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Thomas JM, Sasankan D, Abraham M, Surendran S, Kartha CC, Rajavelu A. DNA methylation signatures on vascular differentiation genes are aberrant in vessels of human cerebral arteriovenous malformation nidus. Clin Epigenetics 2022; 14:127. [PMID: 36229855 PMCID: PMC9563124 DOI: 10.1186/s13148-022-01346-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 10/02/2022] [Indexed: 12/04/2022] Open
Abstract
Arteriovenous malformation (AVM) is a tangle of arteries and veins, rupture of which can result in catastrophic hemorrhage in vulnerable sites such as the brain. Cerebral AVM is associated with a high mortality rate in humans. The causative factor or the stimulus at the artery-venous junction and the molecular basis of the development and progression of cerebral AVM remain unknown. While it is known that aberrant hemodynamic forces in the artery-vein junction contribute to the development of AVMs, the mechanistic pathways are unclear. Given that various environmental stimuli modulate epigenetic modifications on the chromatin of cells, we speculated that misregulated DNA methylome could lead to cerebral AVM development. To identify the aberrant epigenetic signatures, we used AVM nidus tissues and analyzed the global DNA methylome using the Infinium DNA methylome array. We observed significant alterations of DNA methylation in the genes associated with the vascular developmental pathway. Further, we validated the DNA hypermethylation by DNA bisulfite sequencing analysis of selected genes from human cerebral AVM nidus. Taken together, we provide the first experimental evidence for aberrant epigenetic signatures on the genes of vascular development pathway, in human cerebral AVM nidus.
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Affiliation(s)
- Jaya Mary Thomas
- Cardio Vascular Diseases and Diabetes Biology, Rajiv Gandhi Centre for Biotechnology, Poojappura, Thycaud, Thiruvananthapuram, Kerala, India, 695014
| | - Dhakshmi Sasankan
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology, Madras, Chennai, Tamil Nadu, 600036, India
| | - Mathew Abraham
- Department of Neurosurgery, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala, India, 695011
| | - Sumi Surendran
- Cardio Vascular Diseases and Diabetes Biology, Rajiv Gandhi Centre for Biotechnology, Poojappura, Thycaud, Thiruvananthapuram, Kerala, India, 695014
| | - Chandrasekharan C Kartha
- Department of Neurology, Amrita Institute of Medical Sciences, Amrita Vishwa Vidyapeetham, Kochi, 682041, Kerala, India.
| | - Arumugam Rajavelu
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology, Madras, Chennai, Tamil Nadu, 600036, India.
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Jabeena CA, Govindaraju G, Rawat M, Gopi S, Sethumadhavan DV, Jaleel A, Sasankan D, Karmodiya K, Rajavelu A. Dynamic association of the H3K64 trimethylation mark with genes encoding exported proteins in Plasmodium falciparum. J Biol Chem 2021; 296:100614. [PMID: 33839154 PMCID: PMC8095176 DOI: 10.1016/j.jbc.2021.100614] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/23/2021] [Accepted: 03/29/2021] [Indexed: 12/03/2022] Open
Abstract
Epigenetic modifications have emerged as critical regulators of virulence genes and stage-specific gene expression in Plasmodium falciparum. However, the specific roles of histone core epigenetic modifications in regulating the stage-specific gene expression are not well understood. In this study, we report an unconventional trimethylation at lysine 64 on histone 3 (H3K64me3) and characterize its functional relevance in P. falciparum. We show that PfSET4 and PfSET5 proteins of P. falciparum methylate H3K64 and that they prefer the nucleosome as a substrate over free histone 3 proteins. Structural analysis of PfSET5 revealed that it interacts with the nucleosome as a dimer. The H3K64me3 mark is dynamic, being enriched in the ring and trophozoite stages and drastically reduced in the schizont stages. Stage-specific global chromatin immunoprecipitation –sequencing analysis of the H3K64me3 mark revealed the selective enrichment of this methyl mark on the genes of exported family proteins in the ring and trophozoite stages and a significant reduction of the same in the schizont stages. Collectively, our data identify a novel epigenetic mark that is associated with the subset of genes encoding for exported proteins, which may regulate their expression in different stages of P. falciparum.
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Affiliation(s)
- C A Jabeena
- Pathogen Biology Group, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, Kerala, India; Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | - Gayathri Govindaraju
- Pathogen Biology Group, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, Kerala, India; Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | - Mukul Rawat
- Department of Biology, Indian Institute of Science Education and Research, Pune, Maharashtra, India
| | - Soundhararajan Gopi
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India
| | - Devadathan Valiyamangalath Sethumadhavan
- Pathogen Biology Group, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, Kerala, India; Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | - Abdul Jaleel
- Cardiovascular Disease Biology, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, Kerala, India
| | - Dhakshmi Sasankan
- Pathogen Biology Group, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, Kerala, India
| | - Krishanpal Karmodiya
- Department of Biology, Indian Institute of Science Education and Research, Pune, Maharashtra, India
| | - Arumugam Rajavelu
- Pathogen Biology Group, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, Kerala, India.
