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Abbasi AF, Asim MN, Ahmed S, Vollmer S, Dengel A. Survival prediction landscape: an in-depth systematic literature review on activities, methods, tools, diseases, and databases. Front Artif Intell 2024; 7:1428501. [PMID: 39021434 PMCID: PMC11252047 DOI: 10.3389/frai.2024.1428501] [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: 05/07/2024] [Accepted: 06/12/2024] [Indexed: 07/20/2024] Open
Abstract
Survival prediction integrates patient-specific molecular information and clinical signatures to forecast the anticipated time of an event, such as recurrence, death, or disease progression. Survival prediction proves valuable in guiding treatment decisions, optimizing resource allocation, and interventions of precision medicine. The wide range of diseases, the existence of various variants within the same disease, and the reliance on available data necessitate disease-specific computational survival predictors. The widespread adoption of artificial intelligence (AI) methods in crafting survival predictors has undoubtedly revolutionized this field. However, the ever-increasing demand for more sophisticated and effective prediction models necessitates the continued creation of innovative advancements. To catalyze these advancements, it is crucial to bring existing survival predictors knowledge and insights into a centralized platform. The paper in hand thoroughly examines 23 existing review studies and provides a concise overview of their scope and limitations. Focusing on a comprehensive set of 90 most recent survival predictors across 44 diverse diseases, it delves into insights of diverse types of methods that are used in the development of disease-specific predictors. This exhaustive analysis encompasses the utilized data modalities along with a detailed analysis of subsets of clinical features, feature engineering methods, and the specific statistical, machine or deep learning approaches that have been employed. It also provides insights about survival prediction data sources, open-source predictors, and survival prediction frameworks.
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Affiliation(s)
- Ahtisham Fazeel Abbasi
- Department of Computer Science, Rhineland-Palatinate Technical University of Kaiserslautern-Landau, Kaiserslautern, Germany
- Smart Data & Knowledge Services, Deutsches Forschungszentrum für Künstliche Intelligenz (DFKI), Kaiserslautern, Germany
| | - Muhammad Nabeel Asim
- Smart Data & Knowledge Services, Deutsches Forschungszentrum für Künstliche Intelligenz (DFKI), Kaiserslautern, Germany
| | - Sheraz Ahmed
- Smart Data & Knowledge Services, Deutsches Forschungszentrum für Künstliche Intelligenz (DFKI), Kaiserslautern, Germany
| | - Sebastian Vollmer
- Department of Computer Science, Rhineland-Palatinate Technical University of Kaiserslautern-Landau, Kaiserslautern, Germany
- Smart Data & Knowledge Services, Deutsches Forschungszentrum für Künstliche Intelligenz (DFKI), Kaiserslautern, Germany
| | - Andreas Dengel
- Department of Computer Science, Rhineland-Palatinate Technical University of Kaiserslautern-Landau, Kaiserslautern, Germany
- Smart Data & Knowledge Services, Deutsches Forschungszentrum für Künstliche Intelligenz (DFKI), Kaiserslautern, Germany
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Zhan F, Guo Y, He L. A novel defined programmed cell death related gene signature for predicting the prognosis of serous ovarian cancer. J Ovarian Res 2024; 17:92. [PMID: 38685095 PMCID: PMC11057167 DOI: 10.1186/s13048-024-01419-y] [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: 12/07/2023] [Accepted: 04/19/2024] [Indexed: 05/02/2024] Open
Abstract
PURPOSE This study aims to explore the contribution of differentially expressed programmed cell death genes (DEPCDGs) to the heterogeneity of serous ovarian cancer (SOC) through single-cell RNA sequencing (scRNA-seq) and assess their potential as predictors for clinical prognosis. METHODS SOC scRNA-seq data were extracted from the Gene Expression Omnibus database, and the principal component analysis was used for cell clustering. Bulk RNA-seq data were employed to analyze SOC-associated immune cell subsets key genes. CIBERSORT and single-sample gene set enrichment analysis (ssGSEA) were utilized to calculate immune cell scores. Prognostic models and nomograms were developed through univariate and multivariate Cox analyses. RESULTS Our analysis revealed that 48 DEPCDGs are significantly correlated with apoptotic signaling and oxidative stress pathways and identified seven key DEPCDGs (CASP3, GADD45B, GNA15, GZMB, IL1B, ISG20, and RHOB) through survival analysis. Furthermore, eight distinct cell subtypes were characterized using scRNA-seq. It was found that G protein subunit alpha 15 (GNA15) exhibited low expression across these subtypes and a strong association with immune cells. Based on the DEGs identified by the GNA15 high- and low-expression groups, a prognostic model comprising eight genes with significant prognostic value was constructed, effectively predicting patient overall survival. Additionally, a nomogram incorporating the RS signature, age, grade, and stage was developed and validated using two large SOC datasets. CONCLUSION GNA15 emerged as an independent and excellent prognostic marker for SOC patients. This study provides valuable insights into the prognostic potential of DEPCDGs in SOC, presenting new avenues for personalized treatment strategies.
