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Ma Z, Han H, Zhou Z, Wang S, Liang F, Wang L, Ji H, Yang Y, Chen J. Machine learning-based establishment and validation of age-related patterns for predicting prognosis in non-small cell lung cancer within the context of the tumor microenvironment. IUBMB Life 2023; 75:941-956. [PMID: 37548145 DOI: 10.1002/iub.2768] [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: 05/01/2023] [Accepted: 06/20/2023] [Indexed: 08/08/2023]
Abstract
Lung cancer (LC) is a leading cause of cancer-related mortality worldwide, with non-small cell lung cancer (NSCLC) accounting for over 80% of cases. The impact of aging on clinical outcomes in NSCLC remains poorly understood, particularly with respect to the immune response. In this study, we explored the effects of aging on NSCLC using 307 genes associated with human aging from the Human Ageing Genomic Resources. We identified 53 aging-associated genes that significantly correlate with overall survival of NSCLC patients, including the clinically validated gene BUB1B. Furthermore, we developed an aging-associated enrichment score to categorize patients based on their aging subtypes and evaluated their prognostic and therapeutic response values in LC. Our analyses yielded two aging-associated subtypes with unique profiles in the tumor microenvironment, demonstrating varying responses to immunotherapy. Consensus clustering based on transcriptome profiles provided insights into the effects of aging on NSCLC and highlighted the potential of personalized therapeutic approaches tailored to aging subtypes. Our findings provide a new target and theoretical support for personalized therapeutic approaches in patients with NSCLC, offering insights into the potential impact of aging on cancer outcomes.
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Affiliation(s)
- Zeming Ma
- Department of Thoracic Surgery II, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital and Institute, Beijing, China
| | - Haibo Han
- Department of Clinical Laboratory, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital and Institute, Beijing, China
| | - Zhiwei Zhou
- Department of Thoracic Surgery II, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital and Institute, Beijing, China
| | - Shijie Wang
- Department of Thoracic Surgery II, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital and Institute, Beijing, China
| | - Fan Liang
- Department of Thoracic Surgery II, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital and Institute, Beijing, China
- Department of Clinical Laboratory, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital and Institute, Beijing, China
| | - Liang Wang
- Department of Thoracic Surgery II, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital and Institute, Beijing, China
| | - Hong Ji
- Department of Clinical Laboratory, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital and Institute, Beijing, China
| | - Yue Yang
- Department of Thoracic Surgery II, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital and Institute, Beijing, China
| | - Jinfeng Chen
- Department of Thoracic Surgery II, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital and Institute, Beijing, China
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Kong L, Wang L, Wang Z, Xiao X, You Y, Wu H, Wu M, Liu P, Li L. Cytological DNA methylation for cervical cancer screening: a validation set. Front Oncol 2023; 13:1181982. [PMID: 37671063 PMCID: PMC10475939 DOI: 10.3389/fonc.2023.1181982] [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: 03/08/2023] [Accepted: 08/03/2023] [Indexed: 09/07/2023] Open
Abstract
Background In a previous training set with a case-controlled design, cutoff values for host EPB41L3 and JAM3 gene methylation were obtained for the detection of cervical intraepithelial neoplasia (CIN) 2 or more severe lesions (CIN2+). This validation trial was conducted to evaluate the role of DNA methylation in screening for CIN2+ by cervical cytology among unselected participants. Methods From June 1, 2019, to September 1, 2019, in our study center, we collected liquid-based samples from cervical swabs for methylation assays and hrHPV testing in eligible patients. The primary endpoint was the diagnostic accuracy of DNA methylation and hrHPV genotyping for CIN2+ according to confirmed histology results. Results Among 307 participants, compared with hrHPV testing, the methylation assay for CIN2+ had lower sensitivity (68.7% versus 86.1%, p=0.002) but higher specificity (96.7% versus 0.696, p<0.001). The methylation assay also had favorable sensitivity and specificity in patients with negative hrHPV testing (56.3% and 96.9%) and in patients with cervical adenocarcinoma (73.7% and 92.7%). DNA methylation had higher specificity than the hrHPV assay (100.0% versus 44.4%, p<0.001) for identifying residual CIN2+ in patients without residual lesions. Positive cervical DNA methylation was associated with a diagnostic probability of endometrial carcinoma (odds ratio 15.5 [95% confidence interval 4.1-58.6]) but not of ovarian epithelial carcinoma (1.4 [0.3-6.5]). Conclusions The host EPB41L3 and JAM3 gene methylation assay in cervical cytology had favorable diagnostic accuracy for CIN2+ and was highly specific for residual CIN2+ lesions The methylation assay is a promising triage tool in hrHPV+ women, or even an independent tool for cervical cancer screening. The methylation status in cervical cytology could also serve as a prognostic biomarker. Its role in detecting endometrial carcinomas is worthy of further exploration.
