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Izadi M, Sadri N, Abdi A, Serajian S, Jalalei D, Tahmasebi S. Epigenetic biomarkers in aging and longevity: Current and future application. Life Sci 2024; 351:122842. [PMID: 38879158 DOI: 10.1016/j.lfs.2024.122842] [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: 12/29/2023] [Revised: 06/06/2024] [Accepted: 06/12/2024] [Indexed: 06/20/2024]
Abstract
The aging process has been one of the most necessary research fields in the current century, and knowing different theories of aging and the role of different genetic, epigenetic, molecular, and environmental modulating factors in increasing the knowledge of aging mechanisms and developing appropriate diagnostic, therapeutic, and preventive ways would be helpful. One of the most conserved signs of aging is epigenetic changes, including DNA methylation, histone modifications, chromatin remodeling, noncoding RNAs, and extracellular RNAs. Numerous biological processes and hallmarks are vital in aging development, but epigenomic alterations are especially notable because of their importance in gene regulation and cellular identity. The mounting evidence points to a possible interaction between age-related epigenomic alterations and other aging hallmarks, like genome instability. To extend a healthy lifespan and possibly reverse some facets of aging and aging-related diseases, it will be crucial to comprehend global and locus-specific epigenomic modifications and recognize corresponding regulators of health and longevity. In the current study, we will aim to discuss the role of epigenomic mechanisms in aging and the most recent developments in epigenetic diagnostic biomarkers, which have the potential to focus efforts on reversing the destructive signs of aging and extending the lifespan.
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Affiliation(s)
- Mehran Izadi
- Department of Infectious and Tropical Diseases, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran; Synapse Laboratory Diagnostic Technologies Accelerator, Tehran, Iran; Department of Research & Technology, Zeenome Longevity Research Institute, Tehran, Iran
| | - Nariman Sadri
- Synapse Laboratory Diagnostic Technologies Accelerator, Tehran, Iran; Department of Research & Technology, Zeenome Longevity Research Institute, Tehran, Iran; School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Amirhossein Abdi
- Synapse Laboratory Diagnostic Technologies Accelerator, Tehran, Iran; Department of Research & Technology, Zeenome Longevity Research Institute, Tehran, Iran; Royan Institute for Stem Cell Biology and Technology, Tehran, Iran
| | - Sahar Serajian
- Synapse Laboratory Diagnostic Technologies Accelerator, Tehran, Iran; Department of Research & Technology, Zeenome Longevity Research Institute, Tehran, Iran; Royan Institute for Stem Cell Biology and Technology, Tehran, Iran
| | - Dorsa Jalalei
- Synapse Laboratory Diagnostic Technologies Accelerator, Tehran, Iran; Department of Research & Technology, Zeenome Longevity Research Institute, Tehran, Iran; School of Pharmacy, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Safa Tahmasebi
- Synapse Laboratory Diagnostic Technologies Accelerator, Tehran, Iran; Department of Research & Technology, Zeenome Longevity Research Institute, Tehran, Iran; Department of Immunology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Ji XY, Li H, Chen HH, Lin J. Diagnostic performance of RASSF1A and SHOX2 methylation combined with EGFR mutations for differentiation between small pulmonary nodules. J Cancer Res Clin Oncol 2023:10.1007/s00432-023-04745-8. [PMID: 37097393 DOI: 10.1007/s00432-023-04745-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 04/03/2023] [Indexed: 04/26/2023]
Abstract
BACKGROUND AND AIM Aberrant methylation of Ras association domain family 1, isoform A (RASSF1A), and short-stature homeobox gene 2 (SHOX2) promoters has been validated as a pair of valuable biomarkers for diagnosing early lung adenocarcinomas (LUADs). Epidermal growth factor receptor (EGFR) is the key driver mutation in lung carcinogenesis. This study aimed to investigate the aberrant promoter methylation of RASSF1A and SHOX2, and the genetic mutation of EGFR in 258 specimens of early LUADs. METHODS We retrospectively selected 258 paraffin-embedded samples of pulmonary nodules measuring 2 cm or less in diameter and evaluated the diagnostic performance of individual biomarker assays and multiple panels between noninvasive (group 1) and invasive lesions (groups 2A and 2B). Then, we investigated the interaction between genetic and epigenetic alterations. RESULTS The degree of RASSF1A and SHOX2 promoter methylation and EGFR mutation was significantly higher in invasive lesions than in noninvasive lesions. The three biomarkers distinguished between noninvasive and invasive lesions with reliable sensitivity and specificity: 60.9% sensitivity [95% confidence interval (CI) 52.41-68.78] and 80.0% specificity (95% CI 72.14-86.07). The novel panel biomarkers could further discriminate among three invasive pathological subtypes (area under the curve value > 0.6). The distribution of RASSF1A methylation and EGFR mutation was considerably exclusive in early LUAD (P = 0.002). CONCLUSION DNA methylation of RASSF1A and SHOX2 is a pair of promising biomarkers, which may be used in combination with other driver alterations, such as EGFR mutation, to support the differential diagnosis of LUADs, especially for stage I.
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Affiliation(s)
- Xiang-Yu Ji
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, People's Republic of China
| | - Hong Li
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Hui-Hui Chen
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Jie Lin
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China.
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, People's Republic of China.
- National Virtual and Reality Experimental Education Center for Medical Morphology, Southern Medical University, Guangzhou, People's Republic of China.
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Zhang J, Huang H, Yu F, Bian Y, Wang R, Liu H, Kang S, She B, Shi Z. A comprehensive diagnostic scheme of morphological combined molecular methylation under bronchoscopy. Front Oncol 2023; 13:1133675. [PMID: 37182143 PMCID: PMC10174301 DOI: 10.3389/fonc.2023.1133675] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 04/12/2023] [Indexed: 05/16/2023] Open
Abstract
Methylated SHOX2 and RASSF1A genes are potential biomarkers for lung cancer diagnosis. Therefore, we explored the role of methylation detection combined with morphological bronchoscopic evaluation for lung cancer diagnosis. Bronchoscopy, methylation outcome, and pathological data were collected from 585 patients with lung cancer and 101 controls. The methylation status of the SHOX2 and RASSF1A genes were detected using real-time polymerase chain reaction quantification. Further, the sensitivity and area under the receiver operating characteristic curve of the three methods were analyzed. Among 686 patients, 57.1% had new lesions detected through bronchoscopy and 93.1% of these patients were diagnosed with malignant tumors. Besides, 42.9% of patients had no visible changes under bronchoscopy but there were still 74.8% of them diagnosed with malignant tumors. Bronchoscopy revealed that lung adenocarcinoma, lung squamous cell carcinoma, and small cell lung cancer mainly occurred in the upper and middle lobes. The sensitivity and specificity of methylation detection were 72.8% and 87.1% (vs. cytology 10.4% & 100%), respectively. Therefore, methylated SHOX2 and RASSF1A genes may be promising tumor markers in lung cancer diagnosis. Methylation detection can be an excellent supplementary tool for cytological diagnosis and, combined with bronchoscopy, could form a more effective diagnostic process.
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Affiliation(s)
- Jinze Zhang
- Department of Thoracic Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Haoran Huang
- Department of Academic Development, Tellgen Corporation, Shanghai, China
| | - Fan Yu
- Department of Thoracic Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Yuanyuan Bian
- Department of Thoracic Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Rui Wang
- The Cancer Center, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Hui Liu
- Department of Thoracic Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Saisai Kang
- Department of Thoracic Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Bin She
- Department of Academic Development, Tellgen Corporation, Shanghai, China
| | - Zhihua Shi
- Department of Thoracic Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
- *Correspondence: Zhihua Shi,
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Dye CK, Corley MJ, Ing C, Lum-Jones A, Li D, Mau MKLM, Maunakea AK. Shifts in the immunoepigenomic landscape of monocytes in response to a diabetes-specific social support intervention: a pilot study among Native Hawaiian adults with diabetes. Clin Epigenetics 2022; 14:91. [PMID: 35851422 PMCID: PMC9295496 DOI: 10.1186/s13148-022-01307-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 07/04/2022] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Native Hawaiians are disproportionately affected by type 2 diabetes mellitus (DM), a chronic metabolic, non-communicable disease characterized by hyperglycemia and systemic inflammation. Unrelenting systemic inflammation frequently leads to a cascade of multiple comorbidities associated with DM, including cardiovascular disease, microvascular complications, and renal dysfunction. Yet few studies have examined the link between chronic inflammation at a cellular level and its relationship to standard DM therapies such as diabetes-specific lifestyle and social support education, well recognized as the cornerstone of clinical standards of diabetes care. This pilot study was initiated to explore the association of monocyte inflammation using epigenetic, immunologic, and clinical measures following a 3-month diabetes-specific social support program among high-risk Native Hawaiian adults with DM. RESULTS From a sample of 16 Native Hawaiian adults with DM, monocytes enriched from peripheral blood mononuclear cells (PBMCs) of 8 individuals were randomly selected for epigenomic analysis. Using the Illumina HumanMethylation450 BeadChip microarray, 1,061 differentially methylated loci (DML) were identified in monocytes of participants at baseline and 3 months following a DM-specific social support program (DM-SSP). Gene ontology analysis showed that these DML were enriched within genes involved in immune, metabolic, and cardiometabolic pathways, a subset of which were also significantly differentially expressed. Ex vivo analysis of immune function showed improvement post-DM-SSP compared with baseline, characterized by attenuated interleukin 1β and IL-6 secretion from monocytes. Altered cytokine secretion in response to the DM-SSP was significantly associated with changes in the methylation and gene expression states of immune-related genes in monocytes between intervention time points. CONCLUSIONS Our pilot study provides preliminary evidence of changes to inflammatory monocyte activity, potentially driven by epigenetic modifications, 3 months following a DM-specific SSP intervention. These novel alterations in the trajectory of monocyte inflammatory states were identified at loci that regulate transcription of immune and metabolic genes in high-risk Native Hawaiians with DM, suggesting a relationship between improvements in psychosocial behaviors and shifts in the immunoepigenetic patterns following a diabetes-specific SSP. Further research is warranted to investigate how social support influences systemic inflammation via immunoepigenetic modifications in chronic inflammatory diseases such as DM.
