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Song L, Qi J, Zhao J, Bai S, Wu Q, Xu R. Diagnostic value of CA125, HE4, and systemic immune-inflammation index in the preoperative investigation of ovarian masses. Medicine (Baltimore) 2023; 102:e35240. [PMID: 37713838 PMCID: PMC10508492 DOI: 10.1097/md.0000000000035240] [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: 07/03/2023] [Accepted: 08/24/2023] [Indexed: 09/17/2023] Open
Abstract
This study aimed to ascertain the diagnostic accuracy of CA125, HE4, systemic immune-inflammation index (SII), fibrinogen-to-albumin ratio (FAR), prognostic nutritional index (PNI), and their combination for ovarian cancer (OC) to discover an optimal combined diagnostic index for early diagnosis of OC. A thorough investigation was conducted to ascertain the correlation between these markers and the pathological characteristics of OC, thereby providing a foundation for early identification and treatment of this disorder. One hundred seventy patients with documented OC and benign ovarian tumors (BOTs) treated at Hebei General Hospital between January 2019 and December 2022 were included in this retrospective study. Data analysis was conducted using IBM SPSS Statistics version V26.0, MedCalc Statistical Software version 19.4.0, and the R Environment for Statistical Computing software (R Foundation for Statistical Computing). Isolated CA125 showed the best application value for differentiating benign ovarian tumors from OC when the defined variables were compared separately. The combination of CA125, HE4, FAR, SII, and PNI displayed a greater area under the operating characteristic curve curve than any one of them or other combinations of the 5 variables. Compared to CA125 alone, the combination of CA125, HE4, FAR, SII, and PNI showed a slight gain in sensitivity (83.91%), negative predictive value (83.91%), accuracy (85.88%), and a decrease in negative likelihood ratio (0.180%). Higher preoperative CA125, HE4, SII, and FAR levels, and lower PNI levels predicted a higher probability of advanced OC progression and lymph node metastasis. FAR has better application value than other inflammation-related markers (PNI and SII). This study suggests that preoperative serum SII, PNI, and FAR may be clinically valuable markers in patients with OC. FAR has better application value than other inflammation-related markers (PNI and SII). As we delve deeper into the inflammatory mechanisms associated with tumors, we may discover more effective combinations of tumor and inflammatory biomarkers.
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Affiliation(s)
- Liyun Song
- Department of Gynecology, Hebei General Hospital, Shijiazhuang, China
| | - Jie Qi
- Department of Gynecology, Hebei General Hospital, Shijiazhuang, China
| | - Jing Zhao
- Department of Gynecology, Hebei General Hospital, Shijiazhuang, China
| | - Suning Bai
- Department of Gynecology, Hebei General Hospital, Shijiazhuang, China
| | - Qi Wu
- Department of Gynecology, Hebei General Hospital, Shijiazhuang, China
| | - Ren Xu
- Department of Gynecology, Hebei General Hospital, Shijiazhuang, China
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Zhu S, Bao H, Zhang MC, Liu H, Wang Y, Lin C, Zhao X, Liu SL. KAZN as a diagnostic marker in ovarian cancer: a comprehensive analysis based on microarray, mRNA-sequencing, and methylation data. BMC Cancer 2022; 22:662. [PMID: 35710397 PMCID: PMC9204993 DOI: 10.1186/s12885-022-09747-2] [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: 05/12/2021] [Accepted: 06/09/2022] [Indexed: 11/29/2022] Open
Abstract
Background Ovarian cancer (OC) is among the deadliest malignancies in women and the lack of appropriate markers for early diagnosis leads to poor prognosis in most cases. Previous studies have shown that KAZN is involved in multiple biological processes during development, such as cell proliferation, differentiation, and apoptosis, so defects or aberrant expression of KAZN might cause queer cell behaviors such as malignancy. Here we evaluated the KAZN expression and methylation levels for possible use as an early diagnosis marker for OC. Methods We used data from Gene Expression Omnibus (GEO) microarrays, The Cancer Genome Atlas (TCGA), and Clinical Proteomic Tumor Analysis Consortium (CPTAC) to investigate the correlations between KAZN expression and clinical characteristics of OC by comparing methylation levels of normal and OC samples. The relationships among differentially methylated sites in the KAZN gene, corresponding KAZN mRNA expression levels and prognosis were analyzed. Results KAZN was up-regulated in ovarian epithelial tumors and the expression of KAZN was correlated with the patients’ survival time. KAZN CpG site cg17657618 was positively correlated with the expression of mRNA and the methylation levels were significantly differential between the group of stage “I and II” and the group of stage “III and IV”. This study also presents a new method to classify tumor and normal tissue in OC using DNA methylation pattern in the KAZN gene body region. Conclusions KAZN was involved in ovarian cancer pathogenesis. Our results demonstrate a new direction for ovarian cancer research and provide a potential diagnostic biomarker as well as a novel therapeutic target for clinical application. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-09747-2.
