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Wang K, Liu CY, Fang B, Li B, Li YH, Xia QQ, Zhao Y, Cheng XL, Yang SM, Zhang MH, Wang K. The function and therapeutic potential of transfer RNA-derived small RNAs in cardiovascular diseases: A review. Pharmacol Res 2024; 206:107279. [PMID: 38942340 DOI: 10.1016/j.phrs.2024.107279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 06/20/2024] [Accepted: 06/20/2024] [Indexed: 06/30/2024]
Abstract
Transfer RNA-derived small RNAs (tsRNAs) are a class of small non-coding RNA (sncRNA) molecules derived from tRNA, including tRNA derived fragments (tRFs) and tRNA halfs (tiRNAs). tsRNAs can affect cell functions by participating in gene expression regulation, translation regulation, intercellular signal transduction, and immune response. They have been shown to play an important role in various human diseases, including cardiovascular diseases (CVDs). Targeted regulation of tsRNAs expression can affect the progression of CVDs. The tsRNAs induced by pathological conditions can be detected when released into the extracellular, giving them enormous potential as disease biomarkers. Here, we review the biogenesis, degradation process and related functional mechanisms of tsRNAs, and discuss the research progress and application prospects of tsRNAs in different CVDs, to provide a new perspective on the treatment of CVDs.
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Affiliation(s)
- Kai Wang
- Key Laboratory of Maternal & Fetal Medicine of National Health Commission of China, Shandong Provincial Maternal and Child Health Care Hospital affiliated to Qingdao University, Jinan 250014, China; Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Cui-Yun Liu
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Bo Fang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Bo Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Ying-Hui Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Qian-Qian Xia
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Yan Zhao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Xue-Li Cheng
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Su-Min Yang
- Department of Cardiovascular Surgery, The Affiliated Hospital of Qingdao University, Qingdao 266003, China.
| | - Mei-Hua Zhang
- Key Laboratory of Maternal & Fetal Medicine of National Health Commission of China, Shandong Provincial Maternal and Child Health Care Hospital affiliated to Qingdao University, Jinan 250014, China.
| | - Kun Wang
- Key Laboratory of Maternal & Fetal Medicine of National Health Commission of China, Shandong Provincial Maternal and Child Health Care Hospital affiliated to Qingdao University, Jinan 250014, China; Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China.
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Panduga S, Vasishta S, Subramani R, Vincent S, Mutalik S, Joshi MB. Epidrugs in the clinical management of atherosclerosis: Mechanisms, challenges and promises. Eur J Pharmacol 2024; 980:176827. [PMID: 39038635 DOI: 10.1016/j.ejphar.2024.176827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 07/03/2024] [Accepted: 07/18/2024] [Indexed: 07/24/2024]
Abstract
Atherosclerosis is a complex and multigenic pathology associated with significant epigenetic reprogramming. Traditional factors (age, sex, obesity, hyperglycaemia, dyslipidaemia, hypertension) and non-traditional factors (foetal indices, microbiome alteration, clonal hematopoiesis, air pollution, sleep disorders) induce endothelial dysfunction, resulting in reduced vascular tone and increased vascular permeability, inflammation and shear stress. These factors induce paracrine and autocrine interactions between several cell types, including vascular smooth muscle cells, endothelial cells, monocytes/macrophages, dendritic cells and T cells. Such cellular interactions lead to tissue-specific epigenetic reprogramming regulated by DNA methylation, histone modifications and microRNAs, which manifests in atherosclerosis. Our review outlines epigenetic signatures during atherosclerosis, which are viewed as potential clinical biomarkers that may be adopted as new therapeutic targets. Additionally, we emphasize epigenetic modifiers referred to as 'epidrugs' as potential therapeutic molecules to correct gene expression patterns and restore vascular homeostasis during atherosclerosis. Further, we suggest nanomedicine-based strategies involving the use of epidrugs, which may selectively target cells in the atherosclerotic microenvironment and reduce off-target effects.
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Affiliation(s)
- Sushma Panduga
- Department of Biochemistry, Palamur Biosciences Private Limited, Hyderabad, 500026, Telangana, India; PhD Program, Manipal Academy of Higher Education (MAHE), Manipal, India
| | - Sampara Vasishta
- Department of Ageing Research, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Ramamoorthy Subramani
- Department of Biochemistry, Palamur Biosciences Private Limited, Hyderabad, 500026, Telangana, India
| | - Sthevaan Vincent
- Department of Pathology, Palamur Biosciences Private Limited, Hyderabad, 500026, Telangana, India
| | - Srinivas Mutalik
- Department of Pharmaceutics, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Manjunath B Joshi
- Department of Ageing Research, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India.
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Rajan S, Schwarz E. Network-based artificial intelligence approaches for advancing personalized psychiatry. Am J Med Genet B Neuropsychiatr Genet 2024:e32997. [PMID: 39031613 DOI: 10.1002/ajmg.b.32997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 05/24/2024] [Accepted: 06/06/2024] [Indexed: 07/22/2024]
Abstract
Psychiatric disorders have a complex biological underpinning likely involving an interplay of genetic and environmental risk contributions. Substantial efforts are being made to use artificial intelligence approaches to integrate features within and across data types to increase our etiological understanding and advance personalized psychiatry. Network science offers a conceptual framework for exploring the often complex relationships across different levels of biological organization, from cellular mechanistic to brain-functional and phenotypic networks. Utilizing such network information effectively as part of artificial intelligence approaches is a promising route toward a more in-depth understanding of illness biology, the deciphering of patient heterogeneity, and the identification of signatures that may be sufficiently predictive to be clinically useful. Here, we present examples of how network information has been used as part of artificial intelligence within psychiatry and beyond and outline future perspectives on how personalized psychiatry approaches may profit from a closer integration of psychiatric research, artificial intelligence development, and network science.
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Affiliation(s)
- Sivanesan Rajan
- Hector Institute for Artificial Intelligence in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Emanuel Schwarz
- Hector Institute for Artificial Intelligence in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
- German Center for Mental Health (DZPG), partner site Mannheim-Heidelberg-Ulm, Mannheim, Germany
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Benincasa G, Strozziero MG, Di Pastena MA, Criscuolo C, Cetani G, Trama U, Napoli C. Epigenetic challenges on the horizon of chimeric antigen receptor-T. Cytotherapy 2024; 26:411-412. [PMID: 38466261 DOI: 10.1016/j.jcyt.2024.02.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 02/15/2024] [Accepted: 02/15/2024] [Indexed: 03/12/2024]
Affiliation(s)
- Giuditta Benincasa
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania "Luigi Vanvitelli," Naples, Italy.
| | | | - Maria Assunta Di Pastena
- U.O.C. Division of Clinical Immunology, Immunohematology, Transfusion Medicine and Transplant Immunology, Department of Internal Medicine and Specialistics, University of Campania "Luigi Vanvitelli," Naples, Italy
| | - Clelia Criscuolo
- Division of Hematology, Hospital of Aversa (ASLCE), Aversa, Italy
| | - Giusy Cetani
- Division of Hematology, Antonio Cardarelli Hospital, Naples, Italy
| | - Ugo Trama
- Regional Pharmaceutical Unit, Campania Region, Naples, Italy
| | - Claudio Napoli
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania "Luigi Vanvitelli," Naples, Italy; U.O.C. Division of Clinical Immunology, Immunohematology, Transfusion Medicine and Transplant Immunology, Department of Internal Medicine and Specialistics, University of Campania "Luigi Vanvitelli," Naples, Italy
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Benincasa G, Napoli C, DeMeo DL. Transgenerational Epigenetic Inheritance of Cardiovascular Diseases: A Network Medicine Perspective. Matern Child Health J 2024; 28:617-630. [PMID: 38409452 DOI: 10.1007/s10995-023-03886-z] [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] [Accepted: 12/19/2023] [Indexed: 02/28/2024]
Abstract
INTRODUCTION The ability to identify early epigenetic signatures underlying the inheritance of cardiovascular risk, including trans- and intergenerational effects, may help to stratify people before cardiac symptoms occur. METHODS Prospective and retrospective cohorts and case-control studies focusing on DNA methylation and maternal/paternal effects were searched in Pubmed from 1997 to 2023 by using the following keywords: DNA methylation, genomic imprinting, and network analysis in combination with transgenerational/intergenerational effects. RESULTS Maternal and paternal exposures to traditional cardiovascular risk factors during critical temporal windows, including the preconceptional period or early pregnancy, may perturb the plasticity of the epigenome (mainly DNA methylation) of the developing fetus especially at imprinted loci, such as the insulin-like growth factor type 2 (IGF2) gene. Thus, the epigenome is akin to a "molecular archive" able to memorize parental environmental insults and predispose an individual to cardiovascular diseases onset in later life. Direct evidence for human transgenerational epigenetic inheritance (at least three generations) of cardiovascular risk is lacking but it is supported by epidemiological studies. Several blood-based association studies showed potential intergenerational epigenetic effects (single-generation studies) which may mediate the transmittance of cardiovascular risk from parents to offspring. DISCUSSION In this narrative review, we discuss some relevant examples of trans- and intergenerational epigenetic associations with cardiovascular risk. In our perspective, we propose three network-oriented approaches which may help to clarify the unsolved issues regarding transgenerational epigenetic inheritance of cardiovascular risk and provide potential early biomarkers for primary prevention.