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Affiliation(s)
- Christian K Dye
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, HI, 96822, USA
- Department of Native Hawaiian Health, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, 96813, USA
- Department of Anatomy, Biochemistry and Physiology, John A. Burns School of Medicine, University of Hawaii, 651 Ilalo St. BSB222-K, Honolulu, HI, 96813, USA
| | - Michael J Corley
- Cornell Center for Immunology, Weill Cornell Medical Center, Cornell University, New York, NY, 10065, USA
- Department of Native Hawaiian Health, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, 96813, USA
| | - Claire Ing
- Department of Native Hawaiian Health, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, 96813, USA
| | - Annette Lum-Jones
- Department of Native Hawaiian Health, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, 96813, USA
- University of Hawaii Cancer Center, University of Hawaii, Honolulu, HI, 96813, USA
| | - Dongmei Li
- Department of Clinical and Translational Research, School of Medicine and Dentistry, University of Rochester, Rochester, NY, 14642, USA
| | - Marjorie K L M Mau
- Department of Native Hawaiian Health, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, 96813, USA
| | - Alika K Maunakea
- Department of Anatomy, Biochemistry and Physiology, John A. Burns School of Medicine, University of Hawaii, 651 Ilalo St. BSB222-K, Honolulu, HI, 96813, USA.
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Wu Y, Chen J, Tan F, Wang B, Xu W, Yuan C. ITGA9: Potential Biomarkers and Therapeutic Targets in Different Tumors. Curr Pharm Des 2022; 28:1412-1418. [DOI: 10.2174/1381612828666220501165644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 02/24/2022] [Indexed: 11/22/2022]
Abstract
Abstract:
Integrins are a class of a cell surface adhesion molecule which composed of α subunit (ITGA) and β subunit (ITGB). They belong to heterodimer transmembrane glycoproteins. Its main function in organisms is as the receptor of cell adhesion molecules (CAMs) and extracellular matrix (ECM). According to the current research integration analysis, integrin α9 (ITGA9) is one of the integrin subunits, and there are few studies on ITGA9 among integrins. ITGA9 can improve cell migration and regulate various cellular biological functions, such as tumor cell proliferation, adhesion, invasion, and angiogenesis. But its abnormal expression mechanism in cancer and its specific role in tumor growth and metastasis are still unknown to a great extent. This review reveals the role of ITGA9 in the complex pathogenesis of many tumors and cancers, providing a new direction for the treatment of tumors and cancers. Relevant studies were retrieved and collected through the PubMed system. After determining ITGA9 as the research object, we found the close relationship between ITGA9 and tumorigenesis through the analysis of the research articles on ITGA9 in the PubMed system in the last 15 years, and further determined the references mainly based on the influencing factors of the articles. Thus, the role of ITGA9 in tumor and cancer genesis, proliferation, and metastasis was reviewed and analyzed.
ITGA9 is an integrin subunit, which has been proved to be abnormally expressed in many tumors. After sorting and analyzing the research data, it was found that the abnormal expression of ITGA9 in a variety of tumors, including glioblastoma, rhabdomyosarcoma, melanoma, hepatocellular carcinoma, nasopharyngeal carcinoma, multiple myeloma, non-small cell lung cancer, and prostate cancer, was closely related to the proliferation, metastasis, adhesion, and angiogenesis of tumor cells. These results suggest that ITGA9 plays an important role in the occurrence and development of tumors. The integrin subunit ITGA9 may serve as a biomarker for the diagnosis of tumors and a potential therapeutic target for anti-tumor therapies.
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Affiliation(s)
- Yinxin Wu
- Third-grade Pharmacological Laboratory on Traditional Chinese Medicine,State Administration of Traditional Chinese Medicine, China Three Gorges University, Yichang 443002, China
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy,China Three Gorges University, Yichang 443002, China
- Medical College,China Three Gorges University, Yichang 443002, China
| | - Jinlan Chen
- Third-grade Pharmacological Laboratory on Traditional Chinese Medicine,State Administration of Traditional Chinese Medicine, China Three Gorges University, Yichang 443002, China
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy,China Three Gorges University, Yichang 443002, China
- Medical College,China Three Gorges University, Yichang 443002, China
| | - Fangshun Tan
- Third-grade Pharmacological Laboratory on Traditional Chinese Medicine,State Administration of Traditional Chinese Medicine, China Three Gorges University, Yichang 443002, China
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy,China Three Gorges University, Yichang 443002, China
- Medical College,China Three Gorges University, Yichang 443002, China
| | - Bei Wang
- Third-grade Pharmacological Laboratory on Traditional Chinese Medicine,State Administration of Traditional Chinese Medicine, China Three Gorges University, Yichang 443002, China
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy,China Three Gorges University, Yichang 443002, China
- Medical College,China Three Gorges University, Yichang 443002, China
| | - Wen Xu
- Third-grade Pharmacological Laboratory on Traditional Chinese Medicine,State Administration of Traditional Chinese Medicine, China Three Gorges University, Yichang 443002, China
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy,China Three Gorges University, Yichang 443002, China
- Medical College,China Three Gorges University, Yichang 443002, China
| | - Chengfu Yuan
- Third-grade Pharmacological Laboratory on Traditional Chinese Medicine,State Administration of Traditional Chinese Medicine, China Three Gorges University, Yichang 443002, China
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy,China Three Gorges University, Yichang 443002, China
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Fatmi A, Chabni N, Cernada M, Vento M, González-López M, Aribi M, Pallardó FV, García-Giménez JL. Clinical and immunological aspects of microRNAs in neonatal sepsis. Biomed Pharmacother 2021; 145:112444. [PMID: 34808550 DOI: 10.1016/j.biopha.2021.112444] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 11/08/2021] [Accepted: 11/16/2021] [Indexed: 12/12/2022] Open
Abstract
Neonatal sepsis constitutes a highly relevant public health challenge and is the most common cause of infant morbidity and mortality worldwide. Recent studies have demonstrated that during infection epigenetic changes may occur leading to reprogramming of gene expression. Post-transcriptional regulation by short non-coding RNAs (e.g., microRNAs) have recently acquired special relevance because of their role in the regulation of the pathophysiology of sepsis and their potential clinical use as biomarkers. ~22-nucleotide of microRNAs are not only involved in regulating multiple relevant cellular and molecular functions, such as immune cell function and inflammatory response, but have also been proposed as good candidates as biomarkers in sepsis. Nevertheless, establishing clinical practice guidelines based on microRNA patterns as biomarkers for diagnosis and prognosis in neonatal sepsis has yet to be achieved. Given their differential expression across tissues in neonates, the release of specific microRNAs to blood and their expression pattern can differ compared to sepsis in adult patients. Further in-depth research is necessary to fully understand the biological relevance of microRNAs and assess their potential use in clinical settings. This review provides a general overview of microRNAs, their structure, function and biogenesis before exploring their potential clinical interest as diagnostic and prognostic biomarkers of neonatal sepsis. An important part of the review is focused on immune and inflammatory aspects of selected microRNAs that may become biomarkers for clinical use and therapeutic intervention.
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Affiliation(s)
- Ahlam Fatmi
- Laboratory of Applied Molecular Biology and Immunology, University of Tlemcen, W0414100, 13000 Tlemcen, Algeria
| | - Nafissa Chabni
- Faculty of Medicine, Tlemcen Medical Centre University, 13000 Tlemcen, Algeria
| | - María Cernada
- Division of Neonatology, University and Polytechnic Hospital La Fe, Valencia, Spain; Neonatal Research Group, Health Research Institute La Fe, Valencia, Spain, University and Polytechnic Hospital La Fe, Valencia, Spain
| | - Máximo Vento
- Division of Neonatology, University and Polytechnic Hospital La Fe, Valencia, Spain; Neonatal Research Group, Health Research Institute La Fe, Valencia, Spain, University and Polytechnic Hospital La Fe, Valencia, Spain
| | - María González-López
- Department of Pediatrics. Hospital Regional Universitario de Málaga, Málaga, Spain
| | - Mourad Aribi
- Laboratory of Applied Molecular Biology and Immunology, University of Tlemcen, W0414100, 13000 Tlemcen, Algeria; Biotechnology Center of Constantine (CRBt), 25000 Constantine, Algeria
| | - Federico V Pallardó
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Valencia, Spain; INCLIVA Health Research Institute, Mixed Unit for Rare Diseases INCLIVA-CIPF, Valencia, Spain; Department of Physiology, Faculty of Medicine and Dentistry, University of Valencia, Valencia, Spain
| | - José Luis García-Giménez
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Valencia, Spain; INCLIVA Health Research Institute, Mixed Unit for Rare Diseases INCLIVA-CIPF, Valencia, Spain; Department of Physiology, Faculty of Medicine and Dentistry, University of Valencia, Valencia, Spain.
