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Ziemann M, Abeysooriya M, Bora A, Lamon S, Kasu MS, Norris MW, Wong YT, Craig JM. Direction-aware functional class scoring enrichment analysis of infinium DNA methylation data. Epigenetics 2024; 19:2375022. [PMID: 38967555 PMCID: PMC11229754 DOI: 10.1080/15592294.2024.2375022] [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: 02/22/2024] [Accepted: 06/26/2024] [Indexed: 07/06/2024] Open
Abstract
Infinium Methylation BeadChip arrays remain one of the most popular platforms for epigenome-wide association studies, but tools for downstream pathway analysis have their limitations. Functional class scoring (FCS) is a group of pathway enrichment techniques that involve the ranking of genes and evaluation of their collective regulation in biological systems, but the implementations described for Infinium methylation array data do not retain direction information, which is important for mechanistic understanding of genomic regulation. Here, we evaluate several candidate FCS methods that retain directional information. According to simulation results, the best-performing method involves the mean aggregation of probe limma t-statistics by gene followed by a rank-ANOVA enrichment test using the mitch package. This method, which we call 'LAM,' outperformed an existing over-representation analysis method in simulations, and showed higher sensitivity and robustness in an analysis of real lung tumour-normal paired datasets. Using matched RNA-seq data, we examine the relationship of methylation differences at promoters and gene bodies with RNA expression at the level of pathways in lung cancer. To demonstrate the utility of our approach, we apply it to three other contexts where public data were available. First, we examine the differential pathway methylation associated with chronological age. Second, we investigate pathway methylation differences in infants conceived with in vitro fertilization. Lastly, we analyse differential pathway methylation in 19 disease states, identifying hundreds of novel associations. These results show LAM is a powerful method for the detection of differential pathway methylation complementing existing methods. A reproducible vignette is provided to illustrate how to implement this method.
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Affiliation(s)
- Mark Ziemann
- Bioinformatics Working Group, Burnet Institute, Melbourne, Australia
- School of Life and Environmental Sciences, Deakin University, Geelong, Australia
| | - Mandhri Abeysooriya
- School of Life and Environmental Sciences, Deakin University, Geelong, Australia
- School of Exercise and Nutrition Sciences, Institute for Physical Activity and Nutrition, Deakin University, Geelong, Australia
| | - Anusuiya Bora
- Bioinformatics Working Group, Burnet Institute, Melbourne, Australia
- School of Life and Environmental Sciences, Deakin University, Geelong, Australia
| | - Séverine Lamon
- School of Exercise and Nutrition Sciences, Institute for Physical Activity and Nutrition, Deakin University, Geelong, Australia
| | - Mary Sravya Kasu
- School of Life and Environmental Sciences, Deakin University, Geelong, Australia
| | - Mitchell W. Norris
- School of Life and Environmental Sciences, Deakin University, Geelong, Australia
| | - Yen Ting Wong
- School of Medicine, Deakin University, Geelong, Australia
- Murdoch Children’s Research Institute, Melbourne, Australia
| | - Jeffrey M. Craig
- School of Medicine, Deakin University, Geelong, Australia
- Murdoch Children’s Research Institute, Melbourne, Australia
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Zamuner FT, Ramos-López A, García-Negrón A, Purcell-Wiltz A, Cortés-Ortiz A, Cuevas AR, Gosala K, Winkler E, Sidransky D, Guerrero-Preston R. Evaluation of silica spin‑column and magnetic bead formats for rapid DNA methylation analysis in clinical and point‑of‑care settings. Biomed Rep 2024; 21:112. [PMID: 38912171 PMCID: PMC11190640 DOI: 10.3892/br.2024.1800] [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: 01/17/2024] [Accepted: 05/20/2024] [Indexed: 06/25/2024] Open
Abstract
Late-stage cancers lack effective treatment, underscoring the need for early diagnosis to improve prognosis and decrease mortality rates. Molecular markers, such as DNA methylation, offer promise in early cancer detection. The present study compared commercial kits for analyzing DNA from cervical liquid cytology samples in cancer screening. Rapid bisulfite conversion kits using silica spin-columns and magnetic beads were assessed against standard DNA extraction and bisulfite conversion methods for profiling DNA methylation using quantitative methylation-specific PCR. β-actin amplification indicated the suitability of small sample volumes for methylation studies using either the pellet or supernatant (cell-free DNA) parts. Comparison of Bisulfite Conversion Kit-Whole Cell (Abcam), Methylamp Bisulfite Modification (Epigentek), EpiTect Fast LyseAll Bisulfite Kit (Qiagen GmbH) and EZ DNA Methylation-Direct Kit (Zymo Research Corp.) showed no significant differences in β-actin cycle threshold values. EZ-96 DNA Methylation-Lightning MagPrep (Zymo Research Corp.), a hybrid kit in a 96-well plate format, exhibited swift turnaround time and similar amplification efficiency. Automation with magnetic bead kits increased throughput without compromising amplification efficiency in open PCR systems. Cost analysis favored direct kits over the gold standard manual protocol. This comparison aids in selecting cost-effective DNA methylation diagnostic tests. The present study confirmed comparable kit performance in methylation-based analysis, highlighting the adequacy of cytology samples and the potential of bodily fluids as alternatives for liquid biopsy.
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Affiliation(s)
- Fernando T. Zamuner
- Department of Otolaryngology and Head and Neck Surgery, Head and Neck Cancer Research Laboratory, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Ashley Ramos-López
- LifeGene-Biomarks, Research and Development Unit, Toa Baja 00949, Puerto Rico
| | | | - Ana Purcell-Wiltz
- LifeGene-Biomarks, Research and Development Unit, Toa Baja 00949, Puerto Rico
- Department of Medicine, San Juan Bautista School of Medicine, Caguas 00725, Puerto Rico
| | - Andrea Cortés-Ortiz
- LifeGene-Biomarks, Research and Development Unit, Toa Baja 00949, Puerto Rico
- Department of Medicine, San Juan Bautista School of Medicine, Caguas 00725, Puerto Rico
| | - Aniris Román Cuevas
- LifeGene-Biomarks, Research and Development Unit, Toa Baja 00949, Puerto Rico
- Department of Biology, University of Puerto Rico, Río Piedras 00931, Puerto Rico
| | - Keerthana Gosala
- Department of Otolaryngology and Head and Neck Surgery, Head and Neck Cancer Research Laboratory, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Eli Winkler
- Department of Otolaryngology and Head and Neck Surgery, Head and Neck Cancer Research Laboratory, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- New York University Langone Health, New York, NY 10016, USA
| | - David Sidransky
- Department of Otolaryngology and Head and Neck Surgery, Head and Neck Cancer Research Laboratory, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Rafael Guerrero-Preston
- LifeGene-Biomarks, Research and Development Unit, Toa Baja 00949, Puerto Rico
- LifeGene-Biomarks, FastForward Innovation Hub, Baltimore, MD 21205, USA
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3
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Pan B, Liu C, Su J, Xia C. Activation of AMPK inhibits cervical cancer growth by hyperacetylation of H3K9 through PCAF. Cell Commun Signal 2024; 22:306. [PMID: 38831454 PMCID: PMC11145780 DOI: 10.1186/s12964-024-01687-7] [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: 12/19/2023] [Accepted: 05/28/2024] [Indexed: 06/05/2024] Open
Abstract
BACKGROUND Dysregulation in histone acetylation, a significant epigenetic alteration closely associated with major pathologies including cancer, promotes tumorigenesis, inactivating tumor-suppressor genes and activating oncogenic pathways. AMP-activated protein kinase (AMPK) is a cellular energy sensor that regulates a multitude of biological processes. Although a number of studies have identified the mechanisms by which AMPK regulates cancer growth, the underlying epigenetic mechanisms remain unknown. METHODS The impact of metformin, an AMPK activator, on cervical cancer was evaluated through assessments of cell viability, tumor xenograft model, pan-acetylation analysis, and the role of the AMPK-PCAF-H3K9ac signaling pathway. Using label-free quantitative acetylproteomics and chromatin immunoprecipitation-sequencing (ChIP) technology, the activation of AMPK-induced H3K9 acetylation was further investigated. RESULTS In this study, we found that metformin, acting as an AMPK agonist, activates AMPK, thereby inhibiting the proliferation of cervical cancer both in vitro and in vivo. Mechanistically, AMPK activation induces H3K9 acetylation at epigenetic level, leading to chromatin remodeling in cervical cancer. This also enhances the binding of H3K9ac to the promoter regions of multiple tumor suppressor genes, thereby promoting their transcriptional activation. Furthermore, the absence of PCAF renders AMPK activation incapable of inducing H3K9 acetylation. CONCLUSIONS In conclusion, our findings demonstrate that AMPK mediates the inhibition of cervical cancer growth through PCAF-dependent H3K9 acetylation. This discovery not only facilitates the clinical application of metformin but also underscores the essential role of PCAF in AMPK activation-induced H3K9 hyperacetylation.
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Affiliation(s)
- Botao Pan
- Foshan Women and Children Hospital, Foshan, 528000, China
| | - Can Liu
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 515150, China
| | - Jiyan Su
- Foshan Women and Children Hospital, Foshan, 528000, China
| | - Chenglai Xia
- Foshan Women and Children Hospital, Foshan, 528000, China.
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 515150, China.
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Mojtaba Mousavi S, Alireza Hashemi S, Yari Kalashgrani M, Rahmanian V, Riazi M, Omidifar N, Hamed Althomali R, Rahman MM, Chiang WH, Gholami A. Recent Progress in Prompt Molecular Detection of Exosomes Using CRISPR/Cas and Microfluidic-Assisted Approaches Toward Smart Cancer Diagnosis and Analysis. ChemMedChem 2024; 19:e202300359. [PMID: 37916531 DOI: 10.1002/cmdc.202300359] [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: 07/11/2023] [Revised: 10/28/2023] [Accepted: 11/01/2023] [Indexed: 11/03/2023]
Abstract
Exosomes are essential indicators of molecular mechanisms involved in interacting with cancer cells and the tumor environment. As nanostructures based on lipids and nucleic acids, exosomes provide a communication pathway for information transfer by transporting biomolecules from the target cell to other cells. Importantly, these extracellular vesicles are released into the bloodstream by the most invasive cells, i. e., cancer cells; in this way, they could be considered a promising specific biomarker for cancer diagnosis. In this matter, CRISPR-Cas systems and microfluidic approaches could be considered practical tools for cancer diagnosis and understanding cancer biology. CRISPR-Cas systems, as a genome editing approach, provide a way to inactivate or even remove a target gene from the cell without affecting intracellular mechanisms. These practical systems provide vital information about the factors involved in cancer development that could lead to more effective cancer treatment. Meanwhile, microfluidic approaches can also significantly benefit cancer research due to their proper sensitivity, high throughput, low material consumption, low cost, and advanced spatial and temporal control. Thereby, employing CRISPR-Cas- and microfluidics-based approaches toward exosome monitoring could be considered a valuable source of information for cancer therapy and diagnosis. This review assesses the recent progress in these promising diagnosis approaches toward accurate cancer therapy and in-depth study of cancer cell behavior.
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Affiliation(s)
- Seyyed Mojtaba Mousavi
- Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei City, 106335, Taiwan
| | - Seyyed Alireza Hashemi
- Health Policy Research Center, Health Institute, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | - Vahid Rahmanian
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, Lodz, 90-363, Poland
| | - Mohsen Riazi
- Biotechnology Research Center, Shiraz University of Medical Science, Shiraz, 71468-64685, Iran
| | - Navid Omidifar
- Department of Pathology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | - Mohammed M Rahman
- Center of Excellence for Advanced Materials Research (CEAMR) & Department of Chemistry, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah, 21589, Saudi Arabia
| | - Wei-Hung Chiang
- Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei City, 106335, Taiwan
| | - Ahmad Gholami
- Biotechnology Research Center, Shiraz University of Medical Science, Shiraz, 71468-64685, Iran
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He L, Luo X, Bu Q, Jin J, Zhou S, He S, Zhang L, Lin Y, Hong X. PAX1 and SEPT9 methylation analyses in cervical exfoliated cells are highly efficient for detecting cervical (pre)cancer in hrHPV-positive women. J OBSTET GYNAECOL 2023; 43:2179916. [PMID: 36799003 DOI: 10.1080/01443615.2023.2179916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Studies have investigated PAX1 and SEPT methylation were closely associated with cervical cancer. For this study, we verified the expressions of PAX1 and SEPT9 methylation in 236 hrHPV women cervical exfoliated cells by using quantitative methylation-specific PCR and we further explored their diagnostic value in cervical (pre)cancer detection. Our results identified that the methylation rates and levels of PAX1 and SEPT9 increased with cervical lesion severity. For a diagnosis of cervical (pre)cancer, the area under the curve (AUC) of PAX1 methylation was 0.77 (95% CI 0.71-0.83) and the AUC of SEPT9 methylation was 0.86 (95% CI 0.81∼0.90). Analyses of the PAX1 and SEPT9 methylation statuses alone or combined with commonly used tests can efficiently identify cervical (pre)cancer. In particular, SEPT9 methylation might serve as an effective and powerful biomarker for the diagnosis of cervical (pre)cancer and as an alternative triage test in HPV-based cervical (pre)cancer screening programs.Impact StatementWhat is already known on this subject? This subject showed that PAX1 and SEPT9 methylation were closely associated with cervical cancer. The methylation rates and levels of PAX1 and SEPT9 increased with cervical lesion severity and reached a peak in cervical cancer exfoliated cells. We further assessed the diagnostic performances of PAX1 and SEPT9 methylation in cervical cancer screening. In detecting cervical (pre)cancer, the sensitivity values of PAX1 and SEPT9 methylation were up to 61.18% and 82.35%, respectively, and the specificity values of PAX1 and SEPT9 methylation were up to 95.36% and 86.75%, respectively. Moreover, the ROC curve analysis showed AUC values of 0.77 for PAX1 methylation and 0.86 for SEPT9 methylation tests, which were significantly superior to other commonly used tests. These findings suggest that PAX1 and SEPT9 methylation detection may have great clinical potential in cervical cancer screening.What the results of this study add? The rates and levels of PAX1 and SEPT9 methylation increased with the severity of the cervical lesions. For a diagnosis of cervical (pre)cancer, the area under the curve (AUC) of PAX1 methylation was 0.77 (95% CI 0.71-0.83), and the sensitivity and specificity values were 61.18% and 95.36%, respectively. The AUC value of the SEPT9 methylation was 0.86 (95% CI 0.81 ∼ 0.90), and the sensitivity and specificity values were 82.35% and 86.75%, respectively. Compared with the various tests we conducted, the PAX1 methylation showed the highest specificity (95.36%), and the SEPT9 methylation demonstrated the highest accuracy(86.00%).What the implications are of these findings for clinical practice and/or further research? The methylation levels of PAX1 and SEPT9 had a certain predictive effect on the severity of cervical lesions in hrHPV-positive women. In addition, SEPT9 methylation analysis performs better than PAX1 methylation analysis and commonly used tests in cervical exfoliated cells for detecting cervical (pre)cancer in hrHPV-positive women. SEPT9 methylation analysis merits consideration as an effective and objective, alternative triage test in HPV-based cervical (pre)cancer screening programs.