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Affiliation(s)
- Linghua Kong
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric & Gynecologic Diseases, Peking Union Medical College Hospital, Beijing, China
| | - Linhai Wang
- Department of Technology, Beijing OriginPoly Biotechnology CO., Ltd., Beijing, China
| | - Ziyun Wang
- Department of Technology, Beijing OriginPoly Biotechnology CO., Ltd., Beijing, China
| | - Xiaoping Xiao
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric & Gynecologic Diseases, Peking Union Medical College Hospital, Beijing, China
| | - Yan You
- Department of Pathology, Peking Union Medical College Hospital, Beijing, China
| | - Huanwen Wu
- Department of Pathology, Peking Union Medical College Hospital, Beijing, China
| | - Ming Wu
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric & Gynecologic Diseases, Peking Union Medical College Hospital, Beijing, China
| | - Pei Liu
- Department of Technology, Beijing OriginPoly Biotechnology CO., Ltd., Beijing, China
| | - Lei Li
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric & Gynecologic Diseases, Peking Union Medical College Hospital, Beijing, China
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Hao J, Liu T, Xiu Y, Yuan H, Xu D. High DNA methylation age deceleration defines an aggressive phenotype with immunoexclusion environments in endometrial carcinoma. Front Immunol 2023; 14:1208223. [PMID: 37388735 PMCID: PMC10303802 DOI: 10.3389/fimmu.2023.1208223] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 05/30/2023] [Indexed: 07/01/2023] Open
Abstract
Like telomere shortening, global DNA hypomethylation occurs progressively with cellular divisions or in vivo aging and functions as a mitotic clock to restrain malignant transformation/progression. Several DNA-methylation (DNAm) age clocks have been established to precisely predict chronological age using normal tissues, but show DNAm age drift in tumors, which suggests disruption of this mitotic clock during carcinogenesis. Little is known about DNAm age alterations and biological/clinical implications in endometrial cancer (EC). Here we address these issues by analyzing TCGA and GSE67116 cohorts of ECs. Horvath clock analysis of these tumors unexpectedly revealed that almost 90% of them exhibited DNAm age deceleration (DNAmad) compared to patient chronological age. Combined with an additional clock named Phenoage, we identified a subset of tumors (82/429) with high DNAmad (hDNAmad+) as assessed by both clocks. Clinically, hDNAmad+ tumors were associated with advanced diseases and shorter patient survival, compared to hDNAmad- ones. Genetically, hDNAmad+ tumors were characterized by higher copy number alterations (CNAs) whereas lower tumor mutation burden. Functionally, hDNAmad+ tumors were enriched with cell cycle and DNA mismatch repair pathways. Increased PIK3CA alterations and downregulation of SCGB2A1, the inhibitor of PI3K kinase, in hDNAmad+ tumors, might promote tumor growth/proliferation and stemness. In addition, the inactivation of aging drivers/tumor suppressors (TP53, RB1, and CDKN2A) while enhanced telomere maintenance occurred more frequently in hDNAmad+ tumors, which supports sustained tumor growth. Prominently, hDNAmad+ tumors were featured with immunoexclusion microenvironments, accompanied by significantly higher levels of VTCN1 expression while lower PD-L1 and CTLA4 expression, which indicates their poor response to immune checkpoint inhibitor (ICI)-based immunotherapy. We further showed significantly higher levels of DNMT3A and 3B expression in hDNAmad+ than in hDNAmad- tumors. Thus, the tumor suppressive function of aging-like DNA hypomethylation is severely impaired in hDNAmad+ tumors, likely due to enhanced expression of DNMT3A/3B and dysregulated aging regulators. Our findings not only enrich biological knowledge of EC pathogenesis but also help improve EC risk stratification and precision ICI immunotherapy.