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Lassandro G, Ciaccia L, Amoruso A, Palladino V, Palmieri VV, Giordano P. Focus on MicroRNAs as Biomarker in Pediatric Diseases. Curr Pharm Des 2021; 27:826-832. [PMID: 33087027 DOI: 10.2174/1381612826666201021125512] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 09/25/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND MiRNAs are a class of small non-coding RNAs that are involved in the post-transcriptional regulation of gene expression. MiRNAs are considered a class of epigenetic biomarkers. These biomarkers can investigate disease at different stages: diagnosis, therapy or clinical follow-up. OBJECTIVE The aim of this paper is to highlight the innovative use of miRNAs in several childhood diseases. METHODS We conducted a literature review to search the usage of miRNAs in pediatric clinical routine or experimental trials. RESULTS We found a possible key role of miRNAs in different pediatric illnesses (metabolic alterations, coagulation defects, cancer). CONCLUSION The modest literature production denotes that further investigation is needed to assess and validate the promising role of miRNAs as non-invasive biomarkers in pediatric disorders.
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Affiliation(s)
- Giuseppe Lassandro
- Department of Biomedical Science and Human Oncology, University of Bari "Aldo Moro", Bari, Italy
| | - Loredana Ciaccia
- Department of Biomedical Science and Human Oncology, University of Bari "Aldo Moro", Bari, Italy
| | - Anna Amoruso
- Department of Biomedical Science and Human Oncology, University of Bari "Aldo Moro", Bari, Italy
| | - Valentina Palladino
- Department of Biomedical Science and Human Oncology, University of Bari "Aldo Moro", Bari, Italy
| | - Viviana V Palmieri
- Department of Biomedical Science and Human Oncology, University of Bari "Aldo Moro", Bari, Italy
| | - Paola Giordano
- Department of Biomedical Science and Human Oncology, University of Bari "Aldo Moro", Bari, Italy
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García-Giménez JL, Mena-Molla S, Tarazona-Santabalbina FJ, Viña J, Gomez-Cabrera MC, Pallardó FV. Implementing Precision Medicine in Human Frailty through Epigenetic Biomarkers. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:1883. [PMID: 33672064 PMCID: PMC7919465 DOI: 10.3390/ijerph18041883] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 12/15/2022]
Abstract
The main epigenetic features in aging are: reduced bulk levels of core histones, altered pattern of histone post-translational modifications, changes in the pattern of DNA methylation, replacement of canonical histones with histone variants, and altered expression of non-coding RNA. The identification of epigenetic mechanisms may contribute to the early detection of age-associated subclinical changes or deficits at the molecular and/or cellular level, to predict the development of frailty, or even more interestingly, to improve health trajectories in older adults. Frailty reflects a state of increased vulnerability to stressors as a result of decreased physiologic reserves, and even dysregulation of multiple physiologic systems leading to adverse health outcomes for individuals of the same chronological age. A key approach to overcome the challenges of frailty is the development of biomarkers to improve early diagnostic accuracy and to predict trajectories in older individuals. The identification of epigenetic biomarkers of frailty could provide important support for the clinical diagnosis of frailty, or more specifically, to the evaluation of its associated risks. Interventional studies aimed at delaying the onset of frailty and the functional alterations associated with it, would also undoubtedly benefit from the identification of frailty biomarkers. Specific to the article yet reasonably common within the subject discipline.
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Affiliation(s)
- José Luis García-Giménez
- U733, Centre for Biomedical Network Research on Rare Diseases (CIBERER-ISCIII), 28029 Madrid, Spain; (J.L.G.-G.); (F.V.P.)
- Mixed Unit for Rare Diseases INCLIVA-CIPF, INCLIVA Health Research Institute, 46010 Valencia, Spain
- Department of Physiology, Faculty of Medicine, University of Valencia, 46003 Valencia, Spain;
- EpiDisease S.L., Parc Cientific de la Universitat de València, 46980 Paterna, Spain
| | - Salvador Mena-Molla
- Department of Physiology, Faculty of Medicine, University of Valencia, 46003 Valencia, Spain;
- EpiDisease S.L., Parc Cientific de la Universitat de València, 46980 Paterna, Spain
| | | | - Jose Viña
- Freshage Research Group, Department of Physiology, Faculty of Medicine, Institute of Health Research-INCLIVA, University of Valencia and CIBERFES, 46010 Valencia, Spain;
| | - Mari Carmen Gomez-Cabrera
- Freshage Research Group, Department of Physiology, Faculty of Medicine, Institute of Health Research-INCLIVA, University of Valencia and CIBERFES, 46010 Valencia, Spain;
| | - Federico V. Pallardó
- U733, Centre for Biomedical Network Research on Rare Diseases (CIBERER-ISCIII), 28029 Madrid, Spain; (J.L.G.-G.); (F.V.P.)
- Mixed Unit for Rare Diseases INCLIVA-CIPF, INCLIVA Health Research Institute, 46010 Valencia, Spain
- Department of Physiology, Faculty of Medicine, University of Valencia, 46003 Valencia, Spain;
- EpiDisease S.L., Parc Cientific de la Universitat de València, 46980 Paterna, Spain
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Epigenetic Markers Associated with Schistosomiasis. Helminthologia 2021; 58:28-40. [PMID: 33664616 PMCID: PMC7912237 DOI: 10.2478/helm-2021-0009] [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: 02/18/2020] [Accepted: 12/01/2020] [Indexed: 11/21/2022] Open
Abstract
It is important to consider the use of the epigenome as source of complementary data for genome knowledge, which is suitable for the diagnosis of schistosomiasis. Usually, a laboratory diagnosis of schistosomiasis is performed by means of 1. Egg detection in the stool or urine by microscopy remains with limited sensitivity; 2. Immunological screening, in which positivity persists after treatment, and 3. Molecular appraisals prevail over the disadvantages of the currently used methods. In this sense, molecular methodologies are being developed based on epigenetic biomarkers, aiming to improve the diagnosis of the disease and clinical treatment as early as possible to prevent the occurrence of serious liver damage.
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Han Y, Huang L, Zhou F. A dynamic recursive feature elimination framework (dRFE) to further refine a set of OMIC biomarkers. Bioinformatics 2021; 37:2183-2189. [PMID: 33515240 DOI: 10.1093/bioinformatics/btab055] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/23/2020] [Accepted: 01/25/2021] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION A feature selection algorithm may select the subset of features with the best associations with the class labels. The recursive feature elimination (RFE) is a heuristic feature screening framework and has been widely used to select the biological OMIC biomarkers. This study proposed a dynamic recursive feature elimination (dRFE) framework with more flexible feature elimination operations. The proposed dRFE was comprehensively compared with 11 existing feature selection algorithms and five classifiers on the eight difficult transcriptome datasets from a previous study, the ten newly collected transcriptome datasets and the five methylome datasets. RESULTS The experimental data suggested that the regular RFE framework did not perform well, and dRFE outperformed the existing feature selection algorithms in most cases. The dRFE-detected features achieved Acc=1.0000 for the two methylome datasets GSE53045 and GSE66695. The best prediction accuracies of the dRFE-detected features were 0.9259, 0.9424, and 0.8601 for the other three methylome datasets GSE74845, GSE103186, and GSE80970, respectively. Four transcriptome datasets received Acc=1.0000 using the dRFE-detected features, and the prediction accuracies for the other six newly collected transcriptome datasets were between 0.6301 and 0.9917. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yuanyuan Han
- College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin, China, 130012
| | - Lan Huang
- College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin, China, 130012
| | - Fengfeng Zhou
- College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin, China, 130012
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Deng Q, Su B, Ji X, Fang Q, Zhou S, Zhou C. Predictive value of unmethylated RASSF1A on disease progression in non-small cell lung cancer patients receiving pemetrexed-based chemotherapy. Cancer Biomark 2020; 27:313-323. [PMID: 31839603 DOI: 10.3233/cbm-190258] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND OBJECTIVE Chemotherapy remains the basis of the treatment of lung cancer, and screening biomarkers with predictive value for chemotherapy is of great interest. The present study focused on status of genes methylation in NSCLC patients receiving pemetrexed- or gemcitabine-based chemotherapy. PATIENTS AND METHODS Promoter methylation of Ras association domain family (RASSF1A) and short stature homeobox 2 (SHOX2) was examined in bronchoalveolar lavage (BAL) from 117 NSCLC patients treated with chemotherapy. Multivariate analysis was used to identify the predictive value of gene methylation. Progression-free survival (PFS) rather than overall survival (OS) was used as the clinical outcome to minimize the impact of chemotherapy on gene methylation. RESULTS The methylation of RASSF1A and SHOX2 was significantly associated with shorter PFS (RASSF1A: HR = 2.355, 95% CI: 1.533-3.617, P< 0.0001; SHOX2: HR = 2.123, 95% CI: 1.392-3.236, P= 0.0004). After adjusting for confounding factors, RASSF1A methylation was still a predictive factor for PFS (HR = 1.765, 95% CI: 1.064-2.928, P= 0.0278). In the pemetrexed group, unmethylated RASSF1A could be used to predict longer PFS (P= 0.0001), and no predictive value was found in the gemcitabine group. CONCLUSION Unmethylated RASSF1A is a favorable prognostic indicator for patients receiving pemetrexed doublets. Because of the promoting effect of most chemotherapeutic drugs on gene methylation, unmethylated RASSF1A is not suitable as a predictor for gemcitabine doublets.
