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Qian Y, Wang X, Cai L, Han J, Huang Z, Lou Y, Zhang B, Wang Y, Sun X, Zhang Y, Zhu A. Model informed precision medicine of Chinese herbal medicines formulas-A multi-scale mechanistic intelligent model. J Pharm Anal 2024; 14:100914. [PMID: 38694562 PMCID: PMC11061219 DOI: 10.1016/j.jpha.2023.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 11/21/2023] [Accepted: 12/07/2023] [Indexed: 05/04/2024] Open
Abstract
Recent trends suggest that Chinese herbal medicine formulas (CHM formulas) are promising treatments for complex diseases. To characterize the precise syndromes, precise diseases and precise targets of the precise targets between complex diseases and CHM formulas, we developed an artificial intelligence-based quantitative predictive algorithm (DeepTCM). DeepTCM has gone through multilevel model calibration and validation against a comprehensive set of herb and disease data so that it accurately captures the complex cellular signaling, molecular and theoretical levels of traditional Chinese medicine (TCM). As an example, our model simulated the optimal CHM formulas for the treatment of coronary heart disease (CHD) with depression, and through model sensitivity analysis, we calculated the balanced scoring of the formulas. Furthermore, we constructed a biological knowledge graph representing interactions by associating herb-target and gene-disease interactions. Finally, we experimentally confirmed the therapeutic effect and pharmacological mechanism of a novel model-predicted intervention in humans and mice. This novel multiscale model opened up a new avenue to combine "disease syndrome" and "macro micro" system modeling to facilitate translational research in CHM formulas.
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Affiliation(s)
- Yuanyuan Qian
- Zhejiang Key Laboratory of Blood-Stasis-Toxin Syndrome, Zhejiang Chinese Medical University, Hangzhou, 310000, China
- Zhejiang Engineering Research Center for “Preventive Treatment” Smart Health of Traditional Chinese Medicine, Zhejiang Chinese Medical University, Hangzhou, 310000, China
- College of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310000, China
| | - Xiting Wang
- Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China
| | - Lulu Cai
- Zhejiang Key Laboratory of Blood-Stasis-Toxin Syndrome, Zhejiang Chinese Medical University, Hangzhou, 310000, China
- Zhejiang Engineering Research Center for “Preventive Treatment” Smart Health of Traditional Chinese Medicine, Zhejiang Chinese Medical University, Hangzhou, 310000, China
- College of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310000, China
- Academy of Chinese Medical Science, Zhejiang Chinese Medical University, Hangzhou, 310000, China
| | - Jiangxue Han
- Zhejiang Key Laboratory of Blood-Stasis-Toxin Syndrome, Zhejiang Chinese Medical University, Hangzhou, 310000, China
- Zhejiang Engineering Research Center for “Preventive Treatment” Smart Health of Traditional Chinese Medicine, Zhejiang Chinese Medical University, Hangzhou, 310000, China
- College of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310000, China
- Academy of Chinese Medical Science, Zhejiang Chinese Medical University, Hangzhou, 310000, China
| | - Zhu Huang
- Zhejiang Key Laboratory of Blood-Stasis-Toxin Syndrome, Zhejiang Chinese Medical University, Hangzhou, 310000, China
- Zhejiang Engineering Research Center for “Preventive Treatment” Smart Health of Traditional Chinese Medicine, Zhejiang Chinese Medical University, Hangzhou, 310000, China
- College of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310000, China
| | - Yahui Lou
- Zhejiang Key Laboratory of Blood-Stasis-Toxin Syndrome, Zhejiang Chinese Medical University, Hangzhou, 310000, China
- Zhejiang Engineering Research Center for “Preventive Treatment” Smart Health of Traditional Chinese Medicine, Zhejiang Chinese Medical University, Hangzhou, 310000, China
- College of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310000, China
| | - Bingyue Zhang
- Zhejiang Key Laboratory of Blood-Stasis-Toxin Syndrome, Zhejiang Chinese Medical University, Hangzhou, 310000, China
- Zhejiang Engineering Research Center for “Preventive Treatment” Smart Health of Traditional Chinese Medicine, Zhejiang Chinese Medical University, Hangzhou, 310000, China
- College of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310000, China
| | - Yanjie Wang
- Zhejiang Key Laboratory of Blood-Stasis-Toxin Syndrome, Zhejiang Chinese Medical University, Hangzhou, 310000, China
- Zhejiang Engineering Research Center for “Preventive Treatment” Smart Health of Traditional Chinese Medicine, Zhejiang Chinese Medical University, Hangzhou, 310000, China
- College of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310000, China
| | - Xiaoning Sun
- Affiliated Hospital of Liaoning University of Traditional Chinese Medicine, Shenyang, 110032, China
| | - Yan Zhang
- Affiliated Hospital of Liaoning University of Traditional Chinese Medicine, Shenyang, 110032, China
| | - Aisong Zhu