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Affiliation(s)
- Lulu He
- Department of Gynecology, Guangdong Women and Children Hospital, Guangzhou, China
| | - Xiping Luo
- Department of Gynecology, Guangdong Women and Children Hospital, Guangzhou, China
| | - Qiaowen Bu
- Department of Gynecology, Guangdong Women and Children Hospital, Guangzhou, China
| | - Jing Jin
- Department of Gynecology, Guangdong Women and Children Hospital, Guangzhou, China
| | - Shuai Zhou
- Translational Medicine Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Shaoyi He
- Department of Gynecology, Guangdong Women and Children Hospital, Guangzhou, China
| | - Liang Zhang
- Translational Medicine Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Yu Lin
- Nanfang Hospital, Southern Medical University, Guangzhou, China.,Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xiaoshan Hong
- Department of Gynecology, Guangdong Women and Children Hospital, Guangzhou, China
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Jiang Y, Wang C, Zhou S. Artificial intelligence-based risk stratification, accurate diagnosis and treatment prediction in gynecologic oncology. Semin Cancer Biol 2023; 96:82-99. [PMID: 37783319 DOI: 10.1016/j.semcancer.2023.09.005] [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: 12/17/2022] [Revised: 08/27/2023] [Accepted: 09/25/2023] [Indexed: 10/04/2023]
Abstract
As data-driven science, artificial intelligence (AI) has paved a promising path toward an evolving health system teeming with thrilling opportunities for precision oncology. Notwithstanding the tremendous success of oncological AI in such fields as lung carcinoma, breast tumor and brain malignancy, less attention has been devoted to investigating the influence of AI on gynecologic oncology. Hereby, this review sheds light on the ever-increasing contribution of state-of-the-art AI techniques to the refined risk stratification and whole-course management of patients with gynecologic tumors, in particular, cervical, ovarian and endometrial cancer, centering on information and features extracted from clinical data (electronic health records), cancer imaging including radiological imaging, colposcopic images, cytological and histopathological digital images, and molecular profiling (genomics, transcriptomics, metabolomics and so forth). However, there are still noteworthy challenges beyond performance validation. Thus, this work further describes the limitations and challenges faced in the real-word implementation of AI models, as well as potential solutions to address these issues.
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Affiliation(s)
- Yuting Jiang
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan 610041, China; Department of Pulmonary and Critical Care Medicine, State Key Laboratory of Respiratory Health and Multimorbidity, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Chengdi Wang
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan 610041, China; Department of Pulmonary and Critical Care Medicine, State Key Laboratory of Respiratory Health and Multimorbidity, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Shengtao Zhou
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan 610041, China; Department of Pulmonary and Critical Care Medicine, State Key Laboratory of Respiratory Health and Multimorbidity, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China.
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Liu C, Tang H, Hu N, Li T. Methylomics and cancer: the current state of methylation profiling and marker development for clinical care. Cancer Cell Int 2023; 23:242. [PMID: 37840147 PMCID: PMC10577916 DOI: 10.1186/s12935-023-03074-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 09/20/2023] [Indexed: 10/17/2023] Open
Abstract
Epigenetic modifications have long been recognized as an essential level in transcriptional regulation linking behavior and environmental conditions or stimuli with biological processes and disease development. Among them, methylation is the most abundant of these reversible epigenetic marks, predominantly occurring on DNA, RNA, and histones. Methylation modification is intimately involved in regulating gene transcription and cell differentiation, while aberrant methylation status has been linked with cancer development in several malignancies. Early detection and precise restoration of dysregulated methylation form the basis for several epigenetics-based therapeutic strategies. In this review, we summarize the current basic understanding of the regulation and mechanisms responsible for methylation modification and cover several cutting-edge research techniques for detecting methylation across the genome and transcriptome. We then explore recent advances in clinical diagnostic applications of methylation markers of various cancers and address the current state and future prospects of methylation modifications in therapies for different diseases, especially comparing pharmacological methylase/demethylase inhibitors with the CRISPRoff/on methylation editing systems. This review thus provides a resource for understanding the emerging role of epigenetic methylation in cancer, the use of methylation-based biomarkers in cancer detection, and novel methylation-targeted drugs.
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Affiliation(s)
- Chengyin Liu
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Georgetown University, Washington, DC, USA
| | - Han Tang
- BioChain (Beijing) Science & Technology Inc., Beijing, People's Republic of China
| | - Nana Hu
- BioChain (Beijing) Science & Technology Inc., Beijing, People's Republic of China
| | - Tianbao Li
- Department of Molecular Medicine, The University of Texas Health, San Antonio, USA.
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Kim S, Xu Z, Forno E, Qin Y, Park HJ, Yue M, Yan Q, Manni ML, Acosta-Pérez E, Canino G, Chen W, Celedón JC. Cis- and trans-eQTM analysis reveals novel epigenetic and transcriptomic immune markers of atopic asthma in airway epithelium. J Allergy Clin Immunol 2023; 152:887-898. [PMID: 37271320 PMCID: PMC10592527 DOI: 10.1016/j.jaci.2023.05.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 04/03/2023] [Accepted: 05/02/2023] [Indexed: 06/06/2023]
Abstract
BACKGROUND Expression quantitative trait methylation (eQTM) analyses uncover associations between DNA methylation markers and gene expression. Most eQTM analyses of complex diseases have focused on cis-eQTM pairs (within 1 megabase). OBJECTIVES This study sought to identify cis- and trans-methylation markers associated with gene expression in airway epithelium from youth with and without atopic asthma. METHODS In this study, the investigators conducted both cis- and trans-eQTM analyses in nasal (airway) epithelial samples from 158 Puerto Rican youth with atopic asthma and 100 control subjects without atopy or asthma. The investigators then attempted to replicate their findings in nasal epithelial samples from 2 studies of children, while also examining whether their results in nasal epithelium overlap with those from an eQTM analysis in white blood cells from the Puerto Rican subjects. RESULTS This study identified 9,108 cis-eQTM pairs and 2,131,500 trans-eQTM pairs. Trans-associations were significantly enriched for transcription factor and microRNA target genes. Furthermore, significant cytosine-phosphate-guanine sites (CpGs) were differentially methylated in atopic asthma and significant genes were enriched for genes differentially expressed in atopic asthma. In this study, 50.7% to 62.6% of cis- and trans-eQTM pairs identified in Puerto Rican youth were replicated in 2 smaller cohorts at false discovery rate-adjusted P < .1. Replicated genes in the trans-eQTM analysis included biologically plausible asthma-susceptibility genes (eg, HDC, NLRP3, ITGAE, CDH26, and CST1) and are enriched in immune pathways. CONCLUSIONS Studying both cis- and trans-epigenetic regulation of airway epithelial gene expression can identify potential causal and regulatory pathways or networks for childhood asthma. Trans-eQTM CpGs may regulate gene expression in airway epithelium through effects on transcription factor and microRNA target genes.
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Affiliation(s)
- Soyeon Kim
- Division of Pediatric Pulmonary Medicine, University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pa; Department of Pediatrics, School of Medicine, University of Pittsburgh, Pittsburgh, Pa
| | - Zhongli Xu
- Division of Pediatric Pulmonary Medicine, University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pa; School of Medicine, Tsinghua University, Beijing, China
| | - Erick Forno
- Division of Pediatric Pulmonary Medicine, University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pa; Department of Pediatrics, School of Medicine, University of Pittsburgh, Pittsburgh, Pa
| | - Yidi Qin
- Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, Pa
| | - Hyun Jung Park
- Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, Pa
| | - Molin Yue
- Department of Biostatistics, School of Public Health, University of Pittsburgh, Pittsburgh, Pa
| | - Qi Yan
- Department of Obstetrics and Gynecology, Columbia University, New York, NY
| | - Michelle L Manni
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh
| | - Edna Acosta-Pérez
- Behavioral Sciences Research Institute, University of Puerto Rico, San Juan, Puerto Rico
| | - Glorisa Canino
- Behavioral Sciences Research Institute, University of Puerto Rico, San Juan, Puerto Rico
| | - Wei Chen
- Division of Pediatric Pulmonary Medicine, University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pa; School of Medicine, Tsinghua University, Beijing, China
| | - Juan C Celedón
- Division of Pediatric Pulmonary Medicine, University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pa; Department of Pediatrics, School of Medicine, University of Pittsburgh, Pittsburgh, Pa.
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9
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Li Z, Chen G, Sang Q, Wang L, Wuyun Q, Wang Z, Amin B, Lian D, Zhang N. A nomogram based on adipogenesis-related methylation sites in intraoperative visceral fat to predict EWL% at 1 year following laparoscopic sleeve gastrectomy. Surg Obes Relat Dis 2023; 19:990-999. [PMID: 37080886 DOI: 10.1016/j.soard.2023.02.021] [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: 11/02/2022] [Revised: 01/12/2023] [Accepted: 02/24/2023] [Indexed: 03/14/2023]
Abstract
BACKGROUND Laparoscopic sleeve gastrectomy (LSG) is a crucial surgical procedure for patients with obesity. However, epigenetic research in LSG is still in its infancy from the perspective of adipogenesis. OBJECTIVES This work aims to develop a model to predict 1 year excess weight loss percentage (EWL)% following LSG in Chinese patients with obesity by examining the DNA methylation profiles of intraoperative visceral fat. SETTING University hospital, Beijing, China. METHODS Firstly, we classified patients with obesity as either the satisfied group or unsatisfied group depending on whether their EWL% was 50% or higher at 1 year following LSG. After that, we analyzed differentially methylated sites (DMSs) between the satisfied group and unsatisfied group. DMSs were mapped to the corresponding differentially methylated genes. Then, we took the intersection of adipogenesis-related genes and differentially methylated genes and obtained adipogenesis-related DMSs. Next, hub methylation sites were identified by least absolute shrinkage and selection operator analysis. Finally, a nomogram was developed to predict EWL% of Chinese patients with obesity at 1 -year following LSG. RESULTS A total of 26 patients with obesity were enrolled in the study, including 13 in the satisfied group and 13 in the unsatisfied group. A total of 16 genes and 31 DMSs were involved in the adipogenesis signaling pathway. Finally, 4 hub methylation sites (cg06093355, cg00294552, cg00753924, and cg17092065) were identified and a predictive nomogram was established. CONCLUSIONS The predictive nomogram based on methylation sites including cg06093355, cg00294552, cg00753924, and cg17092065 can predict EWL% at 1 year following LSG in Chinese patients with obesity efficiently.
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Affiliation(s)
- Zhehong Li
- Department of General Surgery, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Guanyang Chen
- Department of General Surgery, Peking University Ninth School of Clinical Medicine, Beijing, China
| | - Qing Sang
- Department of General Surgery, Peking University Ninth School of Clinical Medicine, Beijing, China
| | - Liang Wang
- Department of General Surgery, Peking University Ninth School of Clinical Medicine, Beijing, China
| | - Qiqige Wuyun
- Department of General Surgery, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Zheng Wang
- Department of General Surgery, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Buhe Amin
- Department of General Surgery, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Dongbo Lian
- Department of General Surgery, Beijing Shijitan Hospital, Capital Medical University, Beijing, China.
| | - Nengwei Zhang
- Department of General Surgery, Beijing Shijitan Hospital, Capital Medical University, Beijing, China.
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Zhang D, Yin G, Zheng S, Chen Q, Li Y. Construction of a prediction model for prognosis of bladder cancer based on the expression of ion channel-related genes. Zhejiang Da Xue Xue Bao Yi Xue Ban 2023; 52:499-509. [PMID: 37643983 PMCID: PMC10495249 DOI: 10.3724/zdxbyxb-2023-0051] [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: 02/07/2023] [Accepted: 07/06/2023] [Indexed: 08/24/2023]
Abstract
OBJECTIVES To construct a prediction model for the prognosis of bladder cancer patients based on the expression of ion channel-related genes (ICRGs). METHODS ICRGs were obtained from the existing researches. The clinical information and the expression of ICRGs mRNA in breast cancer patients were obtained from the Cancer Genome Atlas database. Cox regression analysis, minimum absolute shrinkage and selection operator regression analysis were used to screen breast cancer prognosis related genes, which were verified by immunohistochemistry and qRT-PCR. The risk scoring equation for predicting the prognosis of patients with bladder cancer was constructed, and the patients were divided into high-risk group and low-risk group according to the median risk score. Immune cell infiltration was compared between the two groups. Kaplan-Meier survival curve and receiver operating characteristic (ROC) curve were used to evaluate the accuracy and clinical application value of the risk scoring equation. The factors related to the prognosis of bladder cancer patients were analyzed by univariate and multivariate Cox regression, and a nomogram for predicting the prognosis of bladder cancer patients was constructed. RESULTS By comparing the expression levels of ICRGs in bladder cancer tissues and normal bladder tissues, 73 differentially expressed ICRGs were dentified, of which 11 were related to the prognosis of bladder cancer patients. Kaplan-Meier survival curve suggested that the risk score based on these 11 genes was negatively correlated with the prognosis of patients. The area under the ROC curve of the risk score for predicting the prognosis of patients at 1, 3 and 5 year was 0.634, 0.665 and 0.712, respectively. Stratified analysis showed that the ICRGs-based risk score performed well in predicting the prognosis of patients with American Joint Committee on Cancer (AJCC) stage Ⅲ-Ⅳ bladder cancer (P<0.05), while it had a poor value in predicting the prognosis of patients with AJCC stage Ⅰ-Ⅱ (P>0.05). There were significant differences in the infiltration of plasma cells, activated natural killer cells, resting mast cells and M2 macrophages between the high-risk group and the low-risk group. Cox regression analysis showed that risk score, smoking, age and AJCC stage were independently associated with the prognosis of patients with bladder cancer (P<0.05). The nomogram constructed by combining risk score and clinical parameters has high accuracy in predicting the 1, 3 and 5 year overall survival rate of bladder cancer patients. CONCLUSIONS The study shows the potential value of ICRGs in the prognostic risk assessment of bladder cancer patients. The constructed prognostic nomogram based on ICRGs risk score has high accuracy in predicting the prognosis of bladder cancer patients.
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Affiliation(s)
- Dianfeng Zhang
- Department of Urology, Xuchang Central Hospital of Henan Province, Xuchang 461000, Henan Province, China.
| | - Guicao Yin
- Department of Urology, the Affiliated Hospital of Yangzhou University, Yangzhou 225000, Jiangsu Province, China
| | - Shengqi Zheng
- Department of Urology, the Affiliated Hospital of Yangzhou University, Yangzhou 225000, Jiangsu Province, China
| | - Qiu Chen
- Department of Urology, the Affiliated Hospital of Yangzhou University, Yangzhou 225000, Jiangsu Province, China
| | - Yifan Li
- Department of Urology, the Affiliated Hospital of Yangzhou University, Yangzhou 225000, Jiangsu Province, China.
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11
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Zhang N, Pang C, Li Z, Xu F, Zhao L. Serum CXCL8 and CXCR2 as diagnostic biomarkers for noninvasive screening of cervical cancer. Medicine (Baltimore) 2023; 102:e34977. [PMID: 37653753 PMCID: PMC10470760 DOI: 10.1097/md.0000000000034977] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 07/25/2023] [Accepted: 08/07/2023] [Indexed: 09/02/2023] Open
Abstract
BACKGROUND Cervical cancer (CC) is the fourth most frequently diagnosed cancer and the fourth leading cause of cancer-related death in women. Identifying new biomarkers for the early detection of CC is an essential requirement in this field. CXCL8 was originally discovered because of its role in inflammation by binding to CXCR1 and CXCR2; however, it is now known to play an important role in cancer. In this study, we aimed to evaluate the expression levels of potential biomarkers (CXCL8, CXCR1, and CXCR2) and to explore their diagnostic potential in CC. METHODS The expression levels of serum CXCL8, CXCR1, and CXCR2 were investigated by kit method on Immulite-1000 in 30 healthy volunteers, 30 precancerous patients and 70 CC patients. RESULTS The results indicated that the expression of CXCL8 and CXCR2 was significantly higher in the serum of CC patients than in healthy volunteers, similar to the well-established tumor marker (squamous-cell cancerantigen [SCC]). Receiver operating characteristic analyses showed that the combination of CXCL8, CXCR2, and SCC had the highest diagnostic sensitivity and area under the curve value. Meanwhile, the positive predictive value and negative predictive value were not very low. Moreover, high concentrations of CXCL8 and CXCR2 are associated with an increased risk of CC. CONCLUSIONS In conclusion, our data demonstrated that combined serum CXCL8, CXCR2, and SCC measurements are helpful for CC diagnosis and can be used as potential biomarkers for the early detection of CC. Cytokines, such as CXCL8 and CXCR2, can be easily measured in most university hospital laboratories and in some private laboratories with a routine test.