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Affiliation(s)
- Qinfang Deng
- Medical College of Soochow University, Soochow, China.,Department of Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China.,Medical College of Soochow University, Soochow, China
| | - Bo Su
- Central Laboratory, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China.,Medical College of Soochow University, Soochow, China
| | - Xianxiu Ji
- Department of Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Qiyu Fang
- Department of Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Songwen Zhou
- Department of Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Caicun Zhou
- Medical College of Soochow University, Soochow, China.,Department of Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
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12
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de Oliveira DT, Guerra-Sá R. Uncovering epigenetic landscape: a new path for biomarkers identification and drug development. Mol Biol Rep 2020; 47:9097-9122. [PMID: 33089404 DOI: 10.1007/s11033-020-05916-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 10/10/2020] [Indexed: 12/31/2022]
Abstract
Scientific advances in recent decades have revealed an incredible degree of plasticity in gene expression in response to various environmental, nutritional, physiological, pathological, and behavioral conditions. Epigenetics emerges in this sense, as the link between the internal (genetic) and external (environmental) factors underlying the expression of the phenotype. Methylation of DNA and histone post-translationa modifications are canonical epigenetic events. Additionally, noncoding RNAs molecules (microRNAs and lncRNAs) have also been proposed as another layer of epigenetic regulation. Together, these events are responsible for regulating gene expression throughout life, controlling cellular fate in both normal and pathological development. Despite being a relatively recent science, epigenetics has been arousing the interest of researchers from different segments of the life sciences and the general public. This review highlights the recent advances in the characterization of the epigenetic events and points promising use of these brands for the diagnosis, prognosis, and therapy of diseases. We also present several classes of epigenetic modifying compounds with therapeutic applications (so-call epidrugs) and their current status in clinical trials and approved by the FDA. In summary, hopefully, we provide the reader with theoretical bases for a better understanding of the epigenetic mechanisms and of the promising application of these marks and events in the medical clinic.
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Affiliation(s)
- Daiane Teixeira de Oliveira
- Programa de Pós-graduação em Ciências Farmacêuticas, Escola de Farmácia, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil.
| | - Renata Guerra-Sá
- Programa de Pós-graduação em Ciências Farmacêuticas, Escola de Farmácia, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil.,Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil
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13
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Davis KD, Aghaeepour N, Ahn AH, Angst MS, Borsook D, Brenton A, Burczynski ME, Crean C, Edwards R, Gaudilliere B, Hergenroeder GW, Iadarola MJ, Iyengar S, Jiang Y, Kong JT, Mackey S, Saab CY, Sang CN, Scholz J, Segerdahl M, Tracey I, Veasley C, Wang J, Wager TD, Wasan AD, Pelleymounter MA. Discovery and validation of biomarkers to aid the development of safe and effective pain therapeutics: challenges and opportunities. Nat Rev Neurol 2020; 16:381-400. [PMID: 32541893 PMCID: PMC7326705 DOI: 10.1038/s41582-020-0362-2] [Citation(s) in RCA: 201] [Impact Index Per Article: 50.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/21/2020] [Indexed: 02/06/2023]
Abstract
Pain medication plays an important role in the treatment of acute and chronic pain conditions, but some drugs, opioids in particular, have been overprescribed or prescribed without adequate safeguards, leading to an alarming rise in medication-related overdose deaths. The NIH Helping to End Addiction Long-term (HEAL) Initiative is a trans-agency effort to provide scientific solutions to stem the opioid crisis. One component of the initiative is to support biomarker discovery and rigorous validation in collaboration with industry leaders to accelerate high-quality clinical research into neurotherapeutics and pain. The use of objective biomarkers and clinical trial end points throughout the drug discovery and development process is crucial to help define pathophysiological subsets of pain, evaluate target engagement of new drugs and predict the analgesic efficacy of new drugs. In 2018, the NIH-led Discovery and Validation of Biomarkers to Develop Non-Addictive Therapeutics for Pain workshop convened scientific leaders from academia, industry, government and patient advocacy groups to discuss progress, challenges, gaps and ideas to facilitate the development of biomarkers and end points for pain. The outcomes of this workshop are outlined in this Consensus Statement.
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Affiliation(s)
- Karen D Davis
- Department of Surgery and Institute of Medical Science, University of Toronto, Toronto, ON, Canada.
- Division of Brain, Imaging and Behaviour, Krembil Brain Institute, Toronto Western Hospital, University Health Network, Toronto, ON, Canada.
| | - Nima Aghaeepour
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Martin S Angst
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - David Borsook
- Center for Pain and the Brain, Harvard Medical School, Boston, MA, USA
| | | | | | | | - Robert Edwards
- Pain Management Center, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Brice Gaudilliere
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Georgene W Hergenroeder
- The Vivian L. Smith Department of Neurosurgery, The University of Texas Health Science Center at Houston, McGovern Medical School, Houston, TX, USA
| | - Michael J Iadarola
- Department of Perioperative Medicine, Clinical Center, NIH, Rockville, MD, USA
| | - Smriti Iyengar
- Division of Translational Research, National Institute of Neurological Disorders and Stroke, NIH, Rockville, MD, USA
| | - Yunyun Jiang
- The Biostatistics Center, Milken Institute School of Public Health, The George Washington University, Washington, DC, USA
| | - Jiang-Ti Kong
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Sean Mackey
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Carl Y Saab
- Department of Neuroscience and Department of Neurosurgery, Carney Institute for Brain Science, Brown University, Providence, RI, USA
| | - Christine N Sang
- Department of Anesthesiology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Joachim Scholz
- Neurocognitive Disorders, Pain and New Indications, Biogen, Cambridge, MA, USA
| | | | - Irene Tracey
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | | | - Jing Wang
- Department of Anesthesiology, Perioperative Care and Pain Medicine, NYU School of Medicine, New York, NY, USA
| | - Tor D Wager
- Department of Psychological and Brain Sciences, Dartmouth College, Hanover, NH, USA
| | - Ajay D Wasan
- Anesthesiology and Perioperative Medicine and Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Mary Ann Pelleymounter
- Division of Translational Research, National Institute of Neurological Disorders and Stroke, NIH, Rockville, MD, USA
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14
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Yin W, Wang X, Li Y, Wang B, Song M, Hulbert A, Chen C, Yu F. Promoter hypermethylation of cysteine dioxygenase type 1 in patients with non-small cell lung cancer. Oncol Lett 2020; 20:967-973. [PMID: 32566027 DOI: 10.3892/ol.2020.11592] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 02/28/2020] [Indexed: 12/19/2022] Open
Abstract
In the present study, promoter hypermethylation of cysteine dioxygenase type 1 (CDO1) was evaluated in non-small cell lung cancer (NSCLC) tissues to assess the value of CDO1 as a novel biomarker to improve the diagnosis of NSCLC. Tumor tissue samples and corresponding normal lung tissue samples from 42 patients with NSCLC were obtained at the Department of Thoracic Surgery, The Second Xiangya Hospital (Changsha, China). Conventional methylation-specific PCR (cMSP) and methylation-on-beads followed by quantitative methylation-specific PCR (MOB-qMSP) were used to analyze the tumor and normal lung tissue samples. Using these two methods, promoter DNA hypermethylation of the CDO1 gene was detected in 59.4 and 71.0% of tumor tissues of patients with NSCLC and in 9.4 and 0% of normal lung tissue, respectively. Compared with the rate of methylation in the well-differentiated NSCLC tissues (15.4 and 55.6%, respectively), the rate of CDO1 gene promoter methylation was higher in the poorly differentiated tissues (89.5 and 92.3%, respectively). Overall, it was demonstrated that the MOB-qMSP method had a higher positive detection rate for CDO1 hypermethylation compared with the cMSP method. In conclusion, CDO1 gene promoter hypermethylation was more frequently observed in NSCLC tissues compared with in normal lung tissues, and a high methylation frequency of the CDO1 gene in biopsy specimens of NSCLC was associated with the degree of differentiation.
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Affiliation(s)
- Wei Yin
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, P.R. China
| | - Xiang Wang
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, P.R. China
| | - Yunping Li
- Department of Ophthalmology, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, P.R. China
| | - Bin Wang
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, P.R. China
| | - Mingzhe Song
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, P.R. China
| | - Alicia Hulbert
- Department of Surgery, University of Illinois at Chicago School of Medicine, Chicago, IL 60607, USA
| | - Chen Chen
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, P.R. China
| | - Fenglei Yu
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, P.R. China
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15
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Dyke SOM, Saulnier KM, Dupras C, Webster AP, Maschke K, Rothstein M, Siebert R, Walter J, Beck S, Pastinen T, Joly Y. Points-to-consider on the return of results in epigenetic research. Genome Med 2019; 11:31. [PMID: 31122281 PMCID: PMC6533659 DOI: 10.1186/s13073-019-0646-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
As epigenetic studies become more common and lead to new insights into health and disease, the return of individual epigenetic results to research participants, in particular in large-scale epigenomic studies, will be of growing importance. Members of the International Human Epigenome Consortium (IHEC) Bioethics Workgroup considered the potential ethical, legal, and social issues (ELSI) involved in returning epigenetic research results and incidental findings in order to produce a set of 'Points-to-consider' (P-t-C) for the epigenetics research community. These P-t-C draw on existing guidance on the return of genetic research results, while also integrating the IHEC Bioethics Workgroup's ELSI research on and discussion of the issues associated with epigenetic data as well as the experience of a return of results pilot study by the Personal Genome Project UK (PGP-UK). Major challenges include how to determine the clinical validity and actionability of epigenetic results, and considerations related to environmental exposures and epigenetic marks, including circumstances warranting the sharing of results with family members and third parties. Interdisciplinary collaboration and good public communication regarding epigenetic risk will be important to advance the return of results framework for epigenetic science.