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Affiliation(s)
- Jing Hao
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, China
- Shandong Engineering Research Center of Biomarker and Artificial Intelligence Application, Jinan, China
| | - Tiantian Liu
- Department of Pathology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Yuchen Xiu
- Department of Pathology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Huiyang Yuan
- Department of Urology, Qilu Hospital of Shandong University, Jinan, China
| | - Dawei Xu
- Department of Medicine, Bioclinicum and Center for Molecular Medicine (CMM), Karolinska Institutet and Karolinska University Hospital Solna, Stockholm, Sweden
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Teulière J, Bernard C, Bonnefous H, Martens J, Lopez P, Bapteste E. Interactomics: Dozens of Viruses, Co-evolving With Humans, Including the Influenza A Virus, may Actively Distort Human Aging. Mol Biol Evol 2023; 40:6989791. [PMID: 36649176 PMCID: PMC9897028 DOI: 10.1093/molbev/msad012] [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: 06/10/2022] [Revised: 12/07/2022] [Accepted: 01/09/2023] [Indexed: 01/18/2023] Open
Abstract
Some viruses (e.g., human immunodeficiency virus 1 and severe acute respiratory syndrome coronavirus 2) have been experimentally proposed to accelerate features of human aging and of cellular senescence. These observations, along with evolutionary considerations on viral fitness, raised the more general puzzling hypothesis that, beyond documented sources in human genetics, aging in our species may also depend on virally encoded interactions distorting our aging to the benefits of diverse viruses. Accordingly, we designed systematic network-based analyses of the human and viral protein interactomes, which unraveled dozens of viruses encoding proteins experimentally demonstrated to interact with proteins from pathways associated with human aging, including cellular senescence. We further corroborated our predictions that specific viruses interfere with human aging using published experimental evidence and transcriptomic data; identifying influenza A virus (subtype H1N1) as a major candidate age distorter, notably through manipulation of cellular senescence. By providing original evidence that viruses may convergently contribute to the evolution of numerous age-associated pathways through co-evolution, our network-based and bipartite network-based methodologies support an ecosystemic study of aging, also searching for genetic causes of aging outside a focal aging species. Our findings, predicting age distorters and targets for anti-aging therapies among human viruses, could have fundamental and practical implications for evolutionary biology, aging study, virology, medicine, and demography.
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Affiliation(s)
| | | | - Hugo Bonnefous
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d’Histoire Naturelle, EPHE, Université des Antilles, Paris, France
| | - Johannes Martens
- Sciences, Normes, Démocratie (SND), Sorbonne Université, CNRS, Paris, France
| | - Philippe Lopez
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d’Histoire Naturelle, EPHE, Université des Antilles, Paris, France
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Prevalence of Human Papillomavirus Infection in the Female Partner of Infertile Couples Undergoing IVF/ICSI-ET and Subsequent Reproductive Outcomes. J Clin Med 2022; 11:jcm11237185. [PMID: 36498761 PMCID: PMC9741338 DOI: 10.3390/jcm11237185] [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: 11/21/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
We investigated the prevalence of human papillomavirus (HPV) infection in the female partner of infertile couples and the reproductive outcomes after in vitro fertilization/intracytoplasmic sperm injection-embryo transfer (IVF/ICSI-ET). We conducted a retrospective analysis on 8117 women from infertile couples who underwent IVF/ICSI treatment and evaluated the prevalence of HPV infection in these women. The prevalence of HPV infection in the female partner of infertile couples was 9.2% (747/8117). These HPV-infected female patients undergoing ART were divided into high-risk HPV (hrHPV) (n = 130) and low-risk HPV (lrHPV) groups (n = 94), and non-infected women patients formed the negative group (n = 126). Of the 747 cases infected with HPV, 529 showed hrHPV infection (70.82%; primarily genotypes 16, 52, 53, 58, and 59); 175 exhibited lrHPV infection (23.43%; primarily genotypes 6, 43, 44, 55, 61, and 81); and 43 cases were co-infected with hrHPV and lrHPV (5.76%). Except for the Day-3 high-quality embryo rate, there were no differences in ovum maturation, fertilization, implantation, clinical pregnancy, live birth, or miscarriage rates between women infected with HPV and non-infected women (p > 0.05); however, we noted an increased miscarriage rate after logistic regression analyses (OR, 0.16; 95% CI, 0.03−0.84; p = 0.041). For single-male-factor-induced infertility in couples (smHPV), although we likewise observed no differences in ovum maturation, fertilization, or implantation rates (p > 0.05) between the smHPV group and the negative group, we discerned diminutions in the Day-3 high-quality embryo rate (46.01% vs. 70.04%, p = 0.013), clinical pregnancy rate (46.67% vs. 57.94%, p = 0.003), and live birth rate (33.33% vs. 46.83%, p = 0.027) as well as an augmented miscarriage rate (11.11% vs. 4.76%, p = 0.003), respectively. Logistic regression analyses indicated that smHPV was a risk factor for decreased clinical pregnancy rate (OR, 4.17; 95% CI, 2.31−7.53; p < 0.001) and live birth rate (OR, 1.83; 95% CI, 0.81−2.14; p = 0.045) and elevated miscarriage rate (OR, 6.83; 95% CI, 2.22−21.00; p = 0.001). HPV infection in women was associated with increased miscarriage rate, and single-male-factor infertility influenced reproductive outcomes in couples undergoing IVF/ICSI treatment. Both were potentially due to HPV infection in the couple.