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Affiliation(s)
- Giuditta Benincasa
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania "Luigi Vanvitelli", 80138, Naples, Italy
| | - Claudio Napoli
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania "Luigi Vanvitelli", 80138, Naples, Italy.
| | - Dawn L DeMeo
- Channing Division of Network Medicine and the Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
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Zong Y, Hu Y, Zheng M, Wang Z. Bioinformatics analysis of the microRNA genes associated with type 2 cardiorenal syndrome. BMC Cardiovasc Disord 2024; 24:142. [PMID: 38443814 PMCID: PMC10913659 DOI: 10.1186/s12872-024-03816-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 02/26/2024] [Indexed: 03/07/2024] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are important regulatory factors in the normal developmental stages of the heart and kidney. However, it is currently unclear how miRNA is expressed in type 2 cardiorenal syndrome (CRS). This study aimed to detect the differential expression of miRNAs and to clarify the main enrichment pathways of differentially expressed miRNA target genes in type 2 CRS. METHODS Five cases of healthy control (Group 1), eight of chronic heart failure (CHF, Group 2) and seven of type 2 CRS (Group 3) were enrolled, respectively. Total RNA was extracted from the peripheral blood of each group. To predict the miRNA target genes and biological signalling pathways closely related to type 2 CRS, the Agilent miRNA microarray platform was used for miRNA profiling and bioinformatics analysis of the isolated total RNA samples. RESULTS After the microarray analysis was done to screen for differentially expressed circulating miRNAs among the three different groups of samples, the target genes and bioinformatic pathways of the differential miRNAs were predicted. A total of 38 differential miRNAs (15 up- and 23 down-regulated) were found in Group 3 compared with Group 1, and a total of 42 differential miRNAs (11 up- and 31 down-regulated) were found in Group 3 compared to Group 2. According to the Gene Ontology (GO) function and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis, the top 10 lists of molecular functions, cellular composition and biological processes, and the top 30 signalling pathways of predicted gene targets of the differentially expressed miRNAs were discriminated among the three groups. CONCLUSION Between the patients with CHF and type 2 CRS, miRNAs were differentially expressed. Prediction of target genes of differentially expressed miRNAs and the use of GO function and KEGG pathway analysis may reveal the molecular mechanisms of CRS. Circulating miRNAs may contribute to the diagnosis of CRS, and further and larger studies are needed to enhance the robustness of our findings.
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Affiliation(s)
- Yani Zong
- Department of Cardiovascular Medicine, Affiliated Nanjing Brain Hospital, Nanjing Medical University, Nanjing, China
- Department of Cardiovascular Medicine, Nanjing Chest Hospital, Nanjing, China
| | - Yuexin Hu
- Department of Cardiovascular Medicine, Affiliated Nanjing Brain Hospital, Nanjing Medical University, Nanjing, China
- Department of Cardiovascular Medicine, Nanjing Chest Hospital, Nanjing, China
| | - Mengdi Zheng
- Department of Cardiovascular Medicine, Affiliated Nanjing Brain Hospital, Nanjing Medical University, Nanjing, China
- Department of Cardiovascular Medicine, Nanjing Chest Hospital, Nanjing, China
| | - Zhi Wang
- Department of Cardiovascular Medicine, Affiliated Nanjing Brain Hospital, Nanjing Medical University, Nanjing, China.
- Department of Cardiovascular Medicine, Nanjing Chest Hospital, Nanjing, China.
- Department of Cardiology Affiliated Nanjing Brain Hospital, Nanjing Medical University, No. 264 Guangzhou Road, Nanjing, Jiangsu, 210029, China.
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Seem K, Kaur S, Kumar S, Mohapatra T. Epigenome editing for targeted DNA (de)methylation: a new perspective in modulating gene expression. Crit Rev Biochem Mol Biol 2024; 59:69-98. [PMID: 38440883 DOI: 10.1080/10409238.2024.2320659] [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: 12/15/2023] [Accepted: 02/15/2024] [Indexed: 03/06/2024]
Abstract
Traditionally, it has been believed that inheritance is driven as phenotypic variations resulting from changes in DNA sequence. However, this paradigm has been challenged and redefined in the contemporary era of epigenetics. The changes in DNA methylation, histone modification, non-coding RNA biogenesis, and chromatin remodeling play crucial roles in genomic functions and regulation of gene expression. More importantly, some of these changes are inherited to the next generations as a part of epigenetic memory and play significant roles in gene expression. The sum total of all changes in DNA bases, histone proteins, and ncRNA biogenesis constitutes the epigenome. Continuous progress in deciphering epigenetic regulations and the existence of heritable epigenetic/epiallelic variations associated with trait of interest enables to deploy epigenome editing tools to modulate gene expression. DNA methylation marks can be utilized in epigenome editing for the manipulation of gene expression. Initially, genome/epigenome editing technologies relied on zinc-finger protein or transcriptional activator-like effector protein. However, the discovery of clustered regulatory interspaced short palindromic repeats CRISPR)/deadCRISPR-associated protein 9 (dCas9) enabled epigenome editing to be more specific/efficient for targeted DNA (de)methylation. One of the major concerns has been the off-target effects, wherein epigenome editing may unintentionally modify gene/regulatory element which may cause unintended change/harmful effects. Moreover, epigenome editing of germline cell raises several ethical/safety issues. This review focuses on the recent developments in epigenome editing tools/techniques, technological limitations, and future perspectives of this emerging technology in therapeutics for human diseases as well as plant improvement to achieve sustainable developmental goals.
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Affiliation(s)
- Karishma Seem
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Simardeep Kaur
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Suresh Kumar
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Trilochan Mohapatra
- Protection of Plant Varieties and Farmers' Rights Authority, New Delhi, India
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Gladwell LR, Ahiarah C, Rasheed S, Rahman SM, Choudhury M. Traditional Therapeutics and Potential Epidrugs for CVD: Why Not Both? Life (Basel) 2023; 14:23. [PMID: 38255639 PMCID: PMC10820772 DOI: 10.3390/life14010023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/07/2023] [Accepted: 12/18/2023] [Indexed: 01/24/2024] Open
Abstract
Cardiovascular disease (CVD) is the leading cause of death worldwide. In addition to the high mortality rate, people suffering from CVD often endure difficulties with physical activities and productivity that significantly affect their quality of life. The high prevalence of debilitating risk factors such as obesity, type 2 diabetes mellitus, smoking, hypertension, and hyperlipidemia only predicts a bleak future. Current traditional CVD interventions offer temporary respite; however, they compound the severe economic strain of health-related expenditures. Furthermore, these therapeutics can be prescribed indefinitely. Recent advances in the field of epigenetics have generated new treatment options by confronting CVD at an epigenetic level. This involves modulating gene expression by altering the organization of our genome rather than altering the DNA sequence itself. Epigenetic changes are heritable, reversible, and influenced by environmental factors such as medications. As CVD is physiologically and pathologically diverse in nature, epigenetic interventions can offer a ray of hope to replace or be combined with traditional therapeutics to provide the prospect of addressing more than just the symptoms of CVD. This review discusses various risk factors contributing to CVD, perspectives of current traditional medications in practice, and a focus on potential epigenetic therapeutics to be used as alternatives.
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Affiliation(s)
- Lauren Rae Gladwell
- Department of Pharmaceutical Sciences, Texas A&M Irma Lerma Rangel College of Pharmacy, 1114 TAMU, College Station, TX 77843, USA
| | - Chidinma Ahiarah
- Department of Pharmaceutical Sciences, Texas A&M Irma Lerma Rangel College of Pharmacy, 1114 TAMU, College Station, TX 77843, USA
| | - Shireen Rasheed
- Department of Pharmaceutical Sciences, Texas A&M Irma Lerma Rangel College of Pharmacy, 1114 TAMU, College Station, TX 77843, USA
| | - Shaikh Mizanoor Rahman
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat Al-Mouz, Nizwa 616, Oman
| | - Mahua Choudhury
- Department of Pharmaceutical Sciences, Texas A&M Irma Lerma Rangel College of Pharmacy, 1114 TAMU, College Station, TX 77843, USA
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Benincasa G, Suades R, Padró T, Badimon L, Napoli C. Bioinformatic platforms for clinical stratification of natural history of atherosclerotic cardiovascular diseases. EUROPEAN HEART JOURNAL. CARDIOVASCULAR PHARMACOTHERAPY 2023; 9:758-769. [PMID: 37562936 DOI: 10.1093/ehjcvp/pvad059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 07/19/2023] [Accepted: 08/09/2023] [Indexed: 08/12/2023]
Abstract
Although bioinformatic methods gained a lot of attention in the latest years, their use in real-world studies for primary and secondary prevention of atherosclerotic cardiovascular diseases (ASCVD) is still lacking. Bioinformatic resources have been applied to thousands of individuals from the Framingham Heart Study as well as health care-associated biobanks such as the UK Biobank, the Million Veteran Program, and the CARDIoGRAMplusC4D Consortium and randomized controlled trials (i.e. ODYSSEY, FOURIER, ASPREE, and PREDIMED). These studies contributed to the development of polygenic risk scores (PRS), which emerged as novel potent genetic-oriented tools, able to calculate the individual risk of ASCVD and to predict the individual response to therapies such as statins and proprotein convertase subtilisin/kexin type 9 inhibitor. ASCVD are the first cause of death around the world including coronary heart disease (CHD), peripheral artery disease, and stroke. To achieve the goal of precision medicine and personalized therapy, advanced bioinformatic platforms are set to link clinically useful indices to heterogeneous molecular data, mainly epigenomics, transcriptomics, metabolomics, and proteomics. The DIANA study found that differential methylation of ABCA1, TCF7, PDGFA, and PRKCZ significantly discriminated patients with acute coronary syndrome from healthy subjects and their expression levels positively associated with CK-MB serum concentrations. The ARIC Study revealed several plasma proteins, acting or not in lipid metabolism, with a potential role in determining the different pleiotropic effects of statins in each subject. The implementation of molecular high-throughput studies and bioinformatic techniques into traditional cardiovascular risk prediction scores is emerging as a more accurate practice to stratify patients earlier in life and to favour timely and tailored risk reduction strategies. Of note, radiogenomics aims to combine imaging features extracted for instance by coronary computed tomography angiography and molecular biomarkers to create CHD diagnostic algorithms useful to characterize atherosclerotic lesions and myocardial abnormalities. The current view is that such platforms could be of clinical value for prevention, risk stratification, and treatment of ASCVD.