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Affiliation(s)
- Stephanie O M Dyke
- Centre of Genomics and Policy, Faculty of Medicine, McGill University, Montreal, Quebec, H3A 0G1, Canada.
- Montreal Neurological Institute, Faculty of Medicine, McGill University, Montreal, Quebec, H3A 2B4, Canada.
| | - Katie M Saulnier
- Centre of Genomics and Policy, Faculty of Medicine, McGill University, Montreal, Quebec, H3A 0G1, Canada
| | - Charles Dupras
- Centre of Genomics and Policy, Faculty of Medicine, McGill University, Montreal, Quebec, H3A 0G1, Canada
| | - Amy P Webster
- UCL Cancer Institute, University College London, London, WC1E 6DD, UK
| | | | - Mark Rothstein
- Institute for Bioethics, Health Policy and Law, University of Louisville School of Medicine, Louisville, KY, 40202, USA
| | - Reiner Siebert
- Institute of Human Genetics, Ulm University Medical Center, 89091, Ulm, Germany
| | - Jörn Walter
- Saarland University, 66123, Saarbrücken, Germany
| | - Stephan Beck
- UCL Cancer Institute, University College London, London, WC1E 6DD, UK
| | - Tomi Pastinen
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, H3A 0G1, Canada
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Yann Joly
- Centre of Genomics and Policy, Faculty of Medicine, McGill University, Montreal, Quebec, H3A 0G1, Canada
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16
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Wang Q, Peng WX, Wang L, Ye L. Toward multiomics-based next-generation diagnostics for precision medicine. Per Med 2019; 16:157-170. [PMID: 30816060 DOI: 10.2217/pme-2018-0085] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Our healthcare system is experiencing a paradigm shift to precision medicine, aiming at an early prediction of individual disease risks and targeted interventions. Whole-genome sequencing is currently gaining momentum, as it has the potential to capture all classes of genetic variation, thus providing a more complete picture of the individual's genetic makeup, which could be utilized in genetic testing; however, this will also lead to difficulties in interpreting the test results, necessitating careful integration of genomic data with other layers of information, both molecular multiomics measurements of epigenome, transcriptome, proteome, metabolome and even microbiome, as well as comprehensive information on diet, lifestyle and environment. Overall, the translation of patient-specific data into actionable diagnostic tools will be a challenging task, requiring expertise from multiple disciplines, secure data sharing in large reference databases and a strong computational infrastructure.
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Affiliation(s)
- Qi Wang
- Department of Emergency Medicine, Hangzhou Hospital of Traditional Chinese Medicine, Hangzhou 310007, Zhejiang Province, China
| | - Wei-Xian Peng
- Department of Emergency Medicine, Hangzhou Hospital of Traditional Chinese Medicine, Hangzhou 310007, Zhejiang Province, China
| | - Lu Wang
- Department of Emergency Medicine, Hangzhou Hospital of Traditional Chinese Medicine, Hangzhou 310007, Zhejiang Province, China
| | - Li Ye
- Department of Nursing, Tongde Hospital of Zhejiang Province, Hangzhou 310012, Zhejiang Province, China
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17
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Xu C, Liu J, Yang W, Shu Y, Wei Z, Zheng W, Feng X, Zhou F. An OMIC biomarker detection algorithm TriVote and its application in methylomic biomarker detection. Epigenomics 2018; 10:335-347. [DOI: 10.2217/epi-2017-0097] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Aim: Transcriptomic and methylomic patterns represent two major OMIC data sources impacted by both inheritable genetic information and environmental factors, and have been widely used as disease diagnosis and prognosis biomarkers. Materials & methods: Modern transcriptomic and methylomic profiling technologies detect the status of tens of thousands or even millions of probing residues in the human genome, and introduce a major computational challenge for the existing feature selection algorithms. This study proposes a three-step feature selection algorithm, TriVote, to detect a subset of transcriptomic or methylomic residues with highly accurate binary classification performance. Results & conclusion: TriVote outperforms both filter and wrapper feature selection algorithms with both higher classification accuracy and smaller feature number on 17 transcriptomes and two methylomes. Biological functions of the methylome biomarkers detected by TriVote were discussed for their disease associations. An easy-to-use Python package is also released to facilitate the further applications.
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Affiliation(s)
- Cheng Xu
- College of Software, Jilin University, Changchun, Jilin 130012, PR China
| | - Jiamei Liu
- College of Software, Jilin University, Changchun, Jilin 130012, PR China
| | - Weifeng Yang
- College of Software, Jilin University, Changchun, Jilin 130012, PR China
| | - Yayun Shu
- College of Software, Jilin University, Changchun, Jilin 130012, PR China
| | - Zhipeng Wei
- Key Laboratory of Symbolic Computation & Knowledge Engineering of Ministry of Education, College of Computer Science & Technology, Jilin University, Changchun, Jilin 130012, PR China
| | - Weiwei Zheng
- Key Laboratory of Symbolic Computation & Knowledge Engineering of Ministry of Education, College of Computer Science & Technology, Jilin University, Changchun, Jilin 130012, PR China
| | - Xin Feng
- Key Laboratory of Symbolic Computation & Knowledge Engineering of Ministry of Education, College of Computer Science & Technology, Jilin University, Changchun, Jilin 130012, PR China
| | - Fengfeng Zhou
- College of Software, Jilin University, Changchun, Jilin 130012, PR China
- Key Laboratory of Symbolic Computation & Knowledge Engineering of Ministry of Education, College of Computer Science & Technology, Jilin University, Changchun, Jilin 130012, PR China
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18
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García-Giménez JL, Rubio-Belmar PA, Peiró-Chova L, Hervás D, González-Rodríguez D, Ibañez-Cabellos JS, Bas-Hermida P, Mena-Mollá S, García-López EM, Pallardó FV, Bas T. Circulating miRNAs as diagnostic biomarkers for adolescent idiopathic scoliosis. Sci Rep 2018; 8:2646. [PMID: 29422531 PMCID: PMC5805715 DOI: 10.1038/s41598-018-21146-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 01/31/2018] [Indexed: 11/09/2022] Open
Abstract
The aetiology of adolescent idiopathic scoliosis (AIS) has been linked to many factors, such as asymmetric growth, neuromuscular condition, bone strength and genetic background. Recently, epigenetic factors have been proposed as contributors of AIS physiopathology, but information about the molecular mechanisms and pathways involved is scarce. Regarding epigenetic factors, microRNAs (miRNAs) are molecules that contribute to gene expression modulation by regulating important cellular pathways. We herein used Next-Generation Sequencing to discover a series of circulating miRNAs detected in the blood samples of AIS patients, which yielded a unique miRNA biomarker signature that diagnoses AIS with high sensitivity and specificity. We propose that these miRNAs participate in the epigenetic control of signalling pathways by regulating osteoblast and osteoclast differentiation, thus modulating the genetic background of AIS patients. Our study yielded two relevant results: 1) evidence for the deregulated miRNAs that participate in osteoblast/osteoclast differentiation mechanisms in AIS; 2) this miRNA-signature can be potentially used as a clinical tool for molecular AIS diagnosis. Using miRNAs as biomarkers for AIS diagnostics is especially relevant since miRNAs can serve for early diagnoses and for evaluating the positive effects of applied therapies to therefore reduce the need of high-risk surgical interventions.
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Affiliation(s)
- José Luis García-Giménez
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Valencia, Spain.
- Instituto de Investigación Sanitaria INCLIVA, Avenida de Menéndez y Pelayo, 4, 46010, Valencia, Spain.