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Affiliation(s)
- Songling Zhu
- Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), College of Pharmacy, Harbin Medical University, Harbin, China.,HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Hongxia Bao
- Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), College of Pharmacy, Harbin Medical University, Harbin, China.,HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Meng-Chun Zhang
- Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), College of Pharmacy, Harbin Medical University, Harbin, China.,HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Huidi Liu
- Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), College of Pharmacy, Harbin Medical University, Harbin, China.,HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Yao Wang
- Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), College of Pharmacy, Harbin Medical University, Harbin, China.,HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Caiji Lin
- Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), College of Pharmacy, Harbin Medical University, Harbin, China.,HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Xingjuan Zhao
- Physical Examination Center, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Shu-Lin Liu
- Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), College of Pharmacy, Harbin Medical University, Harbin, China. .,HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China. .,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China. .,Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Canada.
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Konigsberg IR, Barnes B, Campbell M, Davidson E, Zhen Y, Pallisard O, Boorgula MP, Cox C, Nandy D, Seal S, Crooks K, Sticca E, Harrison GF, Hopkinson A, Vest A, Arnold CG, Kahn MG, Kao DP, Peterson BR, Wicks SJ, Ghosh D, Horvath S, Zhou W, Mathias RA, Norman PJ, Porecha R, Yang IV, Gignoux CR, Monte AA, Taye A, Barnes KC. Host methylation predicts SARS-CoV-2 infection and clinical outcome. COMMUNICATIONS MEDICINE 2021; 1:42. [PMID: 35072167 PMCID: PMC8767772 DOI: 10.1038/s43856-021-00042-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 09/24/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Since the onset of the SARS-CoV-2 pandemic, most clinical testing has focused on RT-PCR1. Host epigenome manipulation post coronavirus infection2-4 suggests that DNA methylation signatures may differentiate patients with SARS-CoV-2 infection from uninfected individuals, and help predict COVID-19 disease severity, even at initial presentation. METHODS We customized Illumina's Infinium MethylationEPIC array to enhance immune response detection and profiled peripheral blood samples from 164 COVID-19 patients with longitudinal measurements of disease severity and 296 patient controls. RESULTS Epigenome-wide association analysis revealed 13,033 genome-wide significant methylation sites for case-vs-control status. Genes and pathways involved in interferon signaling and viral response were significantly enriched among differentially methylated sites. We observe highly significant associations at genes previously reported in genetic association studies (e.g. IRF7, OAS1). Using machine learning techniques, models built using sparse regression yielded highly predictive findings: cross-validated best fit AUC was 93.6% for case-vs-control status, and 79.1%, 80.8%, and 84.4% for hospitalization, ICU admission, and progression to death, respectively. CONCLUSIONS In summary, the strong COVID-19-specific epigenetic signature in peripheral blood driven by key immune-related pathways related to infection status, disease severity, and clinical deterioration provides insights useful for diagnosis and prognosis of patients with viral infections.
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Affiliation(s)
- Iain R. Konigsberg
- School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO USA
| | | | - Monica Campbell
- School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO USA
| | - Elizabeth Davidson
- School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO USA
| | - Yingfei Zhen
- School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO USA
| | - Olivia Pallisard
- School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO USA
| | | | - Corey Cox
- School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO USA
| | - Debmalya Nandy
- Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO USA
| | - Souvik Seal
- Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO USA
| | - Kristy Crooks
- School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO USA
| | - Evan Sticca
- School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO USA
| | - Genelle F. Harrison
- School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO USA
| | - Andrew Hopkinson
- School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO USA
| | - Alexis Vest
- School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO USA
| | - Cosby G. Arnold
- School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO USA
| | - Michael G. Kahn
- School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO USA
| | - David P. Kao
- School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO USA
| | - Brett R. Peterson
- School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO USA
| | - Stephen J. Wicks
- School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO USA
| | - Debashis Ghosh
- Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO USA
| | - Steve Horvath
- University of California Los Angeles, Los Angeles, CA USA
| | - Wanding Zhou
- The Children’s Hospital of Philadelphia, Philadelphia, PA USA
| | - Rasika A. Mathias
- School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO USA
- Johns Hopkins University, Baltimore, MD USA
| | - Paul J. Norman
- School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO USA
| | | | - Ivana V. Yang
- School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO USA
| | | | - Andrew A. Monte
- School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO USA
| | | | - Kathleen C. Barnes
- School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO USA