- Zhejiang Key Laboratory of Blood-Stasis-Toxin Syndrome, Zhejiang Chinese Medical University, Hangzhou, 310000, China
- Zhejiang Engineering Research Center for “Preventive Treatment” Smart Health of Traditional Chinese Medicine, Zhejiang Chinese Medical University, Hangzhou, 310000, China
- College of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310000, China
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Jang MK, Markowitz TE, Andargie TE, Apalara Z, Kuhn S, Agbor-Enoh S. Cell-free chromatin immunoprecipitation to detect molecular pathways in heart transplantation. Life Sci Alliance 2023; 6:e202302003. [PMID: 37730434 PMCID: PMC10511822 DOI: 10.26508/lsa.202302003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 09/11/2023] [Accepted: 09/13/2023] [Indexed: 09/22/2023] Open
Abstract
Existing monitoring approaches in heart transplantation lack the sensitivity to provide deep molecular assessments to guide management, or require endomyocardial biopsy, an invasive and blind procedure that lacks the precision to reliably obtain biopsy samples from diseased sites. This study examined plasma cell-free DNA chromatin immunoprecipitation sequencing (cfChIP-seq) as a noninvasive proxy to define molecular gene sets and sources of tissue injury in heart transplant patients. In healthy controls and in heart transplant patients, cfChIP-seq reliably detected housekeeping genes. cfChIP-seq identified differential gene signals of relevant immune and nonimmune molecular pathways that were predominantly down-regulated in immunosuppressed heart transplant patients compared with healthy controls. cfChIP-seq also identified cell-free DNA tissue sources. Compared with healthy controls, heart transplant patients demonstrated greater cell-free DNA from tissue types associated with heart transplant complications, including the heart, hematopoietic cells, lungs, liver, and vascular endothelium. cfChIP-seq may therefore be a reliable approach to profile dynamic assessments of molecular pathways and sources of tissue injury in heart transplant patients.
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Affiliation(s)
- Moon Kyoo Jang
- https://ror.org/01cwqze88 Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, MD, USA
| | - Tovah E Markowitz
- https://ror.org/01cwqze88 NIAID Collaborative Bioinformatics Resource, Integrated Data Sciences Section, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Temesgen E Andargie
- https://ror.org/01cwqze88 Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, MD, USA
- Department of Biology, Howard University, Washington, DC, USA
| | - Zainab Apalara
- https://ror.org/01cwqze88 Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, MD, USA
| | - Skyler Kuhn
- https://ror.org/01cwqze88 NIAID Collaborative Bioinformatics Resource, Integrated Data Sciences Section, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Sean Agbor-Enoh
- https://ror.org/01cwqze88 Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, MD, USA
- Department of Medicine, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
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3
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Li W, Liu P, Liu H, Zhang F, Fu Y. Integrative analysis of genes reveals endoplasmic reticulum stress-related immune responses involved in dilated cardiomyopathy with fibrosis. Apoptosis 2023; 28:1406-1421. [PMID: 37462883 PMCID: PMC10425499 DOI: 10.1007/s10495-023-01871-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] [Accepted: 06/30/2023] [Indexed: 08/11/2023]
Abstract
Endoplasmic reticulum (ER) stress has been implicated in the mechanisms underlying the fibrotic process in dilated cardiomyopathy (DCM) and results in disease exacerbation; however, the molecular details of this mechanism remain unclear. Through microarray and bioinformatic analyses, we explored genetic alterations in myocardial fibrosis (MF) and identified potential biomarkers related to ER stress. We integrated two public microarray datasets, including 19 DCM and 16 control samples, and comprehensively analyzed differential expression, biological functions, molecular interactions, and immune infiltration levels. The immune cell signatures suggest that inflammatory immune imbalance may promote MF progression. Both innate and adaptive immunity are involved in MF development, and T-cell subsets account for a considerable proportion of immune infiltration. The immune subtypes were further compared, and 103 differentially expressed ER stress-related genes were identified. These genes were mainly enriched in neuronal apoptosis, protein modification, oxidative stress reaction, glycolysis and gluconeogenesis, and NOD-like receptor signaling pathways. Furthermore, the 15 highest-scoring core genes were identified. Seven hub genes (AK1, ARPC3, GSN, KPNA2, PARP1, PFKL, and PRKC) might participate in immune-related mechanisms. Our results offer a new integrative view of the pathways and interaction networks of ER stress-related genes and provide guidance for developing novel therapeutic strategies for MF.