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Affiliation(s)
- Nianzhu Zhang
- Department of Laboratory Medicine, The Second Hospital of Dalian Medical University, Dalian, China
| | - Chunsong Pang
- Department of Laboratory Medicine, The Second Hospital of Dalian Medical University, Dalian, China
| | - Zhenguo Li
- Department of Laboratory Medicine, The Second Hospital of Dalian Medical University, Dalian, China
| | - Fang Xu
- Department of Laboratory Medicine, The Second Hospital of Dalian Medical University, Dalian, China
| | - Lifen Zhao
- Department of Laboratory Medicine, The Second Hospital of Dalian Medical University, Dalian, China
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12
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Zhang S, Luo Y, Sun W, Tan W, Zeng H. Prognostic Values of Core Genes in Pilocytic Astrocytom. World Neurosurg 2023; 176:e101-e108. [PMID: 37169070 DOI: 10.1016/j.wneu.2023.05.006] [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: 02/24/2023] [Revised: 05/01/2023] [Accepted: 05/02/2023] [Indexed: 05/13/2023]
Abstract
BACKGROUND Pilocytic astrocytoma (PA) is the most common primary brain tumor in children and adolescents. Treatment strategy largely depends on its key genes and molecular mutations. This study aimed to identify potential biomarkers of PA closely related to its prognosis. METHODS The gene expression profiles (series numbers GSE50161, GSE66354, and GSE86574) of PA and normal brain tissues were downloaded from the Gene Expression Omnibus database. The Gene Expression Omnibus2R was used to identify differentially expressed genes. The overlapping differentially expressed genes were subjected to Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses using the Database for Annotation, Visualization, and Integrated Discovery (DAVID) database. A protein-protein interaction network was constructed using Search Tool for the Retrieval of Interacting Genes (STRING) and Cytoscape. The Gene Expression Profiling Interactive Analysis 2 (GEPIA2) tool analyzed the impact of hub genes on PA prognosis based on the Kaplan-Meier curves. RESULTS Compared with normal brain tissues (n = 36), a total of 37 upregulated and 144 downregulated genes were identified in PA (n = 40). In the protein-protein interaction network construction and GEPIA2 survival analysis, 2 of the top 10 hub genes were significantly associated with decreased overall survival of PA patients, namely Gamma-aminobutyric acid A receptor alpha 2 (hazard ratio = 2.8, P < 0.01) and regulating synaptic membrane exocytosis protein 1) (hazard ratio = 3.2, P < 0.01). CONCLUSIONS This bioinformatics analysis reveals that low expression of Gamma-aminobutyric acid A receptor alpha 2 and regulating synaptic membrane exocytosis protein 1 is associated with a favorable prognosis for PA patients. These 2 hub genes could be novel biomarkers for prognosis assessment, furthermore a key element for treatment decisions in the future.
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Affiliation(s)
- Siqi Zhang
- Shantou University Medical College, Shantou University, Shantou, China; Department of Radiology, Shenzhen Children's Hospital, Shenzhen, China
| | - Yi Luo
- Shantou University Medical College, Shantou University, Shantou, China; Department of Radiology, Shenzhen Children's Hospital, Shenzhen, China
| | - Weisheng Sun
- Shantou University Medical College, Shantou University, Shantou, China; Department of Radiology, Shenzhen Children's Hospital, Shenzhen, China
| | - Weiting Tan
- Department of Radiology, Shenzhen Children's Hospital, Shenzhen, China
| | - Hongwu Zeng
- Department of Radiology, Shenzhen Children's Hospital, Shenzhen, China.
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13
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Ye Z, Song G, Liang J, Yi S, Gao Y, Jiang H. Optimized screening of DNA methylation sites combined with gene expression analysis to identify diagnostic markers of colorectal cancer. BMC Cancer 2023; 23:617. [PMID: 37400791 DOI: 10.1186/s12885-023-10922-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 05/05/2023] [Indexed: 07/05/2023] Open
Abstract
BACKGROUND The prognosis of patients with colorectal cancer is related to early detection. However, commonly used screening markers lack sensitivity and specificity. In this study, we identified diagnostic methylation sites for colorectal cancer. METHODS After screening the colorectal cancer methylation dataset, diagnostic sites were identified via survival analysis, difference analysis, and ridge regression dimensionality reduction. The correlation between the selected methylation sites and the estimation of immune cell infiltration was analyzed. The accuracy of the diagnosis was verified using different datasets and the 10-fold crossover method. RESULTS According to Gene Ontology, the main enrichment pathways of genes with hypermethylation sites are axon development, axonogenesis, and pattern specification processes. However, the Kyoto Encyclopedia of Genes and Genomes (KEGG) suggests the following main enrichment pathways: neuroactive ligand-receptor interaction, calcium signaling, and cAMP signaling. In The Cancer Genome Atlas (TCGA) and GSE131013 datasets, the area under the curve of cg07628404 was > 0.95. For the NaiveBayes machine model of cg02604524, cg07628404, and cg27364741, the accuracies of 10-fold cross-validation in the GSE131013 and TCGA datasets were 95% and 99.4%, respectively. The survival prognosis of the hypomethylated group (cg02604524, cg07628404, and cg27364741) was better than that of the hypermethylated group. The mutation risk did not differ between the hypermethylated and hypomethylated groups. The correlation coefficient between the three loci and CD4 central memory T cells, hematological stem cells, and other immune cells was not high (p < 0.05). CONCLUSION In cases of colorectal cancer, the main enrichment pathway of genes with hypermethylated sites was axon and nerve development. In the biopsy tissues, the hypermethylation sites were diagnostic for colorectal cancer, and the NaiveBayes machine model of the three loci showed good diagnostic performance. Site (cg02604524, cg07628404, and cg27364741) hypermethylation predicts poor survival for colorectal cancer. Three methylation sites were weakly correlated with individual immune cell infiltration. Hypermethylation sites may be a useful repository for diagnosing colorectal cancer.
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Affiliation(s)
- Zhen Ye
- Department of Health Management, The First Affiliated Hospital, Shandong Provincial Qianfoshan Hospital, Shandong First Medical University, Jinan, 250013, Shandong, China
| | - Guangle Song
- Department of Health Management, The First Affiliated Hospital, Shandong Provincial Qianfoshan Hospital, Shandong First Medical University, Jinan, 250013, Shandong, China
| | - Jianwei Liang
- Department of General Surgery, Tai'an City Center Hospital, Taian, 271000, Shandong, China
| | - Shuying Yi
- Department of Health Management, The First Affiliated Hospital, Shandong Provincial Qianfoshan Hospital, Shandong First Medical University, Jinan, 250013, Shandong, China
| | - Yuqi Gao
- Department of Health Management, The First Affiliated Hospital, Shandong Provincial Qianfoshan Hospital, Shandong First Medical University, Jinan, 250013, Shandong, China.
| | - Hanming Jiang
- Department of Health Management, The First Affiliated Hospital, Shandong Provincial Qianfoshan Hospital, Shandong First Medical University, Jinan, 250013, Shandong, China.
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14
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Guan X, Du Y, Ma R, Teng N, Ou S, Zhao H, Li X. Construction of the XGBoost model for early lung cancer prediction based on metabolic indices. BMC Med Inform Decis Mak 2023; 23:107. [PMID: 37312179 DOI: 10.1186/s12911-023-02171-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 04/05/2023] [Indexed: 06/15/2023] Open
Abstract
BACKGROUND Lung cancer is a malignant tumour, and early diagnosis has been shown to improve the survival rate of lung cancer patients. In this study, we assessed the use of plasma metabolites as biomarkers for lung cancer diagnosis. In this work, we used a novel interdisciplinary mechanism, applied for the first time to lung cancer, to detect biomarkers for early lung cancer diagnosis by combining metabolomics and machine learning approaches. RESULTS In total, 478 lung cancer patients and 370 subjects with benign lung nodules were enrolled from a hospital in Dalian, Liaoning Province. We selected 47 serum amino acid and carnitine indicators from targeted metabolomics studies using LC‒MS/MS and age and sex demographic indicators of the subjects. After screening by a stepwise regression algorithm, 16 metrics were included. The XGBoost model in the machine learning algorithm showed superior predictive power (AUC = 0.81, accuracy = 75.29%, sensitivity = 74%), with the metabolic biomarkers ornithine and palmitoylcarnitine being potential biomarkers to screen for lung cancer. The machine learning model XGBoost is proposed as an tool for early lung cancer prediction. This study provides strong support for the feasibility of blood-based screening for metabolites and provide a safer, faster and more accurate tool for early diagnosis of lung cancer. CONCLUSIONS This study proposes an interdisciplinary approach combining metabolomics with a machine learning model (XGBoost) to predict early the occurrence of lung cancer. The metabolic biomarkers ornithine and palmitoylcarnitine showed significant power for early lung cancer diagnosis.
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Affiliation(s)
- Xiuliang Guan
- School of Public Health, Dalian Medical University, Dalian, 116000, China
| | - Yue Du
- School of Public Health, Dalian Medical University, Dalian, 116000, China
| | - Rufei Ma
- School of Public Health, Dalian Medical University, Dalian, 116000, China
| | - Nan Teng
- School of Public Health, Dalian Medical University, Dalian, 116000, China
| | - Shu Ou
- School of Public Health, Dalian Medical University, Dalian, 116000, China
| | - Hui Zhao
- Department of Health Examination Center, The Second Affiliated Hospital of Dalian Medical University, Dalian, China.
| | - Xiaofeng Li
- School of Public Health, Dalian Medical University, Dalian, 116000, China.
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15
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Magi A, Mattei G, Mingrino A, Caprioli C, Ronchini C, Frigè G, Semeraro R, Bolognini D, Rambaldi A, Candoni A, Colombo E, Mazzarella L, Pelicci PG. High-resolution Nanopore methylome-maps reveal random hyper-methylation at CpG-poor regions as driver of chemoresistance in leukemias. Commun Biol 2023; 6:382. [PMID: 37031307 PMCID: PMC10082806 DOI: 10.1038/s42003-023-04756-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 03/24/2023] [Indexed: 04/10/2023] Open
Abstract
Aberrant DNA methylation at CpG dinucleotides is a cancer hallmark that is associated with the emergence of resistance to anti cancer treatment, though molecular mechanisms and biological significance remain elusive. Genome scale methylation maps by currently used methods are based on chemical modification of DNA and are best suited for analyses of methylation at CpG rich regions (CpG islands). We report the first high coverage whole-genome map in cancer using the long read nanopore technology, which allows simultaneous DNA-sequence and -methylation analyses on native DNA. We analyzed clonal epigenomic/genomic evolution in Acute Myeloid Leukemias (AMLs) at diagnosis and relapse, after chemotherapy. Long read sequencing coupled to a novel computational method allowed definition of differential methylation at unprecedented resolution, and showed that the relapse methylome is characterized by hypermethylation at both CpG islands and sparse CpGs regions. Most differentially methylated genes, however, were not differentially expressed nor enriched for chemoresistance genes. A small fraction of under-expressed and hyper-methylated genes at sparse CpGs, in the gene body, was significantly enriched in transcription factors (TFs). Remarkably, these few TFs supported large gene-regulatory networks including 50% of all differentially expressed genes in the relapsed AMLs and highly-enriched in chemoresistance genes. Notably, hypermethylated regions at sparse CpGs were poorly conserved in the relapsed AMLs, under-represented at their genomic positions and showed higher methylation entropy, as compared to CpG islands. Analyses of available datasets confirmed TF binding to their target genes and conservation of the same gene-regulatory networks in large patient cohorts. Relapsed AMLs carried few patient specific structural variants and DNA mutations, apparently not involved in drug resistance. Thus, drug resistance in AMLs can be mainly ascribed to the selection of random epigenetic alterations at sparse CpGs of a few transcription factors, which then induce reprogramming of the relapsing phenotype, independently of clonal genomic evolution.
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Affiliation(s)
- Alberto Magi
- Department of Information Engineering, University of Florence, Florence, Italy.
- Institute for Biomedical Technologies, National Research Council, Segrate, Milano, Italy.
| | - Gianluca Mattei
- Department of Information Engineering, University of Florence, Florence, Italy
| | - Alessandra Mingrino
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Chiara Caprioli
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milano, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Chiara Ronchini
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milano, Italy
| | - GianMaria Frigè
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milano, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Roberto Semeraro
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Davide Bolognini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Alessandro Rambaldi
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
- Azienda Socio-Sanitaria Territoriale Papa Giovanni XXIII, Bergamo, Italy
| | - Anna Candoni
- Clinica Ematologica, Azienda Sanitaria Universitaria Integrata di Udine, Udine, Italy
| | - Emanuela Colombo
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milano, Italy
| | - Luca Mazzarella
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milano, Italy
| | - Pier Giuseppe Pelicci
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milano, Italy.
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy.
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16
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Liu H, Ma H, Li Y, Zhao H. Advances in epigenetic modifications and cervical cancer research. Biochim Biophys Acta Rev Cancer 2023; 1878:188894. [PMID: 37011697 DOI: 10.1016/j.bbcan.2023.188894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 03/19/2023] [Accepted: 03/31/2023] [Indexed: 04/03/2023]
Abstract
Cervical cancer (CC) is an important public health problem for women, and perspectives and information regarding its prevention and treatment are quickly evolving. Human papilloma virus (HPV) has been recognized as a major contributor to CC development; however, HPV infection is not the only cause of CC. Epigenetics refers to changes in gene expression levels caused by non-gene sequence changes. Growing evidence suggests that the disruption of gene expression patterns which were governed by epigenetic modifications can result in cancer, autoimmune diseases, and various other maladies. This article mainly reviews the current research status of epigenetic modifications in CC based on four aspects, respectively DNA methylation, histone modification, noncoding RNA regulation and chromatin regulation, and we also discuss their functions and molecular mechanisms in the occurrence and progression of CC. This review provides new ideas for early screening, risk assessment, molecular targeted therapy and prognostic prediction of CC.
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Salmerón-Bárcenas EG, Mendoza-Catalan MA, Ramírez-Bautista ÁU, Lozano-Santos RA, Torres-Rojas FI, Ávila-López PA, Zacapala-Gómez AE. Identification of Mir-182-3p/FLI-1 Axis as a Key Signaling in Immune Response in Cervical Cancer: A Comprehensive Bioinformatic Analysis. Int J Mol Sci 2023; 24:ijms24076032. [PMID: 37047006 PMCID: PMC10094573 DOI: 10.3390/ijms24076032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/15/2023] [Accepted: 03/17/2023] [Indexed: 04/14/2023] Open
Abstract
miRNAs modulate gene expression and play critical functions as oncomiRs or tumor suppressors. The miR-182-3p is important in chemoresistance and cancer progression in breast, lung, osteosarcoma, and ovarian cancer. However, the role of miR-182-3p in cervical cancer (CC) has not been elucidated. AIM To analyze the role of miR-182-3p in CC through a comprehensive bioinformatic analysis. METHODS Gene Expression Omnibus (GEO) databases were used for the expression analysis. The mRNA targets of miR-182-3p were identified using miRDB, TargetScanHuman, and miRPathDB. The prediction of island CpG was performed using the MethPrimer program. The transcription factor binding sites in the FLI-1 promoter were identified using ConSite+, Alibaba2, and ALGGEN-PROMO. The protein-protein interaction (PPI) analysis was performed in STRING 11.5. RESULTS miR-182-3p was significantly overexpressed in CC patients and has potential as a diagnostic. We identified 330 targets of miR-182-3p including FLI-1, which downregulates its expression in CC. Additionally, the aberrant methylation of the FLI-1 promoter and Ap2a transcription factor could be involved in downregulating FLI1 expression. Finally, we found that FLI-1 is a possible key gene in the immune response in CC. CONCLUSIONS The miR-182-3p/FLI-1 axis plays a critical role in immune response in CC.