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Musa J, Kim K, Zheng Y, Qu Y, Joyce BT, Wang J, Nannini DR, Gursel DB, Silas O, Abdulkareem FB, Imade G, Akanmu AS, Wei JJ, Kocherginsky M, Kim KYA, Wehbe F, Achenbach CJ, Anorlu R, Simon MA, Sagay A, Ogunsola FT, Murphy RL, Hou L. Accelerated Epigenetic Age Among Women with Invasive Cervical Cancer and HIV-Infection in Nigeria. Front Public Health 2022; 10:834800. [PMID: 35570901 PMCID: PMC9099239 DOI: 10.3389/fpubh.2022.834800] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 04/11/2022] [Indexed: 11/13/2022] Open
Abstract
Background Invasive cervical cancer (ICC) is a serious public health burden in Nigeria, where human immunodeficiency virus (HIV) remains highly prevalent. Previous research suggested that epigenetic age acceleration (EAA) could play a role in detection of HIV-associated ICC. However, little research has been conducted on this topic in Africa where the population is most severely affected by HIV-associated ICC. Here, we investigated the association between ICC and EAA using cervical tissues of ICC-diagnosed Nigerian women living with HIV. Methods We included 116 cervical tissue samples from three groups of Nigerian women in this study: (1) HIV+/ICC+ (n = 39); (2) HIV+/ICC- (n = 53); and (3) HIV-/ICC + (n = 24). We utilized four DNA methylation-based EAA estimators; IEAA, EEAA, GrimAA, and PhenoAA. We compared EAA measurements across the 3 HIV/ICC groups using multiple linear regression models. We also compared EAA between 26 tumor tissues and their surrounding normal tissues using paired t-tests. We additionally performed a receiver operating characteristics (ROC) curve analysis to illustrate the area under the curve (AUC) of EAA in ICC. Results We found the most striking associations between HIV/ICC status and PhenoAge acceleration (PhenoAA). Among HIV-positive women, PhenoAA was on average 13.4 years higher in women with ICC compared to cancer-free women (P = 0.005). PhenoAA was 20.7 and 7.1 years higher in tumor tissues compared to surrounding normal tissues among HIV-positive women (P = 0.009) and HIV-negative women (P = 0.284), respectively. We did not find substantial differences in PhenoAA between HIV-positive and HIV-negative women with ICC. Conclusion PhenoAA is associated with ICC in HIV-infected women in our study. Our findings suggest that PhenoAA may serve as a potential biomarker for further risk stratification of HIV-associated ICC in Nigeria and similar resource-constrained settings.