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Affiliation(s)
- Wanpeng Li
- Department of Cardiology, Gansu Provincial Hospital, Lanzhou, 730000, P.R., China
| | - Peiling Liu
- Department of Rheumatology, First Affiliated Hospital of Zhengzhou University Zhengzhou, Henan, 450000, P.R., China
| | - Huilin Liu
- Department of Geriatrics, Peking University Third Hospital, Beijing, 100191, P.R , China
| | - Fuchun Zhang
- Department of Geriatrics, Peking University Third Hospital, Beijing, 100191, P.R , China
| | - Yicheng Fu
- Department of Geriatrics, Peking University Third Hospital, Beijing, 100191, P.R , China.
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4
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Majid A, Hassan FO, Hoque MM, Gbadegoye JO, Lebeche D. Bioactive Compounds and Cardiac Fibrosis: Current Insight and Future Prospect. J Cardiovasc Dev Dis 2023; 10:313. [PMID: 37504569 PMCID: PMC10380727 DOI: 10.3390/jcdd10070313] [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: 06/08/2023] [Revised: 07/14/2023] [Accepted: 07/18/2023] [Indexed: 07/29/2023] Open
Abstract
Cardiac fibrosis is a pathological condition characterized by excessive deposition of collagen and other extracellular matrix components in the heart. It is recognized as a major contributor to the development and progression of heart failure. Despite significant research efforts in characterizing and identifying key molecular mechanisms associated with myocardial fibrosis, effective treatment for this condition is still out of sight. In this regard, bioactive compounds have emerged as potential therapeutic antifibrotic agents due to their anti-inflammatory and antioxidant properties. These compounds exhibit the ability to modulate fibrogenic processes by inhibiting the production of extracellular matrix proteins involved in fibroblast to myofibroblast differentiation, or by promoting their breakdown. Extensive investigation of these bioactive compounds offers new possibilities for preventing or reducing cardiac fibrosis and its detrimental consequences. This comprehensive review aims to provide a thorough overview of the mechanisms underlying cardiac fibrosis, address the limitations of current treatment strategies, and specifically explore the potential of bioactive compounds as therapeutic interventions for the treatment and/or prevention of cardiac fibrosis.
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Affiliation(s)
- Abdul Majid
- Department of Physiology, College of Medicine, The University of Tennessee Health Science Center, Translational Research Building, Room 318H, 71 S. Manassas, Memphis, TN 38163, USA
- College of Graduate Health Sciences, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Fasilat Oluwakemi Hassan
- Department of Physiology, College of Medicine, The University of Tennessee Health Science Center, Translational Research Building, Room 318H, 71 S. Manassas, Memphis, TN 38163, USA
- College of Graduate Health Sciences, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Md Monirul Hoque
- Department of Physiology, College of Medicine, The University of Tennessee Health Science Center, Translational Research Building, Room 318H, 71 S. Manassas, Memphis, TN 38163, USA
- College of Graduate Health Sciences, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Joy Olaoluwa Gbadegoye
- Department of Physiology, College of Medicine, The University of Tennessee Health Science Center, Translational Research Building, Room 318H, 71 S. Manassas, Memphis, TN 38163, USA
- College of Graduate Health Sciences, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Djamel Lebeche
- Department of Physiology, College of Medicine, The University of Tennessee Health Science Center, Translational Research Building, Room 318H, 71 S. Manassas, Memphis, TN 38163, USA
- College of Graduate Health Sciences, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
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5
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Zhang Z, Sun Y, Wang H, Yang Y, Dong R, Xu Y, Zhang M, Lv Q, Chen X, Liu Y. Melatonin pretreatment can improve the therapeutic effect of adipose-derived stem cells on CCl 4-induced liver fibrosis. TOXIN REV 2023. [DOI: 10.1080/15569543.2023.2191263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
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6
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Soboleva AG, Sobolev VV, Karapetyan MM, Mezentsev A, Rud’ko OI, Davydova ED, Mogulevtseva JA, Zhukova OV, Korsunskaya IM. Laser Therapy Changes the Expression of Matrix Metalloproteinases in Bleomycin-Induced Skin Fibrosis. Life (Basel) 2023; 13:life13030810. [PMID: 36983965 PMCID: PMC10056988 DOI: 10.3390/life13030810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/05/2023] [Accepted: 03/15/2023] [Indexed: 03/19/2023] Open
Abstract
Matrix metalloproteinases (MMPs) are often considered biomarkers of skin fibrosis. At the early stages of the pathological process, an elevation of their enzymatic activity causes significant changes in the composition of the extracellular matrix. MMPs secreted by immune cells facilitate their migration to the site of damage. Then, the immune cells eliminate the affected cells and biomolecules. Moreover, bidirectional changes in the activity of proteolytic enzymes, including MMPs, accompany wound healing. This study aimed to assess changes in the expression of Mmp2, Mmp3, and Mmp9 after treating mice with laser therapy using the experimental model of bleomycin-induced skin fibrosis. Using immunohistochemistry, we characterized the histological features of scarred skin. We also analyzed changes in the expression of MMPs using real-time polymerase chain reaction before and after laser irradiation. We showed that treatment of the mice with a CO2 laser partially normalized the histological features of scarred skin. We also noticed a decrease in the expression of Mmp2, Mmp3 (both p < 0.05), and Mmp9 (p = 0.065) during scar healing. The obtained results suggest that normalization of skin homeostasis requires control of MMP activity via induction of genes.