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Affiliation(s)
- Eric Genaro Salmerón-Bárcenas
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, CINVESTAV, Ciudad de México 07360, Mexico
| | - Miguel Angel Mendoza-Catalan
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo 39070, Mexico
| | - Ángela Uray Ramírez-Bautista
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo 39070, Mexico
| | - Rafael Acxel Lozano-Santos
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo 39070, Mexico
| | - Francisco Israel Torres-Rojas
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo 39070, Mexico
| | - Pedro Antonio Ávila-López
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Ana Elvira Zacapala-Gómez
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo 39070, Mexico
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18
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Kefayati F, Karimi Babaahmadi A, Mousavi T, Hodjat M, Abdollahi M. Epigenotoxicity: a danger to the future life. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2023; 58:382-411. [PMID: 36942370 DOI: 10.1080/10934529.2023.2190713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 02/17/2023] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
Environmental toxicants can regulate gene expression in the absence of DNA mutations via epigenetic mechanisms such as DNA methylation, histone modifications, and non-coding RNAs' (ncRNAs). Here, all three epigenetic modifications for seven important categories of diseases and the impact of eleven main environmental factors on epigenetic modifications were discussed. Epigenetic-related mechanisms are among the factors that could explain the root cause of a wide range of common diseases. Its overall impression on the development of diseases can help us diagnose and treat diseases, and besides, predict transgenerational and intergenerational effects. This comprehensive article attempted to address the relationship between environmental factors and epigenetic modifications that cause diseases in different categories. The studies main gap is that the precise role of environmentally-induced epigenetic alterations in the etiology of the disorders is unknown; thus, still more well-designed researches need to be accomplished to fill this gap. The present review aimed to first summarize the adverse effect of certain chemicals on the epigenome that may involve in the onset of particular disease based on in vitro and in vivo models. Subsequently, the possible adverse epigenetic changes that can lead to many human diseases were discussed.
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Affiliation(s)
- Farzaneh Kefayati
- Toxicology and Diseases Group (TDG), Pharmaceutical Sciences Research Center (PSRC), Tehran University of Medical Sciences, Tehran, Iran
- Department of Toxicology and Pharmacology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Atoosa Karimi Babaahmadi
- Toxicology and Diseases Group (TDG), Pharmaceutical Sciences Research Center (PSRC), Tehran University of Medical Sciences, Tehran, Iran
- Department of Toxicology and Pharmacology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Taraneh Mousavi
- Toxicology and Diseases Group (TDG), Pharmaceutical Sciences Research Center (PSRC), Tehran University of Medical Sciences, Tehran, Iran
- Department of Toxicology and Pharmacology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahshid Hodjat
- Toxicology and Diseases Group (TDG), Pharmaceutical Sciences Research Center (PSRC), Tehran University of Medical Sciences, Tehran, Iran
- Dental Research Center, Dentistry Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Abdollahi
- Toxicology and Diseases Group (TDG), Pharmaceutical Sciences Research Center (PSRC), Tehran University of Medical Sciences, Tehran, Iran
- Department of Toxicology and Pharmacology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
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19
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Luciani LL, Miller LM, Zhai B, Clarke K, Hughes Kramer K, Schratz LJ, Balasubramani GK, Dauer K, Nowalk MP, Zimmerman RK, Shoemaker JE, Alcorn JF. Blood Inflammatory Biomarkers Differentiate Inpatient and Outpatient Coronavirus Disease 2019 From Influenza. Open Forum Infect Dis 2023; 10:ofad095. [PMID: 36949873 PMCID: PMC10026548 DOI: 10.1093/ofid/ofad095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 02/20/2023] [Indexed: 02/25/2023] Open
Abstract
Background The ongoing circulation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses a diagnostic challenge because symptoms of coronavirus disease 2019 (COVID-19) are difficult to distinguish from other respiratory diseases. Our goal was to use statistical analyses and machine learning to identify biomarkers that distinguish patients with COVID-19 from patients with influenza. Methods Cytokine levels were analyzed in plasma and serum samples from patients with influenza and COVID-19, which were collected as part of the Centers for Disease Control and Prevention's Hospitalized Adult Influenza Vaccine Effectiveness Network (inpatient network) and the US Flu Vaccine Effectiveness (outpatient network). Results We determined that interleukin (IL)-10 family cytokines are significantly different between COVID-19 and influenza patients. The results suggest that the IL-10 family cytokines are a potential diagnostic biomarker to distinguish COVID-19 and influenza infection, especially for inpatients. We also demonstrate that cytokine combinations, consisting of up to 3 cytokines, can distinguish SARS-CoV-2 and influenza infection with high accuracy in both inpatient (area under the receiver operating characteristics curve [AUC] = 0.84) and outpatient (AUC = 0.81) groups, revealing another potential screening tool for SARS-CoV-2 infection. Conclusions This study not only reveals prospective screening tools for COVID-19 infections that are independent of polymerase chain reaction testing or clinical condition, but it also emphasizes potential pathways involved in disease pathogenesis that act as potential targets for future mechanistic studies.
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Affiliation(s)
- Lauren L Luciani
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Leigh M Miller
- Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Bo Zhai
- Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Karen Clarke
- Department of Family Medicine and Clinical Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Kailey Hughes Kramer
- Department of Internal Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Lucas J Schratz
- Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - G K Balasubramani
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Klancie Dauer
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - M Patricia Nowalk
- Department of Family Medicine and Clinical Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Richard K Zimmerman
- Department of Family Medicine and Clinical Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Jason E Shoemaker
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - John F Alcorn
- Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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20
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Hosseini M, Lotfi‐Shahreza M, Nikpour P. Integrative analysis of DNA methylation and gene expression through machine learning identifies stomach cancer diagnostic and prognostic biomarkers. J Cell Mol Med 2023; 27:714-726. [PMID: 36779430 PMCID: PMC9983314 DOI: 10.1111/jcmm.17693] [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: 10/15/2022] [Revised: 01/15/2023] [Accepted: 01/18/2023] [Indexed: 02/14/2023] Open
Abstract
DNA methylation is an early event in tumorigenesis. Here, by integrative analysis of DNA methylation and gene expression and utilizing machine learning approaches, we introduced potential diagnostic and prognostic methylation signatures for stomach cancer. Differentially-methylated positions (DMPs) and differentially-expressed genes (DEGs) were identified using The Cancer Genome Atlas (TCGA) stomach adenocarcinoma (STAD) data. A total of 256 DMPs consisting of 140 and 116 hyper- and hypomethylated positions were identified between 443 tumour and 27 nontumour STAD samples. Gene expression analysis revealed a total of 2821 DEGs with 1247 upregulated and 1574 downregulated genes. By analysing the impact of cis and trans regulation of methylation on gene expression, a dominant negative correlation between methylation and expression was observed, while for trans regulation, in hypermethylated and hypomethylated genes, there was mainly a negative and positive correlation with gene expression, respectively. To find diagnostic biomarkers, we used 28 hypermethylated probes locating in the promoter of 27 downregulated genes. By implementing a feature selection approach, eight probes were selected and then used to build a support vector machine diagnostic model, which had an area under the curve of 0.99 and 0.97 in the training and validation (GSE30601 with 203 tumour and 94 nontumour samples) cohorts, respectively. Using 412 TCGA-STAD samples with both methylation and clinical data, we also identified four prognostic probes by implementing univariate and multivariate Cox regression analysis. In summary, our study introduced potential diagnostic and prognostic biomarkers for STAD, which demands further validation.
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Affiliation(s)
- Maryam Hosseini
- Department of Genetics and Molecular Biology, Faculty of MedicineIsfahan University of Medical SciencesIsfahanIran
| | | | - Parvaneh Nikpour
- Department of Genetics and Molecular Biology, Faculty of MedicineIsfahan University of Medical SciencesIsfahanIran
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Non-Association of Driver Alterations in PTEN with Differential Gene Expression and Gene Methylation in IDH1 Wildtype Glioblastomas. Brain Sci 2023; 13:brainsci13020186. [PMID: 36831729 PMCID: PMC9953940 DOI: 10.3390/brainsci13020186] [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: 12/05/2022] [Revised: 01/18/2023] [Accepted: 01/20/2023] [Indexed: 01/24/2023] Open
Abstract
During oncogenesis, alterations in driver genes called driver alterations (DAs) modulate the transcriptome, methylome and proteome through oncogenic signaling pathways. These modulatory effects of any DA may be analyzed by examining differentially expressed mRNAs (DEMs), differentially methylated genes (DMGs) and differentially expressed proteins (DEPs) between tumor samples with and without that DA. We aimed to analyze these modulations with 12 common driver genes in Isocitrate Dehydrogenase 1 wildtype glioblastomas (IDH1-W-GBs). Using Cbioportal, groups of tumor samples with and without DAs in these 12 genes were generated from the IDH1-W-GBs available from "The Cancer Genomics Atlas Firehose Legacy Study Group" (TCGA-FL-SG) on Glioblastomas (GBs). For all 12 genes, samples with and without DAs were compared for DEMs, DMGs and DEPs. We found that DAs in PTEN were unassociated with any DEM or DMG in contrast to DAs in all other drivers, which were associated with several DEMs and DMGs. This contrasting PTEN-related property of being unassociated with differential gene expression or methylation in IDH1-W-GBs was unaffected by concurrent DAs in other common drivers or by the types of DAs affecting PTEN. From the lists of DEMs and DMGs associated with some common drivers other than PTEN, enriched gene ontology terms and insights into the co-regulatory effects of these drivers on the transcriptome were obtained. The findings from this study can improve our understanding of the molecular mechanisms underlying gliomagenesis with potential therapeutic benefits.
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22
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Zhang W, Liang G, Zhou H, Zeng X, Zhang Z, Xu X, Lai K. Identification of potential biomarkers for systemic lupus erythematosus by integrated analysis of gene expression and methylation data. Clin Rheumatol 2023; 42:1423-1433. [PMID: 36595110 DOI: 10.1007/s10067-022-06495-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 12/07/2022] [Accepted: 12/18/2022] [Indexed: 01/04/2023]
Abstract
INTRODUCTION Systemic lupus erythematosus (SLE) is a heterogeneous and chronic autoimmune disease. Aberrant DNA methylation occurs during various processes of SLE development regulating the mRNA expression of interrelated genes. This study aims to screen potential DNA methylation markers for SLE. METHODS Gene expression and methylation datasets were downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) between SLE patients and healthy controls were screened using the limma R package, and differentially methylated positions (DMPs) and regions (DMRs) were identified using dmpfinder and bumphunter (minfi). Additionally, the DNA methylation markers to distinguish SLE patients from healthy controls were explored through receiver operating characteristic (ROC) curves and logistic regression analyses. Finally, we validated the results of the bioinformatic analysis by pyrosequencing. RESULTS In total, 91 DEGs, 90,092 DMPs, 15 DMRs, and 13 DMR-associated genes were identified. Through the integrative analysis of DEG- and DMR-associated genes, we identified five type I interferon (IFN)-related genes as key epigenetic-driven genes in SLE. GO enrichment analysis showed that the five SLE-associated epigenetic-driven genes were mainly enriched in the type I IFN signaling pathway involved in immune response and defense response to virus. Moreover, we identified two SLE-specific DNA methylation markers, three SLE without lupus nephritis (SLE-LN-)-specific DNA methylation markers, and two SLE with lupus nephritis (SLE-LN+)-specific DNA methylation markers by stepwise logistic regression. CONCLUSIONS Overall, our study demonstrates potential DNA methylation markers of SLE, SLE-LN-, and SLE-LN+, which may help the diagnosis, boost the development of new epigenetic therapy, and contribute to individualized treatment. Key Points • This study identified five type I IFN-related genes as key epigenetic-driven genes in SLE, which support the importance of the type I IFN pathway in the pathogenesis of SLE • We identified novel DNA methylation biomarkers in SLE, SLE-LN-, and SLE-LN+ by a comprehensive analysis of bioinformatics methods and executed experimental validation, and binary logistic regression analysis showed that they have excellent potential • These results may provide new insights into the biological mechanisms of SLE, and identify reliable biomarkers for SLE, SLE-LN-, and SLE-LN+, which may contribute to diagnosis and individualized treatment.
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Affiliation(s)
- Wenjing Zhang
- Department of Dermatology, Nanfang Hospital, Southern Medical University, Baiyun District, No. 1838, North Guangzhou Avenue, Guangzhou, 510515, China.,Department of Dermatology, The First Affiliated Hospital of Jinan University, Guangzhou, 510632, China
| | - Guixin Liang
- Department of Dermatology, Nanfang Hospital, Southern Medical University, Baiyun District, No. 1838, North Guangzhou Avenue, Guangzhou, 510515, China
| | - Huifeng Zhou
- Department of Dermatology, Nanfang Hospital, Southern Medical University, Baiyun District, No. 1838, North Guangzhou Avenue, Guangzhou, 510515, China
| | - Xuedan Zeng
- Department of Dermatology, Nanfang Hospital, Southern Medical University, Baiyun District, No. 1838, North Guangzhou Avenue, Guangzhou, 510515, China
| | - Zhiwen Zhang
- Department of Dermatology, Nanfang Hospital, Southern Medical University, Baiyun District, No. 1838, North Guangzhou Avenue, Guangzhou, 510515, China
| | - Xia Xu
- Guangzhou Institute of Dermatology, Guangzhou, 510030, China
| | - Kuan Lai
- Department of Dermatology, Nanfang Hospital, Southern Medical University, Baiyun District, No. 1838, North Guangzhou Avenue, Guangzhou, 510515, China.
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Townsend J, Braz CU, Taylor T, Khatib H. Effects of paternal methionine supplementation on sperm DNA methylation and embryo transcriptome in sheep. ENVIRONMENTAL EPIGENETICS 2022; 9:dvac029. [PMID: 36727109 PMCID: PMC9885981 DOI: 10.1093/eep/dvac029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 12/18/2022] [Accepted: 12/22/2022] [Indexed: 06/18/2023]
Abstract
Environmental effects on gene expression and offspring development can be mediated by epigenetic modifications. It is well established that maternal diet influences DNA methylation patterns and phenotypes in the offspring; however, the epigenetic effects of paternal diet on developing offspring warrants further investigation. Here, we examined how a prepubertal methionine-enriched paternal diet affected sperm DNA methylation and its subsequent effects on embryo gene expression. Three treatment and three control rams were bred to seven ewes, and blastocysts were flushed for RNA extraction. Semen was collected from all rams and submitted for reduced representation bisulfite sequencing analysis. In total, 166 differentially methylated cytosines were identified in the sperm from treatment versus control rams. Nine genes were found to be differentially expressed in embryos produced from treatment versus control rams, and seven differentially methylated cytosines in the sperm were found to be highly correlated with gene expression in the embryos. Our results demonstrate that sperm methylation differences induced by diet may influence fetal programming.
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Affiliation(s)
- Jessica Townsend
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, 1675 Observatory Dr., Madison, WI 53706, USA
| | - Camila U Braz
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, 1675 Observatory Dr., Madison, WI 53706, USA
| | - Todd Taylor
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, 1675 Observatory Dr., Madison, WI 53706, USA
| | - Hasan Khatib
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, 1675 Observatory Dr., Madison, WI 53706, USA
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24
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Yu W, Lu Y, Shou H, Xu H, Shi L, Geng X, Song T. A 5‐year survival status prognosis of nonmetastatic cervical cancer patients through machine learning algorithms. Cancer Med 2022; 12:6867-6876. [PMID: 36479910 PMCID: PMC10067071 DOI: 10.1002/cam4.5477] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 10/31/2022] [Accepted: 11/11/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Prediction models with high accuracy rates for nonmetastatic cervical cancer (CC) patients are limited. This study aimed to construct and compare predictive models on the basis of machine learning (ML) algorithms for predicting the 5-year survival status of CC patients through using the Surveillance, Epidemiology, and End Results public database of the National Cancer Institute. METHODS The data registered from 2004 to 2016 were extracted and randomly divided into training and validation cohorts (8:2). The least absolute shrinkage and selection operator (LASSO) regression was employed to identify significant factors. Then, four predictive models were constructed, including logistic regression (LR), random forest (RF), support vector machine (SVM), and extreme gradient boosting (XGBoost). The predictive models were evaluated and compared using Receiver-operating characteristics with areas under the curves (AUCs) and decision curve analysis (DCA), respectively. RESULTS A total of 13,802 patients were involved and classified into training (N = 11,041) and validation (N = 2761) cohorts. By using the LASSO regression method, seven factors were identified. In the training cohort, the XGBoost model showed the best performance (AUC = 0.8400) compared to the other three models (all p < 0.05 by Delong's test). In the validation cohort, the XGBoost model also demonstrated a superior prediction ability (AUC = 0.8365) than LR and SVM models (both p < 0.05 by Delong's test), although the difference was not statistically significant between the XGBoost and the RF models (p = 0.4251 by Delong's test). Based on the DCA results, the XGBoost model was also superior, and feature importance analysis indicated that the tumor stage was the most important variable among the seven factors. CONCLUSIONS The XGBoost model proved to be an effective algorithm with better prediction abilities. This model is proposed to support better decision-making for nonmetastatic CC patients in the future.