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Kosvyra A, Ntzioni E, Chouvarda I. Network analysis with biological data of cancer patients: A scoping review. J Biomed Inform 2021; 120:103873. [PMID: 34298154 DOI: 10.1016/j.jbi.2021.103873] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 06/30/2021] [Accepted: 07/18/2021] [Indexed: 12/25/2022]
Abstract
BACKGROUND & OBJECTIVE Network Analysis (NA) is a mathematical method that allows exploring relations between units and representing them as a graph. Although NA was initially related to social sciences, the past two decades was introduced in Bioinformatics. The recent growth of the networks' use in biological data analysis reveals the need to further investigate this area. In this work, we attempt to identify the use of NA with biological data, and specifically: (a) what types of data are used and whether they are integrated or not, (b) what is the purpose of this analysis, predictive or descriptive, and (c) the outcome of such analyses, specifically in cancer diseases. METHODS & MATERIALS The literature review was conducted on two databases, PubMed & IEEE, and was restricted to journal articles of the last decade (January 2010 - December 2019). At a first level, all articles were screened by title and abstract, and at a second level the screening was conducted by reading the full text article, following the predefined inclusion & exclusion criteria leading to 131 articles of interest. A table was created with the information of interest and was used for the classification of the articles. The articles were initially classified to analysis studies and studies that propose a new algorithm or methodology. Each one of these categories was further screened by the following clustering criteria: (a) data used, (b) study purpose, (c) study outcome. Specifically for the studies proposing a new algorithm, the novelty presented in each one was detected. RESULTS & Conclusions: In the past five years researchers are focusing on creating new algorithms and methodologies to enhance this field. The articles' classification revealed that only 25% of the analyses are integrating multi-omics data, although 50% of the new algorithms developed follow this integrative direction. Moreover, only 20% of the analyses and 10% of the newly developed methodologies have a predictive purpose. Regarding the result of the works reviewed, 75% of the studies focus on identifying, prognostic or not, gene signatures. Concluding, this review revealed the need for deploying predictive and multi-omics integrative algorithms and methodologies that can be used to enhance cancer diagnosis, prognosis and treatment.
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Affiliation(s)
- A Kosvyra
- Laboratory of Computing, Medical Informatics and Biomedical Imaging Technologies, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece.
| | - E Ntzioni
- Laboratory of Computing, Medical Informatics and Biomedical Imaging Technologies, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - I Chouvarda
- Laboratory of Computing, Medical Informatics and Biomedical Imaging Technologies, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
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Li H, Jiang F, Du Y, Li N, Chen Z, Cai H, Guo Y, Hong G. Identification of differential DNA methylation alterations of ovarian cancer in peripheral whole blood based on within-sample relative methylation orderings. Epigenetics 2021; 17:314-326. [PMID: 33749504 DOI: 10.1080/15592294.2021.1900029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Leukocyte cell proportion changes affect the detection of cancer-associated aberrant DNA methylation alterations in peripheral blood samples. We aimed to detect cellular DNA methylation changes in ovarian cancer (OVC) blood samples avoiding the above-mentioned cell-composition effects. Based on the within-sample relative methylation orderings (RMOs) of CpG loci in leukocyte subtypes, we developed the Ref-RMO method to detect aberrant methylation alterations from OVC blood samples. Stable CpG pairs with consistent RMOs in different leukocyte subtypes were determined, more than 99% of which retained their RMO patterns in peripheral whole blood (PWB) in independent datasets. Based on the stable CpG pairs, significantly reversed CpG pairs were detected from OVC PWB samples, which were relative to clinical information such as age, subtype, grade, stage, or CA125 level. Results showed 439 CpG loci were determined to be significant differential DNA methylations between OVC and healthy blood samples. They were mainly enriched in KEGG pathways, such as cytokine-cytokine receptor interaction, apoptosis, proteoglycans in cancer, and immune-associated Gene Ontology terms. STRING analysis showed that they tended to have functional interactions with cancer-associated genes recorded in the COSMIC database. Leukocyte cellular differential DNA methylations could be identified by the proposed RMO-based method from OVC PWB samples, which were cancer-associated aberrant signals against cell-composition effects.
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Affiliation(s)
- Hongdong Li
- School of Medical Information Engineering, Gannan Medical University, Ganzhou, China
| | - Fengle Jiang
- Department of Bioinformatics, Fujian Medical University, Fuzhou, China
| | - Yuhui Du
- School of Medical Information Engineering, Gannan Medical University, Ganzhou, China
| | - Na Li
- School of Medical Information Engineering, Gannan Medical University, Ganzhou, China
| | - Zhihong Chen
- School of Medical Information Engineering, Gannan Medical University, Ganzhou, China
| | - Hao Cai
- Medical Big Data and Bioinformatics Research Centre, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - You Guo
- Medical Big Data and Bioinformatics Research Centre, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Guini Hong
- School of Medical Information Engineering, Gannan Medical University, Ganzhou, China.,Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Gannan Medical University, Ganzhou, PR China
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