- Dept. Physiology. Faculty of Medicine and Dentistry, University of Valencia, Av/Blasco Ibañez, 15, 46010, Valencia, Spain.
| | - Pedro Antonio Rubio-Belmar
- Instituto de Investigación Sanitaria IISLAFE, Av/Fernando Abril Martorell, 106. Torre A 7, 46026, Valencia, Spain
- Unidad de Raquis. Hospital Universitari i Politècnic La Fe, Av/Fernando Abril Martorell, 106, 46026, Valencia, Spain
| | - Lorena Peiró-Chova
- Instituto de Investigación Sanitaria INCLIVA, Avenida de Menéndez y Pelayo, 4, 46010, Valencia, Spain
| | - David Hervás
- Unidad de Bioestadística, Instituto de Investigación Sanitaria IISLAFE, Av/Fernando Abril Martorell, 106, 46026, Valencia, Spain
| | - Daymé González-Rodríguez
- Instituto de Investigación Sanitaria INCLIVA, Avenida de Menéndez y Pelayo, 4, 46010, Valencia, Spain
| | - José Santiago Ibañez-Cabellos
- Instituto de Investigación Sanitaria INCLIVA, Avenida de Menéndez y Pelayo, 4, 46010, Valencia, Spain
- Dept. Physiology. Faculty of Medicine and Dentistry, University of Valencia, Av/Blasco Ibañez, 15, 46010, Valencia, Spain
| | - Paloma Bas-Hermida
- Instituto de Investigación Sanitaria IISLAFE, Av/Fernando Abril Martorell, 106. Torre A 7, 46026, Valencia, Spain
- Unidad de Raquis. Hospital Universitari i Politècnic La Fe, Av/Fernando Abril Martorell, 106, 46026, Valencia, Spain
| | - Salvador Mena-Mollá
- Dept. Physiology. Faculty of Medicine and Dentistry, University of Valencia, Av/Blasco Ibañez, 15, 46010, Valencia, Spain
| | - Eva María García-López
- Instituto de Investigación Sanitaria INCLIVA, Avenida de Menéndez y Pelayo, 4, 46010, Valencia, Spain
- Dept. Physiology. Faculty of Medicine and Dentistry, University of Valencia, Av/Blasco Ibañez, 15, 46010, Valencia, Spain
| | - Federico V Pallardó
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Valencia, Spain
- Instituto de Investigación Sanitaria INCLIVA, Avenida de Menéndez y Pelayo, 4, 46010, Valencia, Spain
- Dept. Physiology. Faculty of Medicine and Dentistry, University of Valencia, Av/Blasco Ibañez, 15, 46010, Valencia, Spain
| | - Teresa Bas
- Instituto de Investigación Sanitaria IISLAFE, Av/Fernando Abril Martorell, 106. Torre A 7, 46026, Valencia, Spain
- Unidad de Raquis. Hospital Universitari i Politècnic La Fe, Av/Fernando Abril Martorell, 106, 46026, Valencia, Spain
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19
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Zhang C, Yu W, Wang L, Zhao M, Guo Q, Lv S, Hu X, Lou J. DNA Methylation Analysis of the SHOX2 and RASSF1A Panel in Bronchoalveolar Lavage Fluid for Lung Cancer Diagnosis. J Cancer 2017; 8:3585-3591. [PMID: 29151944 PMCID: PMC5687174 DOI: 10.7150/jca.21368] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 08/28/2017] [Indexed: 12/22/2022] Open
Abstract
Introduction: Currently the majority of lung cancer patients are diagnosed as advanced diseases for no sensitive and specific biomarkers exist, noninvasive biomarkers with high sensitivity and specificity are urgently needed in lung cancer diagnosis. Bronchoscopy is a standard procedure of the diagnostic work-up of patients with suspected lung cancer despite of the limited diagnostic accuracy. Besides, epigenetic changes through DNA methylation play an important role in tumorigenesis. Thus, we examined the aberrant methylation of the SHOX2 and RASSF1A in bronchoalveolar lavage fluid (BALF) in comparing with conventional cytology examination and serum CEA in order to evaluate the new diagnostic method. Patients and Methods: BALF and serum samples were collected from 322 patients at the time of diagnosis, 284 of them were pathologically confirmed lung cancer, 35 were benign lung diseases and 3 were malignancies in other systems. For all of the 322 patients, the methylation status of the SHOX2 and RASSF1A gene were detected by a new RT-PCR platform and then confirmed by sanger sequencing. Serum CEA were detected using electrochemiluminescence immunoassay. Results: Profiling data showed the consistency of RT-PCR and sanger sequencing in detecting the methylation of the SHOX2 and RASSF1A. Besides, the combination of SHOX2 and RASSF1A methylation in BALF yielded a diagnostic sensitivity of 81.0% and specificity of 97.4%. When compared with established cytology examination (sensitivity: 68.3%, specificity: 97.4%) and serum biomarker carcinoembryonic antigen (CEA) (sensitivity: 30.6%, specificity: 100.0%), the SHOX2 and RASSF1A methylation panel showed the highest diagnostic efficiency. Notably, the combination of cytology and the SHOX2 and RASSF1A methylation panel could significantly improve the diagnostic efficacy. Conclusion: The methylation analysis of the SHOX2 and RASSF1A panel in BALF with RT-PCR achieved a satisfactory sensitivity and specificity in lung cancer diagnosis, especially in an early stage. It could be used as a promising noninvasive biomarker for auxiliary diagnosis of lung cancer.
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Affiliation(s)
- Chenzi Zhang
- Department of Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Wenjun Yu
- Department of Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Lin Wang
- Department of Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Mingna Zhao
- Department of Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Qiaomei Guo
- Department of Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Shaogang Lv
- Department of Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Xiaomeng Hu
- Department of Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Jiatao Lou
- Department of Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, China
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20
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Ashraf W, Ibrahim A, Alhosin M, Zaayter L, Ouararhni K, Papin C, Ahmad T, Hamiche A, Mély Y, Bronner C, Mousli M. The epigenetic integrator UHRF1: on the road to become a universal biomarker for cancer. Oncotarget 2017; 8:51946-51962. [PMID: 28881702 PMCID: PMC5584303 DOI: 10.18632/oncotarget.17393] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 04/02/2017] [Indexed: 12/12/2022] Open
Abstract
Cancer is one of the deadliest diseases in the world causing record number of mortalities in both developed and undeveloped countries. Despite a lot of advances and breakthroughs in the field of oncology still, it is very hard to diagnose and treat the cancers at early stages. Here in this review we analyze the potential of Ubiquitin-like containing PHD and Ring Finger domain 1 (UHRF1) as a universal biomarker for cancers. UHRF1 is an important epigenetic regulator maintaining DNA methylation and histone code in the cell. It is highly expressed in a variety of cancers and is a well-known oncogene that can disrupt the epigenetic code and override the senescence machinery. Many studies have validated UHRF1 as a powerful diagnostic and prognostic tool to differentially diagnose cancer, predict the therapeutic response and assess the risk of tumor progression and recurrence. Highly sensitive, non-invasive and cost effective approaches are therefore needed to assess the level of UHRF1 in patients, which can be deployed in diagnostic laboratories to detect cancer and monitor disease progression.
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Affiliation(s)
- Waseem Ashraf
- Laboratory of Biophotonics and Pharmacology, Faculty of Pharmacy, University of Strasbourg, Illkirch, France
| | - Abdulkhaleg Ibrahim
- Institute of Genetics and Molecular and Cellular Biology, University of Strasbourg, Illkirch-Graffenstaden, France
| | - Mahmoud Alhosin
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Cancer Metabolism and Epigenetic Unit, King Abdulaziz University, Jeddah, Saudi Arabia
- Cancer and Mutagenesis Unit, King Fahd Centre for Medical Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Liliyana Zaayter
- Laboratory of Biophotonics and Pharmacology, Faculty of Pharmacy, University of Strasbourg, Illkirch, France
| | - Khalid Ouararhni
- Institute of Genetics and Molecular and Cellular Biology, University of Strasbourg, Illkirch-Graffenstaden, France
| | - Christophe Papin
- Institute of Genetics and Molecular and Cellular Biology, University of Strasbourg, Illkirch-Graffenstaden, France
| | - Tanveer Ahmad
- Laboratory of Biophotonics and Pharmacology, Faculty of Pharmacy, University of Strasbourg, Illkirch, France
| | - Ali Hamiche
- Institute of Genetics and Molecular and Cellular Biology, University of Strasbourg, Illkirch-Graffenstaden, France
| | - Yves Mély
- Laboratory of Biophotonics and Pharmacology, Faculty of Pharmacy, University of Strasbourg, Illkirch, France
| | - Christian Bronner
- Institute of Genetics and Molecular and Cellular Biology, University of Strasbourg, Illkirch-Graffenstaden, France
| | - Marc Mousli
- Laboratory of Biophotonics and Pharmacology, Faculty of Pharmacy, University of Strasbourg, Illkirch, France
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Weinhouse C, Bergin IL, Harris C, Dolinoy DC. Stat3 is a candidate epigenetic biomarker of perinatal Bisphenol A exposure associated with murine hepatic tumors with implications for human health. Epigenetics 2016; 10:1099-110. [PMID: 26542749 DOI: 10.1080/15592294.2015.1107694] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Bisphenol A (BPA) is an endocrine disrupting chemical (EDC) that has been implicated as a potential carcinogen and epigenotoxicant. We have previously reported dose-dependent incidence of hepatic tumors in 10-month-old isogenic mice perinatally exposed to BPA. Here, we evaluated DNA methylation at 3 candidate genes (Esr1, Il-6st, and Stat3) in liver tissue of BPA-exposed mice euthanized at 2 time points: post-natal day 22 (PND22; n = 147) or 10-months of age (n = 78, including n = 18 with hepatic tumors). Additionally, DNA methylation profiles were analyzed at human homologs of murine candidate genes in human fetal liver samples (n = 50) with known liver tissue BPA levels. Candidate genes were chosen based on reported expression changes in both rodent and human hepatocellular carcinoma (HCC). Regions for bisulfite sequencing were chosen by mining whole genome next generation sequencing methylation datasets of both mice and human liver samples with known perinatal BPA exposures. One of 3 candidate genes, Stat3, displayed dose-dependent DNA methylation changes in both 10-month mice with liver tumors as compared to those without liver tumors and 3-week sibling mice from the same exposure study, implicating Stat3 as a potential epigenetic biomarker of both early life BPA exposure and adult disease in mice. DNA methylation profiles within STAT3 varied with liver tissue BPA level in human fetal liver samples as well, suggesting STAT3 may be a translationally relevant candidate biomarker. These data implicate Stat3 as a potential early life biomarker of adult murine liver tumor risk following early BPA exposure with early evidence of relevance to human health.