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Affiliation(s)
- Giuditta Benincasa
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania 'Luigi Vanvitelli', 80138 Naples, Italy
- Cardiovascular Program ICCC, Research Institute of Hospital Santa Creu i Sant Pau, IIB Sant Pau, Avinguda Sant Antoni Maria Claret 167, Pavelló 11 (Antic Convent), 08049 Barcelona, Spain
| | - Rosa Suades
- Cardiovascular Program ICCC, Research Institute of Hospital Santa Creu i Sant Pau, IIB Sant Pau, Avinguda Sant Antoni Maria Claret 167, Pavelló 11 (Antic Convent), 08049 Barcelona, Spain
- Centro de Investigación Biomédica en Red Cardiovascular (CIBERCV) Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Teresa Padró
- Cardiovascular Program ICCC, Research Institute of Hospital Santa Creu i Sant Pau, IIB Sant Pau, Avinguda Sant Antoni Maria Claret 167, Pavelló 11 (Antic Convent), 08049 Barcelona, Spain
- Centro de Investigación Biomédica en Red Cardiovascular (CIBERCV) Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Lina Badimon
- Cardiovascular Program ICCC, Research Institute of Hospital Santa Creu i Sant Pau, IIB Sant Pau, Avinguda Sant Antoni Maria Claret 167, Pavelló 11 (Antic Convent), 08049 Barcelona, Spain
- Centro de Investigación Biomédica en Red Cardiovascular (CIBERCV) Instituto de Salud Carlos III, 28029 Madrid, Spain
- Cardiovascular Research Chair, Universitat Autònoma de Barcelona (UAB), 08193 Barcelona, Spain
| | - Claudio Napoli
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania 'Luigi Vanvitelli', 80138 Naples, Italy
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Yang Q, Gao J, Wang TY, Ding JC, Hu PF. Integration of RNA-Seq and Machine Learning Identifies Hub Genes for Empagliflozin Benefitable Heart Failure with Reduced Ejection Fraction. J Inflamm Res 2023; 16:4733-4749. [PMID: 37872956 PMCID: PMC10590560 DOI: 10.2147/jir.s429096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 10/12/2023] [Indexed: 10/25/2023] Open
Abstract
Purpose This study aimed to analyze the hub genes of heart failure with reduced ejection fraction (HFrEF) treated with Empagliflozin using RNA sequencing (RNA-seq) and bioinformatics methods, including machine learning. Methods From February 2021 to February 2023, nine patients with HFrEF were enrolled from our hospital's cardiovascular department. In addition to routine drug treatment, these patients received 10 mg of Empagliflozin once daily for two months. Efficacy was assessed and RNA-seq was performed on peripheral blood before and after treatment with empagliflozin. HFrEF-related hub genes were identified through bioinformatics analyses including differential gene expression analysis, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses, immune infiltration analysis, machine learning, immune cell correlation analysis and clinical indicator correlation analysis. Results The nine patients included in this study completed a two-month treatment regimen, with an average age of 62.11 ± 6.36 years. By performing bioinformatics analysis on the transcriptome from the treatment groups, 42 differentially expressed genes were identified, with six being up-regulated and 36 being down-regulated (|log2FC|>1 and adj.pvalue<0.05). Immune infiltration analysis of these genes demonstrated a significant difference in the proportion of plasma between the pre-treatment and post-treatment groups (p<0.05). Two hub genes, GTF2IP14 and MTLN, were finally identified through machine learning. Further analysis of the correlation between the hub genes and immune cells suggested a negative correlation between GTF2IP14 and naive B cells, and a positive correlation between MTLN and regulatory T cells and resting memory CD4+ T cells (p<0.05). Conclusion Through RNA-seq and bioinformatics analysis, this study identified GTF2IP14 and MTLN as the hub genes of HFrEF, and their mechanisms may be related to immune inflammatory responses and various immune cells.
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Affiliation(s)
- Qiang Yang
- Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang Province, 310053, People’s Republic of China
| | - Jing Gao
- Department of Cardiology, Sir Run Run Shaw Hospital, College of Medicine Zhejiang University, Hangzhou, Zhejiang Province, 310018, People’s Republic of China
| | - Tian-Yu Wang
- Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang Province, 310053, People’s Republic of China
| | - Jun-Can Ding
- Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang Province, 310053, People’s Republic of China
| | - Peng-Fei Hu
- Department of Cardiology, the Second Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang Province, 310005, People’s Republic of China
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Napoli C, Coscioni E, Trama U, Strozziero MG, Benincasa G. An evidence-based debate on epigenetics and immunosenescence in COVID-19. CURRENT RESEARCH IN IMMUNOLOGY 2023; 4:100069. [PMID: 37781451 PMCID: PMC10539895 DOI: 10.1016/j.crimmu.2023.100069] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 09/01/2023] [Accepted: 09/06/2023] [Indexed: 10/03/2023] Open
Abstract
Immunosenescence contributes to the decline of immune function leading to a reduced ability to respond to severe coronavirus disease 2019 (COVID-19) in elderly patients. Clinical course of COVID-19 is widely heterogeneous and guided by the possible interplay between genetic background and epigenetic-sensitive mechanisms underlying the immunosenescence which could explain, at least in part, the higher percentage of disease severity in elderly individuals. The most convincing evidence regards the hypomethylation of the angiotensin-converting enzyme 2 (ACE2) promoter gene in lungs as well as the citrullination of histone H3 in neutrophils which have been associated with worsening of COVID-19 outcome in elderly patients. In contrast, centenarians who have showed milder symptoms have been associated to a younger "epigenetic age" based on DNA methylation profiles at specific genomic sites (epigenetic clock). Some large prospective studies showed that the acceleration of epigenetic aging as well as the shortening of telomeres were significantly associated with lymphopenia and poor outcome suggesting prognostic biomarkers in elderly COVID-19 patients. Furthermore, randomized clinical trials showed that statins, L-arginine, and resveratrol could mediate anti-inflammatory effects via indirect epigenetic interference and might improve COVID-19 outcome. Here, we discuss the epigenetic-sensitive events which might contribute to increase the risk of severity and mortality in older subjects and possible targeted therapies to counteract immunosenescence.
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Affiliation(s)
- Claudio Napoli
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania “Luigi Vanvitelli”, Naples, Italy
- U.O.C. Division of Clinical Immunology, Immunohematology, Transfusion Medicine and Transplant Immunology, Department of Internal Medicine and Specialistics, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Enrico Coscioni
- Division of Cardiac Surgery, AOU San Giovanni di Dio e Ruggid'Aragona, 84131, Salerno, Italy
| | - Ugo Trama
- Regional Pharmaceutical Unit, Campania Region, 80143 Naples, Italy
| | - Maria Grazia Strozziero
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania “Luigi Vanvitelli”, Naples, Italy
- IRCCS Synlab SDN Naples Italy
| | - Giuditta Benincasa
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania “Luigi Vanvitelli”, Naples, Italy
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12
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Benincasa G, Napoli C. Unexplored horizons on sex bias and progression of heart failure with preserved ejection fraction. EUROPEAN HEART JOURNAL. CARDIOVASCULAR PHARMACOTHERAPY 2023; 9:502-504. [PMID: 37486244 DOI: 10.1093/ehjcvp/pvad050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 07/13/2023] [Indexed: 07/25/2023]
Affiliation(s)
- Giuditta Benincasa
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania "Luigi Vanvitelli", Pz. Miraglia, 2, 80138 Naples, Italy
| | - Claudio Napoli
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania "Luigi Vanvitelli", Pz. Miraglia, 2, 80138 Naples, Italy
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13
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Palmieri V, Montisci A, Vietri MT, Colombo PC, Sala S, Maiello C, Coscioni E, Donatelli F, Napoli C. Artificial intelligence, big data and heart transplantation: Actualities. Int J Med Inform 2023; 176:105110. [PMID: 37285695 DOI: 10.1016/j.ijmedinf.2023.105110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 05/21/2023] [Accepted: 05/22/2023] [Indexed: 06/09/2023]
Abstract
BACKGROUND As diagnostic and prognostic models developed by traditional statistics perform poorly in real-world, artificial intelligence (AI) and Big Data (BD) may improve the supply chain of heart transplantation (HTx), allocation opportunities, correct treatments, and finally optimize HTx outcome. We explored available studies, and discussed opportunities and limits of medical application of AI to the field of HTx. METHOD A systematic overview of studies published up to December 31st, 2022, in English on peer-revied journals, have been identified through PUBMED-MEDLINE-WEB of Science, referring to HTx, AI, BD. Studies were grouped in 4 domains based on main studies' objectives and results: etiology, diagnosis, prognosis, treatment. A systematic attempt was made to evaluate studies by the Prediction model Risk Of Bias ASsessment Tool (PROBAST) and the Transparent Reporting of a multivariable prediction model for Individual Prognosis Or Diagnosis (TRIPOD). RESULTS Among the 27 publications selected, none used AI applied to BD. Of the selected studies, 4 fell in the domain of etiology, 6 in the domain of diagnosis, 3 in the domain of treatment, and 17 in that of prognosis, as AI was most frequently used for algorithmic prediction and discrimination of survival, but in retrospective cohorts and registries. AI-based algorithms appeared superior to probabilistic functions to predict patterns, but external validation was rarely employed. Indeed, based on PROBAST, selected studies showed, to some extent, significant risk of bias (especially in the domain of predictors and analysis). In addition, as example of applicability in the real-world, a free-use prediction algorithm developed through AI failed to predict 1-year mortality post-HTx in cases from our center. CONCLUSIONS While AI-based prognostic and diagnostic functions performed better than those developed by traditional statistics, risk of bias, lack of external validation, and relatively poor applicability, may affect AI-based tools. More unbiased research with high quality BD meant for AI, transparency and external validations, are needed to have medical AI as a systematic aid to clinical decision making in HTx.