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Affiliation(s)
- Wenke Yu
- Department of Radiology Qingchun Hospital of Zhejiang Province Hangzhou Zhejiang China
| | - Yanwei Lu
- Cancer Center, Department of Radiation Oncology Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College Hangzhou Zhejiang China
| | - Huafeng Shou
- Department of Gynecology Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College Hangzhou Zhejiang China
| | - Hong’en Xu
- Cancer Center, Department of Radiation Oncology Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College Hangzhou Zhejiang China
| | - Lei Shi
- Cancer Center, Department of Radiation Oncology Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College Hangzhou Zhejiang China
| | - Xiaolu Geng
- Department of Radiology Qingchun Hospital of Zhejiang Province Hangzhou Zhejiang China
| | - Tao Song
- Cancer Center, Department of Radiation Oncology Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College Hangzhou Zhejiang China
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25
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Piña-Sánchez P. Human Papillomavirus: Challenges and Opportunities for the Control of Cervical Cancer. Arch Med Res 2022; 53:753-769. [PMID: 36462952 DOI: 10.1016/j.arcmed.2022.11.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 11/18/2022] [Indexed: 12/05/2022]
Abstract
Viruses are the most abundant and genetically diverse entities on the planet, infect all life forms and have evolved with their hosts. To date, 263 viral species have been identified that infect humans, of which only seven are considered type I oncogenic. Human papillomavirus (HPV) is the main virus associated with cancer and is responsible for practically all cases of cervical carcinoma. Screening tests for early detection have been available since the 1960s. Undoubtedly, the entailment between knowledge of HPV biology and the natural history of cervical cancer has contributed to the significant advances that have been made for its prevention since the 21st century, with the development of prophylactic vaccines and improved screening strategies. Therefore, it is possible to eradicate invasive cervical cancer as a worldwide public health problem, as proposed by the WHO with the 90-70-90 initiative based on vaccination coverage, screening, and treatment, respectively. In addition, the emerging knowledge of viral biology generates opportunities that will contribute to strengthening prevention and treatment strategies in HPV-associated neoplasms.
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Affiliation(s)
- Patricia Piña-Sánchez
- Laboratorio Molecular de Oncología, Unidad de Investigación Oncológica, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, México.
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26
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Moradi A, Shahsavari M, Gowdini E, Mohammadian K, Alizamir A, Khalilollahi M, Abgarmi ZM, Ganji SM. Consequences of aberrated DNA methylation in Colon Adenocarcinoma: a bioinformatic-based multi-approach. BMC Genom Data 2022; 23:83. [PMID: 36443682 PMCID: PMC9706923 DOI: 10.1186/s12863-022-01100-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 11/21/2022] [Indexed: 12/03/2022] Open
Abstract
INTRODUCTION The biology of colorectal cancer (CRC) is remained to be elucidated. Numerous genetic and epigenetic modifications are in concert to create and progress CRC. DNA methylation as a principal epigenetic factor has gained increased attention and could be utilized for biological studies. This study aims to find novel methylated and downregulated genes with a focus on HAND2 in CRC and decipher the biological consequences. MATERIAL AND METHOD Data on DNA methylation from GEO and SMART databases and the expression GEPIA2 database were downloaded. Afterward, a set of hypermethylated and downregulated genes in CRC was chosen by overlapping genes. Consequently, HAND2 was selected as a key gene for further investigation and confirmed with cell lines methylation and expression data. The functions of HAND2 were further analyzed using gene ontology analyses and the protein-protein interaction network. RESULTS The methylation (p < 0.01) and expression (p < 0.01) of HAND2 are significantly varied in CRC compared to normal control. The correlation analysis (Pearson's correlation coefficient = -0.44, p = 6.6e-14) conveys that HAND2 significantly downregulated and has a reverse correlation with the methylation status of CpG islands. The biological process analysis of HAND2 target genes conveyed that disruption in HAND2 expression could dysregulate ERK1 and ERK2 signaling pathways. CONCLUSION Together, the findings showed that DNA hypermethylation of HAND2 was critical evidence in CRC. Further validation and prospective studies are needed to utilize HAND2 methylation as a promising biomarker.
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Affiliation(s)
- Arash Moradi
- grid.419420.a0000 0000 8676 7464Department of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Shahrak-E Pajoohesh, Km 15, P.O. Box 14965/161, Tehran - Karaj Highway, Tehran, Iran
| | - Milad Shahsavari
- grid.411463.50000 0001 0706 2472Department of Biology, Faculty of Biological Sciences, North Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Erfan Gowdini
- grid.419420.a0000 0000 8676 7464Department of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Shahrak-E Pajoohesh, Km 15, P.O. Box 14965/161, Tehran - Karaj Highway, Tehran, Iran
| | - Kamal Mohammadian
- grid.411950.80000 0004 0611 9280Department of Radiation Oncology, Hamadan University of Medical Sciences, Mahdieh Center, Hamadan, Iran
| | - Aida Alizamir
- grid.411950.80000 0004 0611 9280Department of Pathology, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Mohammad Khalilollahi
- grid.411463.50000 0001 0706 2472Department of Microbiology, Islamic Azad University, North Tehran Branch, Tehran, Iran
| | - Zahara Mohammadi Abgarmi
- grid.412266.50000 0001 1781 3962Department of Clinical Biochemistry, Faculty of Medical Science, Tarbiat Modares University, Tehran, Iran
| | - Shahla Mohammad Ganji
- grid.419420.a0000 0000 8676 7464Department of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Shahrak-E Pajoohesh, Km 15, P.O. Box 14965/161, Tehran - Karaj Highway, Tehran, Iran
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Methylation-Mediated Silencing of RBP7 Promotes Breast Cancer Progression through PPAR and PI3K/AKT Pathway. JOURNAL OF ONCOLOGY 2022; 2022:9039110. [PMID: 36276273 PMCID: PMC9584705 DOI: 10.1155/2022/9039110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 07/06/2022] [Accepted: 09/26/2022] [Indexed: 11/17/2022]
Abstract
Retinoid-binding protein7 (RBP7) is a member of the cellular retinol-binding protein (CRBP) family, which is involved in the pathogenesis of breast cancer. The study aims to illustrate the prognostic value and the potential regulatory mechanisms of RBP7 expression in breast cancer. Bioinformatics analysis with the TCGA and CPTAC databases revealed that the mRNA and protein expression levels of RBP7 in normal were higher compared to breast cancer tissues. Survival analysis displayed that the lower expression of RBP7, the worse the prognosis in ER-positive (ER+) breast cancer patients. Genomic analysis showed that low expression of RBP7 correlates with its promoter hypermethylation in breast cancer. Functional enrichment analysis demonstrated that downregulation of RBP7 expression may exert its biological influence on breast cancer through the PPAR pathway and the PI3K/AKT pathway. In summary, we identified RBP7 as a novel biomarker that is helpful for the prognosis of ER+ breast cancer patients. Promoter methylation of RBP7 is involved in its gene silencing in breast cancer, thus regulating the occurrence and development of ER+ breast cancer through the PPAR and PI3K/AKT pathways.
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28
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Hong J, Rhee JK. Genomic Effect of DNA Methylation on Gene Expression in Colorectal Cancer. BIOLOGY 2022; 11:biology11101388. [PMID: 36290295 PMCID: PMC9598958 DOI: 10.3390/biology11101388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/16/2022] [Accepted: 09/20/2022] [Indexed: 11/25/2022]
Abstract
Simple Summary Abnormal DNA methylation is known to regulate gene expression, and its features have been frequently observed in colorectal cancer (CRC) patients. In addition, alterations in DNA methylation can be proposed as biomarkers for cancer prognosis, as they occur in the early stage of carcinogenesis. Although numerous studies have attempted to shed light on the impacts of DNA methylation on gene expression, it is still unclear which specific regions regulate gene expression and how they are associated with patient survival. In this study, we elucidated the intricate relationship between DNA methylation and gene expression. Furthermore, we found genes that were influenced by DNA methylation and were associated with survival; these genes were mainly enriched in immune-related pathways. Abstract The aberrant expression of cancer-related genes can lead to colorectal cancer (CRC) carcinogenesis, and DNA methylation is one of the causes of abnormal expression. Although many studies have been conducted to reveal how DNA methylation affects transcription regulation, the ways in which it modulates gene expression and the regions that significantly affect DNA methylation-mediated gene regulation remain unclear. In this study, we investigated how DNA methylation in specific genomic areas can influence gene expression. Several regression models were constructed for gene expression prediction based on DNA methylation. Among these models, ElasticNet, which had the best performance, was chosen for further analysis. DNA methylation near transcription start sites (TSS), especially from 2 kb upstream to 7 kb downstream of TSS, had an essential regulatory role in gene expression. Moreover, methylation-affected and survival-associated genes were compiled and found to be mainly enriched in immune-related pathways. This study investigated genomic regions in which methylation changes can affect gene expression. In addition, this study proposed that aberrantly expressed genes due to DNA methylation can lead to CRC pathogenesis by the immune system.
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Iser IC, Vedovatto S, Oliveira FD, Beckenkamp LR, Lenz G, Wink MR. The crossroads of adenosinergic pathway and epithelial-mesenchymal plasticity in cancer. Semin Cancer Biol 2022; 86:202-213. [PMID: 35779713 DOI: 10.1016/j.semcancer.2022.06.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/24/2022] [Accepted: 06/26/2022] [Indexed: 10/31/2022]
Abstract
Epithelial-mesenchymal transition (EMT) is a key mechanism related to tumor progression, invasion, metastasis, resistance to therapy and poor prognosis in several types of cancer. However, targeting EMT or partial-EMT, as well as the molecules involved in this process, has remained a challenge. Recently, the CD73 enzyme, which hydrolyzes AMP to produce adenosine (ADO), has been linked to the EMT process. This relationship is not only due to the production of the immunosuppressant ADO but also to its role as a receptor for extracellular matrix proteins, being involved in cell adhesion and migration. This article reviews the crosstalk between the adenosinergic pathway and the EMT program and the impact of this interrelation on cancer development and progression. An in silico analysis of RNAseq datasets showed that several tumor types have a significant correlation between an EMT score and NT5E (CD73) and ENTPD1 (CD39) expressions, with the strongest correlations in prostate adenocarcinoma. Furthermore, it is evident that the cooperation between EMT and adenosinergic pathway in tumor progression is context and tumor-dependent. The increased knowledge about this topic will help broaden the view to explore new treatments and therapies for different types of cancer.
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Affiliation(s)
- Isabele Cristiana Iser
- Department of Basics Health Sciences and Laboratory of Cell Biology, Federal University of Health Sciences of Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil
| | - Samlai Vedovatto
- Department of Biophysics and Center of Biotechnology, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Fernanda Dittrich Oliveira
- Department of Biophysics and Center of Biotechnology, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Liziane Raquel Beckenkamp
- Department of Basics Health Sciences and Laboratory of Cell Biology, Federal University of Health Sciences of Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil
| | - Guido Lenz
- Department of Biophysics and Center of Biotechnology, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Márcia Rosângela Wink
- Department of Basics Health Sciences and Laboratory of Cell Biology, Federal University of Health Sciences of Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil.
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Castro-Oropeza R, Piña-Sánchez P. Epigenetic and Transcriptomic Regulation Landscape in HPV+ Cancers: Biological and Clinical Implications. Front Genet 2022; 13:886613. [PMID: 35774512 PMCID: PMC9237502 DOI: 10.3389/fgene.2022.886613] [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: 02/28/2022] [Accepted: 05/24/2022] [Indexed: 11/13/2022] Open
Abstract
Human Papillomavirus (HPV) is an oncogenic virus that causes the highest number of viral-associated cancer cases and deaths worldwide, with more than 690,000 new cases per year and 342,000 deaths only for cervical cancer (CC). Although the incidence and mortality rates for CC are declining in countries where screening and vaccination programs have been implemented, other types of cancer in which HPV is involved, such as oropharyngeal cancer, are increasing, particularly in men. Mutational and transcriptional profiles of various HPV-associated neoplasms have been described, and accumulated evidence has shown the oncogenic capacity of E6, E7, and E5 genes of high-risk HPV. Interestingly, transcriptomic analysis has revealed that although a vast majority of the human genome is transcribed into RNAs, only 2% of transcripts are translated into proteins. The remaining transcripts lacking protein-coding potential are called non-coding RNAs. In addition to the transfer and ribosomal RNAs, there are regulatory non-coding RNAs classified according to size and structure in long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and small RNAs; such as microRNAs (miRNAs), piwi-associated RNAs (piRNAs), small nucleolar RNAs (snoRNAs) and endogenous short-interfering RNAs. Recent evidence has shown that lncRNAs, miRNAs, and circRNAs are aberrantly expressed under pathological conditions such as cancer. In addition, those transcripts are dysregulated in HPV-related neoplasms, and their expression correlates with tumor progression, metastasis, poor prognosis, and recurrence. Nuclear lncRNAs are epigenetic regulators involved in controlling gene expression at the transcriptional level through chromatin modification and remodeling. Moreover, disruption of the expression profiles of those lncRNAs affects multiple biological processes such as cell proliferation, apoptosis, and migration. This review highlights the epigenetic alterations induced by HPV, from infection to neoplastic transformation. We condense the epigenetic role of non-coding RNA alterations and their potential as biomarkers in transformation’s early stages and clinical applications. We also summarize the molecular mechanisms of action of nuclear lncRNAs to understand better their role in the epigenetic control of gene expression and how they can drive the malignant phenotype of HPV-related neoplasia. Finally, we review several chemical and epigenetic therapy options to prevent and treat HPV-associated neoplasms.
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Review of the Standard and Advanced Screening, Staging Systems and Treatment Modalities for Cervical Cancer. Cancers (Basel) 2022; 14:cancers14122913. [PMID: 35740578 PMCID: PMC9220913 DOI: 10.3390/cancers14122913] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/10/2022] [Accepted: 06/10/2022] [Indexed: 12/13/2022] Open
Abstract
Simple Summary This review discusses the timeline and development of the recommended screening tests, diagnosis system, and therapeutics implemented in clinics for precancer and cancer of the uterine cervix. The incorporation of the latest automation, machine learning modules, and state-of-the-art technologies into these aspects are also discussed. Abstract Cancer arising from the uterine cervix is the fourth most common cause of cancer death among women worldwide. Almost 90% of cervical cancer mortality has occurred in low- and middle-income countries. One of the major aetiologies contributing to cervical cancer is the persistent infection by the cancer-causing types of the human papillomavirus. The disease is preventable if the premalignant lesion is detected early and managed effectively. In this review, we outlined the standard guidelines that have been introduced and implemented worldwide for decades, including the cytology, the HPV detection and genotyping, and the immunostaining of surrogate markers. In addition, the staging system used to classify the premalignancy and malignancy of the uterine cervix, as well as the safety and efficacy of the various treatment modalities in clinical trials for cervical cancers, are also discussed. In this millennial world, the advancements in computer-aided technology, including robotic modules and artificial intelligence (AI), are also incorporated into the screening, diagnostic, and treatment platforms. These innovations reduce the dependence on specialists and technologists, as well as the work burden and time incurred for sample processing. However, concerns over the practicality of these advancements remain, due to the high cost, lack of flexibility, and the judgment of a trained professional that is currently not replaceable by a machine.
