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Zhao J, Li J, Yao J, Lin G, Chen C, Ye H, He X, Qu S, Chen Y, Wang D, Liang Y, Gao Z, Wu F. Enhanced PSO feature selection with Runge-Kutta and Gaussian sampling for precise gastric cancer recurrence prediction. Comput Biol Med 2024; 175:108437. [PMID: 38669732 DOI: 10.1016/j.compbiomed.2024.108437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/14/2024] [Accepted: 04/07/2024] [Indexed: 04/28/2024]
Abstract
Gastric cancer (GC), characterized by its inconspicuous initial symptoms and rapid invasiveness, presents a formidable challenge. Overlooking postoperative intervention opportunities may result in the dissemination of tumors to adjacent areas and distant organs, thereby substantially diminishing prospects for patient survival. Consequently, the prompt recognition and management of GC postoperative recurrence emerge as a matter of paramount urgency to mitigate the deleterious implications of the ailment. This study proposes an enhanced feature selection model, bRSPSO-FKNN, integrating boosted particle swarm optimization (RSPSO) with fuzzy k-nearest neighbor (FKNN), for predicting GC. It incorporates the Runge-Kutta search, for improved model accuracy, and Gaussian sampling, enhancing the search performance and helping to avoid locally optimal solutions. It outperforms the sophisticated variants of particle swarm optimization when evaluated in the CEC 2014 test suite. Furthermore, the bRSPSO-FKNN feature selection model was introduced for GC recurrence prediction analysis, achieving up to 82.082 % and 86.185 % accuracy and specificity, respectively. In summation, this model attains a notable level of precision, poised to ameliorate the early warning system for GC recurrence and, in turn, advance therapeutic options for afflicted patients.
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Affiliation(s)
- Jungang Zhao
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China.
| | - JiaCheng Li
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China.
| | - Jiangqiao Yao
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China.
| | - Ganglian Lin
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China.
| | - Chao Chen
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China.
| | - Huajun Ye
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China.
| | - Xixi He
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China.
| | - Shanghu Qu
- Department of Urology, Yunnan Tumor Hospital and the Third Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China.
| | - Yuxin Chen
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China.
| | - Danhong Wang
- Wenzhou Medical University, Wenzhou, Zhejiang, China.
| | - Yingqi Liang
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China.
| | - Zhihong Gao
- Zhejiang Engineering Research Center of Intelligent Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China.
| | - Fang Wu
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China.
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Luo Y, Zhao J. The dynamic changes of peripheral blood cell counts predict the clinical outcomes of aneurysmal subarachnoid hemorrhage. Heliyon 2024; 10:e29763. [PMID: 38681624 PMCID: PMC11053216 DOI: 10.1016/j.heliyon.2024.e29763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 05/01/2024] Open
Abstract
Background Aneurysmal subarachnoid hemorrhage (aSAH) is a serious type of hemorrhagic stroke. It is very important to predict the prognosis at early phase. In this work, we intend to characterize early changes in peripheral blood cells after aSAH and explore the association between peripheral blood cells and clinical outcomes after aSAH. Methods aSAH patients admitted between December 2019 and September 2022 were enrolled. A retrospective observational study was performed. Total leukocytes, monocytes, neutrophils, erythrocytes, lymphocytes and platelets counts were recorded on the day of admission (day 1), day 3, day 5 and day 7. Statistical tests included Chi-square test, analysis of variance and multivariate logistic regression (MLR) models. 197 patients were analyzed. Results Leukocytes and neutrophils were higher in poor outcome groups from day 1 to day 7 and in delayed cerebral ischemia (DCI) groups from day 3 to day 7. Lymphocytes were higher at day 5 and day 7 in good outcome groups and no DCI groups. Neutrophil-to-lymphocyte ratio (NLR) was lower from day 3 to day 7 in good outcome groups and no DCI groups. Erythrocytes were higher from day 3 to day 7 in good outcome groups and no DCI groups. Lymphocytes were negatively related to poor outcomes on day 1 (OR = 0.457), indicating higher lymphocytes predicted good outcomes, Neutrophils were positively related to poor outcomes on day 3 (OR = 3.003) indicating higher neutrophils predicted poor outcomes. Lymphocytes were negatively related to DCI on day 5 (OR = 0.388) indicating higher lymphocytes predicted no DCI, Erythrocytes were negatively related to DCI on day 5 (OR = 0.335) and day 7 (OR = 0.204) indicating higher erythrocytes predicted no DCI. The improved ability of neutrophils, lymphocytes and erythrocytes to predict DCI or poor functional outcomes were revealed by ROC curve analysis. Conclusions The dynamic changes of peripheral blood cell counts were related to poor functional outcomes and DCI after aSAH. Elevated neutrophils, leukocytes, NLR, and decreased lymphocytes, erythrocytes were accompanied by DCI and poor outcome. Neutrophils, lymphocytes and erythrocytes counts could be beneficial to predict DCI and outcomes after aSAH.