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Affiliation(s)
- Vittorio Palmieri
- Azienda Ospedaliera dei Colli Monaldi-Cotugno-CTO, Department of Cardiac Surgery and Transplantation, Naples, Italy.
| | - Andrea Montisci
- Division of Cardiothoracic Intensive Care, Cardiothoracic Department, ASST Spedali Civili, Brescia, Italy
| | - Maria Teresa Vietri
- Department of Precision Medicine, "Luigi Vanvitelli" University of Campania School of Medicine, Naples, Italy
| | - Paolo C Colombo
- Milstein Division of Cardiology, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Silvia Sala
- Chair of Anesthesia and Intensive Care, University of Brescia, Brescia, Italy
| | - Ciro Maiello
- Azienda Ospedaliera dei Colli Monaldi-Cotugno-CTO, Department of Cardiac Surgery and Transplantation, Naples, Italy
| | - Enrico Coscioni
- Department of Cardiac Surgery, AOU San Giovanni di Dio e Ruggi d'Aragona, Salerno, Italy
| | - Francesco Donatelli
- Department of Cardiac Surgery, Istituto Clinico Sant'Ambrogio, Milan, Italy; Chair of Cardiac Surgery, University of Milan, Milan, Italy
| | - Claudio Napoli
- Department of Advanced Medical and Surgical Sciences (DAMSS), "Luigi Vanvitelli" University of Campania School of Medicine, Naples, Italy
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14
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Schiano C, Balbi C, de Nigris F, Napoli C. Basic Pathogenic Mechanisms and Epigenetic Players Promoted by Extracellular Vesicles in Vascular Damage. Int J Mol Sci 2023; 24:ijms24087509. [PMID: 37108672 PMCID: PMC10138986 DOI: 10.3390/ijms24087509] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 04/14/2023] [Accepted: 04/16/2023] [Indexed: 04/29/2023] Open
Abstract
Both progression from the early pathogenic events to clinically manifest cardiovascular diseases (CVD) and cancer impact the integrity of the vascular system. Pathological vascular modifications are affected by interplay between endothelial cells and their microenvironment. Soluble factors, extracellular matrix molecules and extracellular vesicles (EVs) are emerging determinants of this network that trigger specific signals in target cells. EVs have gained attention as package of molecules with epigenetic reversible activity causing functional vascular changes, but their mechanisms are not well understood. Valuable insights have been provided by recent clinical studies, including the investigation of EVs as potential biomarkers of these diseases. In this paper, we review the role and the mechanism of exosomal epigenetic molecules during the vascular remodeling in coronary heart disease as well as in cancer-associated neoangiogenesis.
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Affiliation(s)
- Concetta Schiano
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania Luigi Vanvitelli, 80138 Naples, Italy
- Laboratory of Cellular and Molecular Cardiology, Cardiocentro Ticino Institute, 6807 Taverne-Torricella, Switzerland
| | - Carolina Balbi
- Laboratory of Cellular and Molecular Cardiology, Cardiocentro Ticino Institute, 6807 Taverne-Torricella, Switzerland
| | - Filomena de Nigris
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, 80138 Naples, Italy
| | - Claudio Napoli
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania Luigi Vanvitelli, 80138 Naples, Italy
- Clinical Department of Internal Medicine and Specialistic Units, Division of Clinical Immunology and Immunohematology, Transfusion Medicine and Transplant Immunology (SIMT), Azienda Universitaria Policlinico (AOU), 80138 Naples, Italy
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15
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Benincasa G, Napoli C, Loscalzo J, Maron BA. Pursuing functional biomarkers in complex disease: Focus on pulmonary arterial hypertension. Am Heart J 2023; 258:96-113. [PMID: 36565787 DOI: 10.1016/j.ahj.2022.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 12/12/2022] [Accepted: 12/19/2022] [Indexed: 05/11/2023]
Abstract
A major gap in diagnosis, classification, risk stratification, and prediction of therapeutic response exists in pulmonary arterial hypertension (PAH), driven in part by a lack of functional biomarkers that are also disease-specific. In this regard, leveraging big data-omics analyses using innovative approaches that integrate network medicine and machine learning correlated with clinically useful indices or risk stratification scores is an approach well-positioned to advance PAH precision medicine. For example, machine learning applied to a panel of 48 cytokines, chemokines, and growth factors could prognosticate PAH patients with immune-dominant subphenotypes at elevated or low-risk for mortality. Here, we discuss strengths and weaknesses of the most current studies evaluating omics-derived biomarkers in PAH. Progress in this field is offset by studies with small sample size, pervasive limitations in bioinformatics, and lack of standardized methods for data processing and interpretation. Future success in this field, in turn, is likely to hinge on mechanistic validation of data outputs in order to couple functional biomarker data with target-specific therapeutics in clinical practice.
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Affiliation(s)
- Giuditta Benincasa
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania "Luigi Vanvitelli", Naples, Italy.
| | - Claudio Napoli
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Joseph Loscalzo
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA
| | - Bradley A Maron
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA.
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16
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Wang RS, Maron BA, Loscalzo J. Multiomics Network Medicine Approaches to Precision Medicine and Therapeutics in Cardiovascular Diseases. Arterioscler Thromb Vasc Biol 2023; 43:493-503. [PMID: 36794589 PMCID: PMC10038904 DOI: 10.1161/atvbaha.122.318731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 01/30/2023] [Indexed: 02/17/2023]
Abstract
Cardiovascular diseases (CVD) are the leading cause of death worldwide and display complex phenotypic heterogeneity caused by many convergent processes, including interactions between genetic variation and environmental factors. Despite the identification of a large number of associated genes and genetic loci, the precise mechanisms by which these genes systematically influence the phenotypic heterogeneity of CVD are not well understood. In addition to DNA sequence, understanding the molecular mechanisms of CVD requires data from other omics levels, including the epigenome, the transcriptome, the proteome, as well as the metabolome. Recent advances in multiomics technologies have opened new precision medicine opportunities beyond genomics that can guide precise diagnosis and personalized treatment. At the same time, network medicine has emerged as an interdisciplinary field that integrates systems biology and network science to focus on the interactions among biological components in health and disease, providing an unbiased framework through which to integrate systematically these multiomics data. In this review, we briefly present such multiomics technologies, including bulk omics and single-cell omics technologies, and discuss how they can contribute to precision medicine. We then highlight network medicine-based integration of multiomics data for precision medicine and therapeutics in CVD. We also include a discussion of current challenges, potential limitations, and future directions in the study of CVD using multiomics network medicine approaches.
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Affiliation(s)
- Rui-Sheng Wang
- Division of Cardiovascular Medicine
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
| | | | - Joseph Loscalzo
- Division of Cardiovascular Medicine
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
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17
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Benincasa G, Viglietti M, Coscioni E, Napoli C. "Transplantomics" for predicting allograft rejection: real-life applications and new strategies from Network Medicine. Hum Immunol 2023; 84:89-97. [PMID: 36424231 DOI: 10.1016/j.humimm.2022.11.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 11/08/2022] [Accepted: 11/09/2022] [Indexed: 11/23/2022]
Abstract
Although decades of the reductionist approach achieved great milestones in optimizing the immunosuppression therapy, traditional clinical parameters still fail in predicting both acute and chronic (mainly) rejection events leading to higher rates across all solid organ transplants. To clarify the underlying immune-related cellular and molecular mechanisms, current biomedical research is increasingly focusing on "transplantomics" which relies on a huge quantity of big data deriving from genomics, transcriptomics, epigenomics, proteomics, and metabolomics platforms. The AlloMap (gene expression) and the AlloSure (donor-derived cell-free DNA) tests represent two successful examples of how omics and liquid biopsy can really improve the precision medicine of heart and kidney transplantation. One of the major challenges in translating big data in clinically useful biomarkers is the integration and interpretation of the different layers of omics datasets. Network Medicine offers advanced bioinformatic-molecular strategies which were widely used to integrate large omics datasets and clinical information in end-stage patients to prioritize potential biomarkers and drug targets. The application of network-oriented approaches to clarify the complex nature of graft rejection is still in its infancy. Here, we briefly discuss the real-life clinical applications derived from omics datasets as well as novel opportunities for establishing predictive tests in solid organ transplantation. Also, we provide an original "graft rejection interactome" and propose network-oriented strategies which can be useful to improve precision medicine of solid organ transplantation.
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Affiliation(s)
- Giuditta Benincasa
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania "Luigi Vanvitelli", 80138, Naples, Italy.
| | - Mario Viglietti
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania "Luigi Vanvitelli", 80138, Naples, Italy
| | - Enrico Coscioni
- Division of Cardiac Surgery, AOU San Giovanni di Dio e Ruggi d'Aragona, 84131, Salerno, Italy
| | - Claudio Napoli
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania "Luigi Vanvitelli", 80138, Naples, Italy; U.O.C. Division of Clinical Immunology, Immunohematology, Transfusion Medicine and Transplant Immunology, Department of Internal Medicine and Specialistics, University of Campania "Luigi Vanvitelli", Naples, Italy
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18
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Fiorentino G, Benincasa G, Coppola A, Franzese M, Annunziata A, Affinito O, Viglietti M, Napoli C. Targeted genetic analysis unveils novel associations between ACE I/D and APO T158C polymorphisms with D-dimer levels in severe COVID-19 patients with pulmonary embolism. J Thromb Thrombolysis 2023; 55:51-59. [PMID: 36371754 PMCID: PMC9660132 DOI: 10.1007/s11239-022-02728-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/25/2022] [Indexed: 11/14/2022]
Abstract
Only a percentage of COVID-19 patients develop thrombotic complications. We hypothesized that genetic profiles may explain part of the inter-individual differences. Our goal was to evaluate the genotypic distribution of targeted DNA polymorphisms in COVID-19 patients complicated (PE+) or not (PE-) by pulmonary embolism. We designed a retrospective observational study enrolling N = 94 consecutive patients suffering severe COVID-19 with pulmonary embolism (PE+, N = 47) or not (PE-, N = 47) during hospitalization. A panel of N = 13 prothrombotic DNA polymorphisms (FV R506Q and H1299R, FII G20210A, MTHFR C677T and A1298C, CBS 844ins68, PAI-1 4G/5G, GPIIIa HPA-1 a/b, ACE I/D, AGT T9543C, ATR-1 A1166C, FGB - 455G > A, FXIII103G > T) and N = 2 lipid metabolism-related DNA polymorphisms (APOE T 112C and T158C) were investigated using Reverse Dot Blot technique. Then, we investigated possible associations between genotypic subclasses and demographic, clinical, and laboratory parameters including age, obesity, smoking, pro-inflammatory cytokines, drug therapy, and biomarkers of thrombotic risk such as D-dimer (DD). We found that 58.7% of PE+ had homozygous mutant D/D genotype at ACE I/D locus vs. PE- (40.4%) and 87% of PE+ had homozygous mutant C/C genotype at APOE T158C locus vs. PE- (68.1%). In PE+ group, DD levels were significantly higher in D/D and I/D genotypes at ACE I/D locus (P = 0.00066 and P = 0.00023, respectively) and in C/C and T/C genotypes at APOE T158C locus (P = 1.6e-06 and P = 0.0012, respectively) than PE- group. For the first time, we showed significant associations between higher DD levels and ACE I/D and APOE T158C polymorphisms in PE+ vs. PE- patients suggesting potential useful biomarkers of poor clinical outcome.