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Affiliation(s)
- Feng Zhan
- College of Engineering, Fujian Jiangxia University, Fuzhou, Fujian, 350108, China
- School of Electronic Information Engineering, Taiyuan University of Science and Technology, Taiyuan, Shanxi, 030024, China
| | - Yina Guo
- School of Electronic Information Engineering, Taiyuan University of Science and Technology, Taiyuan, Shanxi, 030024, China
| | - Lidan He
- Department of Obstetrics and Gynecology, the First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, 350004, China.
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Wu X, Zhang W, Zhao X, Zhang L, Xu M, Hao Y, Xiao J, Zhang B, Li J, Kraft P, Smoller JW, Jiang X. Investigating the relationship between depression and breast cancer: observational and genetic analyses. BMC Med 2023; 21:170. [PMID: 37143087 PMCID: PMC10161423 DOI: 10.1186/s12916-023-02876-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 04/20/2023] [Indexed: 05/06/2023] Open
Abstract
BACKGROUND Both depression and breast cancer (BC) contribute to a substantial global burden of morbidity and mortality among women, and previous studies have observed a potential depression-BC link. We aimed to comprehensively characterize the phenotypic and genetic relationships between depression and BC. METHODS We first evaluated phenotypic association using longitudinal follow-up data from the UK Biobank (N = 250,294). We then investigated genetic relationships leveraging summary statistics from the hitherto largest genome-wide association study of European individuals conducted for depression (N = 500,199), BC (N = 247,173), and its subtypes based on the status of estrogen receptor (ER + : N = 175,475; ER - : N = 127,442). RESULTS Observational analysis suggested an increased hazard of BC in depression patients (HR = 1.10, 95%CIs = 0.95-1.26). A positive genetic correlation between depression and overall BC was observed ([Formula: see text] = 0.08, P = 3.00 × 10-4), consistent across ER + ([Formula: see text] = 0.06, P = 6.30 × 10-3) and ER - subtypes ([Formula: see text] = 0.08, P = 7.20 × 10-3). Several specific genomic regions showed evidence of local genetic correlation, including one locus at 9q31.2, and four loci at, or close, to 6p22.1. Cross-trait meta-analysis identified 17 pleiotropic loci shared between depression and BC. TWAS analysis revealed five shared genes. Bi-directional Mendelian randomization suggested risk of depression was causally associated with risk of overall BC (OR = 1.12, 95%Cis = 1.04-1.19), but risk of BC was not causally associated with risk of depression. CONCLUSIONS Our work demonstrates a shared genetic basis, pleiotropic loci, and a putative causal relationship between depression and BC, highlighting a biological link underlying the observed phenotypic relationship; these findings may provide important implications for future studies aimed reducing BC risk.