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Affiliation(s)
- Anna G. Soboleva
- Center for Theoretical Problems in Physico-Chemical Pharmacology, Russian Academy of Sciences, 30 Srednaya Kalitnikovskaya Street, 109029 Moscow, Russia
- Avtsyn Research Institute of Human Morphology of Petrovsky National Research Centre of Surgery, 3 Tsyurupy Street, 117418 Moscow, Russia
| | - Vladimir V. Sobolev
- Center for Theoretical Problems in Physico-Chemical Pharmacology, Russian Academy of Sciences, 30 Srednaya Kalitnikovskaya Street, 109029 Moscow, Russia
- Correspondence:
| | | | - Alexandre Mezentsev
- Center for Theoretical Problems in Physico-Chemical Pharmacology, Russian Academy of Sciences, 30 Srednaya Kalitnikovskaya Street, 109029 Moscow, Russia
| | - Olga I. Rud’ko
- Faculty of Biology, M.V. Lomonosov Moscow State University, 1-12 Leninskie Gory, 119991 Moscow, Russia
| | | | - Julia A. Mogulevtseva
- Department of Agronomy and Biotechnology, Russian Agrarian University (Moscow Timiryazev Agricultural Academy), 49 Timiryazeva Street, 127550 Moscow, Russia
| | - Olga V. Zhukova
- Moscow Center of Dermatology and Cosmetology, 17 Leninsky Avenue, 119071 Moscow, Russia
| | - Irina M. Korsunskaya
- Center for Theoretical Problems in Physico-Chemical Pharmacology, Russian Academy of Sciences, 30 Srednaya Kalitnikovskaya Street, 109029 Moscow, Russia
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7
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Quaife NM, Chothani S, Schulz JF, Lindberg EL, Vanezis K, Adami E, O'Fee K, Greiner J, Litviňuková M, van Heesch S, Whiffin N, Hubner N, Schafer S, Rackham O, Cook SA, Barton PJR. LINC01013 Is a Determinant of Fibroblast Activation and Encodes a Novel Fibroblast-Activating Micropeptide. J Cardiovasc Transl Res 2023; 16:77-85. [PMID: 35759180 PMCID: PMC9944705 DOI: 10.1007/s12265-022-10288-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 06/09/2022] [Indexed: 10/17/2022]
Abstract
Myocardial fibrosis confers an almost threefold mortality risk in heart disease. There are no prognostic therapies and novel therapeutic targets are needed. Many thousands of unannotated small open reading frames (smORFs) have been identified across the genome with potential to produce micropeptides (< 100 amino acids). We sought to investigate the role of smORFs in myocardial fibroblast activation.Analysis of human cardiac atrial fibroblasts (HCFs) stimulated with profibrotic TGFβ1 using RNA sequencing (RNA-Seq) and ribosome profiling (Ribo-Seq) identified long intergenic non-coding RNA LINC01013 as TGFβ1 responsive and containing an actively translated smORF. Knockdown of LINC01013 using siRNA reduced expression of profibrotic markers at baseline and blunted their response to TGFβ1. In contrast, overexpression of a codon-optimised smORF invoked a profibrotic response comparable to that seen with TGFβ1 treatment, whilst FLAG-tagged peptide associated with the mitochondria.Together, these data support a novel LINC01013 smORF micropeptide-mediated mechanism of fibroblast activation. TGFβ1 stimulation of atrial fibroblasts induces expression of LINC01013, whose knockdown reduces fibroblast activation. Overexpression of a smORF contained within LINC01013 localises to mitochondria and activates fibroblasts.