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Wu Q, Zheng X, Leung KS, Wong MH, Tsui SKW, Cheng L. meGPS: a multi-omics signature for hepatocellular carcinoma detection integrating methylome and transcriptome data. Bioinformatics 2022; 38:3513-3522. [PMID: 35674358 DOI: 10.1093/bioinformatics/btac379] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 05/08/2022] [Accepted: 06/01/2022] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Hepatocellular carcinoma (HCC) is a primary malignancy with poor prognosis. Recently, multi-omics molecular-level measurement enables HCC diagnosis and prognosis prediction, which is crucial for early intervention of personalized therapy to diminish mortality. Here, we introduce a novel strategy utilizing DNA methylation and RNA expression data to achieve a multi-omics gene pair signature (GPS) for HCC discrimination. RESULTS The immune genes with negative correlations between expression and promoter methylation are enriched in the highly connected cancer-related pathway network, which are considered as the candidates for HCC detection. After that, we separately construct a methylation GPS (mGPS) and an expression GPS (eGPS), and then assemble them as a meGPS with five gene pairs, in which the significant methylation and expression changes occur between HCC tumor and non-tumor groups. Reliable performance has been validated by independent tissue (age, gender, and etiology) and blood datasets. This study proposes a procedure for multi-omics GPS identification and develops a novel HCC signature using both methylome and transcriptome data, suggesting potential molecular targets for the detection and therapy of HCC. AVAILABILITY AND IMPLEMENTATION Models are available at https://github.com/bioinformaticStudy/meGPS.git. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Qiong Wu
- Shenzhen People's Hospital, First Affiliated Hospital of Southern University of Science and Technology, Second Clinical Medicine College of Jinan University, Shenzhen, 518020, China.,School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Paediatrics, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Xubin Zheng
- Shenzhen People's Hospital, First Affiliated Hospital of Southern University of Science and Technology, Second Clinical Medicine College of Jinan University, Shenzhen, 518020, China.,Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Kwong-Sak Leung
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Man-Hon Wong
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Stephen Kwok-Wing Tsui
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Lixin Cheng
- Shenzhen People's Hospital, First Affiliated Hospital of Southern University of Science and Technology, Second Clinical Medicine College of Jinan University, Shenzhen, 518020, China
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Yang X, Chen Y, Li M, Zhu W. ERBB3 methylation and immune infiltration in tumor microenvironment of cervical cancer. Sci Rep 2022; 12:8112. [PMID: 35581263 PMCID: PMC9114106 DOI: 10.1038/s41598-022-11415-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 04/22/2022] [Indexed: 11/09/2022] Open
Abstract
ERBB3, a member of the ERBB family of receptor tyrosine kinases, plays an important role in cancer, despite its lack of intrinsic carcinogenic mechanism of cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC). Research on bioinformatics methods through multi-omics, this work proves that ERBB3 gene mutation, methylation modification have extensive regulatory mechanisms on the CESC microenvironment. We found that ERBB3 is involved in carcinogenesis of cervical cancer and is not associated with its prognosis. The carcinogenic mechanism is mainly related to the suppression of the immune system between tumor infiltrating lymphocytes (TILs) and the methylation of the RNA level. Our study indicated ERBB3 is more likely to be a carcinogenic factor than a key prognostic factor for cervical cancer. Methylation of ERBB3 may work as a checkpoint immunotherapy target in CESC, DNA methylation modification of the 4480 base pair downstream of ERBB3 transcription initiation site was the highest.
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Affiliation(s)
- Xiaoyue Yang
- Department of Obstetrics and Gynecology, Affiliated Hospital of Jiangsu University, Jiefang Road 438, Zhenjiang, 212001, Jiangsu, China.,Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Soochow University, Sanxiang Road 1055, Suzhou, 215000, Jiangsu, China
| | - Ying Chen
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Soochow University, Sanxiang Road 1055, Suzhou, 215000, Jiangsu, China
| | - Mei Li
- Department of Pathology, Affiliated Hospital of Jiangsu University, Jiefang Road 438, Zhenjiang, 212001, Jiangsu, China.
| | - Weipei Zhu
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Soochow University, Sanxiang Road 1055, Suzhou, 215000, Jiangsu, China.
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Braz CU, Taylor T, Namous H, Townsend J, Crenshaw T, Khatib H. Paternal diet induces transgenerational epigenetic inheritance of DNA methylation signatures and phenotypes in sheep model. PNAS NEXUS 2022; 1:pgac040. [PMID: 36713326 PMCID: PMC9802161 DOI: 10.1093/pnasnexus/pgac040] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/05/2022] [Accepted: 04/02/2022] [Indexed: 06/18/2023]
Abstract
Transgenerational epigenetic inheritance (TEI) requires transmission of environmentally induced epigenetic changes and associated phenotypes to subsequent generations without continued exposure to the environmental factor that originated the change. TEI is well-established in plants and Caenorhabditis elegans; however, occurrence in mammals is debated and poorly understood. Here, we examined whether paternal diet from weaning to puberty-induced changes in sperm DNA methylation that were transmitted to subsequent generations. Over 100 methylated cytosines, environmentally altered in the F0 generation, were inherited by the F1 and F2 generations. Furthermore, the F0 paternal diet was associated with growth and male fertility phenotypes in subsequent generations. Differentially methylated cytosines were correlated with gene expression. Our results demonstrate that some sperm methylation sites may escape DNA methylation erasure and are transmitted to subsequent generations despite the 2 waves of epigenetic programming: in primordial germ cells and in embryos after fertilization. These results advance our understanding of the complex relationships between nature and nurture.
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Affiliation(s)
- Camila U Braz
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Todd Taylor
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Hadjer Namous
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jessica Townsend
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Thomas Crenshaw
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
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Deng Y, Li Y, Wu T, Chen X, Li X, Cai K, Wu X. RAD6 Positively Affects Tumorigenesis of Esophageal Squamous Cell Carcinoma by Regulating Histone Ubiquitination of CCNB1. Biol Proced Online 2022; 24:4. [PMID: 35321657 PMCID: PMC8943946 DOI: 10.1186/s12575-022-00165-z] [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: 09/13/2021] [Accepted: 02/21/2022] [Indexed: 11/23/2022] Open
Abstract
Objective Esophageal carcinoma (ESCA) is deadly cancer worldwide with unknown etiology. This study aimed to investigate the impact and mechanism of RAD6 on the development of Esophageal squamous cell carcinoma (ESCC). Expressions of RAD6A and RAD6B in ESCA were investigated from TCGA dataset and their expressions in tissue sample of ESCA patients and cells were determined. Functional experiments were conducted to explore the impact of RAD6A and RAD6B on malignant characteristics of several kinds of ESCC cells. Animal experiment was established and injected with RAD6A and RAD6B shRNA to evaluate the effect on tumor growth. RAD6A and RAD6B were up-regulated in ESCC cells and tissues. Overexpressed RAD6A and RAD6B similarly increased ESCC cell proliferation, invasion and migration and silencing of RAD6 exerted opposite effects. Knockdown of RAD6A suppressed tumor growth and decreased the level of H2B, as data demonstrated positive correlation between RAD6A and CCNB1 in ESCC tissues. Collectively, this study elucidates that RAD6 is up-regulated in ESCC and promotes the progression of ESCC through up-regulation of CCNB1 to enhance H2B ubiquitination. These evidence provide a novel insight into the pathogenesis of ESCC and might contribute to the development of targeted therapy.
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Affiliation(s)
- Yu Deng
- Department of Thoracic Surgery, Nanfang Hospital of Southern Medical University, Guangzhou, China
| | - Yujiang Li
- Department of Thoracic Surgery, Nanfang Hospital of Southern Medical University, Guangzhou, China.,Department of Thoracic and Cardiovascular Surgery, Affiliated Dongguan People's Hospital, Southern Medical University, Dongguan, China
| | - Tiantong Wu
- Department of General Surgery, Nanfang Hospital of Southern Medical University, Guangzhou, China
| | - Xuyuan Chen
- Department of Thoracic Surgery, Nanfang Hospital of Southern Medical University, Guangzhou, China
| | - Xiang Li
- Department of Emergency Medicine, Nanfang Hospital of Southern Medical University, Guangzhou, China
| | - Kaican Cai
- Department of Thoracic Surgery, Nanfang Hospital of Southern Medical University, Guangzhou, China.
| | - Xu Wu
- Department of Thoracic Surgery, Nanfang Hospital of Southern Medical University, Guangzhou, China.
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Integration of Multimodal Data from Disparate Sources for Identifying Disease Subtypes. BIOLOGY 2022; 11:biology11030360. [PMID: 35336734 PMCID: PMC8945377 DOI: 10.3390/biology11030360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/17/2022] [Accepted: 02/23/2022] [Indexed: 11/17/2022]
Abstract
Simple Summary The diagnostic and treatment strategies of cancer remain generally suboptimal resulting in over-diagnosis or under-treatment. Though many attempts on optimizing treatment decisions by early prediction of disease progression have been undertaken, these efforts yielded only modest success so far due to the heterogeneity of cancer with multifactorial etiology. Here, we propose a deep-learning based data integration model capable of predicting disease progression by integrating collective information available through multiple studies with different cohorts and heterogeneous data types. The results have shown that the proposed data integration pipeline is able to identify disease progression with higher accuracy and robustness compared to using a single cohort, by offering a more complete picture of the specific disease on patients with brain, blood, and pancreatic cancers. Abstract Studies over the past decade have generated a wealth of molecular data that can be leveraged to better understand cancer risk, progression, and outcomes. However, understanding the progression risk and differentiating long- and short-term survivors cannot be achieved by analyzing data from a single modality due to the heterogeneity of disease. Using a scientifically developed and tested deep-learning approach that leverages aggregate information collected from multiple repositories with multiple modalities (e.g., mRNA, DNA Methylation, miRNA) could lead to a more accurate and robust prediction of disease progression. Here, we propose an autoencoder based multimodal data fusion system, in which a fusion encoder flexibly integrates collective information available through multiple studies with partially coupled data. Our results on a fully controlled simulation-based study have shown that inferring the missing data through the proposed data fusion pipeline allows a predictor that is superior to other baseline predictors with missing modalities. Results have further shown that short- and long-term survivors of glioblastoma multiforme, acute myeloid leukemia, and pancreatic adenocarcinoma can be successfully differentiated with an AUC of 0.94, 0.75, and 0.96, respectively.
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Yates J, Boeva V. Deciphering the etiology and role in oncogenic transformation of the CpG island methylator phenotype: a pan-cancer analysis. Brief Bioinform 2022; 23:6520307. [PMID: 35134107 PMCID: PMC8921629 DOI: 10.1093/bib/bbab610] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/06/2021] [Accepted: 12/30/2021] [Indexed: 12/25/2022] Open
Abstract
Numerous cancer types have shown to present hypermethylation of CpG islands, also known as a CpG island methylator phenotype (CIMP), often associated with survival variation. Despite extensive research on CIMP, the etiology of this variability remains elusive, possibly due to lack of consistency in defining CIMP. In this work, we utilize a pan-cancer approach to further explore CIMP, focusing on 26 cancer types profiled in the Cancer Genome Atlas (TCGA). We defined CIMP systematically and agnostically, discarding any effects associated with age, gender or tumor purity. We then clustered samples based on their most variable DNA methylation values and analyzed resulting patient groups. Our results confirmed the existence of CIMP in 19 cancers, including gliomas and colorectal cancer. We further showed that CIMP was associated with survival differences in eight cancer types and, in five, represented a prognostic biomarker independent of clinical factors. By analyzing genetic and transcriptomic data, we further uncovered potential drivers of CIMP and classified them in four categories: mutations in genes directly involved in DNA demethylation; mutations in histone methyltransferases; mutations in genes not involved in methylation turnover, such as KRAS and BRAF; and microsatellite instability. Among the 19 CIMP-positive cancers, very few shared potential driver events, and those drivers were only IDH1 and SETD2 mutations. Finally, we found that CIMP was strongly correlated with tumor microenvironment characteristics, such as lymphocyte infiltration. Overall, our results indicate that CIMP does not exhibit a pan-cancer manifestation; rather, general dysregulation of CpG DNA methylation is caused by heterogeneous mechanisms.
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Affiliation(s)
- Josephine Yates
- Institute for Machine Learning, Department of Computer Science, ETH Zürich, Zurich 8092, Switzerland
| | - Valentina Boeva
- Institute for Machine Learning, Department of Computer Science, ETH Zürich, Zurich 8092, Switzerland.,Swiss Institute for Bioinformatics (SIB), Zürich, Switzerland.,Cochin Institute, Inserm U1016, CNRS UMR 8104, Paris Descartes University UMR-S1016, Paris 75014, France
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Epigenome-Wide DNA Methylation Profiling in Colorectal Cancer and Normal Adjacent Colon Using Infinium Human Methylation 450K. Diagnostics (Basel) 2022; 12:diagnostics12010198. [PMID: 35054365 PMCID: PMC8775085 DOI: 10.3390/diagnostics12010198] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/31/2021] [Accepted: 01/03/2022] [Indexed: 01/20/2023] Open
Abstract
The aims were to profile the DNA methylation in colorectal cancer (CRC) and to explore cancer-specific methylation biomarkers. Fifty-four pairs of CRCs and the adjacent normal tissues were subjected to Infinium Human Methylation 450K assay and analysed using ChAMP R package. A total of 26,093 differentially methylated probes were identified, which represent 6156 genes; 650 probes were hypermethylated, and 25,443 were hypomethylated. Hypermethylated sites were common in CpG islands, while hypomethylated sites were in open sea. Most of the hypermethylated genes were associated with pathways in cancer, while the hypomethylated genes were involved in the PI3K-AKT signalling pathway. Among the identified differentially methylated probes, we found evidence of four potential probes in CRCs versus adjacent normal; HOXA2 cg06786372, OPLAH cg17301223, cg15638338, and TRIM31 cg02583465 that could serve as a new biomarker in CRC since these probes were aberrantly methylated in CRC as well as involved in the progression of CRC. Furthermore, we revealed the potential of promoter methylation ADHFE1 cg18065361 in differentiating the CRC from normal colonic tissue from the integrated analysis. In conclusion, aberrant DNA methylation is significantly involved in CRC pathogenesis and is associated with gene silencing. This study reports several potential important methylated genes in CRC and, therefore, merit further validation as novel candidate biomarker genes in CRC.
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Zhao J, Liu Z, Zheng X, Gao H, Li L. Prognostic Model and Nomogram Construction Based on a Novel Ferroptosis-Related Gene Signature in Lower-Grade Glioma. Front Genet 2021; 12:753680. [PMID: 34819946 PMCID: PMC8606636 DOI: 10.3389/fgene.2021.753680] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 10/04/2021] [Indexed: 01/31/2023] Open
Abstract
Background: Low-grade glioma (LGG) is considered a fatal disease for young adults, with overall survival widely ranging from 1 to 15 years depending on histopathologic and molecular subtypes. As a novel type of programmed cell death, ferroptosis was reported to be involved in tumorigenesis and development, which has been intensively studied in recent years. Methods: For the discovery cohort, data from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) were used to identify the differentially expressed and prognostic ferroptosis-related genes (FRGs). The least absolute shrinkage and selection operator (LASSO) and multivariate Cox were used to establish a prognostic signature with the above-selected FRGs. Then, the signature was developed and validated in TCGA and Chinese Glioma Genome Atlas (CGGA) databases. By combining clinicopathological features and the FRG signature, a nomogram was established to predict individuals’ one-, three-, and five-year survival probability, and its predictive performance was evaluated by Harrell’s concordance index (C-index) and calibration curves. Enrichment analysis was performed to explore the signaling pathways regulated by the signature. Results: A novel risk signature contains seven FRGs that were constructed and were used to divide patients into two groups. Kaplan–Meier (K−M) survival curve and receiver-operating characteristic (ROC) curve analyses confirmed the prognostic performance of the risk model, followed by external validation based on data from the CGGA. The nomogram based on the risk signature and clinical traits was validated to perform well for predicting the survival rate of LGG. Finally, functional analysis revealed that the immune statuses were different between the two risk groups, which might help explain the underlying mechanisms of ferroptosis in LGG. Conclusion: In conclusion, this study constructed a novel and robust seven-FRG signature and established a prognostic nomogram for LGG survival prediction.