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Affiliation(s)
- Xueyao Wu
- Department of Epidemiology and Health Statistics, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16 Ren Min Nan Lu, Chengdu, Sichuan, 610041, People's Republic of China
| | - Wenqiang Zhang
- Department of Epidemiology and Health Statistics, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16 Ren Min Nan Lu, Chengdu, Sichuan, 610041, People's Republic of China
| | - Xunying Zhao
- Department of Epidemiology and Health Statistics, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16 Ren Min Nan Lu, Chengdu, Sichuan, 610041, People's Republic of China
| | - Li Zhang
- Department of Epidemiology and Health Statistics, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16 Ren Min Nan Lu, Chengdu, Sichuan, 610041, People's Republic of China
| | - Minghan Xu
- Department of Epidemiology and Health Statistics, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16 Ren Min Nan Lu, Chengdu, Sichuan, 610041, People's Republic of China
| | - Yu Hao
- Department of Epidemiology and Health Statistics, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16 Ren Min Nan Lu, Chengdu, Sichuan, 610041, People's Republic of China
| | - Jinyu Xiao
- Department of Epidemiology and Health Statistics, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16 Ren Min Nan Lu, Chengdu, Sichuan, 610041, People's Republic of China
| | - Ben Zhang
- Department of Epidemiology and Health Statistics, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16 Ren Min Nan Lu, Chengdu, Sichuan, 610041, People's Republic of China
| | - Jiayuan Li
- Department of Epidemiology and Health Statistics, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16 Ren Min Nan Lu, Chengdu, Sichuan, 610041, People's Republic of China
| | - Peter Kraft
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jordan W Smoller
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, and Department of Psychiatry, Massachusetts General Hospital, MA, Boston, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, MA, Cambridge, USA
| | - Xia Jiang
- Department of Epidemiology and Health Statistics, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16 Ren Min Nan Lu, Chengdu, Sichuan, 610041, People's Republic of China.
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Solna, Sweden.
- Department of Nutrition and Food Hygiene, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China.
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The Modifying Effect of Obesity on the Association of Matrix Metalloproteinase Gene Polymorphisms with Breast Cancer Risk. Biomedicines 2022; 10:biomedicines10102617. [PMID: 36289879 PMCID: PMC9599943 DOI: 10.3390/biomedicines10102617] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/10/2022] [Accepted: 10/13/2022] [Indexed: 11/17/2022] Open
Abstract
Objective: We investigated the possible modifying effect of obesity on the association of matrix metalloproteinase (MMP) gene polymorphisms with breast cancer (BC) risk. Methods: A total of 1104 women divided into two groups according to their body mass index (BMI): BMI ≥ 30 (119 BC, and 190 control) and BMI < 30 (239 BC, and 556 control) were genotyped for specially selected (according to their association with BC in the previous study) 10 single-nucleotide polymorphisms (SNP) of MMP1, 2, 3, 8, and 9 genes. Logistic regression association analysis was performed in each studied group of women (with/without obesity). Functional annotation of BC-correlated MMP polymorphic variants was analyzed by in silico bioinformatics. Results: We observed significant differences in the involvement of MMP SNPs in BC in obese and non-obese women. Polymorphic loci MMP9 (c.836 A > G (rs17576) and c. 1721 C > G (rs2250889)) were BC-protective factors in obese women (OR 0.71, allelic model, and OR 0.55, additive model, respectively). Genotypes TT MMP2 (c.-1306 C > T,rs243865) and AA MMP9 (c. 1331-163 G > A,rs3787268) determined BC susceptibility in non-obese women (OR 0.31, and OR 2.36, respectively). We found in silico substantial multidirectional influences on gene expression in adipose tissue BC-related polymorphic loci: BC risk allele A-rs3787268 in non-obese women is associated with low expression NEURL2, PLTP, RP3-337O18.9, SPATA25, and ZSWIM1, whereas BC risk allele A-rs17576 in obese women is associated with high expression in the same genes in visceral and/or subcutaneous adipose. Conclusions: our study indicated that obesity has a significant modifying effect on the association of MMP genes with BC risk in postmenopausal women.