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Affiliation(s)
- N M Quaife
- National Heart and Lung Institute, Imperial College London, London, UK
- MRC London Institute of Medical Sciences, London, UK
| | - S Chothani
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore, 169857, Singapore
| | - J F Schulz
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- DZHK (German Center for Cardiovascular Research), partner site Berlin, Berlin, Germany
| | - E L Lindberg
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - K Vanezis
- National Heart and Lung Institute, Imperial College London, London, UK
- MRC London Institute of Medical Sciences, London, UK
| | - E Adami
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore, 169857, Singapore
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - K O'Fee
- MRC London Institute of Medical Sciences, London, UK
| | - J Greiner
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - M Litviňuková
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - S van Heesch
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - N Whiffin
- National Heart and Lung Institute, Imperial College London, London, UK
- Cardiovascular Research Centre, Royal Brompton and Harefield Hospitals, Guy's and St Thomas NHS Foundation Trust, London, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - N Hubner
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- DZHK (German Center for Cardiovascular Research), partner site Berlin, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - S Schafer
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore, 169857, Singapore
| | - O Rackham
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore, 169857, Singapore
| | - S A Cook
- MRC London Institute of Medical Sciences, London, UK
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore, 169857, Singapore
- National Heart Centre Singapore, Singapore, Singapore
| | - P J R Barton
- National Heart and Lung Institute, Imperial College London, London, UK.
- MRC London Institute of Medical Sciences, London, UK.
- Cardiovascular Research Centre, Royal Brompton and Harefield Hospitals, Guy's and St Thomas NHS Foundation Trust, London, UK.
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Jang MK, Markowitz TE, Andargie TE, Apalara Z, Kuhn S, Agbor-Enoh S. Cell-free Chromatin Immunoprecipitation to detect molecular pathways in Physiological and Disease States. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.24.525414. [PMID: 36789421 PMCID: PMC9928031 DOI: 10.1101/2023.01.24.525414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Patient monitoring is a cornerstone in clinical practice to define disease phenotypes and guide clinical management. Unfortunately, this is often reliant on invasive and/or less sensitive methods that do not provide deep phenotype assessments of disease state to guide treatment. This paper examined plasma cell-free DNA chromatin immunoprecipitation sequencing (cfChIP-seq) to define molecular gene sets in physiological and heart transplant patients taking immunosuppression medications. We show cfChIP-seq reliably detect gene signals that correlate with gene expression. In healthy controls and in heart transplant patients, cfChIP-seq reliably detected housekeeping genes. cfChIP-seq identified differential gene signals of the relevant immune and non-immune molecular pathways that were predominantly downregulated in immunosuppressed heart transplant patients compared to healthy controls. cfChIP-seq also identified tissue sources of cfDNA, detecting greater cell-free DNA from cardiac, hematopoietic, and other non-hematopoietic tissues such as the pulmonary, digestive, and neurological tissues in transplant patients than healthy controls. cfChIP-seq gene signals were reproducible between patient populations and blood collection methods. cfChIP-seq may therefore be a reliable approach to provide dynamic assessments of molecular pathways and tissue injury associated to disease.
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Affiliation(s)
- Moon K. Jang
- Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision. Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, MD
| | - Tovah E. Markowitz
- NIAID Collaborative Bioinformatics Resource, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
| | - Temesgen E. Andargie
- Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision. Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, MD
| | - Zainab Apalara
- Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision. Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, MD
| | - Skyler Kuhn
- NIAID Collaborative Bioinformatics Resource, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
| | - Sean Agbor-Enoh
- Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision. Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, MD
- Department of Medicine, Johns Hopkins University, School of Medicine, Baltimore, MD
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9
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Shirvaliloo M. The landscape of histone modifications in epigenomics since 2020. Epigenomics 2022; 14:1465-1477. [PMID: 36710634 DOI: 10.2217/epi-2022-0437] [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] [Indexed: 01/31/2023] Open
Abstract
Histone proteins are a primary component of chromatin; therefore, any modifications to their structure are anticipated to affect the behavior of our genetic material, which is manifested in the form of phenotypic changes at a molecular, cellular or organic level. The majority of histone modifications are of either methylation or acetylation type that regulate gene expression. Though, not all of these modifications are concerned with the direct regulation of gene transcription. Throughout its 13-year run, Epigenomics has never ceased to cover these most gripping epigenetic stories, a significant proportion of which is in the matter of histones and their modifications. As such, the current perspective piece is intended to highlight original histone-oriented contributions published in Epigenomics since 2020.