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Affiliation(s)
- Junsheng Zhao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhengtao Liu
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaoping Zheng
- Department of Pathology, Hangzhou Tongchuang Medical Laboratory, Hangzhou, China
| | - Hainv Gao
- Department of Infectious Diseases, ShuLan (Hangzhou) Hospital Affiliated to Zhejiang Shuren University, Shulan International Medical College, Hangzhou, China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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Celaya-Padilla JM, Villagrana-Bañuelos KE, Oropeza-Valdez JJ, Monárrez-Espino J, Castañeda-Delgado JE, Oostdam ASHV, Fernández-Ruiz JC, Ochoa-González F, Borrego JC, Enciso-Moreno JA, López JA, López-Hernández Y, Galván-Tejada CE. Kynurenine and Hemoglobin as Sex-Specific Variables in COVID-19 Patients: A Machine Learning and Genetic Algorithms Approach. Diagnostics (Basel) 2021; 11:2197. [PMID: 34943434 PMCID: PMC8700648 DOI: 10.3390/diagnostics11122197] [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: 10/07/2021] [Revised: 11/21/2021] [Accepted: 11/21/2021] [Indexed: 11/16/2022] Open
Abstract
Differences in clinical manifestations, immune response, metabolic alterations, and outcomes (including disease severity and mortality) between men and women with COVID-19 have been reported since the pandemic outbreak, making it necessary to implement sex-specific biomarkers for disease diagnosis and treatment. This study aimed to identify sex-associated differences in COVID-19 patients by means of a genetic algorithm (GALGO) and machine learning, employing support vector machine (SVM) and logistic regression (LR) for the data analysis. Both algorithms identified kynurenine and hemoglobin as the most important variables to distinguish between men and women with COVID-19. LR and SVM identified C10:1, cough, and lysoPC a 14:0 to discriminate between men with COVID-19 from men without, with LR being the best model. In the case of women with COVID-19 vs. women without, SVM had a higher performance, and both models identified a higher number of variables, including 10:2, lysoPC a C26:0, lysoPC a C28:0, alpha-ketoglutaric acid, lactic acid, cough, fever, anosmia, and dysgeusia. Our results demonstrate that differences in sexes have implications in the diagnosis and outcome of the disease. Further, genetic and machine learning algorithms are useful tools to predict sex-associated differences in COVID-19.
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Affiliation(s)
- Jose M. Celaya-Padilla
- Unidad Académica de Ingeniería Eléctrica, Universidad Autónoma de Zacatecas, Jardín Juárez 147, Centro, Zacatecas 98000, Mexico; (J.M.C.-P.); (K.E.V.-B.)
| | - Karen E. Villagrana-Bañuelos
- Unidad Académica de Ingeniería Eléctrica, Universidad Autónoma de Zacatecas, Jardín Juárez 147, Centro, Zacatecas 98000, Mexico; (J.M.C.-P.); (K.E.V.-B.)
| | - Juan José Oropeza-Valdez
- Unidad de Investigación Biomédica de Zacatecas, Instituto Mexicano del Seguro Social, Centro, Zacatecas 98000, Mexico; (J.J.O.-V.); (J.E.C.-D.); (J.C.F.-R.); (F.O.-G.); (J.A.E.-M.)
| | - Joel Monárrez-Espino
- Department of Health Research, Christus Muguerza del Parque Hospital Chihuahua, University of Monterrey, San Pedro Garza García 66238, Mexico;
| | - Julio E. Castañeda-Delgado
- Unidad de Investigación Biomédica de Zacatecas, Instituto Mexicano del Seguro Social, Centro, Zacatecas 98000, Mexico; (J.J.O.-V.); (J.E.C.-D.); (J.C.F.-R.); (F.O.-G.); (J.A.E.-M.)
- Cátedras-CONACyT, Consejo Nacional de Ciencia y Tecnología, Ciudad de México 03940, Mexico
| | - Ana Sofía Herrera-Van Oostdam
- Doctorado en Ciencias Biomédicas Básicas, Centro de Investigación en Ciencias de la Salud y Biomedicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí 78210, Mexico;
| | - Julio César Fernández-Ruiz
- Unidad de Investigación Biomédica de Zacatecas, Instituto Mexicano del Seguro Social, Centro, Zacatecas 98000, Mexico; (J.J.O.-V.); (J.E.C.-D.); (J.C.F.-R.); (F.O.-G.); (J.A.E.-M.)
| | - Fátima Ochoa-González
- Unidad de Investigación Biomédica de Zacatecas, Instituto Mexicano del Seguro Social, Centro, Zacatecas 98000, Mexico; (J.J.O.-V.); (J.E.C.-D.); (J.C.F.-R.); (F.O.-G.); (J.A.E.-M.)
- Área de Ciencias de la Salud, Universidad Autónoma de Zacatecas, Carretera Zacatecas–Guadalajara kilometro 6, Ejido la Escondida, Zacatecas 98160, Mexico
| | - Juan Carlos Borrego
- Departamento de Epidemiología, Hospital General de Zona #1 “Emilio Varela Luján”, Instituto Mexicano del Seguro Social, Centro, Zacatecas 98000, Mexico;
| | - Jose Antonio Enciso-Moreno
- Unidad de Investigación Biomédica de Zacatecas, Instituto Mexicano del Seguro Social, Centro, Zacatecas 98000, Mexico; (J.J.O.-V.); (J.E.C.-D.); (J.C.F.-R.); (F.O.-G.); (J.A.E.-M.)
| | - Jesús Adrián López
- Laboratorio de MicroRNAs y Cáncer, Unidad Académica de Ciencias Biológicas, Universidad Autónoma de Zacatecas, Zacatecas 98000, Mexico;
| | - Yamilé López-Hernández
- Cátedras-CONACyT, Consejo Nacional de Ciencia y Tecnología, Ciudad de México 03940, Mexico
- Metabolomics and Proteomics Laboratory, Autonomous University of Zacatecas, Zacatecas 98000, Mexico
| | - Carlos E. Galván-Tejada
- Unidad Académica de Ingeniería Eléctrica, Universidad Autónoma de Zacatecas, Jardín Juárez 147, Centro, Zacatecas 98000, Mexico; (J.M.C.-P.); (K.E.V.-B.)
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Shi K, Lin W, Zhao XM. Identifying Molecular Biomarkers for Diseases With Machine Learning Based on Integrative Omics. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021; 18:2514-2525. [PMID: 32305934 DOI: 10.1109/tcbb.2020.2986387] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Molecular biomarkers are certain molecules or set of molecules that can be of help for diagnosis or prognosis of diseases or disorders. In the past decades, thanks to the advances in high-throughput technologies, a huge amount of molecular 'omics' data, e.g., transcriptomics and proteomics, have been accumulated. The availability of these omics data makes it possible to screen biomarkers for diseases or disorders. Accordingly, a number of computational approaches have been developed to identify biomarkers by exploring the omics data. In this review, we present a comprehensive survey on the recent progress of identification of molecular biomarkers with machine learning approaches. Specifically, we categorize the machine learning approaches into supervised, un-supervised and recommendation approaches, where the biomarkers including single genes, gene sets and small gene networks. In addition, we further discuss potential problems underlying bio-medical data that may pose challenges for machine learning, and provide possible directions for future biomarker identification.
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Dlamini Z, Mbele M, Makhafola TJ, Hull R, Marima R. HIV-Associated Cancer Biomarkers: A Requirement for Early Diagnosis. Int J Mol Sci 2021; 22:ijms22158127. [PMID: 34360891 PMCID: PMC8348540 DOI: 10.3390/ijms22158127] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/18/2021] [Accepted: 07/19/2021] [Indexed: 02/07/2023] Open
Abstract
Globally, HIV/AIDS and cancer are increasingly public health problems and continue to exist as comorbidities. The sub-Saharan African region has the largest number of HIV infections. Malignancies previously associated with HIV/AIDS, also known as the AIDS-defining cancers (ADCs) have been documented to decrease, while the non-AIDS defining cancer (NADCs) are on the rise. On the other hand, cancer is a highly heterogeneous disease and precision oncology as the most effective cancer therapy is gaining attraction. Among HIV-infected individuals, the increased risk for developing cancer is due to the immune system of the patient being suppressed, frequent coinfection with oncogenic viruses and an increase in risky behavior such as poor lifestyle. The core of personalised medicine for cancer depends on the discovery and the development of biomarkers. Biomarkers are specific and highly sensitive markers that reveal information that aid in leading to the diagnosis, prognosis and therapy of the disease. This review focuses mainly on the risk assessment, diagnostic, prognostic and therapeutic role of various cancer biomarkers in HIV-positive patients. A careful selection of sensitive and specific HIV-associated cancer biomarkers is required to identify patients at most risk of tumour development, thus improving the diagnosis and prognosis of the disease.
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Zhao D, Kim DY, Chen P, Yu P, Ho S, Cheng SW, Zhao C, Guo JA, Li YR. Pan-Cancer Survival Classification With Clinicopathological and Targeted Gene Expression Features. Cancer Inform 2021; 20:11769351211035137. [PMID: 34376966 PMCID: PMC8330450 DOI: 10.1177/11769351211035137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 07/05/2021] [Indexed: 11/15/2022] Open
Abstract
Prognostication for patients with cancer is important for clinical planning and management, but remains challenging given the large number of factors that can influence outcomes. As such, there is a need to identify features that can robustly predict patient outcomes. We evaluated 8608 patient tumor samples across 16 cancer types from The Cancer Genome Atlas and generated distinct survival classifiers for each using clinical and histopathological data accessible to standard oncology workflows. For cancers that had poor model performance, we deployed a random-forest-embedded sequential forward selection approach that began with an initial subset of the 15 most predictive clinicopathological features before sequentially appending the next most informative gene as an additional feature. With classifiers derived from clinical and histopathological features alone, we observed cancer-type-dependent model performance and an area under the receiver operating curve (AUROC) range of 0.65 to 0.91 across all 16 cancer types for 1- and 3-year survival prediction, with some classifiers consistently outperforming those for others. As such, for cancers that had poor model performance, we posited that the addition of more complex biomolecular features could enhance our ability to prognose patients where clinicopathological features were insufficient. With the inclusion of gene expression data, model performance for 3 select cancers (glioblastoma, stomach/gastric adenocarcinoma, ovarian serous carcinoma) markedly increased from initial AUROC scores of 0.66, 0.69, and 0.67 to 0.76, 0.77, and 0.77, respectively. As a whole, this study provides a thorough examination of the relative contributions of clinical, pathological, and gene expression data in predicting overall survival and reveals cancer types for which clinical features are already strong predictors and those where additional biomolecular information is needed.
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Affiliation(s)
- Daniel Zhao
- School of Medicine, New York Medical College, Valhalla, NY, USA
| | - Daniel Y Kim
- Molecular Pathology, Massachusetts General Hospital, Charlestown, MA, USA
| | - Peter Chen
- Raytheon Technologies, Brooklyn, NY, USA
| | - Patrick Yu
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,College of Engineering, University of Illinois at Urbana-Champaign, Champaign, IL, USA
| | - Sophia Ho
- Northeastern University, Boston, MA, USA
| | | | - Cindy Zhao
- Northeastern University, Boston, MA, USA
| | - Jimmy A Guo
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA.,School of Medicine, UCSF, San Francisco, CA, USA
| | - Yun R Li
- Department of Radiation Oncology, UCSF, San Francisco, CA, USA
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Li B, Huang Z, Yu W, Liu S, Zhang J, Wang Q, Wu L, Kou F, Yang L. Molecular subtypes based on CNVs related gene signatures identify candidate prognostic biomarkers in lung adenocarcinoma. Neoplasia 2021; 23:704-717. [PMID: 34139453 PMCID: PMC8208901 DOI: 10.1016/j.neo.2021.05.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 05/06/2021] [Indexed: 12/26/2022]
Abstract
The classical factors for predicting prognosis currently cannot meet the developing requirements of individualized and accurate prognostic evaluation in lung adenocarcinoma (LUAD). With the rapid development of high-throughput DNA sequencing technologies, genomic changes have been discovered. These sequencing data provide unprecedented opportunities for identifying cancer molecular subtypes. In this article, we classified LUAD into two distinct molecular subtypes (Cluster 1 and Cluster 2) based on Copy Number Variations (CNVs) and mRNA expression data from the Cancer Genome Atlas (TCGA) based on non-negative matrix factorization. Patients in Cluster 1 had worse outcomes than that in Cluster 2. Molecular features in subtypes were assessed to explain this phenomenon by analyzing differential expression genes expression pattern, which involved in cellular processes and environmental information processing. Analysis of immune cell populations suggested different distributions of CD4+ T cells, CD8+ T cells, and dendritic cells in the two subtypes. Subsequently, two novel genes, TROAP and RASGRF1, were discovered to be prognostic biomarkers in TCGA, which were confirmed in GSE31210 and Tianjin Medical University Cancer Institute and Hospital LUAD cohorts. We further proved their crucial roles in cancers by vitro experiments. TROAP mediates tumor cell proliferation, cycle, invasion, and migration, not apoptosis. RASGRF1 has a significant effect on tumor microenvironment. In conclusion, our study provides a novel insight into molecular classification based on CNVs related genes in LUAD, which may contribute to identify new molecular subtypes and target genes.
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Affiliation(s)
- Baihui Li
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China; National Clinical Research Center for Cancer, Tianjin, China; Key Laboratory of Cancer Prevention and Therapy, Tianjin, China; Tianjin's Clinical Research Center for Cancer, Tianjin, China; Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China
| | - Ziqi Huang
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China; National Clinical Research Center for Cancer, Tianjin, China; Key Laboratory of Cancer Prevention and Therapy, Tianjin, China; Tianjin's Clinical Research Center for Cancer, Tianjin, China; Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China
| | - Wenwen Yu
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China; National Clinical Research Center for Cancer, Tianjin, China; Key Laboratory of Cancer Prevention and Therapy, Tianjin, China; Tianjin's Clinical Research Center for Cancer, Tianjin, China; Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China
| | - Shaochuan Liu
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China; National Clinical Research Center for Cancer, Tianjin, China; Key Laboratory of Cancer Prevention and Therapy, Tianjin, China; Tianjin's Clinical Research Center for Cancer, Tianjin, China; Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China
| | - Jian Zhang
- School of Medicine, Nankai University, Tianjin, China; Department of Oncology, Oncology Laboratory, General Hospital of Chinese PLA, Beijing, China
| | - Qingqing Wang
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China; National Clinical Research Center for Cancer, Tianjin, China; Key Laboratory of Cancer Prevention and Therapy, Tianjin, China; Tianjin's Clinical Research Center for Cancer, Tianjin, China; Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China
| | - Lei Wu
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China; National Clinical Research Center for Cancer, Tianjin, China; Key Laboratory of Cancer Prevention and Therapy, Tianjin, China; Tianjin's Clinical Research Center for Cancer, Tianjin, China; Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China
| | - Fan Kou
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China; National Clinical Research Center for Cancer, Tianjin, China; Key Laboratory of Cancer Prevention and Therapy, Tianjin, China; Tianjin's Clinical Research Center for Cancer, Tianjin, China; Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China
| | - Lili Yang
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China; National Clinical Research Center for Cancer, Tianjin, China; Key Laboratory of Cancer Prevention and Therapy, Tianjin, China; Tianjin's Clinical Research Center for Cancer, Tianjin, China; Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China.
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Katopodis P, Kerslake R, Zikopoulos A, Beri N, Anikin V. p38β - MAPK11 and its role in female cancers. J Ovarian Res 2021; 14:84. [PMID: 34174910 PMCID: PMC8236201 DOI: 10.1186/s13048-021-00834-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 06/07/2021] [Indexed: 12/24/2022] Open
Abstract
Background The p38MAPK family of Mitogen Activated Protein Kinases are a group of signalling molecules involved in cell growth, survival, proliferation and differentiation. The widely studied p38α isoform is ubiquitously expressed and is implicated in a number of cancer pathologies, as are p38γ and p38δ. However, the mechanistic role of the isoform, p38β, remains fairly elusive. Recent studies suggest a possible role of p38β in both breast and endometrial cancer with research suggesting involvement in bone metastasis and cancer cell survival. Female tissue specific cancers such as breast, endometrial, uterine and ovary account for over 3,000,000 cancer related incidents annually; advancements in therapeutics and treatment however require a deeper understanding of the molecular aetiology associated with these diseases. This study provides an overview of the MAPK signalling molecule p38β (MAPK11) in female cancers using an in-silico approach. Methods A detailed gene expression and methylation analysis was performed using datasets from cBioportal, CanSar and MEXPRESS. Breast, Uterine Endometrial, Cervical, Ovarian and Uterine Carcinosarcoma TCGA cancer datasets were used and analysed. Results Data using cBioportal and CanSAR suggest that expression of p38β is lower in cancers: BRCA, UCEC, UCS, CESC and OV compared to normal tissue. Methylation data from SMART and MEXPRESS indicate significant probe level variation of CpG island methylation status of the gene MAPK11. Analysis of the genes’ two CpG islands shows that the gene was hypermethylated in the CpG1 with increased methylation seen in BRCA, CESC and UCEC cancer data sets with a slight increase of expression recorded in cancer samples. CpG2 exhibited hypomethylation with no significant difference between samples and high levels of expression. Further analysis from MEXPRESS revealed no significance between probe methylation and altered levels of expression. In addition, no difference in the expression of BRCA oestrogen/progesterone/HER2 status was seen. Conclusion This data provides an overview of the expression of p38β in female tissue specific cancers, showing a decrease in expression of the gene in BRCA, UCEC, CESC, UCS and OV, increasing the understanding of p38β MAPK expression and offering insight for future in-vitro investigation and therapeutic application. Supplementary Information The online version contains supplementary material available at 10.1186/s13048-021-00834-9.