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Affiliation(s)
- Jonah Musa
- Department of Preventive Medicine, Division of Cancer Epidemiology and Prevention, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
- Center for Global Oncology, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
- Department of Obstetrics and Gynecology, College of Health Sciences, University of Jos, Jos, Nigeria
| | - Kyeezu Kim
- Department of Preventive Medicine, Division of Cancer Epidemiology and Prevention, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Yinan Zheng
- Department of Preventive Medicine, Division of Cancer Epidemiology and Prevention, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
- Center for Global Oncology, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Yishu Qu
- Department of Preventive Medicine, Division of Cancer Epidemiology and Prevention, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Brian T. Joyce
- Department of Preventive Medicine, Division of Cancer Epidemiology and Prevention, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
- Center for Global Oncology, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Jun Wang
- Department of Preventive Medicine, Division of Cancer Epidemiology and Prevention, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
- Center for Global Oncology, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Drew R. Nannini
- Department of Preventive Medicine, Division of Cancer Epidemiology and Prevention, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Demirkan B. Gursel
- Center for Global Oncology, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | | | | | - Godwin Imade
- Department of Obstetrics and Gynecology, College of Health Sciences, University of Jos, Jos, Nigeria
| | - Alani S. Akanmu
- Department of Hematology and Blood Transfusion, Lagos University Teaching Hospital and College of Medicine, University of Lagos, Lagos, Nigeria
| | - Jian-Jun Wei
- Center for Global Oncology, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Masha Kocherginsky
- Department of Preventive Medicine, Division of Cancer Epidemiology and Prevention, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
- Center for Global Oncology, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Kwang-Youn A. Kim
- Department of Preventive Medicine, Division of Cancer Epidemiology and Prevention, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
- Center for Global Oncology, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Firas Wehbe
- Center for Global Oncology, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
- Department of Preventive Medicine, Division of Health and Biomedical Informatics, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Chad J. Achenbach
- Center for Global Oncology, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Rose Anorlu
- Department of Obstetrics and Gynecology, College of Medicine, University of Lagos, Lagos, Nigeria
| | - Melissa A. Simon
- Department of Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Atiene Sagay
- Department of Obstetrics and Gynecology, College of Health Sciences, University of Jos, Jos, Nigeria
| | - Folasade T. Ogunsola
- Department of Medical Microbiology, College of Medicine, University of Lagos, Lagos, Nigeria
| | - Robert L. Murphy
- Center for Global Oncology, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Lifang Hou
- Department of Preventive Medicine, Division of Cancer Epidemiology and Prevention, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
- Center for Global Oncology, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
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Liu Y, Liao J, Yi X, Pan Z, Pan J, Sun C, Zhou H, Meng Y. Diagnostic value of colposcopy in patients with cytology-negative and HR-HPV-positive cervical lesions. Arch Gynecol Obstet 2022; 306:1161-1169. [PMID: 35320389 DOI: 10.1007/s00404-022-06415-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 01/20/2022] [Indexed: 12/24/2022]
Abstract
PURPOSE High-risk human papillomavirus (HR-HPV)-positive but cytology-negative cervical cancer screening results are not uncommon. This study aimed to investigate colposcopy's accuracy and diagnostic value in patients with cytology-negative HR-HPV-positive screening results. METHODS This retrospective study included patients with HR-HPV-positive cytology-negative screening results who underwent electronic colposcopy with acetic acid and multi-point cervical biopsy, HPV typing (24 HPV subtypes), and quantitative HPV detection. RESULTS Among 229 patients, 130 had chronic cervicitis, and 99 had cervical lesions (CIN1, n = 37; CIN2/3, n = 55; invasive carcinoma, n = 7). Using colposcopy as a reference, the cervical cytology false-negative rate was 43.2% (99/229). Colposcopy was more accurate in patients with HR-HPV16/18 or high viral loads. Multivariable analyses showed HPV viral load and childbearing history were the independent factors affecting the accuracy of colposcopy (P < 0.05). CONCLUSION Colposcopy in HR-HPV-positive cytology-negative patients has a moderate diagnostic accuracy. The type of cervical transformation zone and HPV viral load are independent factors affecting the accuracy of colposcopy-based diagnosis.
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Affiliation(s)
- Yang Liu
- Department of Reproduction, The Second Affiliated Hospital of Kunming Medical University, Kunming, 650101, China
| | - Jing Liao
- Department of Gynecology, The Second Affiliated Hospital of Kunming Medical University, Kunming, 650101, China
| | - Xiaojia Yi
- Department of Pathology, The Second Affiliated Hospital of Kunming Medical University, Kunming, 650101, China
| | - Zhengmei Pan
- Department of Reproduction, The Second Affiliated Hospital of Kunming Medical University, Kunming, 650101, China
| | - Jing Pan
- Department of Gynecology, The Second Affiliated Hospital of Kunming Medical University, Kunming, 650101, China
| | - Chunyi Sun
- Department of Gynecology, The Second Affiliated Hospital of Kunming Medical University, Kunming, 650101, China
| | - Honglin Zhou
- Department of Gynecology, The Second Affiliated Hospital of Kunming Medical University, Kunming, 650101, China
| | - Yushi Meng
- Department of Reproduction, The Second Affiliated Hospital of Kunming Medical University, Kunming, 650101, China.