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Affiliation(s)
- Yi Luo
- Department of Neurology, The First People's Hospital of Jing Zhou, The First Affiliated Hospital of Yangtze University, Jing zhou, 434000, China
- Department of Stroke Center, The First People's Hospital of Jing Zhou, The First Affiliated Hospital of Yangtze University, Jing zhou, 434000, China
| | - Jian Zhao
- Department of Neurosurgery, The First People's Hospital of Jing Zhou, The First Affiliated Hospital of Yangtze University, Jing zhou, 434000, China
- Department of Stroke Center, The First People's Hospital of Jing Zhou, The First Affiliated Hospital of Yangtze University, Jing zhou, 434000, China
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Xu F, Dirsch O, Dahmen U. Causal relationship between psychological factors and hepatocellular carcinoma as revealed by Mendelian randomization. J Cancer Res Clin Oncol 2024; 150:100. [PMID: 38383696 PMCID: PMC10881603 DOI: 10.1007/s00432-024-05617-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 01/09/2024] [Indexed: 02/23/2024]
Abstract
PURPOSE The impact of psychological factors on the incidence of hepatocellular carcinoma (HCC) in humans remains unclear. Mendelian randomization (MR) study is a novel approach aimed at unbiased detection of causal effects. Therefore, we conducted a two-sample MR to determine if there is a causal relationship between psychological distress (PD), participation in leisure/social activities of religious groups (LARG), and HCC. METHODS The genetic summary data of exposures and outcome were retrieved from genome-wide association studies (GWAS). We used PD and LARG as exposures and HCC as outcome. Five MR methods were used to investigate the causal relationship between PD, LARG, and HCC. The result of inverse variance weighted (IVW) method was deemed as principal result. Besides, we performed a comprehensive sensitivity analysis to verify the robustness of the results. RESULTS The IVW results showed that PD [odds ratio (OR) 1.006, 95% confidence interval (CI) 1.000-1.011, P = 0.033] and LARG (OR 0.994, 95% CI 0.988-1.000, P = 0.035) were causally associated with the incidence of HCC. Sensitivity analysis did not identify any bias in the results. CONCLUSION PD turned out to be a mild risk factor for HCC. In contrast, LARG is a protective factor for HCC. Therefore, it is highly recommended that people with PD are seeking positive leisure activities such as participation in formal religious social activities, which may help them reduce the risk of HCC.
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Affiliation(s)
- Fengming Xu
- Department of Infectious Diseases, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, 310006, China
- Else Kröner Graduate School for Medical Students "JSAM", Jena University Hospital, 07747, Jena, Germany
- Experimental Transplantation Surgery, Department of General, Visceral and Vascular Surgery, Jena University Hospital, 07747, Jena, Germany
| | - Olaf Dirsch
- Institute of Pathology, Klinikum Chemnitz gGmbH, 09111, Chemnitz, Germany
| | - Uta Dahmen
- Experimental Transplantation Surgery, Department of General, Visceral and Vascular Surgery, Jena University Hospital, 07747, Jena, Germany.
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Qin S, Wang J, Yuan H, He J, Luan S, Deng Y. Liver function indicators and risk of hepatocellular carcinoma: a bidirectional mendelian randomization study. Front Genet 2024; 14:1260352. [PMID: 38318289 PMCID: PMC10839095 DOI: 10.3389/fgene.2023.1260352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 12/29/2023] [Indexed: 02/07/2024] Open
Abstract
Observational studies have shown an association between liver dysfunction and hepatocellular carcinoma (HCC), but the causality relationship between them is unclear. We aimed to determine whether there is a bidirectional causal relationship between liver function indicators (alanine aminotransferase, ALT; aspartate aminotransferase, AST; alkaline phosphatase, ALP; γ-glutamyltransferase, GGT) and HCC. Our two-sample Mendelian randomization (MR) study acquired single nucleotide polymorphisms (SNPs) associated with liver function indicators (ALT, n = 134,182; AST, n = 134,154; GGT, n = 118,309; ALP, n = 105,030) and with HCC (n = 197,611) from publicly available genome-wide association studies (GWAS) of East Asian ancestry in Japan (BioBank Japan, BBJ). Univariable MR analyses were performed to identify whether the genetic evidence of exposure was significantly associated with outcome. Multivariable MR analysis was conducted to estimate the independent effects of exposures on outcome. Univariable MR analysis indicated that the level of ALT, AST, and GGT was the risk factor for HCC incidence. Meanwhile, multivariable MR analysis revealed that AST was an independent risk factor for HCC. The hazard ratio (HR) of the probability of HCC was 3.045 [95% confidence interval (95%CI), 1.697-5.463, p = 0.003] for AST. The results of reverse MR analyses showed that gene-predictive HCC incidence could increase the levels of AST (HR = 1.031, 95%CI: 1.009-1.054, p = 2.52 × 10-4) and ALT (HR = 1.040, 95%CI: 1.019-1.063, p = 0.005). Meanwhile, HCC may be negatively correlated with ALP levels (HR = 0.971, 95%CI: 0.947-0.995, p = 0.018). This study provides evidence to support that genetically predicted higher levels of AST are related to increased risk of HCC, with no strong evidence of a causal effect of genetically predicted ALP, ALP, and GGT on HCC. In addition, genetic predisposition to HCC could influence blood concentration of ALT, AST, and ALP. Thus, this may create a vicious cycle.