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Affiliation(s)
- Milad Shirvaliloo
- Infectious & Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, 15731, Iran
- Future Science Group, Unitec House, 2 Albert Place, London, N3 1QB, UK
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10
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Ehrlich M. Risks and rewards of big-data in epigenomics research: an interview with Melanie Ehrlich. Epigenomics 2022; 14:351-358. [PMID: 35255735 DOI: 10.2217/epi-2022-0056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Melanie Ehrlich, PhD, is a professor in the Tulane Cancer Center, the Tulane Center for Medical Bioinformatics and Genomics and the Hayward Human Genetics Program at Tulane Medical School, New Orleans, LA. She obtained her PhD in molecular biology in 1971 from the State University of New York at Stony Brook and completed postdoctoral research at Albert Einstein College of Medicine in 1972. She has been working on various aspects of epigenetics, starting with DNA methylation, since 1973. Her group made many first findings about DNA methylation (see below). For example, in 1982 and 1983, in collaboration with Charles Gehrke at the University of Missouri, she was the first to report tissue-specific and cancer-specific differences in overall DNA methylation in humans. In 1985, Xian-Yang Zhang and Richard Wang in her lab discovered a class of human DNA sequences specifically hypomethylated in sperm. In 1998, her group was the first to describe extensive losses of DNA methylation in pericentromeric and centromeric DNA repeats in human cancer. Her lab's many publications on the prevalence of both DNA hypermethylation and hypomethylation in the same cancers brought needed balance to our understanding of the epigenetics of cancer and to its clinical implications [1]. Besides working on cancer epigenetics, her research group has helped elucidate cytogenetic and gene expression abnormalities in the immunodeficiency, centromeric and facial anomalies (ICF) syndrome, a rare recessive disease often caused by mutations in DNMT3B. Her group also studied the epigenetics and transcriptomics of facioscapulohumeral muscular dystrophy (FSHD), whose disease locus is a tandem 3.3-kb repeat at subtelomeric 4q (that happens to be hypomethylated in ICF DNA [2]). Her study of FSHD has taken her in the direction of muscle (skeletal muscle, heart and aorta) epigenetics [3-6]. Recently, she has led research that applies epigenetics much more rigorously than usual to the evaluation of genetic variants from genome-wide association studies (GWAS) of osteoporosis and obesity. In continued collaboration with Sriharsa Pradhan at New England Biolabs and Michelle Lacey at Tulane University, she has compared 5-hydroxymethylcytosine and 5-methylcytosine clustering in various human tissues [7] and is studying myoblast methylomes that they generated by a new high-resolution enzymatic technique (enzymatic methyl-seq).
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Affiliation(s)
- Melanie Ehrlich
- Tulane Cancer Center, Center for Medical Bioinformatics & Genomics, & Hayward Genetics Center, Tulane University, New Orleans, LA 70112, USA
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11
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BRD4-directed super-enhancer organization of transcription repression programs links to chemotherapeutic efficacy in breast cancer. Proc Natl Acad Sci U S A 2022; 119:2109133119. [PMID: 35105803 PMCID: PMC8832982 DOI: 10.1073/pnas.2109133119] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/15/2021] [Indexed: 12/11/2022] Open
Abstract
BRD4 is well known for its role in super-enhancer organization and transcription activation of several prominent oncogenes including c-MYC and BCL2 As such, BRD4 inhibitors are being pursued as promising therapeutics for cancer treatment. However, drug resistance also occurs for BRD4-targeted therapies. Here, we report that BRD4 unexpectedly interacts with the LSD1/NuRD complex and colocalizes with this repressive complex on super-enhancers. Integrative genomic and epigenomic analyses indicate that the BRD4/LSD1/NuRD complex restricts the hyperactivation of a cluster of genes that are functionally linked to drug resistance. Intriguingly, treatment of breast cancer cells with a small-molecule inhibitor of BRD4, JQ1, results in no immediate activation of the drug-resistant genes, but long-time treatment or destabilization of LSD1 by PELI1 decommissions the BRD4/LSD1/NuRD complex, leading to resistance to JQ1 as well as to a broad spectrum of therapeutic compounds. Consistently, PELI1 is up-regulated in breast carcinomas, its level is negatively correlated with that of LSD1, and the expression level of the BRD4/LSD1/NuRD complex-restricted genes is strongly correlated with a worse overall survival of breast cancer patients. Together, our study uncovers a functional duality of BRD4 in super-enhancer organization of transcription activation and repression linking to oncogenesis and chemoresistance, respectively, supporting the pursuit of a combined targeting of BRD4 and PELI1 in effective treatment of breast cancer.