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Affiliation(s)
- Caren Weinhouse
- a Department of Environmental Health Sciences ; University of Michigan ; Ann Arbor , Michigan , USA
| | - Ingrid L Bergin
- b Unit for Laboratory Animal Medicine; University of Michigan ; Ann Arbor , Michigan , USA
| | - Craig Harris
- a Department of Environmental Health Sciences ; University of Michigan ; Ann Arbor , Michigan , USA
| | - Dana C Dolinoy
- a Department of Environmental Health Sciences ; University of Michigan ; Ann Arbor , Michigan , USA.,c Department of Nutritional Sciences ; University of Michigan ; Ann Arbor , Michigan , USA
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22
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Diaz-Lagares A, Mendez-Gonzalez J, Hervas D, Saigi M, Pajares MJ, Garcia D, Crujerias AB, Pio R, Montuenga LM, Zulueta J, Nadal E, Rosell A, Esteller M, Sandoval J. A Novel Epigenetic Signature for Early Diagnosis in Lung Cancer. Clin Cancer Res 2016; 22:3361-71. [DOI: 10.1158/1078-0432.ccr-15-2346] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 01/16/2016] [Indexed: 11/16/2022]
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23
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Thomas CR. Epigenetics and Child Psychiatry: Ethical and Legal Issues. BEHAVIORAL SCIENCES & THE LAW 2015; 33:644-652. [PMID: 26358684 DOI: 10.1002/bsl.2207] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Epigenetics has the potential to revolutionize diagnosis and treatment in psychiatry, especially child psychiatry, as it may offer the opportunity for early detection and prevention, as well as development of new treatments. As with the previous introduction of genetic research in psychiatry, there is also the problem of unrealistic expectations and new legal and ethical problems. This article reviews the potential contributions and problems of epigenetic research in child psychiatry. Previous legal and ethical issues in genetic research serve as a guide to those in epigenetic research. Recommendations for safeguards and guidelines on the use of epigenetics with children and adolescents are outlined based on the identified issues.
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Dmitriev AA, Rosenberg EE, Krasnov GS, Gerashchenko GV, Gordiyuk VV, Pavlova TV, Kudryavtseva AV, Beniaminov AD, Belova AA, Bondarenko YN, Danilets RO, Glukhov AI, Kondratov AG, Alexeyenko A, Alekseev BY, Klein G, Senchenko VN, Kashuba VI. Identification of Novel Epigenetic Markers of Prostate Cancer by NotI-Microarray Analysis. DISEASE MARKERS 2015; 2015:241301. [PMID: 26491211 PMCID: PMC4602334 DOI: 10.1155/2015/241301] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 07/11/2015] [Accepted: 07/14/2015] [Indexed: 12/30/2022]
Abstract
A significant need for reliable and accurate cancer diagnostics and prognosis compels the search for novel biomarkers that would be able to discriminate between indolent and aggressive tumors at the early stages of disease. The aim of this work was identification of potential diagnostic biomarkers for characterization of different types of prostate tumors. NotI-microarrays with 180 clones associated with chromosome 3 genes/loci were applied to determine genetic and epigenetic alterations in 33 prostate tumors. For 88 clones, aberrations were detected in more than 10% of tumors. The major types of alterations were DNA methylation and/or deletions. Frequent methylation of the discovered loci was confirmed by bisulfite sequencing on selective sampling of genes: FGF12, GATA2, and LMCD1. Three genes (BHLHE40, BCL6, and ITGA9) were tested for expression level alterations using qPCR, and downregulation associated with hypermethylation was shown in the majority of tumors. Based on these data, we proposed the set of potential biomarkers for detection of prostate cancer and discrimination between prostate tumors with different malignancy and aggressiveness: BHLHE40, FOXP1, LOC285205, ITGA9, CTDSPL, FGF12, LOC440944/SETD5, VHL, CLCN2, OSBPL10/ZNF860, LMCD1, FAM19A4, CAND2, MAP4, KY, and LRRC58. Moreover, we probabilistically estimated putative functional relations between the genes within each set using the network enrichment analysis.
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Affiliation(s)
- Alexey A. Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
- P.A. Herzen Moscow Cancer Research Institute, Ministry of Healthcare of the Russian Federation, Moscow 125284, Russia
| | - Eugenia E. Rosenberg
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kiev 03680, Ukraine
| | - George S. Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Ganna V. Gerashchenko
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kiev 03680, Ukraine
| | - Vasily V. Gordiyuk
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kiev 03680, Ukraine
| | - Tatiana V. Pavlova
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, 17177 Stockholm, Sweden
| | - Anna V. Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Artemy D. Beniaminov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Anastasia A. Belova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Yuriy N. Bondarenko
- Institute of Urology, National Academy of Medical Sciences of Ukraine, Kiev 04053, Ukraine
| | - Rostislav O. Danilets
- Institute of Urology, National Academy of Medical Sciences of Ukraine, Kiev 04053, Ukraine
| | - Alexander I. Glukhov
- Department of Molecular Biology, Kurchatov NBIC Centre NRC “Kurchatov Institute”, Moscow 123182, Russia
| | - Aleksandr G. Kondratov
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kiev 03680, Ukraine
| | - Andrey Alexeyenko
- Bioinformatics Infrastructure for Life Sciences, Science for Life Laboratory, Karolinska Institute, 17177 Stockholm, Sweden
| | - Boris Y. Alekseev
- P.A. Herzen Moscow Cancer Research Institute, Ministry of Healthcare of the Russian Federation, Moscow 125284, Russia
| | - George Klein
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, 17177 Stockholm, Sweden
| | - Vera N. Senchenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Vladimir I. Kashuba
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kiev 03680, Ukraine
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, 17177 Stockholm, Sweden
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25
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Paska AV, Hudler P. Aberrant methylation patterns in cancer: a clinical view. Biochem Med (Zagreb) 2015; 25:161-76. [PMID: 26110029 PMCID: PMC4470106 DOI: 10.11613/bm.2015.017] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 04/30/2015] [Indexed: 12/14/2022] Open
Abstract
Epigenetic mechanisms, such as DNA methylation, DNA hydroxymethylation, post-translational modifications (PTMs) of histone proteins affecting nucleosome remodelling, and regulation by small and large non-coding RNAs (ncRNAs) work in concert with cis and trans acting elements to drive appropriate gene expression. Advances in detection methods and development of dedicated platforms and methylation arrays resulted in an explosion of information on aberrantly methylated sequences linking deviations in epigenetic landscape with the initiation and progression of complex diseases. Here, we consider how DNA methylation changes in malignancies, such as breast, pancreatic, colorectal, and gastric cancer could be exploited for the purpose of developing specific diagnostic tools. DNA methylation changes can be applicable as biomarkers for detection of malignant disease in easily accessible tissues. Methylation signatures are already proving to be an important marker for determination of drug sensitivity. Even more, promoter methylation patterns of some genes, such as MGMT, SHOX2, and SEPT9, have already been translated into commercial clinical assays aiding in patient assessment as adjunct diagnostic tools. In conclusion, the changes in DNA methylation patterns in tumour cells are slowly gaining entrance into routine diagnostic tests as promising biomarkers and as potential therapeutic targets.
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Affiliation(s)
- Alja Videtic Paska
- Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Petra Hudler
- Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
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26
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Hudler P, Videtič Paska A, Komel R. Contemporary proteomic strategies for clinical epigenetic research and potential impact for the clinic. Expert Rev Proteomics 2015; 12:197-212. [PMID: 25719543 DOI: 10.1586/14789450.2015.1019479] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Novel proteomic methods are revealing the intricacy of the epigenetic landscape affecting gene regulation and improving our knowledge of the pathogenesis of complex diseases. Despite the enormous amount of data regarding epigenetic modifications present in DNA and histones, deciphering their biological relevance in the context of the disease and health is currently still an ongoing process. Here, we consider the relationship between epigenetic research in tumorigenesis and the prospect of knowledge transfer to clinical use, focusing primarily on the epigenetic histone post-translational modifications, which could be used as biomarkers. We additionally focus on the use of proteomic techniques in research and evaluate their usefulness in clinical setting.
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Affiliation(s)
- Petra Hudler
- Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, SI-1000 Ljubljana, Slovenia
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27
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Wang G, Li B, Fu Y, He M, Wang J, Shen P, Bai L. miR-23a suppresses proliferation of osteosarcoma cells by targeting SATB1. Tumour Biol 2015; 36:4715-21. [PMID: 25619478 DOI: 10.1007/s13277-015-3120-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 01/14/2015] [Indexed: 12/28/2022] Open
Abstract
Accumulating evidence has shown that microRNAs are involved in multiple processes in cancer development and progression. Recent studies have shown that miR-23a functions as an oncogene in various human cancer types, but its role in osteosarcoma remains poorly understood. Here, we demonstrated that miR-23a is frequently downregulated in osteosarcoma specimens and cell lines compared with adjacent noncancerous tissues and cell line. Bioinformatics analysis further revealed SATB1 as a potential target of miR-23a. Data from luciferase reporter assays showed that miR-23a directly binds to the 3'UTR of SATB1 messenger RNA (mRNA). Furthermore, we found that expression patterns of miR-23a were inversely correlated with those of SATB1 in osteosarcoma tissues and cell lines, and overexpression of miR-23a suppressed SATB1 expression at both transcriptional and translational levels in osteosarcoma cell lines. In functional assays, miR-23a inhibited osteosarcoma cell proliferation, which could be reversed by overexpression of SATB1. Furthermore, knockdown of SATB1 reduced osteosarcoma cell proliferation, which resembled the inhibitory effects of miR-23a overexpression. Taken together, our data provide compelling evidence that miR-23a functions as a tumor suppressor in osteosarcoma, and its inhibitory effect on tumor are mediated chiefly through downregulation of SATB1.