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Affiliation(s)
- Shanshan Qin
- Department of Radiology, Qilu Hospital of Shandong University, Jinan, China
| | - Jing Wang
- Shandong Medical College, Jinan, China
| | - Haiqing Yuan
- Intensive Care Unit, Weifang People’s Hospital, Weifang, Shandong, China
| | - Jingzhen He
- Department of Radiology, Qilu Hospital of Shandong University, Jinan, China
| | - Shoujing Luan
- Department of Endocrinology and Metabolism, Weifang People’s Hospital, Weifang, Shandong, China
| | - Yan Deng
- Department of Radiology, Qilu Hospital of Shandong University, Jinan, China
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Lv JH, Hou AJ, Zhang SH, Dong JJ, Kuang HX, Yang L, Jiang H. WGCNA combined with machine learning to find potential biomarkers of liver cancer. Medicine (Baltimore) 2023; 102:e36536. [PMID: 38115320 PMCID: PMC10727608 DOI: 10.1097/md.0000000000036536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/16/2023] [Accepted: 11/17/2023] [Indexed: 12/21/2023] Open
Abstract
The incidence of hepatocellular carcinoma (HCC) has been increasing in recent years. With the development of various detection technologies, machine learning is an effective method to screen disease characteristic genes. In this study, weighted gene co-expression network analysis (WGCNA) and machine learning are combined to find potential biomarkers of liver cancer, which provides a new idea for future prediction, prevention, and personalized treatment. In this study, the "limma" software package was used. P < .05 and log2 |fold-change| > 1 is the standard screening differential genes, and then the module genes obtained by WGCNA analysis are crossed to obtain the key module genes. Gene Ontology and Kyoto Gene and Genome Encyclopedia analysis was performed on key module genes, and 3 machine learning methods including lasso, support vector machine-recursive feature elimination, and RandomForest were used to screen feature genes. Finally, the validation set was used to verify the feature genes, the GeneMANIA (http://www.genemania.org) database was used to perform protein-protein interaction networks analysis on the feature genes, and the SPIED3 database was used to find potential small molecule drugs. In this study, 187 genes associated with HCC were screened by using the "limma" software package and WGCNA. After that, 6 feature genes (AADAT, APOF, GPC3, LPA, MASP1, and NAT2) were selected by RandomForest, Absolute Shrinkage and Selection Operator, and support vector machine-recursive feature elimination machine learning algorithms. These genes are also significantly different on the external dataset and follow the same trend as the training set. Finally, our findings may provide new insights into targets for diagnosis, prevention, and treatment of HCC. AADAT, APOF, GPC3, LPA, MASP1, and NAT2 may be potential genes for the prediction, prevention, and treatment of liver cancer in the future.