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Liu T, Wang J, Xiu Y, Wu Y, Xu D. DNA Methylation Age Drift Is Associated with Poor Outcomes and De-Differentiation in Papillary and Follicular Thyroid Carcinomas. Cancers (Basel) 2021; 13:cancers13194827. [PMID: 34638311 PMCID: PMC8508076 DOI: 10.3390/cancers13194827] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/19/2021] [Accepted: 09/23/2021] [Indexed: 12/17/2022] Open
Abstract
Simple Summary Normal human tissues contain an epigenetic clock resulting from the age-dependent DNA methylation signature, which is the so-called DNA methylation (DNAm) age and can be used to precisely predict chronological age of healthy individuals. Abnormal DNAm age drift has been implicated in cancer risk and pathogenesis. Here, we observed that highly drifted DNAm age (HDDA) occurred in approximately 1/3 tumors derived from patients with papillary and follicular thyroid carcinomas. HDDA is significantly associated with dedifferentiation of tumor cells and poor patient outcomes. Thus, HDDA may serve as a new prognostic factor for thyroid carcinoma. Abstract Alterations in global DNA methylation play a critical role in both aging and cancer, and DNA methylation (DNAm) age drift has been implicated in cancer risk and pathogenesis. In the present study, we analyzed the TCGA cohort of papillary and follicular thyroid carcinoma (PTC and FTC) for their DNAm age and association with clinic-pathological features. In 54 noncancerous thyroid (NT) samples, DNAm age was highly correlated with patient chronological age (R2 = 0.928, p = 2.6 × 10−31), but drifted to younger than chronological age in most specimens, especially those from patients >50 years old. DNAm age in 502 tumors was also correlated with patient chronological age, but to a much lesser extent (R2 = 0.403). Highly drifted DNAm age (HDDA) was identified in 161 tumors, among which were 101 with DNAm age acceleration while 60 with DNAm age deceleration. Tumors with HDDA were characterized by the robust aberrations in metabolic activities, extracellular microenvironment components and inflammation/immunology responses, and dedifferentiation. Importantly, HDDA in tumors independently predicted shorter disease-free survival of patients. Collectively, NT thyroids from TC patients have younger DNAm age, while HDDA frequently occurs in TCs, and contributes to the TC progression and poor patient outcomes. HDDA may serve as a new prognostic factor for TCs.
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Affiliation(s)
- Tiantian Liu
- Pathology Department, School of Basic Medical Science, Shandong University, Jinan 250012, China; (J.W.); (Y.X.)
- Correspondence:
| | - Jiansheng Wang
- Pathology Department, School of Basic Medical Science, Shandong University, Jinan 250012, China; (J.W.); (Y.X.)
| | - Yuchen Xiu
- Pathology Department, School of Basic Medical Science, Shandong University, Jinan 250012, China; (J.W.); (Y.X.)
| | - Yujiao Wu
- Department of Medicine, Division of Hematology, Bioclinicum and Center for Molecular Medicine (CMM), Karolinska University Hospital Solna, Karolinsk Institutet, SE-171 76 Stockholm, Sweden; (Y.W.); (D.X.)
| | - Dawei Xu
- Department of Medicine, Division of Hematology, Bioclinicum and Center for Molecular Medicine (CMM), Karolinska University Hospital Solna, Karolinsk Institutet, SE-171 76 Stockholm, Sweden; (Y.W.); (D.X.)
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Noroozi R, Ghafouri-Fard S, Pisarek A, Rudnicka J, Spólnicka M, Branicki W, Taheri M, Pośpiech E. DNA methylation-based age clocks: From age prediction to age reversion. Ageing Res Rev 2021; 68:101314. [PMID: 33684551 DOI: 10.1016/j.arr.2021.101314] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 02/25/2021] [Accepted: 03/01/2021] [Indexed: 12/12/2022]
Abstract
Aging as an irretrievable occurrence throughout the entire life is characterized by a progressive decline in physiological functionality and enhanced disease vulnerability. Numerous studies have demonstrated that epigenetic modifications, particularly DNA methylation (DNAm), correlate with aging and age-related diseases. Several investigations have attempted to predict chronological age using the age-related alterations in the DNAm of certain CpG sites. Here we categorize different studies that tracked the aging process in the DNAm landscape to show how epigenetic age clocks evolved from a chronological age estimator to an indicator of lifespan and healthspan. We also describe the health and disease predictive potential of estimated epigenetic age acceleration regarding different clinical conditions and lifestyle factors. Considering the revealed age-related epigenetic changes, the recent age-reprogramming strategies are discussed which are promising methods for resetting the aging clocks.