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Affiliation(s)
| | - Giuditta Benincasa
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania "Luigi Vanvitelli", Naples, Italy.
| | - Antonietta Coppola
- Department of Intensive Care, A.O.R.N. Ospedali dei Colli, Naples, Italy
| | | | - Anna Annunziata
- Department of Intensive Care, A.O.R.N. Ospedali dei Colli, Naples, Italy
| | | | - Mario Viglietti
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Claudio Napoli
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania “Luigi Vanvitelli”, Naples, Italy
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19
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Targeting emerging cancer hallmarks by transition metal complexes: Epigenetic reprogramming and epitherapies. Part II. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2022.214899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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20
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Benincasa G, Maron BA, Affinito O, D’Alto M, Franzese M, Argiento P, Schiano C, Romeo E, Bontempo P, Golino P, Berrino L, Loscalzo J, Napoli C. Association Between Circulating CD4 + T Cell Methylation Signatures of Network-Oriented SOCS3 Gene and Hemodynamics in Patients Suffering Pulmonary Arterial Hypertension. J Cardiovasc Transl Res 2023; 16:17-30. [PMID: 35960497 PMCID: PMC9944731 DOI: 10.1007/s12265-022-10294-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 07/19/2022] [Indexed: 02/06/2023]
Abstract
Pathogenic DNA methylation changes may be involved in pulmonary arterial hypertension (PAH) onset and its progression, but there is no data on potential associations with patient-derived hemodynamic parameters. The reduced representation bisulfite sequencing (RRBS) platform identified N = 631 differentially methylated CpG sites which annotated to N = 408 genes (DMGs) in circulating CD4+ T cells isolated from PAH patients vs. healthy controls (CTRLs). A promoter-restricted network analysis established the PAH subnetwork that included 5 hub DMGs (SOCS3, GNAS, ITGAL, NCOR2, NFIC) and 5 non-hub DMGs (NR4A2, GRM2, PGK1, STMN1, LIMS2). The functional analysis revealed that the SOCS3 gene was the most recurrent among the top ten significant pathways enriching the PAH subnetwork, including the growth hormone receptor and the interleukin-6 signaling. Correlation analysis showed that the promoter methylation levels of each network-oriented DMG were associated individually with hemodynamic parameters. In particular, SOCS3 hypomethylation was negatively associated with right atrial pressure (RAP) and positively associated with cardiac index (CI) (|r|≥ 0.6). A significant upregulation of the SOCS3, ITGAL, NFIC, NCOR2, and PGK1 mRNA levels (qRT-PCR) in peripheral blood mononuclear cells from PAH patients vs. CTRLs was found (P ≤ 0.05). By immunoblotting, a significant upregulation of the SOCS3 protein was confirmed in PAH patients vs. CTRLs (P < 0.01). This is the first network-oriented study which integrates circulating CD4+ T cell DNA methylation signatures, hemodynamic parameters, and validation experiments in PAH patients at first diagnosis or early follow-up. Our data suggests that SOCS3 gene might be involved in PAH pathogenesis and serve as potential prognostic biomarker.
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Affiliation(s)
- Giuditta Benincasa
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania "Luigi Vanvitelli", 80138, Naples, Italy.
| | - Bradley A. Maron
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women’s Hospital, MB Boston, USA ,Harvard Medical School, Boston, MA USA
| | | | - Michele D’Alto
- Department of Cardiology, Monaldi Hospital, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | | | - Paola Argiento
- Department of Cardiology, Monaldi Hospital, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Concetta Schiano
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Emanuele Romeo
- Department of Cardiology, Monaldi Hospital, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Paola Bontempo
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Paolo Golino
- Department of Cardiology, Monaldi Hospital, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Liberato Berrino
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Joseph Loscalzo
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women’s Hospital, MB Boston, USA
| | - Claudio Napoli
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy ,IRCCS SDN, Naples, Italy
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21
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Yang Y, Zhang M, Wang Y. The roles of histone modifications in tumorigenesis and associated inhibitors in cancer therapy. JOURNAL OF THE NATIONAL CANCER CENTER 2022; 2:277-290. [PMID: 39036551 PMCID: PMC11256729 DOI: 10.1016/j.jncc.2022.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 09/19/2022] [Accepted: 09/26/2022] [Indexed: 11/25/2022] Open
Abstract
Histone modifications are key factors in chromatin packaging, and are responsible for gene regulation during cell fate determination and development. Abnormal alterations in histone modifications potentially affect the stability of the genome and disrupt gene expression patterns, leading to many diseases, including cancer. In recent years, mounting evidence has shown that various histone modifications altered by aberrantly expressed modifier enzymes contribute to tumor development and metastasis through the induction of epigenetic, transcriptional, and phenotypic changes. In this review, we will discuss the existing histone modifications, both well-studied and rare ones, and their roles in solid tumors and hematopoietic cancers, to identify the molecular pathways involved and investigate targeted therapeutic drugs to reorganize the chromatin and enhance cancer treatment efficiency. Finally, clinical inhibitors of histone modifications are summarized to better understand the developmental stage of cancer therapy in using these drugs to inhibit the histone modification enzymes.
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Affiliation(s)
| | | | - Yan Wang
- Key Laboratory of Cancer and Microbiome, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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22
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Di Rocco L, Ferraro Petrillo U, Rombo SE. DIAMIN: a software library for the distributed analysis of large-scale molecular interaction networks. BMC Bioinformatics 2022; 23:474. [DOI: 10.1186/s12859-022-05026-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 10/29/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
Huge amounts of molecular interaction data are continuously produced and stored in public databases. Although many bioinformatics tools have been proposed in the literature for their analysis, based on their modeling through different types of biological networks, several problems still remain unsolved when the problem turns on a large scale.
Results
We propose , that is, a high-level software library to facilitate the development of applications for the efficient analysis of large-scale molecular interaction networks. relies on distributed computing, and it is implemented in Java upon the framework Apache Spark. It delivers a set of functionalities implementing different tasks on an abstract representation of very large graphs, providing a built-in support for methods and algorithms commonly used to analyze these networks. has been tested on data retrieved from two of the most used molecular interactions databases, resulting to be highly efficient and scalable. As shown by different provided examples, can be exploited by users without any distributed programming experience, in order to perform various types of data analysis, and to implement new algorithms based on its primitives.
Conclusions
The proposed has been proved to be successful in allowing users to solve specific biological problems that can be modeled relying on biological networks, by using its functionalities. The software is freely available and this will hopefully allow its rapid diffusion through the scientific community, to solve both specific data analysis and more complex tasks.
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23
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Montisci A, Palmieri V, Vietri MT, Sala S, Maiello C, Donatelli F, Napoli C. Big Data in cardiac surgery: real world and perspectives. J Cardiothorac Surg 2022; 17:277. [PMID: 36309702 PMCID: PMC9617748 DOI: 10.1186/s13019-022-02025-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 10/14/2022] [Indexed: 11/10/2022] Open
Abstract
Big Data, and the derived analysis techniques, such as artificial intelligence and machine learning, have been considered a revolution in the modern practice of medicine. Big Data comes from multiple sources, encompassing electronic health records, clinical studies, imaging data, registries, administrative databases, patient-reported outcomes and OMICS profiles. The main objective of such analyses is to unveil hidden associations and patterns. In cardiac surgery, the main targets for the use of Big Data are the construction of predictive models to recognize patterns or associations better representing the individual risk or prognosis compared to classical surgical risk scores. The results of these studies contributed to kindle the interest for personalized medicine and contributed to recognize the limitations of randomized controlled trials in representing the real world. However, the main sources of evidence for guidelines and recommendations remain RCTs and meta-analysis. The extent of the revolution of Big Data and new analytical models in cardiac surgery is yet to be determined.
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Increased Risk of Hereditary Prostate Cancer in Italian Families with Hereditary Breast and Ovarian Cancer Syndrome Harboring Mutations in BRCA and in Other Susceptibility Genes. Genes (Basel) 2022; 13:genes13101692. [PMID: 36292577 PMCID: PMC9601514 DOI: 10.3390/genes13101692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/14/2022] [Accepted: 09/16/2022] [Indexed: 11/29/2022] Open
Abstract
Hereditary prostate cancer (HPCa) has the highest heritability of any cancer in men. Interestingly, it occurs in several hereditary syndromes, including breast and ovarian cancer (HBOC) and Lynch syndrome (LS). Several gene mutations related to these syndromes have been identified as biomarkers in HPCa. The goal of this study was to screen for germline mutations in susceptibility genes by using a multigene panel, and to subsequently correlate the results with clinical and laboratory parameters. This was undertaken in 180 HBOC families, which included 217 males with prostate cancer (PCa). Mutational analysis was further extended to 104 family members of mutated patients. Screening of HBOC families revealed that 30.5% harbored germline mutations in susceptibility genes, with 21.6% harboring pathogenic variants (PVs) and 8.9% having variants of uncertain significance (VUS). We found PVs at similar frequency in BRCA1 and BRCA2 genes (8.8% and 9.4%, respectively), while 0.56% of PVs were present in well-established susceptibility genes PALB2, TP53 and RAD51C. Moreover, 0.56% of monoallelic PVs were present in MUTYH, a gene whose function in tumorigenesis in the context of PCa is still unclear. Finally, we reported double heterozygosity (DH) in BRCA1/2 genes in a single family, and found double mutation (DM) present in BRCA2 in a separate family. There was no significant difference between the mean age of onset of PCa in HBOC families with or without germline mutations in susceptibility genes, while the mean survival was highest in mutated patients compared to wild type. Furthermore, PCa is the second most recurrent cancer in our cohort, resulting in 18% of cases in both mutated and non-mutated families. Our investigation shows that PVs were located mostly in the 3′ of BRCA1 and BRCA2 genes, and in BRCA2, most PVs fell in exon 11, suggesting a mutation cluster region relating to risk of HPCa. A total of 65 family members inherited the proband’s mutation; of these, 24 developed cancer, with 41 remaining unaffected.