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Affiliation(s)
- Guangbin Wang
- Department of Orthopedics, Shengjing Hospital, China Medical University, Shenyang, 110004, Liaoning, People's Republic of China
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Abstract
Colorectal cancer (CRC) is one of most common malignancies and a leading cause of cancer related deaths worldwide. Epigenetic change is an important mechanism of colorectal carcinogenesis. Accumulation of epigenetic changes was found in colorectal cancer and other tumors. Aberrant changes in DNA methylation, histone modification, imprinting, and noncoding RNAs were frequently found in human colorectal cancer. Epigenetic changes may serve as a diagnostic, prognostic, and chemo-sensitive marker. It also becomes a cancer preventive or therapeutic target in some circumstances.
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Affiliation(s)
- Wenji Yan
- Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853, China
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29
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Mordente A, Meucci E, Martorana GE, Silvestrini A. Cancer Biomarkers Discovery and Validation: State of the Art, Problems and Future Perspectives. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 867:9-26. [DOI: 10.1007/978-94-017-7215-0_2] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Mendez EF, Sattler R. Biomarker development for C9orf72 repeat expansion in ALS. Brain Res 2014; 1607:26-35. [PMID: 25261695 DOI: 10.1016/j.brainres.2014.09.041] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Revised: 09/09/2014] [Accepted: 09/16/2014] [Indexed: 12/11/2022]
Abstract
The expanded GGGGCC hexanucleotide repeat in the non-coding region of the C9orf72 gene on chromosome 9p21 has been discovered as the cause of approximately 20-50% of familial and up to 5-20% of sporadic amyotrophic lateral sclerosis (ALS) cases, making this the most common known genetic mutation of ALS to date. At the same time, it represents the most common genetic mutation in frontotemporal dementia (FTD; 10-30%). Because of the high prevalence of mutant C9orf72, pre-clinical efforts in identifying therapeutic targets and developing novel therapeutics for this mutation are highly pursued in the hope of providing a desperately needed disease-modifying treatment for ALS patients, as well as other patient populations affected by the C9orf72 mutation. The current lack of effective treatments for ALS is partially due to the lack of appropriate biomarkers that aide in assessing drug efficacy during clinical trials independent of clinical outcome measures, such as increased survival. In this review we will summarize the opportunities for biomarker development specifically targeted to the newly discovered C9orf72 repeat expansion. While drugs are being developed for this mutation, it will be crucial to provide a reliable biomarker to accompany the clinical development of these novel therapeutic interventions to maximize the chances of a successful clinical trial. This article is part of a Special Issue entitled ALS complex pathogenesis.
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Affiliation(s)
- Emily F Mendez
- Brain Science Institute and Department of Neurology, Johns Hopkins University School of Medicine, 855N Wolfe Street, Rangos 2-223, Baltimore, MD 21205, USA
| | - Rita Sattler
- Brain Science Institute and Department of Neurology, Johns Hopkins University School of Medicine, 855N Wolfe Street, Rangos 2-223, Baltimore, MD 21205, USA.
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31
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Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. Nat Methods 2014; 11:834-40. [PMID: 24997861 PMCID: PMC4130351 DOI: 10.1038/nmeth.3022] [Citation(s) in RCA: 115] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 06/01/2014] [Indexed: 12/11/2022]
Abstract
Elucidating the molecular details of how chromatin-associated factors deposit, remove and recognize histone post-translational modification (PTM) signatures remains a daunting task in the epigenetics field. We introduce a versatile platform that greatly accelerates biochemical investigations into chromatin recognition and signaling. This technology is based on the streamlined semisynthesis of DNA-barcoded nucleosome libraries with distinct combinations of PTMs. Chromatin immunoprecipitation of these libraries, once they have been treated with purified chromatin effectors or the combined chromatin recognizing and modifying activities of the nuclear proteome, is followed by multiplexed DNA-barcode sequencing. This ultrasensitive workflow allowed us to collect thousands of biochemical data points revealing the binding preferences of various nuclear factors for PTM patterns and how preexisting PTMs, alone or synergistically, affect further PTM deposition via cross-talk mechanisms. We anticipate that the high throughput and sensitivity of the technology will help accelerate the decryption of the diverse molecular controls that operate at the level of chromatin.
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32
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Zhou J, Bi H, Zhan P, Chang C, Xu C, Huang X, Yu L, Yao X, Yan J. Overexpression of HP1γ is associated with poor prognosis in non-small cell lung cancer cell through promoting cell survival. Tumour Biol 2014; 35:9777-85. [PMID: 24981246 DOI: 10.1007/s13277-014-2182-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2014] [Accepted: 06/02/2014] [Indexed: 11/28/2022] Open
Abstract
Heterochromatin protein 1γ (HP1γ), which binds to di- or trimethylated lysine 9 on histone H3 (H3K9), plays an important role in chromatin packaging and gene transcriptional regulation. Recently, HP1γ has been implicated in cancer development. However, its clinical relevance and functional role in non-small cell lung cancer (NSCLC) remain elusive. In this study, we found that HP1γ expression was elevated in NSCLC samples at the messenger RNA (mRNA) level compared to adjacent normal lung tissues. In a cohort of 108 NSCLC patients, HP1γ overexpression is significantly associated with N stage (P = 0.003), pathological tumor-node-metastasis (TNM) stage (P = 0.013), smoking status (P = 0.009), and gender (P = 0.042). Patients with a high level of HP1γ expression showed a poorer overall survival rate than those with low HP1γ expression (P = 0.017). Multivariate analysis revealed that HP1γ expression is an independent prognostic marker. We also found knockdown of HP1γ in A549 and NCI-H1975 cells induced apoptosis accompanied with suppressed cell proliferation and colony formation. Consistently, pro-apoptotic proteins, Bax and GADD45α, were upregulated in response to HP1γ depletion. Altogether, our data suggested that HP1γ plays an important role in promoting NSCLC and may represent a novel prognostic biomarker and therapeutic target for the disease.
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Affiliation(s)
- Ji Zhou
- Department of Respiratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu, China
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33
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MicroRNA-320 inhibits osteosarcoma cells proliferation by directly targeting fatty acid synthase. Tumour Biol 2014; 35:4177-83. [DOI: 10.1007/s13277-013-1546-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2013] [Accepted: 12/11/2013] [Indexed: 01/09/2023] Open
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34
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Vrtačnik P, Marc J, Ostanek B. Epigenetic mechanisms in bone. Clin Chem Lab Med 2014; 52:589-608. [DOI: 10.1515/cclm-2013-0770] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 11/19/2013] [Indexed: 12/11/2022]
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35
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Peiró-Chova L, Peña-Chilet M, López-Guerrero JA, García-Giménez JL, Alonso-Yuste E, Burgues O, Lluch A, Ferrer-Lozano J, Ribas G. High stability of microRNAs in tissue samples of compromised quality. Virchows Arch 2013; 463:765-74. [PMID: 24197449 DOI: 10.1007/s00428-013-1485-2] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 09/13/2013] [Accepted: 09/17/2013] [Indexed: 12/24/2022]
Abstract
Degradation of tissue samples limits performing RNA-based molecular studies, but little is known about the potential usefulness of samples of compromised quality for studies focused on miRNAs. In this work we analyze a series of cryopreserved tissue samples (n = 14), frozen samples that underwent a severe thawing process (n = 10), and their paired formalin-fixed paraffin-embedded (FFPE) tissue samples (n = 24) from patients with breast cancer obtained during primary surgical resection and collected in 2011. Quality and integrity analyses of the total and small fraction of RNA were carried out. Recovery of specific RNA molecules (miRNAs hsa-miR-21, hsa-miR-125b, and hsa-miR-191; snoRNA RNU6B; and mRNAs GAPDH and HPRT1) was also analyzed by quantitative RT-PCR. Our results suggest that visualisation of the small RNA electrophoretic profiles obtained using the Agilent 2100 bioanalyzer makes it possible to differentiate between the three groups of samples (optimally frozen, thawed, and FFPE). We demonstrate that specific miRNA molecules can be similarly recovered from different tissue sample sources, which supports their high degree of stability. We conclude that miRNAs are robustly detected irrespective of the quality of the tissue sample. In this regard, a word of caution should be raised before degraded samples are discarded: although prior quality assessment of the biological material to be analyzed is recommended, our work demonstrates that degraded tissue samples are also suitable for miRNA studies.
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Affiliation(s)
- Lorena Peiró-Chova
- Biobank, INCLIVA Biomedical Research Institute, Avenida Blasco Ibáñez, 17, 46010, Valencia, Spain
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