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Affiliation(s)
- Rezvan Noroozi
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Aleksandra Pisarek
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Joanna Rudnicka
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | | | - Wojciech Branicki
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
| | - Mohammad Taheri
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Ewelina Pośpiech
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
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10
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Zhou YJ, Lu XF, Meng JL, Wang QW, Chen JN, Zhang QW, Zheng KI, Rocha CS, Martins CB, Yan FR, Li XB. Specific epigenetic age acceleration patterns among four molecular subtypes of gastric cancer and their prognostic value. Epigenomics 2021; 13:767-778. [PMID: 33876652 DOI: 10.2217/epi-2020-0290] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Aims: To determine the association of the methylation age (Horvath epigenetic clock) of gastric cancer (GC) tissues with molecular subtypes and patient survival. Materials & methods: Multivariate regression models were used to determine the association of methylation age acceleration (AA) with the clinical and molecular characteristics of 333 GC patients. Results: Relative to the chromosomal instability subtype, the epigenetic AA was 49.8 (95% CI: 42.7-56.9) years for Epstein-Barr virus, 16.1 (10.6-21.6) years for microsatellite instability, and 6.05 (0.1-11.1) years for genomic stability subtype. GC patients with accelerated aging of tumor tissues had better outcomes (adjusted hazard ratio: 3.13; p = 0.03). Differentially methylated probes in patients with accelerated and decelerated methylation aging enriched in pathways including BMP signaling, HMGB1 signaling, STAT3 signaling and human embryonic stem cell pluripotency. Conclusions: Our results highlight the prognostic value of epigenetic AA in GC and suggest that epigenetic AA is also an indicator of molecular subtype in GC.
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Affiliation(s)
- Yu-Jie Zhou
- Division of Gastroenterology & Hepatology, Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Xiao-Fan Lu
- State Key Laboratory of Natural Medicines, Research Center of Biostatistics and Computational Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Jia-Lin Meng
- Department of Urology, The First Affiliated Hospital of Anhui Medical University and Institute of Urology & Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei 230022, China.,Department of Urology, University of Rochester Medical Center, Rochester 14620, NY, USA
| | - Qi-Wen Wang
- Division of Gastroenterology & Hepatology, Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Jin-Nan Chen
- Division of Gastroenterology & Hepatology, Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Qing-Wei Zhang
- Division of Gastroenterology & Hepatology, Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Kenneth I Zheng
- Department of Hepatology, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Claudia S Rocha
- School of International Studies, Wenzhou Medical University, Wenzhou 325000, China
| | - Carla B Martins
- School of International Studies, Wenzhou Medical University, Wenzhou 325000, China
| | - Fang-Rong Yan
- State Key Laboratory of Natural Medicines, Research Center of Biostatistics and Computational Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Xiao-Bo Li
- Division of Gastroenterology & Hepatology, Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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11
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Hong C, Yang S, Wang Q, Zhang S, Wu W, Chen J, Zhong D, Li M, Li L, Li J, Yu H, Chen H, Zeng Q, Zhang C. Epigenetic Age Acceleration of Stomach Adenocarcinoma Associated With Tumor Stemness Features, Immunoactivation, and Favorable Prognosis. Front Genet 2021; 12:563051. [PMID: 33815458 PMCID: PMC8012546 DOI: 10.3389/fgene.2021.563051] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 02/22/2021] [Indexed: 12/20/2022] Open
Abstract
Background: Abnormal DNA methylation (DNAm) age has been assumed to be an indicator for canceration and all-cause mortality. However, associations between DNAm age and molecular features of stomach adenocarcinoma (STAD), and its prognosis have not been systematically studied. Method: We calculated the DNAm age of 591 STAD samples and 115 normal stomach samples from The Cancer Genome Atlas (TCGA) and gene expression omnibus (GEO) database using the Horvath’s clock model. Meanwhile, we utilized survival analysis to evaluate the prognostic value of DNAm age and epigenetic age acceleration shift. In addition, we performed weighted gene co-expression network analysis (WGCNA) to identify DNAm age-associated gene modules and pathways. Finally, the association between DNAm age and molecular features was performed by correlation analysis. Results: DNA methylation age was significantly correlated with chronological age in normal gastric tissues (r = 0.85, p < 0.0001), but it was not associated with chronological age in STAD samples (r = 0.060, p = 0.2369). Compared with tumor adjacent normal tissue, the DNAm age of STAD tissues was significantly decreased. Meanwhile, chronological age in STAD samples was higher than its DNAm age. Both DNAm age and epigenetic acceleration shift were associated with the prognosis of STAD patients. By using correlation analysis, we also found that DNAm age was associated with immunoactivation and stemness in STAD samples. Conclusion: In summary, epigenetic age acceleration of STAD was associated with tumor stemness, immunoactivation, and favorable prognosis.