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An Optimized Comparative Proteomic Approach as a Tool in Neurodegenerative Disease Research. Cells 2022; 11:cells11172653. [PMID: 36078061 PMCID: PMC9454658 DOI: 10.3390/cells11172653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/16/2022] [Accepted: 08/22/2022] [Indexed: 11/25/2022] Open
Abstract
Recent advances in proteomic technologies now allow unparalleled assessment of the molecular composition of a wide range of sample types. However, the application of such technologies and techniques should not be undertaken lightly. Here, we describe why the design of a proteomics experiment itself is only the first step in yielding high-quality, translatable results. Indeed, the effectiveness and/or impact of the majority of contemporary proteomics screens are hindered not by commonly considered technical limitations such as low proteome coverage but rather by insufficient analyses. Proteomic experimentation requires a careful methodological selection to account for variables from sample collection, through to database searches for peptide identification to standardised post-mass spectrometry options directed analysis workflow, which should be adjusted for each study, from determining when and how to filter proteomic data to choosing holistic versus trend-wise analyses for biologically relevant patterns. Finally, we highlight and discuss the difficulties inherent in the modelling and study of the majority of progressive neurodegenerative conditions. We provide evidence (in the context of neurodegenerative research) for the benefit of undertaking a comparative approach through the application of the above considerations in the alignment of publicly available pre-existing data sets to identify potential novel regulators of neuronal stability.
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Tulsyan S, Aftab M, Sisodiya S, Khan A, Chikara A, Tanwar P, Hussain S. Molecular basis of epigenetic regulation in cancer diagnosis and treatment. Front Genet 2022; 13:885635. [PMID: 36092905 PMCID: PMC9449878 DOI: 10.3389/fgene.2022.885635] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 07/19/2022] [Indexed: 02/01/2023] Open
Abstract
The global cancer cases and mortality rates are increasing and demand efficient biomarkers for accurate screening, detection, diagnosis, and prognosis. Recent studies have demonstrated that variations in epigenetic mechanisms like aberrant promoter methylation, altered histone modification and mutations in ATP-dependent chromatin remodelling complexes play an important role in the development of carcinogenic events. However, the influence of other epigenetic alterations in various cancers was confirmed with evolving research and the emergence of high throughput technologies. Therefore, alterations in epigenetic marks may have clinical utility as potential biomarkers for early cancer detection and diagnosis. In this review, an outline of the key epigenetic mechanism(s), and their deregulation in cancer etiology have been discussed to decipher the future prospects in cancer therapeutics including precision medicine. Also, this review attempts to highlight the gaps in epigenetic drug development with emphasis on integrative analysis of epigenetic biomarkers to establish minimally non-invasive biomarkers with clinical applications.
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Affiliation(s)
- Sonam Tulsyan
- Division of Cellular and Molecular Diagnostics (Molecular Biology Group), ICMR- National Institute of Cancer Prevention and Research, Noida, India
| | - Mehreen Aftab
- Division of Cellular and Molecular Diagnostics (Molecular Biology Group), ICMR- National Institute of Cancer Prevention and Research, Noida, India
| | - Sandeep Sisodiya
- Division of Cellular and Molecular Diagnostics (Molecular Biology Group), ICMR- National Institute of Cancer Prevention and Research, Noida, India
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Pune, India
| | - Asiya Khan
- Laboratory Oncology Unit, Dr. B. R. A. Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Atul Chikara
- Division of Cellular and Molecular Diagnostics (Molecular Biology Group), ICMR- National Institute of Cancer Prevention and Research, Noida, India
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Pune, India
| | - Pranay Tanwar
- Laboratory Oncology Unit, Dr. B. R. A. Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
- *Correspondence: Showket Hussain, ; Pranay Tanwar,
| | - Showket Hussain
- Division of Cellular and Molecular Diagnostics (Molecular Biology Group), ICMR- National Institute of Cancer Prevention and Research, Noida, India
- *Correspondence: Showket Hussain, ; Pranay Tanwar,
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Schiano C, Balbi C, Burrello J, Ruocco A, Infante T, Fiorito C, Panella S, Barile L, Mauro C, Vassalli G, Napoli C. De novo DNA methylation induced by circulating extracellular vesicles from acute coronary syndrome patients. Atherosclerosis 2022; 354:41-52. [PMID: 35830762 DOI: 10.1016/j.atherosclerosis.2022.06.1026] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/25/2022] [Accepted: 06/29/2022] [Indexed: 11/02/2022]
Abstract
BACKGROUND AND AIMS DNA methylation is associated with gene silencing, but its clinical role in cardiovascular diseases (CVDs) remains to be elucidated. We hypothesized that extracellular vesicles (EVs) may carry epigenetic changes, showing themselves as a potentially valuable non-invasive diagnostic liquid biopsy. We isolated and characterized circulating EVs of acute coronary syndrome (ACS) patients and assessed their role on DNA methylation in epigenetic modifications. METHODS EVs were recovered from plasma of 19 ACS patients and 50 healthy subjects (HS). Flow cytometry, qRT-PCR, and Western blot (WB) were performed to evaluate both intra-vesicular and intra-cellular signals. ShinyGO, PANTHER, and STRING tools were used to perform GO and PPI network analyses. RESULTS ACS-derived EVs showed increased levels of DNA methyltransferases (DNMTs) (p<0.001) and Ten-eleven translocation (TET) genes reduction. Specifically, de novo methylation transcripts, as DNMT3A and DNMT3B, were significantly increased in plasma ACS-EVs. DNA methylation analysis on PBMCs from healthy donors treated with HS- and ACS-derived EVs showed an important role of DNMTs carried by EVs. PPI network analysis evidenced that ACS-EVs induced changes in PBMC methylome. In the most enriched subnetwork, the hub gene SRC was connected to NOTCH1, FOXO3, CDC42, IKBKG, RXRA, DGKG, BAIAP2 genes that were showed to have many molecular effects on various cell types into onset of several CVDs. Modulation in gene expression after ACS-EVs treatment was confirmed for SRC, NOTCH1, FOXO3, RXRA, DGKG and BAIAP2 (p<0.05). CONCLUSIONS Our data showed an important role for ACS-derived EVs in gene expression modulation through de novo DNA methylation signals, and modulating signalling pathways in target cells.
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Affiliation(s)
- Concetta Schiano
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania Luigi Vanvitelli, Naples, Italy; Cellular and Molecular Cardiology lab Istituto Cardiocentro Ticino-EOC, Lugano, Switzerland; Laboratories for Translation Research, EOC, Bellinzona, Switzerland.
| | - Carolina Balbi
- Cellular and Molecular Cardiology lab Istituto Cardiocentro Ticino-EOC, Lugano, Switzerland; Laboratories for Translation Research, EOC, Bellinzona, Switzerland; Center for Molecular Cardiology, Zurich, Switzerland
| | - Jacopo Burrello
- Laboratories for Translation Research, EOC, Bellinzona, Switzerland; Cardiovascular Theranostics, Istituto Cardiocentro Ticino-EOC, Lugano, Switzerland
| | - Antonio Ruocco
- Unit of Cardiovascular Diseases and Arrhythmias, Antonio Cardarelli Hospital, Naples, Italy
| | - Teresa Infante
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania Luigi Vanvitelli, Naples, Italy
| | | | - Stefano Panella
- Laboratories for Translation Research, EOC, Bellinzona, Switzerland; Cardiovascular Theranostics, Istituto Cardiocentro Ticino-EOC, Lugano, Switzerland
| | - Lucio Barile
- Laboratories for Translation Research, EOC, Bellinzona, Switzerland; Cardiovascular Theranostics, Istituto Cardiocentro Ticino-EOC, Lugano, Switzerland
| | - Ciro Mauro
- Unit of Cardiovascular Diseases and Arrhythmias, Antonio Cardarelli Hospital, Naples, Italy
| | - Giuseppe Vassalli
- Cellular and Molecular Cardiology lab Istituto Cardiocentro Ticino-EOC, Lugano, Switzerland; Laboratories for Translation Research, EOC, Bellinzona, Switzerland; Center for Molecular Cardiology, Zurich, Switzerland
| | - Claudio Napoli
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania Luigi Vanvitelli, Naples, Italy; Division of Clinical Immunology, Immunohematology, Transfusion Medicine and Transplant Immunology (SIMT), Regional Reference Laboratory of Transplant Immunology (LIT), Azienda Universitaria Policlinico (AOU), Naples, Italy
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28
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Lei MK, Gibbons FX, Gerrard M, Beach SRH, Dawes K, Philibert R. Digital methylation assessments of alcohol and cigarette consumption account for common variance in accelerated epigenetic ageing. Epigenetics 2022; 17:1991-2005. [PMID: 35866695 PMCID: PMC9665121 DOI: 10.1080/15592294.2022.2100684] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Smoking and Heavy Alcohol Consumption (HAC) are established risk factors for myriad complex disorders of ageing. Yet many prior studies of Epigenetic Ageing (EA) have shown only modest effects of smoking and drinking on accelerated ageing. One potential reason for this conundrum might be the reliance of some prior EA studies on self-reported substance use, which may be unreliable in many samples. To test whether novel, non-self-reported indices would show a stronger association of smoking and HAC to EA, we used methylation sensitive digital PCR (MSdPCR) and data from 437 African American subjects from Wave 7 of the Family and Community Health Study Offspring Cohort to examine the effects of subjective and objective measures of smoking and HAC on 7 indices of EA. Because of limited overall correlations between the various EA indices, we examined patterns of association separately for each index. Consistent with expectations, MSdPCR assessments of smoking and HAC, but not self-reported alcohol consumption, were strongly correlated with accelerated EA. MSdPCR assessments of smoking and HAC accounted for 57% of GrimAge acceleration and the shared variance in GrimAge and DunedinPOAM accelerated EA. We conclude that MSdPCR assessments of smoking and HAC are valuable tools for understanding EA, represent directly targetable conditions for the prevention of premature ageing, and substantially improve upon self-reported assessment of smoking and HAC.