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Transplantation of Fibroblast Sheets with Blood Mononuclear Cell Culture Exerts Cardioprotective Effects by Enhancing Anti-Inflammation and Vasculogenic Potential in Rat Experimental Autoimmune Myocarditis Model. BIOLOGY 2022; 11:biology11010106. [PMID: 35053105 PMCID: PMC8772944 DOI: 10.3390/biology11010106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/26/2021] [Accepted: 12/30/2021] [Indexed: 11/28/2022]
Abstract
Simple Summary Fulminant myocarditis (FM) is a serious inflammatory lesion of the myocardium accompanied by cardiac dysfunction, transitioning to end-stage heart failure. Due to such a difficult pathology, a therapeutic strategy that exerts a steadfast effect has yet to be developed. Blood mononuclear cells (MNCs) have been previously shown to enhance the quality and quantity of cellular fractions (QQMNCs) with anti-inflammatory and vasculogenic potential using the one culture system. The aim of this study was to investigate whether transplantation therapy with hybrid cell sheets of fibroblasts and QQMNCs improves cardiac function in a rat model with experimental autoimmune myocarditis (EAM) induced by purified porcine cardiac myosin. The transplanted hybrid cell sheet exerts cardioprotective effects against EAM, resulting in limited left ventricular remodeling and partially improved cardiac functions due to revascularization, anti-inflammation, and anti-fibrosis. Thus, tissue engineering using hybrid cell sheets of fibroblasts constructed with QQMNCs is expected to provide an effective therapeutic option for patients with severe FM. Abstract Fulminant myocarditis causes impaired cardiac function, leading to poor prognosis and heart failure. Cell sheet engineering is an effective therapeutic option for improving cardiac function. Naïve blood mononuclear cells (MNCs) have been previously shown to enhance the quality and quantity of cellular fractions (QQMNCs) with anti-inflammatory and vasculogenic potential using the one culture system. Herein, we investigated whether autologous cell sheet transplant with QQMNCs improves cardiac function in a rat model with experimental autoimmune myocarditis (EAM). Fibroblast sheets (F-sheet), prepared from EAM rats, were co-cultured with or without QQMNCs (QQ+F sheet) on temperature-responsive dishes. QQ+F sheet induced higher expression of anti-inflammatory and vasculogenic genes (Vegf-b, Hgf, Il-10, and Mrc1/Cd206) than the F sheet. EAM rats were transplanted with either QQ+F sheet or F-sheet, and the left ventricular (LV) hemodynamic analysis was performed using cardiac catheterization. Among the three groups (QQ+F sheet, F-sheet, operation control), the QQ+F sheet transplant group showed alleviation of end-diastolic pressure–volume relationship on a volume load to the same level as that in the healthy group. Histological analysis revealed that QQ+F sheet transplantation promoted revascularization and mitigated fibrosis by limiting LV remodeling. Therefore, autologous QQMNC-modified F-sheets may be a beneficial therapeutic option for EAM.
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Chignon A, Argaud D, Boulanger MC, Mkannez G, Bon-Baret V, Li Z, Thériault S, Bossé Y, Mathieu P. Genome-wide chromatin contacts of super-enhancer-associated lncRNA identify LINC01013 as a regulator of fibrosis in the aortic valve. PLoS Genet 2022; 18:e1010010. [PMID: 35041643 PMCID: PMC8797204 DOI: 10.1371/journal.pgen.1010010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 01/28/2022] [Accepted: 12/22/2021] [Indexed: 12/22/2022] Open
Abstract
Calcific aortic valve disease (CAVD) is characterized by a fibrocalcific process. The regulatory mechanisms that drive the fibrotic response in the aortic valve (AV) are poorly understood. Long noncoding RNAs derived from super-enhancers (lncRNA-SE) control gene expression and cell fate. Herein, multidimensional profiling including chromatin immunoprecipitation and sequencing, transposase-accessible chromatin sequencing, genome-wide 3D chromatin contacts of enhancer-promoter identified LINC01013 as an overexpressed lncRNA-SE during CAVD. LINC01013 is within a loop anchor, which has contact with the promoter of CCN2 (CTGF) located at ~180 kb upstream. Investigation showed that LINC01013 acts as a decoy factor for the negative transcription elongation factor E (NELF-E), whereby it controls the expression of CCN2. LINC01013-CCN2 is part of a transforming growth factor beta 1 (TGFB1) network and exerts a control over fibrogenesis. These findings illustrate a novel mechanism whereby a dysregulated lncRNA-SE controls, through a looping process, the expression of CCN2 and fibrogenesis of the AV. Calcific aortic valve disease is the most common heart valve disorder characterized by a thickening of the aortic valve resulting from fibrotic and calcific processes. Because the aortic valve replacement is currently the only therapeutic option, the identification of key molecular processes that control the progression of the disease could lead to the development of novel noninvasive therapies. Growing evidence suggests that long noncoding RNAs (lncRNAs) fine tune gene expression in health and disease states. By using a multidimensional profiling including genome-wide 3D enhancer-promoter looping data, we identified LINC01013, a lncRNA, as a regulator of fibrogenesis. Specifically, we found that LINC01013 is located in a cluster of distant enhancers (super-enhancer) in aortic valve interstitial cells and has significant long-range looping with the promoter of CCN2, a gene that orchestrates fibrogenesis. We discovered that LINC01013 is acting as a decoy factor for a negative transcription elongation factor, whereby it controls the transcription of CCN2. In turn, higher expression of LINC01013 during calcific aortic valve disease promoted the expression of CCN2 and a fibrogenic program. These findings provide evidence that LINC01013 is a key regulator of fibrogenesis in CAVD.