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Affiliation(s)
- Periklis Katopodis
- Biosciences, College of Health and Life Sciences, Brunel University London, Uxbridge, UK. .,Division of Thoracic Surgery, The Royal Brompton & Harefield NHS Foundation Trust, Harefield Hospital, London, UB9 6JH, UK.
| | - Rachel Kerslake
- Biosciences, College of Health and Life Sciences, Brunel University London, Uxbridge, UK
| | - Athanasios Zikopoulos
- Obstetrics and Gynaecology Department, Royal Cornwall Hospitals NHS Foundation Trust, Royal Cornwall Hospital, Truro, TR1 3LJ, UK
| | - Nefeli Beri
- Department of Medicine, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Vladimir Anikin
- Division of Thoracic Surgery, The Royal Brompton & Harefield NHS Foundation Trust, Harefield Hospital, London, UB9 6JH, UK.,Department of Oncology and Reconstructive Surgery, Sechenov First Moscow State Medical University, Moscow, Russian Federation, 119146
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Chen H, Li H, Wang L, Li Y, Yang C. A 5-gene DNA methylation signature is a promising prognostic biomarker for early-stage cervical cancer. J OBSTET GYNAECOL 2021; 42:327-332. [PMID: 34082663 DOI: 10.1080/01443615.2021.1907563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The demographic information and overall survival (OS) of patients with cervical cancer (CC) (pathological stage: IA-IIA) were extracted from the TCGA database. A univariate and multivariate Cox proportional hazard model was performed to identify methylation markers significantly associated with the OS of patients in the training dataset. Then such a prognostic classifier was tested on the validation set and all subgroups. The Kaplan-Meier analysis and ROC analysis were performed to detect the ability to discriminate between patients with different risks and different OS. A DNA methylation signature which contained five genes was found to be significantly associated with the OS of CC patients by the Cox regression analysis in the training dataset. Such a signature could efficiently distinguish the patients into two risk groups with significantly different OS in both datasets. The receiver operating characteristic (ROC) analysis showed it had high sensitivity and specificity. Moreover, such a prognostic model also could be effectively applied to different subgroups, including groups of different ages, tumour sizes, histologic types, etc. A 5-DNA methylation signature identified by this study may act as a novel prognostic indicator for early-stage CC, and it may be helpful for the timely diagnosis and intervention of CC at pathological stages IA-IIA.Impact StatementWhat is already known on this subject? Cervical cancer (CC) is one of the most common gynaecological malignant tumours.What the results of this study add? This study constructed a risk model based on a 5-DNA methylation signature for early-stage CC patients' survival prediction.What the implications are of these findings for clinical practice and/or further research? Methylated markers have the potential to discriminate patients of different risks and different OS. Our results may shed new light on the early diagnosis and intervention, and potential therapeutic targets for CC patients at pathological stages IA-IIA.
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Affiliation(s)
- Hongxia Chen
- Department of Pathophysiology, School of Basic Medicine, Hubei University of Science and Technology, Xianning, China
| | - Hongying Li
- Maternal and Child Health Hospital of Hubei Province, Hongshan District, Wuhan, Hubei, China.,Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Wuhan University of Science and Technology, Wuhan, Hubei, China
| | - Lei Wang
- School of Laboratory Medicine, Hubei University of Chinese Medicine, Wuhan, China
| | - Yaxiong Li
- Information Center of Hubei University of Science and Technology, Xianning, China
| | - ChunYan Yang
- Department of Public Health Management, School of Basic Medicine, Hubei University of Science and Technology, Xianning, China
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Yu R, Zhang L, Yu Q, Zhao H, Yang H, Wang Y. Effect of LHX2 gene methylation level and its function on radiotherapy of cervical cancer. Transl Cancer Res 2021; 10:2944-2961. [PMID: 35116603 PMCID: PMC8797467 DOI: 10.21037/tcr-21-739] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 06/01/2021] [Indexed: 12/29/2022]
Abstract
Background Cervical cancer is the most common malignancy of the female reproductive system, for which radiotherapy is one of the main treatments. Gene methylation in cells is an important factor in tumorigenesis, and radiotherapy can change DNA methylation in cells. At the same time, combined with the clinical effect of radiotherapy, key genes of LIM homeobox 2 (LHX2) significantly related to cervical cancer. The LHX2 are LIM-homeobox genes that play important roles in signal transduction, cell differentiation, tissue-specific differentiation, and body formation. Methods In this study, bisulfite genomic sequencing (BSP-Seq) technology was used to analyze the methylation level of LHX2 in patients with cervical cancer before and after radiotherapy. In addition, combined with the clinical effect of radiotherapy, the function of LHX2 in siHA and C33A cells were analyzed with the help of overexpression, small interfering RNA (siRNA), cell invasion, and migration ability. The expression level of the migration- and apoptosis-related genes which were affected by LHX2 were tested with quantitative real time polymerase chain reaction (qRT-PCR). Results Combined with clinical treatment, methylation level difference, and correlation enrichment analysis, it was found that LHX2 genes were closely related to the occurrence and development of cervical cancer. After 5-aza-2’-deoxycytidine (5-Aza-dC) and radiotherapy, the methylation of LHX2 genes in siHA and C33A squamous cell carcinoma cells was decreased, and the messenger RNA (mRNA) and protein expression levels were relatively increased; meanwhile, the LHX2 could accelerate the ability for cell invasion and migration and inhibited the apoptosis of the cell after treatment with radiotherapy. Conclusions The methylation and expression levels of LHX2 genes are closely related to cervical cancer. The methylation level of LHX2 was reduced after radiation therapy. The LHX2 gene has a positive effect on cervical cancer through acceleration of the cell invasion and migration ability and inhibition of cell apoptosis after radiotherapy treatment.
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Affiliation(s)
- Rong Yu
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China.,Department of Radiation Oncology, Inner Mongolia Cancer Hospital & Affiliated People's Hospital of Inner Mongolia Medical University, Hohhot, Inner Mongolia, China
| | - Lihe Zhang
- Department of Radiation Oncology, Inner Mongolia Cancer Hospital & Affiliated People's Hospital of Inner Mongolia Medical University, Hohhot, Inner Mongolia, China
| | - Qin Yu
- Department of Radiation Oncology, Inner Mongolia Cancer Hospital & Affiliated People's Hospital of Inner Mongolia Medical University, Hohhot, Inner Mongolia, China
| | - Haiping Zhao
- Department of Radiation Oncology, Inner Mongolia Cancer Hospital & Affiliated People's Hospital of Inner Mongolia Medical University, Hohhot, Inner Mongolia, China
| | - Hao Yang
- Department of Radiation Oncology, Inner Mongolia Cancer Hospital & Affiliated People's Hospital of Inner Mongolia Medical University, Hohhot, Inner Mongolia, China
| | - Yadi Wang
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China.,Radiotherapy Department, Oncology Faculty, the Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
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Talukdar FR, Soares Lima SC, Khoueiry R, Laskar RS, Cuenin C, Sorroche BP, Boisson AC, Abedi-Ardekani B, Carreira C, Menya D, Dzamalala CP, Assefa M, Aseffa A, Miranda-Gonçalves V, Jerónimo C, Henrique RM, Shakeri R, Malekzadeh R, Gasmelseed N, Ellaithi M, Gangane N, Middleton DRS, Le Calvez-Kelm F, Ghantous A, Roux ML, Schüz J, McCormack V, Parker MI, Pinto LFR, Herceg Z. Genome-Wide DNA Methylation Profiling of Esophageal Squamous Cell Carcinoma from Global High-Incidence Regions Identifies Crucial Genes and Potential Cancer Markers. Cancer Res 2021; 81:2612-2624. [PMID: 33741694 DOI: 10.1158/0008-5472.can-20-3445] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 01/04/2021] [Accepted: 03/18/2021] [Indexed: 12/24/2022]
Abstract
Epigenetic mechanisms such as aberrant DNA methylation (DNAme) are known to drive esophageal squamous cell carcinoma (ESCC), yet they remain poorly understood. Here, we studied tumor-specific DNAme in ESCC cases from nine high-incidence countries of Africa, Asia, and South America. Infinium MethylationEPIC array was performed on 108 tumors and 51 normal tissues adjacent to the tumors (NAT) in the discovery phase, and targeted pyrosequencing was performed on 132 tumors and 36 NAT in the replication phase. Top genes for replication were prioritized by weighting methylation results using RNA-sequencing data from The Cancer Genome Atlas and GTEx and validated by qPCR. Methylome analysis comparing tumor and NAT identified 6,796 differentially methylated positions (DMP) and 866 differential methylated regions (DMR), with a 30% methylation (Δβ) difference. The majority of identified DMPs and DMRs were hypermethylated in tumors, particularly in promoters and gene-body regions of genes involved in transcription activation. The top three prioritized genes for replication, PAX9, SIM2, and THSD4, had similar methylation differences in the discovery and replication sets. These genes were exclusively expressed in normal esophageal tissues in GTEx and downregulated in tumors. The specificity and sensitivity of these DNAme events in discriminating tumors from NAT were assessed. Our study identified novel, robust, and crucial tumor-specific DNAme events in ESCC tumors across several high-incidence populations of the world. Methylome changes identified in this study may serve as potential targets for biomarker discovery and warrant further functional characterization. SIGNIFICANCE: This largest genome-wide DNA methylation study on ESCC from high-incidence populations of the world identifies functionally relevant and robust DNAme events that could serve as potential tumor-specific markers. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/81/10/2612/F1.large.jpg.
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Affiliation(s)
| | - Sheila C Soares Lima
- Department of Molecular Carcinogenesis, Brazilian National Cancer Institute, Rio de Janeiro, Brazil
| | - Rita Khoueiry
- International Agency for Research on Cancer, Lyon, France
| | | | - Cyrille Cuenin
- International Agency for Research on Cancer, Lyon, France
| | - Bruna Pereira Sorroche
- International Agency for Research on Cancer, Lyon, France
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
| | | | | | | | | | | | | | - Abraham Aseffa
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Vera Miranda-Gonçalves
- Department of Pathology and Cancer Biology and Epigenetics Group, Portuguese Oncology Institute of Porto and Biomedical Sciences Institute of University of Porto, Porto, Portugal
| | - Carmen Jerónimo
- Department of Pathology and Cancer Biology and Epigenetics Group, Portuguese Oncology Institute of Porto and Biomedical Sciences Institute of University of Porto, Porto, Portugal
| | - Rui M Henrique
- Department of Pathology and Cancer Biology and Epigenetics Group, Portuguese Oncology Institute of Porto and Biomedical Sciences Institute of University of Porto, Porto, Portugal
| | - Ramin Shakeri
- Digestive Disease Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Reza Malekzadeh
- Digestive Disease Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Nagla Gasmelseed
- Department of Molecular Biology, National Cancer Institute, University of Gezira, Gezira, Sudan
| | - Mona Ellaithi
- Department of Histopathology and Cytology, Al-Neelain University, Khartoum, Sudan
| | - Nitin Gangane
- Mahatma Gandhi Institute of Medical Sciences, Sevagram, India
| | | | | | - Akram Ghantous
- International Agency for Research on Cancer, Lyon, France
| | | | - Joachim Schüz
- International Agency for Research on Cancer, Lyon, France
| | | | - M Iqbal Parker
- Integrative Biomedical Sciences and IDM, University of Cape Town, Cape Town, South Africa
| | | | - Zdenko Herceg
- International Agency for Research on Cancer, Lyon, France.
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50
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Li L, Gong Y, Xu K, Chen W, Xia J, Cheng Z, Li L, Yu R, Mu J, Le X, Xiang Q, Peng W, Tang J, Xiang T. ZBTB28 induces autophagy by regulation of FIP200 and Bcl-XL facilitating cervical cancer cell apoptosis. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:150. [PMID: 33931087 PMCID: PMC8086320 DOI: 10.1186/s13046-021-01948-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 04/14/2021] [Indexed: 12/21/2022]
Abstract
Background Among the common preventable cancers of women, cervical cancer has the highest morbidity. It is curable if detected at an early stage. However, reliable diagnostic and prognostic markers, which relate to physiologic and pathologic regulation of cervical cancer, are not available. In this study, one such potential marker, ZBTB28, was evaluated for its potential usefulness in cervical cancer assessment. Methods Public database analysis, reverse-transcription polymerase chain reaction (PCR), and methylation-specific PCR were employed to analyze ZBTB28 expression and promoter methylation. The importance of ZBTB28 in cervical cancer cells was assessed by cellular and molecular analysis in vitro and in vivo. Results This study assessed the anti-tumor effects of the transcription factor, ZBTB28, which is often silenced in cervical cancer due to CpG methylation of its promoter. We found ZBTB28 to directly affect cervical cancer cell proliferation, apoptosis, autophagy, and tumorigenesis. Also, it increased cancer cell chemosensitivity to Paclitaxel, Cisplatin, and 5-fluorouracil. Ectopic ZBTB28 expression inhibited the growth of cervical cancer xenografts in nude mice. Furthermore, electron microscopy demonstrated ZBTB28 to induce autophagosomes in cervical cancer cells. ZBTB28 induced cellular autophagy by the degradation of Bcl-XL, reduction of the Bcl-XL-BECN1 complex, and by interaction with the autophagy-related gene FIP200. ZBTB28-induced autophagy of cervical cancer cells was shown to mediate cellular apoptosis through the regulation of FIP200. Conclusion These findings identify ZBTB28 as a tumor suppressor gene that can induce autophagy-related apoptosis in cervical cancer cells. As such, ZBTB28 may be a target for the treatment of uterine-cervical carcinoma. Further, ZBTB28 promoter methylation analysis may offer a new objective strategy for cervical cancer screening. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-021-01948-0.
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Affiliation(s)
- Li Li
- Department of Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, No. 1 Youyi Road, Chongqing, 400016, Yuzhong District, China
| | - Yijia Gong
- Department of Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, No. 1 Youyi Road, Chongqing, 400016, Yuzhong District, China
| | - Ke Xu
- Department of Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, No. 1 Youyi Road, Chongqing, 400016, Yuzhong District, China
| | - Weihong Chen
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, No. 1 Youyi Road, Chongqing, 400016, Yuzhong District, China
| | - Jiuyi Xia
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, No. 1 Youyi Road, Chongqing, 400016, Yuzhong District, China
| | - Zhaobo Cheng
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, No. 1 Youyi Road, Chongqing, 400016, Yuzhong District, China
| | - Lili Li
- Cancer Epigenetics Laboratory, Department of Clinical Oncology, State Key Laboratory of Translational Oncology, Sir YK Pao Center for Cancer and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Renjie Yu
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, No. 1 Youyi Road, Chongqing, 400016, Yuzhong District, China
| | - Junhao Mu
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, No. 1 Youyi Road, Chongqing, 400016, Yuzhong District, China
| | - Xin Le
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, No. 1 Youyi Road, Chongqing, 400016, Yuzhong District, China
| | - Qin Xiang
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, No. 1 Youyi Road, Chongqing, 400016, Yuzhong District, China
| | - Weiyan Peng
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, No. 1 Youyi Road, Chongqing, 400016, Yuzhong District, China
| | - Junying Tang
- Department of Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Tingxiu Xiang
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, No. 1 Youyi Road, Chongqing, 400016, Yuzhong District, China.
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