular shape. However, the CT imaging finding is not enough to predict BRAFV600E status, but an indication.
Objective
This study aimed to examine the correlation between BRAFV600E status and computed tomography (CT) imaging characteristics in papillary thyroid carcinoma (PTC) and determine if suspicious CT imaging features could predict BRAFV600E status.
Methods
This retrospective study included patients with pathologically confirmed PTC at the Department of Thyroid Surgery of Zhongshan Hospital, Xiamen University, between July 2020 and June 2022. We compared the clinicopathologic factors and CT findings of nodules with and without the mutation, and the multiple logistical regression test was used to determine independent parameters of the BRAFV600E mutation.
Results
This study included 381 patients with PTC, among them, BRAFV600E mutation was detected in 314 patients (82.4%). Multivariate logistic regression analysis showed that gender (OR = 0.542, 95% CI [0.296–0.993], P = 0.047) and shape (OR = 0.510, 95% CI [0.275–0.944], P = 0.032) were associated with BRAFV600E mutation.
Conclusions
Compared to BRAFV600E mutation-negative, BRAFV600E-positive PTC lesions were more likely to be found in female patients and were characterized by irregular shape. However, the CT imaging finding is not enough to predict BRAFV600E status, but an indication.Evaluating the relationship between Clinical G6PD enzyme activity and gene variantshttps://peerj.com/articles/165542024-01-032024-01-03Xinyi ZhouZheng QiangSufen ZhangYuqiu ZhouQizhi XiaoGongjun Tan
Glucose-6-phosphate dehydrogenase (G6PD) is a the first and rate-limiting enzyme that plays a critical role in G6PD deficiency, the most common enzyme disorder worldwide, is related to intravascular hemolysis. To determine the clinical enzyme activity level in different G6PD variants, we evaluated 15 variant from 424 clinical blood samples by using multicolor melting curve analysis and DNA sequencing. The results showed that the enzyme activities of the hemizygous deficient were 1.5–2.4 U/gHb, which was significantly lower than those of the heterozygous (P < 0.001) and the compound heterozygous variants (P < 0.05). Since the hemizygous of c.1024C > T (Chinese-5) mutation affects the kinetic parameters of G6PD and increase utilization of analogues, its enzyme activity is more than those of other mutations that mutated in the β+α region of G6PD. The heterozygous enzyme levels ranged from 6.5–20.1 U/gHb; and there was no significant difference among different heterozygous variants (P > 0.05). The enzyme activity levels of the compound heterozygous mutation were mainly in the range of 1.7–3.8 U/gHb, which was much lower than that of the heterozygous mutation (P < 0.001). In summary, our findings revealed that the enzyme activity of G6PD in blood have a significant relationship with genotype of G6PD.
Glucose-6-phosphate dehydrogenase (G6PD) is a the first and rate-limiting enzyme that plays a critical role in G6PD deficiency, the most common enzyme disorder worldwide, is related to intravascular hemolysis. To determine the clinical enzyme activity level in different G6PD variants, we evaluated 15 variant from 424 clinical blood samples by using multicolor melting curve analysis and DNA sequencing. The results showed that the enzyme activities of the hemizygous deficient were 1.5–2.4 U/gHb, which was significantly lower than those of the heterozygous (P < 0.001) and the compound heterozygous variants (P < 0.05). Since the hemizygous of c.1024C > T (Chinese-5) mutation affects the kinetic parameters of G6PD and increase utilization of analogues, its enzyme activity is more than those of other mutations that mutated in the β+α region of G6PD. The heterozygous enzyme levels ranged from 6.5–20.1 U/gHb; and there was no significant difference among different heterozygous variants (P > 0.05). The enzyme activity levels of the compound heterozygous mutation were mainly in the range of 1.7–3.8 U/gHb, which was much lower than that of the heterozygous mutation (P < 0.001). In summary, our findings revealed that the enzyme activity of G6PD in blood have a significant relationship with genotype of G6PD.Progress of circRNA/lncRNA-miRNA-mRNA axis in atrial fibrillationhttps://peerj.com/articles/166042023-12-192023-12-19Jia-le WenZhong-bao RuanFei WangYuhua Hu
Atrial fibrillation (AF) is a prevalent arrhythmia that requires effective biomarkers and therapeutic targets for clinical management. In recent years, non-coding RNAs (ncRNAs) have emerged as key players in the pathogenesis of AF, particularly through the ceRNA (competitive endogenous RNA) mechanism. By acting as ceRNAs, ncRNAs can competitively bind to miRNAs and modulate the expression of target mRNAs, thereby influencing the biological behavior of AF. The ceRNA axis has shown promise as a diagnostic and prognostic biomarker for AF. This review provides a comprehensive overview of the roles of ncRNAs in the development and progression of AF, highlighting the intricate crosstalk between different ncRNAs in AF pathophysiology. Furthermore, we discuss the potential implications of targeting the circRNA/lncRNA-miRNA-mRNA axis for the diagnosis, prognosis, and therapeutic intervention of AF.
Atrial fibrillation (AF) is a prevalent arrhythmia that requires effective biomarkers and therapeutic targets for clinical management. In recent years, non-coding RNAs (ncRNAs) have emerged as key players in the pathogenesis of AF, particularly through the ceRNA (competitive endogenous RNA) mechanism. By acting as ceRNAs, ncRNAs can competitively bind to miRNAs and modulate the expression of target mRNAs, thereby influencing the biological behavior of AF. The ceRNA axis has shown promise as a diagnostic and prognostic biomarker for AF. This review provides a comprehensive overview of the roles of ncRNAs in the development and progression of AF, highlighting the intricate crosstalk between different ncRNAs in AF pathophysiology. Furthermore, we discuss the potential implications of targeting the circRNA/lncRNA-miRNA-mRNA axis for the diagnosis, prognosis, and therapeutic intervention of AF.