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Affiliation(s)
- Jia-Hao Lv
- Key Laboratory of Basic and Application Research of Beiyao, Heilongjiang University of Chinese Medicine, Ministry of Education, Harbin, China
| | - A-Jiao Hou
- Key Laboratory of Basic and Application Research of Beiyao, Heilongjiang University of Chinese Medicine, Ministry of Education, Harbin, China
| | - Shi-Hao Zhang
- Key Laboratory of Basic and Application Research of Beiyao, Heilongjiang University of Chinese Medicine, Ministry of Education, Harbin, China
| | - Jiao-Jiao Dong
- Key Laboratory of Basic and Application Research of Beiyao, Heilongjiang University of Chinese Medicine, Ministry of Education, Harbin, China
| | - Hai-Xue Kuang
- Key Laboratory of Basic and Application Research of Beiyao, Heilongjiang University of Chinese Medicine, Ministry of Education, Harbin, China
| | - Liu Yang
- Key Laboratory of Basic and Application Research of Beiyao, Heilongjiang University of Chinese Medicine, Ministry of Education, Harbin, China
| | - Hai Jiang
- Key Laboratory of Basic and Application Research of Beiyao, Heilongjiang University of Chinese Medicine, Ministry of Education, Harbin, China
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Qin SS, Pan GQ, Meng QB, Liu JB, Tian ZY, Luan SJ. The causal relationship between metabolic factors, drinking, smoking and intrahepatic cholangiocarcinoma: a Mendelian randomization study. Front Oncol 2023; 13:1203685. [PMID: 37427123 PMCID: PMC10325926 DOI: 10.3389/fonc.2023.1203685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 06/05/2023] [Indexed: 07/11/2023] Open
Abstract
Background Intrahepatic cholangiocarcinoma (iCCA) is the second most common primary liver cancer. While multiple risk factors for iCCA have been established, metabolic diseases (obesity, diabetes, NAFLD, dyslipidemia, and hypertension) and other risk factors, including smoking and drinking, are still controversial due to their potential confounders. Here, Mendelian randomization (MR) analysis was performed to identify the causal relationship between them. Method In this study, we obtained GWAS data related to exposures from corresponding large genome-wide association studies. Summary-level statistical data for iCCA were obtained from the UK Biobank (UKB). We performed a univariable MR analysis to identify whether genetic evidence of exposure was significantly associated with iCCA risk. A multivariable MR analysis was conducted to estimate the independent effects of exposures on iCCA. Results Univariable and multivariable MR analysis based on the large GWAS data indicated that there is little evidence to support the genetic role of metabolic factors, smoking, drinking, and NAFLD in iCCA development (P >0.05). In contrast to most current studies, their impact on iCCA development, if any, might be smaller than we thought. The previous positive results might be due to the comorbidities between diseases and potentially unavoidable confounding factors. Conclusion In this MR study, we found no strong evidence to support causal associations between metabolic factors, NAFLD, smoking, drinking, and iCCA risk.
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Affiliation(s)
- Shan-shan Qin
- Department of Radiology, Qilu Hospital, Shandong University, Jinan, China
| | - Guo-qiang Pan
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan, China
| | - Qun-bo Meng
- Department of Orthopaedical Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jin-bo Liu
- Department of Orthopaedical Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Zi-yu Tian
- Department of Radiology, Qilu Hospital, Shandong University, Jinan, China
| | - Shou-jing Luan
- Department of Endocrinology, Weifang People’s Hospital, Weifang, China
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Pan GQ, Jiao Y, Meng GX, Dong ZR, Li T. The relationship between the serum lipid profile and hepatocellular carcinoma in east Asian population: A mendelian randomization study. Heliyon 2023; 9:e17126. [PMID: 37484252 PMCID: PMC10361312 DOI: 10.1016/j.heliyon.2023.e17126] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 06/07/2023] [Accepted: 06/08/2023] [Indexed: 07/25/2023] Open
Abstract
Background Although several studies have found that the serum lipid profile may be correlated with hepatocellular carcinoma (HCC), the causal relationships between the serum lipid profile and HCC have not been determined due to potential confounder. Here, Mendelian randomization (MR) analysis was performed to identify the relationship between the serum lipid profile and HCC in the East Asian population. Method Our study made a MR analysis with the validation of two data sets. We obtained genome-wide association study (GWAS) data related to the serum lipid profile from Asian Genetic Epidemiology Network (AGEN). Then, the data from a recent large GWAS of the East Asian ancestry in Japan (BioBank Japan, BBJ) were extracted. Summary-level statistical data for HCC were obtained from a large GWAS of the East Asian ancestry in Japan. Univariable MR analysis were performed to identify whether the genetic evidence of serum lipid profile was significantly associated with HCC risk. Multivariable MR analysis was conducted to estimate the independent effects of exposures on HCC. Results Univariable and multivariable MR analyses indicated that the serum lipid profile was not a risk factor for HCC incidence in either data set based on the East Asian population. Multivariable MR analysis revealed that the hazard ratios of the probability of HCC in AGEN were 1.134 (95% confidence interval (CI), 0.903-1.424) for TG, 1.010 (95% CI: 0.824-1.237) for HDL-C, 0.974 (95% CI: 0.746-1.271) for TC, 0.918 (95% CI: 0.734-1.147) for LDL-C, while the results in BBJ were also non-significant: 1.111 (95% CI: 0.869-1.419) for TG, 0.957 (95% CI: 0.790-1.158) for HDL-C, 0.917 (95% CI: 0.643-1.308) for TC, 0.932 (95% CI: 0.699-1.243) for LDL-C. Conclusion Our MR study with the validation of two data sets found no strong evidence to support causal associations between the serum lipid profile and HCC risk.
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Affiliation(s)
- Guo-Qiang Pan
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan, China
| | - Yan Jiao
- Department of Hepatobiliary and Pancreatic Surgery, The First Hospital of Jilin University, Changchun, China
| | - Guang-Xiao Meng
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan, China
| | - Zhao-Ru Dong
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan, China
| | - Tao Li
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan, China
- Department of Hepatobiliary Surgery, The Second Hospital of Shandong University, Jinan, 250012, China
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