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Affiliation(s)
- Arnaud Chignon
- Laboratory of Cardiovascular Pathobiology, Quebec Heart and Lung Institute/Research Center, Department of Surgery, Laval University, Quebec, Canada
| | - Déborah Argaud
- Laboratory of Cardiovascular Pathobiology, Quebec Heart and Lung Institute/Research Center, Department of Surgery, Laval University, Quebec, Canada
| | - Marie-Chloé Boulanger
- Laboratory of Cardiovascular Pathobiology, Quebec Heart and Lung Institute/Research Center, Department of Surgery, Laval University, Quebec, Canada
| | - Ghada Mkannez
- Laboratory of Cardiovascular Pathobiology, Quebec Heart and Lung Institute/Research Center, Department of Surgery, Laval University, Quebec, Canada
| | - Valentin Bon-Baret
- Laboratory of Cardiovascular Pathobiology, Quebec Heart and Lung Institute/Research Center, Department of Surgery, Laval University, Quebec, Canada
| | - Zhonglin Li
- Laboratory of Cardiovascular Pathobiology, Quebec Heart and Lung Institute/Research Center, Department of Surgery, Laval University, Quebec, Canada
| | - Sébastien Thériault
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University, Quebec, Canada
| | - Yohan Bossé
- Department of Molecular Medicine, Laval University, Quebec, Canada
| | - Patrick Mathieu
- Laboratory of Cardiovascular Pathobiology, Quebec Heart and Lung Institute/Research Center, Department of Surgery, Laval University, Quebec, Canada
- * E-mail:
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Johnson S. Welcome to the 14th volume of Epigenomics. Epigenomics 2021; 14:1-4. [PMID: 34904443 DOI: 10.2217/epi-2021-0396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Storm Johnson
- Future Medicine, Future Science Group Ltd, London N3 1QB, UK
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Xue T, Qiu X, Liu H, Gan C, Tan Z, Xie Y, Wang Y, Ye T. Epigenetic regulation in fibrosis progress. Pharmacol Res 2021; 173:105910. [PMID: 34562602 DOI: 10.1016/j.phrs.2021.105910] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 08/23/2021] [Accepted: 09/15/2021] [Indexed: 02/08/2023]
Abstract
Fibrosis, a common process of chronic inflammatory diseases, is defined as a repair response disorder when organs undergo continuous damage, ultimately leading to scar formation and functional failure. Around the world, fibrotic diseases cause high mortality, unfortunately, with limited treatment means in clinical practice. With the development and application of deep sequencing technology, comprehensively exploring the epigenetic mechanism in fibrosis has been allowed. Extensive remodeling of epigenetics controlling various cells phenotype and molecular mechanisms involved in fibrogenesis was subsequently verified. In this review, we summarize the regulatory mechanisms of DNA methylation, histone modification, noncoding RNAs (ncRNAs) and N6-methyladenosine (m6A) modification in organ fibrosis, focusing on heart, liver, lung and kidney. Additionally, we emphasize the diversity of epigenetics in the cellular and molecular mechanisms related to fibrosis. Finally, the potential and prospect of targeted therapy for fibrosis based on epigenetic is discussed.
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Affiliation(s)
- Taixiong Xue
- Sichuan University-University of Oxford Huaxi Joint Centre for Gastrointestinal Cancer, Department of Gastroenterology and Hepatology, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Xingyu Qiu
- Sichuan University-University of Oxford Huaxi Joint Centre for Gastrointestinal Cancer, Department of Gastroenterology and Hepatology, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Hongyao Liu
- Sichuan University-University of Oxford Huaxi Joint Centre for Gastrointestinal Cancer, Department of Gastroenterology and Hepatology, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Cailing Gan
- Sichuan University-University of Oxford Huaxi Joint Centre for Gastrointestinal Cancer, Department of Gastroenterology and Hepatology, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Zui Tan
- Sichuan University-University of Oxford Huaxi Joint Centre for Gastrointestinal Cancer, Department of Gastroenterology and Hepatology, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yuting Xie
- Sichuan University-University of Oxford Huaxi Joint Centre for Gastrointestinal Cancer, Department of Gastroenterology and Hepatology, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yuxi Wang
- Sichuan University-University of Oxford Huaxi Joint Centre for Gastrointestinal Cancer, Department of Gastroenterology and Hepatology, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China; Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China.
| | - Tinghong Ye
- Sichuan University-University of Oxford Huaxi Joint Centre for Gastrointestinal Cancer, Department of Gastroenterology and Hepatology, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China.
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