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Zhang H, Qu M, Sun C, Wang Y, Li T, Xu W, Sun Z, Zhang X, Guo K, Chen W, Sun M, Miao C. Association of Mu-Opioid Receptor Expression With Long-Term Survival and Perineural Nerve Invasion in Patients Undergoing Surgery for Ovarian Cancer. Front Oncol 2022; 12:927262. [PMID: 35875149 PMCID: PMC9302566 DOI: 10.3389/fonc.2022.927262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 05/27/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundOpioids are widely used during primary debulking surgery (PDS) for ovarian cancers, and a high mu-opioid receptor (MOR) expression predicts worse cancer outcomes. However, the impact of MOR expression on survival outcomes in ovarian cancers is still not clear.MethodsA retrospective cohort study was conducted in patients who underwent PDS in ovarian cancer patients. MOR expression was measured in tumor and normal tissue. Primary outcomes were overall survival (OS) and disease-free survival (DFS). Secondary outcomes included perineural invasion (PNI), intraoperative sufentanil consumption, length of stay (LOS), and verbal numerical rating scale (VNRS) on postoperative day 1 (POD1), POD3, and POD5.ResultsAfter propensity score matching, a total of 366 patients were finally enrolled in this study. There were no significant differences in OS rates in patients with high versus low levels of MOR (1-year OS: 82.9% versus 83.3%, 3-year: 57.8% versus 59.1%, 5-year: 22.4% versus 23.1%,respectively) in the ovarian cancers. There were no significant differences in DFS between the groups. Intraoperative sufentanil consumption was higher in the MOR high-expression group compared with the MOR low-expression group. Tumors expressing high levels of MOR showed higher rates of PNI. VNRS in the MOR high-expression group was higher on POD1.ConclusionMOR is not an independent predictor of worse survival in ovarian cancers but is associated with high rates of perineural invasion.
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Affiliation(s)
- Hao Zhang
- Department of Anesthesiology, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Perioperative Stress and Protection, Shanghai, China
| | - Mengdi Qu
- Department of Anesthesiology, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Perioperative Stress and Protection, Shanghai, China
| | - Caihong Sun
- Department of Anesthesiology, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Perioperative Stress and Protection, Shanghai, China
| | - Yanghanzhao Wang
- Department of Anesthesiology, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Perioperative Stress and Protection, Shanghai, China
| | - Ting Li
- Department of Anesthesiology, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Perioperative Stress and Protection, Shanghai, China
| | - Wei Xu
- Department of Anesthesiology, Jinshan Hospital, Fudan University, Shanghai, China
| | - Zhirong Sun
- Department of Anesthesiology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiaoguang Zhang
- Department of Anesthesiology, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Perioperative Stress and Protection, Shanghai, China
- Department of Anesthesiology, Jinshan Hospital, Fudan University, Shanghai, China
| | - Kefang Guo
- Department of Anesthesiology, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Perioperative Stress and Protection, Shanghai, China
- *Correspondence: Changhong Miao, ; Wankun Chen, ; Kefang Guo, ; Minli Sun,
| | - Wankun Chen
- Department of Anesthesiology, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Perioperative Stress and Protection, Shanghai, China
- *Correspondence: Changhong Miao, ; Wankun Chen, ; Kefang Guo, ; Minli Sun,
| | - Minli Sun
- Department of Anesthesiology, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Perioperative Stress and Protection, Shanghai, China
- *Correspondence: Changhong Miao, ; Wankun Chen, ; Kefang Guo, ; Minli Sun,
| | - Changhong Miao
- Department of Anesthesiology, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Perioperative Stress and Protection, Shanghai, China
- Department of Anesthesiology, Jinshan Hospital, Fudan University, Shanghai, China
- *Correspondence: Changhong Miao, ; Wankun Chen, ; Kefang Guo, ; Minli Sun,
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