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Affiliation(s)
- Chunhong Hong
- Center of Digestive Disease, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Shaohua Yang
- Center of Digestive Disease, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Qiaojin Wang
- Department of Surgical Intensive Care Unit, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Shiqiang Zhang
- Department of Urology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Wenhui Wu
- Center of Digestive Disease, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Jinyao Chen
- Center of Digestive Disease, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Danhui Zhong
- Department of Physiotherapy, The University of Hongkong-Shenzhen Hospital, Shenzhen, China
| | - Mingzhe Li
- Center of Digestive Disease, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Liang Li
- Center of Digestive Disease, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Jianfeng Li
- Center of Digestive Disease, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Hong Yu
- Center of Digestive Disease, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Hong Chen
- Center of Digestive Disease, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Qianlin Zeng
- Center of Digestive Disease, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Changhua Zhang
- Center of Digestive Disease, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
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12
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Chteinberg E, Vogt J, Kolarova J, Bormann F, van den Oord J, Speel EJ, Winnepenninckx V, Kurz AK, Zenke M, Siebert R, Hausen AZ. The curious case of Merkel cell carcinoma: epigenetic youth and lack of pluripotency. Epigenetics 2020; 15:1319-1324. [PMID: 32475296 PMCID: PMC7678933 DOI: 10.1080/15592294.2020.1773096] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Merkel cell carcinoma (MCC) is a very rare, but highly aggressive skin cancer which occurs mainly in elderly patients. MCC cells show an expression pattern of three cell lineages: epithelial, neuroendocrine, and B-cell progenitor. This trilinear expression pattern suggests stemness activity in MCC. The etiopathogenesis of MCC is either linked to the Merkel cell polyomavirus (MCPyV) or in a smaller proportion (20%) to high levels of UV-induced somatic mutations. Both viral presence and accumulation of mutations have been shown to be associated with accelerated DNA methylation Age (DNAmAge) compared to chronological age. The MCC DNAmAge was significantly lower compared to the chronological age, which was irrespective of the viral presence or mutational burden. Although these features indicate some aspects of stemness in MCC cells, gene-expression-based pluripotency testing did not provide evidence for pluripotency of MCC cells.
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Affiliation(s)
- Emil Chteinberg
- Department of Pathology, GROW-School for Oncology & Developmental Biology, Maastricht University, Medical Centre+ , Maastricht, The Netherlands.,Institute for Biomedical Engineering, Department of Cell Biology, RWTH Aachen, University Hospital , Aachen, Germany.,Helmholtz Institute for Biomedical Engineering, RWTH Aachen University , Aachen, Germany
| | - Julia Vogt
- Institute of Human Genetics, Ulm University and Ulm University Medical Center , Ulm, Germany
| | - Julia Kolarova
- Institute of Human Genetics, Ulm University and Ulm University Medical Center , Ulm, Germany
| | | | - Joost van den Oord
- Department of Pathology and Laboratory Translational Cell and Tissue Research, University of Leuven , KU, Leuven, Belgium
| | - Ernst Jan Speel
- Department of Pathology, GROW-School for Oncology & Developmental Biology, Maastricht University, Medical Centre+ , Maastricht, The Netherlands
| | - Véronique Winnepenninckx
- Department of Pathology, GROW-School for Oncology & Developmental Biology, Maastricht University, Medical Centre+ , Maastricht, The Netherlands
| | - Anna Kordelia Kurz
- Department of Internal Medicine IV, University Hospital Aachen , Aachen, Germany
| | - Martin Zenke
- Institute for Biomedical Engineering, Department of Cell Biology, RWTH Aachen, University Hospital , Aachen, Germany.,Helmholtz Institute for Biomedical Engineering, RWTH Aachen University , Aachen, Germany
| | - Reiner Siebert
- Institute of Human Genetics, Ulm University and Ulm University Medical Center , Ulm, Germany
| | - Axel Zur Hausen
- Department of Pathology, GROW-School for Oncology & Developmental Biology, Maastricht University, Medical Centre+ , Maastricht, The Netherlands
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