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Affiliation(s)
- Man-Kit Lei
- Department of Sociology, University of Georgia, Athens, GA, USA.,Center for Family Research, University of Georgia, Athens, GA, USA
| | - Frederick X Gibbons
- Department of Psychological Sciences, University of Connecticut, Storrs, CT, USA
| | - Meg Gerrard
- Department of Psychological Sciences, University of Connecticut, Storrs, CT, USA
| | - Steven R H Beach
- Center for Family Research, University of Georgia, Athens, GA, USA.,Department of Psychology, University of Georgia, Athens, GA, USA
| | - Kelsey Dawes
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
| | - Robert Philibert
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA.,Behavioral Diagnostics LLC, Coralville, IA, USA
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29
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Napoli C, Benincasa G, Ellahham S. Precision Medicine in Patients with Differential Diabetic Phenotypes: Novel Opportunities from Network Medicine. Curr Diabetes Rev 2022; 18:e221221199301. [PMID: 34951369 DOI: 10.2174/1573399818666211222164400] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 10/05/2021] [Accepted: 10/28/2021] [Indexed: 11/22/2022]
Abstract
INTRODUCTION Diabetes mellitus (DM) comprises differential clinical phenotypes ranging from rare monogenic to common polygenic forms, such as type 1 (T1DM), type 2 (T2DM), and gestational diabetes, which are associated with cardiovascular complications. Also, the high- -risk prediabetic state is rising worldwide, suggesting the urgent need for early personalized strategies to prevent and treat a hyperglycemic state. OBJECTIVE We aim to discuss the advantages and challenges of Network Medicine approaches in clarifying disease-specific molecular pathways, which may open novel ways for repurposing approved drugs to reach diabetes precision medicine and personalized therapy. CONCLUSION The interactome or protein-protein interactions (PPIs) is a useful tool to identify subtle molecular differences between precise diabetic phenotypes and predict putative novel drugs. Despite being previously unappreciated as T2DM determinants, the growth factor receptor-bound protein 14 (GRB14), calmodulin 2 (CALM2), and protein kinase C-alpha (PRKCA) might have a relevant role in disease pathogenesis. Besides, in silico platforms have suggested that diflunisal, nabumetone, niflumic acid, and valdecoxib may be suitable for the treatment of T1DM; phenoxybenzamine and idazoxan for the treatment of T2DM by improving insulin secretion; and hydroxychloroquine reduce the risk of coronary heart disease (CHD) by counteracting inflammation. Network medicine has the potential to improve precision medicine in diabetes care and enhance personalized therapy. However, only randomized clinical trials will confirm the clinical utility of network- oriented biomarkers and drugs in the management of DM.
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Affiliation(s)
- Claudio Napoli
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania "Luigi Vanvitelli", 80138- Naples, Italy
- Clinical Department of Internal and Specialty Medicine (DAI), University Hospital (AOU), University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - Giuditta Benincasa
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania "Luigi Vanvitelli", 80138- Naples, Italy
| | - Samer Ellahham
- Department of Cardiology, Cleveland Clinic Abu Dhabi, Abu Dhabi, United Arab Emirates
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30
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Benedetti R, Benincasa G, Glass K, Chianese U, Vietri MT, Congi R, Altucci L, Napoli C. Effects of novel SGLT2 inhibitors on cancer incidence in hyperglycemic patients: a meta-analysis of randomized clinical trials. Pharmacol Res 2021; 175:106039. [PMID: 34929299 DOI: 10.1016/j.phrs.2021.106039] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 12/10/2021] [Accepted: 12/15/2021] [Indexed: 02/06/2023]
Abstract
Epidemiological evidence shows that diabetic patients have an increased cancer risk and a higher mortality rate. Glucose could play a central role in metabolism and growth of many tumor types, and this possible mechanism is supported by the high rate of glucose demand and uptake in cancer. Thus, growing evidence suggests that hyperglycemia contributes to cancer progression but also to its onset. Many mechanisms underlying this association have been hypothesized, such as insulin resistance, hyperinsulinemia, and increased inflammatory processes. Inflammation is a common pathophysiological feature in both diabetic and oncological patients, and inflammation linked to high glucose levels sensitizes microenvironment to tumorigenesis, promoting the development of malignant lesions by altering and sustaining a pathological condition in tissues. Glycemic control is the first goal of antidiabetic therapy, and glucose level reduction has also been associated with favorable outcomes in cancer. Here, we describe key events in carcinogenesis focusing on hyperglycemia as supporter in tumor progression and in particular, related to the role of a specific hypoglycemic drug class, sodium-glucose linked transporters (SGLTs). We also discuss the use of SGLT2 inhibitors as a novel potential cancer therapy. Our meta-analysis showed that SGLT-2 inhibitors were significantly associated with an overall reduced risk of cancer as compared to placebo (RR = 0.35, CI 0.33-0.37, P = 0. 00) with a particular effectiveness for dapaglifozin and ertuglifozin (RR = 0. 06, CI 0. 06-0. 07 and RR = 0. 22, CI 0. 18-0. 26, respectively). Network Medicine approaches may advance the possible repurposing of these drugs in patients with concomitant diabetes and cancer.
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Affiliation(s)
- Rosaria Benedetti
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Via L. De Crecchio 7, 80138 Naples, Italy
| | - Giuditta Benincasa
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania "Luigi Vanvitelli", Pz. Miraglia 2, 80138 Naples, Italy.
| | - Kimberly Glass
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Ugo Chianese
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Via L. De Crecchio 7, 80138 Naples, Italy
| | - Maria Teresa Vietri
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Via L. De Crecchio 7, 80138 Naples, Italy
| | - Raffaella Congi
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Via L. De Crecchio 7, 80138 Naples, Italy
| | - Lucia Altucci
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Via L. De Crecchio 7, 80138 Naples, Italy; Biogem Institute of Molecular and Genetic Biology, 83031 Ariano Irpino, Italy.
| | - Claudio Napoli
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania "Luigi Vanvitelli", Pz. Miraglia 2, 80138 Naples, Italy; Clinical Department of Internal Medicine and Specialistics, Division of Clinical Immunology, Transfusion Medicine and Transplant Immunology, AOU University of Campania "Luigi Vanvitelli", Via L. De Crecchio 7, 80138 Naples, Italy.
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31
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Vietri MT, D'Elia G, Benincasa G, Ferraro G, Caliendo G, Nicoletti GF, Napoli C. DNA methylation and breast cancer: A way forward (Review). Int J Oncol 2021; 59:98. [PMID: 34726251 DOI: 10.3892/ijo.2021.5278] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 10/01/2021] [Indexed: 11/05/2022] Open
Abstract
The current management of breast cancer (BC) lacks specific non‑invasive biomarkers able to provide an early diagnosis of the disease. Epigenetic‑sensitive signatures are influenced by environmental exposures and are mediated by direct molecular mechanisms, mainly guided by DNA methylation, which regulate the interplay between genetic and non‑genetic risk factors during cancerogenesis. The inactivation of tumor suppressor genes due to promoter hypermethylation is an early event in carcinogenesis. Of note, targeted tumor suppressor genes are frequently hypermethylated in patient‑derived BC tissues and peripheral blood biospecimens. In addition, epigenetic alterations in triple‑negative BC, as the most aggressive subtype, have been identified. Thus, detecting both targeted and genome‑wide DNA methylation changes through liquid‑based assays appears to be a useful clinical strategy for early detection, more accurate risk stratification and a personalized prediction of therapeutic response in patients with BC. Of note, the DNA methylation profile may be mapped by isolating the circulating tumor DNA from the plasma as a more accessible biospecimen. Furthermore, the sensitivity to treatment with chemotherapy, hormones and immunotherapy may be altered by gene‑specific DNA methylation, suggesting novel potential drug targets. Recently, the use of epigenetic drugs administered alone and/or with anticancer therapies has led to remarkable results, particularly in patients with BC resistant to anticancer treatment. The aim of the present review was to provide an update on DNA methylation changes that are potentially involved in BC development and their putative clinical utility in the fields of diagnosis, prognosis and therapy.
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Affiliation(s)
- Maria Teresa Vietri
- Department of Precision Medicine, University of Campania 'Luigi Vanvitelli', I-80138 Naples, Italy
| | - Giovanna D'Elia
- Unit of Clinical and Molecular Pathology, AOU, University of Campania 'Luigi Vanvitelli', I-80138 Naples, Italy
| | - Giuditta Benincasa
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania 'Luigi Vanvitelli', I-80138 Naples, Italy
| | - Giuseppe Ferraro
- Multidisciplinary Department of Medical, Surgical and Dental Sciences, Plastic Surgery Unit, University of Campania 'Luigi Vanvitelli', I-80138 Naples, Italy
| | - Gemma Caliendo
- Unit of Clinical and Molecular Pathology, AOU, University of Campania 'Luigi Vanvitelli', I-80138 Naples, Italy
| | - Giovanni Francesco Nicoletti
- Multidisciplinary Department of Medical, Surgical and Dental Sciences, Plastic Surgery Unit, University of Campania 'Luigi Vanvitelli', I-80138 Naples, Italy
| | - Claudio Napoli
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania 'Luigi Vanvitelli', I-80138 Naples, Italy
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32
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Montisci A, Palmieri V, Liu JE, Vietri MT, Cirri S, Donatelli F, Napoli C. Severe Cardiac Toxicity Induced by Cancer Therapies Requiring Intensive Care Unit Admission. Front Cardiovasc Med 2021; 8:713694. [PMID: 34540917 PMCID: PMC8446380 DOI: 10.3389/fcvm.2021.713694] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 07/27/2021] [Indexed: 12/28/2022] Open
Abstract
A steadying increase of cancer survivors has been observed as a consequence of more effective therapies. However, chemotherapy regimens are often associated with significant toxicity, and cardiac damage emerges as a prominent clinical issue. Many mechanisms sustain chemotherapy-induced cardiac toxicity: direct myocyte damage, arrhythmia induction, coronary vasospasm, and accelerated atherosclerosis. Anthracyclines are the most studied cardiotoxic drugs and represent a clinical model for cardiac damage induced by chemotherapy. In patients suffering from advanced heart failure (HF) because of chemotherapy-related cardiomyopathy, when refractory to optimal medical therapy, mechanical circulatory support or heart transplantation represents an effective treatment. Here, the main mechanisms of cardiac toxicity induced by cancer therapies are analyzed, with a focus on patients requiring intensive care unit (ICU) admission during the course of the disease because of acute cardiac toxicity, takotsubo syndrome, and acute-on-chronic HF in patients suffering from chemotherapy-induced cardiomyopathy. In a subset of patients, cardiac toxicity can be acute and life-threatening, leading to overt cardiogenic shock. The management of critically ill cancer patients poses a unique challenge and requires a multidisciplinary approach. Moreover, no etiologic therapy is available, and only supportive measures can be implemented.
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Affiliation(s)
- Andrea Montisci
- Division of Cardiothoracic Intensive Care, Azienda Socio-Sanitaria Territoriale (ASST) Spedali Civili, Brescia, Italy
| | - Vittorio Palmieri
- Department of Cardiac Surgery and Transplantation, Ospedali dei Colli Monaldi-Cotugno-CTO, Naples, Italy
| | - Jennifer E Liu
- Department of Medicine/Cardiology Service, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Maria T Vietri
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Silvia Cirri
- Department of Anesthesia and Intensive Care, Istituto Clinico Sant'Ambrogio, Milan, Italy
| | | | - Claudio Napoli
- Clinical Department of Internal Medicine and Specialistics, University Department of Advanced Clinical and Surgical Sciences, University of Campania "Luigi Vanvitelli", Naples, Italy.,Istituto di Ricovero e Cura a Carattere Scientifico - Synlab Diagnostica Nucleare (IRCCS SDN), Naples, Italy
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33
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Napoli C, Bontempo P, Palmieri V, Coscioni E, Maiello C, Donatelli F, Benincasa G. Epigenetic Therapies for Heart Failure: Current Insights and Future Potential. Vasc Health Risk Manag 2021; 17:247-254. [PMID: 34079271 PMCID: PMC8164213 DOI: 10.2147/vhrm.s287082] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 04/29/2021] [Indexed: 12/20/2022] Open
Abstract
Despite the current reductionist approach providing an optimal indication for diagnosis and treatment of patients with heart failure with reduced ejection fraction (HFrEF), there are no standard pharmacological therapies for heart failure with preserved ejection fraction (HFpEF). Although in its infancy in cardiovascular diseases, the epigenetic-based therapy ("epidrugs") is capturing the interest of physician community. In fact, an increasing number of controlled clinical trials is evaluating the putative beneficial effects of: 1) direct epigenetic-oriented drugs, eg, apabetalone, and 2) repurposed drugs with a possible indirect epigenetic interference, eg, metformin, statins, sodium glucose transporter inhibitors 2 (SGLT2i), and omega 3 polyunsaturated fatty acids (PUFAs) in both HFrEF and HFpEF, separately. Apabetalone is the first and unique direct epidrug tested in cardiovascular patients to date, and the BETonMACE trial has reported a reduction in first HF hospitalization (any EF value) and cardiovascular death in patients with type 2 diabetes and recent acute coronary syndrome, suggesting a possible role in secondary prevention. Patients with HFpEF seem to benefit from supplementation to the standard therapy with statins, metformin, and SGLT2i owing to their ability in reducing mortality. In contrast, the vasodilator hydralazine, with or without isosorbide dinitrate, did not provide beneficial effects. In HFrEF, metformin and SGLT2i could reduce the risk of incident HF and mortality in affected patients whereas clinical trials based on statins provided mixed results. Furthermore, PUFAs diet supplementation was significantly associated with reduced cardiovascular risk in both HFpEF and HFrEF. Future large trials will reveal whether direct and indirect epitherapy will remain a work in progress or become a useful way to customize the therapy in the real-world management of HFpEF and HFrEF. Our goal is to discuss the recent advancement in the epitherapy as a possible way to improve personalized therapy of HF.
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Affiliation(s)
- Claudio Napoli
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania "Luigi Vanvitelli", Naples, 80138, Italy
| | - Paola Bontempo
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, 80138, Italy
| | - Vittorio Palmieri
- Department of Cardiac Surgery and Transplantation, Heart Transplantation Unit in Adults of the 'Ospedali dei Colli Monaldi-Cotugno-CTO', Naples, Italy
| | - Enrico Coscioni
- Department of Cardiac Surgery, Azienda Ospedaliera Universitaria San Giovanni di Dio e Ruggi d'Aragona, Salerno, Italy
| | - Ciro Maiello
- Department of Cardiovascular Surgery and Transplants, Monaldi Hospital, Azienda dei Colli, Naples, Italy
| | - Francesco Donatelli
- Chair of Cardiac Surgery, Department of Cardiothoracic Center, Istituto Clinico Sant'Ambrogio, University of Milan, Milan, Italy
| | - Giuditta Benincasa
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania "Luigi Vanvitelli", Naples, 80138, Italy
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34
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Epigenetics of addiction. Neurochem Int 2021; 147:105069. [PMID: 33992741 DOI: 10.1016/j.neuint.2021.105069] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 04/16/2021] [Accepted: 05/09/2021] [Indexed: 11/22/2022]
Abstract
Substance use disorders are complex biopsychosocial disorders that have substantial negative neurocognitive impact in various patient populations. These diseases involve the compulsive use of licit or illicit substances despite adverse medicolegal consequences and appear to be secondary to long-lasting epigenetic and transcriptional adaptations in brain reward and non-reward circuits. The accumulated evidence supports the notion that repeated drug use causes changes in post-translational histone modifications and in DNA methylation/hydroxymethylation processes in several brain regions. This review provides an overview of epigenetic changes reported in models of cocaine, methamphetamine, and opioid use disorders. The accumulated data suggest that future therapeutic interventions should focus on the development of epigenetic drugs against addictive diseases.
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35
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Benincasa G, Vasco M, Corrado A, Sansone A, Picascia A, Napoli C. Epigenetic-based therapy in allogenic hematopoietic stem cell transplantation: Novel opportunities for personalized treatment. Clin Transplant 2021; 35:e14306. [PMID: 33792965 DOI: 10.1111/ctr.14306] [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: 02/09/2021] [Revised: 03/23/2021] [Accepted: 03/27/2021] [Indexed: 12/16/2022]
Abstract
Current management of patients undergoing allogeneic hematopoietic stem cell transplantation (allo-HSCT) lacks immunosuppressant drugs able to block the host immune response toward the graft antigens. Novel treatments may include epigenetic compounds (epidrugs) some of which have been yet approved by the Food and Drugs Administration for the treatment of specific blood malignancies. The most investigated in clinical trials for allo-HSCT are DNA demethylating agents (DNMTi), such as azacitidine (Vidaza) and decitabine (Dacogen) as well as histone deacetylases inhibitors (HDACi), such as vorinostat (Zolinza) and panobinostat (Farydak). Indeed, azacitidine monotherapy before allo-HSCT may reduce the conventional chemotherapy-related complications, whereas it may reduce relapse risk and death after allo-HSCT. Besides, a decitabine-containing conditioning regimen could protect against graft versus host disease (GVHD) and respiratory infections after allo-HSCT. Regarding HDACi, the addition of vorinostat and panobinostat to the conditioning regimen after allo-HSCT seems to reduce the incidence of acute GVHD. Furthermore, panobinostat alone or in combination with low-dose decitabine may reduce the relapse rate in high-risk patients with acute myeloid leukemia patients after allo-HSCT. We discuss the phase 1 and 2 clinical trials evaluating the possible beneficial effects of repurposing specific epidrugs which may guide personalized therapy in the setting of allo-HSCT.
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Affiliation(s)
- Giuditta Benincasa
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Maria Vasco
- U.O.C. Division of Clinical Immunology, Immunohematology, Transfusion Medicine and Transplant Immunology, Regional Reference Laboratory of Transplant Immunology, Department of Internal and Specialty Medicine, A.O.U., University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Alessio Corrado
- U.O.C. Division of Clinical Immunology, Immunohematology, Transfusion Medicine and Transplant Immunology, Regional Reference Laboratory of Transplant Immunology, Department of Internal and Specialty Medicine, A.O.U., University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Annunziata Sansone
- U.O.C. Division of Clinical Immunology, Immunohematology, Transfusion Medicine and Transplant Immunology, Regional Reference Laboratory of Transplant Immunology, Department of Internal and Specialty Medicine, A.O.U., University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Antonietta Picascia
- U.O.C. Division of Clinical Immunology, Immunohematology, Transfusion Medicine and Transplant Immunology, Regional Reference Laboratory of Transplant Immunology, Department of Internal and Specialty Medicine, A.O.U., University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Claudio Napoli
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania "Luigi Vanvitelli", Naples, Italy.,U.O.C. Division of Clinical Immunology, Immunohematology, Transfusion Medicine and Transplant Immunology, Regional Reference Laboratory of Transplant Immunology, Department of Internal and Specialty Medicine, A.O.U., University of Campania "Luigi Vanvitelli", Naples, Italy
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