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Thomas JM, Sasankan D, Surendran S, Abraham M, Rajavelu A, Kartha CC. Aberrant regulation of retinoic acid signaling genes in cerebral arterio venous malformation nidus and neighboring astrocytes. J Neuroinflammation 2021; 18:61. [PMID: 33648532 PMCID: PMC7923665 DOI: 10.1186/s12974-021-02094-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 01/29/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cerebral arterio venous malformations (AVM) are a major causal factor for intracranial hemorrhage, which result in permanent disability or death. The molecular mechanisms of AVM are complex, and their pathogenesis remains an enigma. Current research on cerebral AVM is focused on characterizing the molecular features of AVM nidus to elucidate the aberrant signaling pathways. The initial stimuli that lead to the development of AVM nidus structures between a dilated artery and a vein are however not known. METHODS In order to understand the molecular basis of development of cerebral AVM, we used in-depth RNA sequencing with the total RNA isolated from cerebral AVM nidus. Immunoblot and qRT-PCR assays were used to study the differential gene expression in AVM nidus, and immunofluorescence staining was used to study the expression pattern of aberrant proteins in AVM nidus and control tissues. Immunohistochemistry was used to study the expression pattern of aberrant proteins in AVM nidus and control tissues. RESULTS The transcriptome study has identified 38 differentially expressed genes in cerebral AVM nidus, of which 35 genes were upregulated and 3 genes were downregulated. A final modular analysis identified an upregulation of ALDH1A2, a key rate-limiting enzyme of retinoic acid signaling pathway. Further analysis revealed that CYR61, a regulator of angiogenesis, and the target gene for retinoic acid signaling is upregulated in AVM nidus. We observed that astrocytes associated with AVM nidus are abnormal with increased expression of GFAP and Vimentin. Triple immunofluorescence staining of the AVM nidus revealed that CYR61 was also overexpressed in the abnormal astrocytes associated with AVM tissue. CONCLUSION Using high-throughput RNA sequencing analysis and immunostaining, we report deregulated expression of retinoic acid signaling genes in AVM nidus and its associated astrocytes and speculate that this might trigger the abnormal angiogenesis and the development of cerebral AVM in humans.
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Affiliation(s)
- Jaya Mary Thomas
- Cardio Vascular Diseases and Diabetes Biology, Rajiv Gandhi Centre for Biotechnology, Poojapura, Thycaud, Thiruvananthapuram, Kerala, 695014, India
- Manipal Academy of Higher Education, Madhav Nagar, Manipal, Karnataka, 576104, India
| | - Dhakshmi Sasankan
- Cardio Vascular Diseases and Diabetes Biology, Rajiv Gandhi Centre for Biotechnology, Poojapura, Thycaud, Thiruvananthapuram, Kerala, 695014, India
| | - Sumi Surendran
- Cardio Vascular Diseases and Diabetes Biology, Rajiv Gandhi Centre for Biotechnology, Poojapura, Thycaud, Thiruvananthapuram, Kerala, 695014, India
| | - Mathew Abraham
- Department of Neurosurgery, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala, 695011, India
| | - Arumugam Rajavelu
- Pathogen Biology, Rajiv Gandhi Centre for Biotechnology, Poojapura, Thycaud, Thiruvananthapuram, Kerala, 695014, India.
| | - Chandrasekharan C Kartha
- Cardio Vascular Diseases and Diabetes Biology, Rajiv Gandhi Centre for Biotechnology, Poojapura, Thycaud, Thiruvananthapuram, Kerala, 695014, India.
- Society for Continuing Medical Education and Research, Kerala Institute of Medical Sciences, Thiruvananthapuram, Kerala, 695029, India.
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Thomas JM, Surendran S, Abraham M, Sasankan D, Bhaadri S, Rajavelu A, Kartha CC. Gene expression analysis of nidus of cerebral arteriovenous malformations reveals vascular structures with deficient differentiation and maturation. PLoS One 2018; 13:e0198617. [PMID: 29897969 PMCID: PMC5999265 DOI: 10.1371/journal.pone.0198617] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Accepted: 05/22/2018] [Indexed: 12/19/2022] Open
Abstract
Objective Arteriovenous malformations (AVMs) are characterised by tangles of dysplastic blood vessels which shunt blood from arteries to veins with no intervening capillary bed. It is not known at what stage of development and differentiation, AVM vessels became aberrant. To address this, we have analysed the expression of vascular differentiation, vascular maturation and brain capillary specific genes in AVM nidus. Methodology We performed immunohistochemistry and western blot analysis of vascular differentiation (HEY2, DLL4, EFNB2, and COUP-TFII), vascular maturation (ENG and KLF2) and brain capillary specific genes (GGTP and GLUT1) on ten surgically excised human brain AVMs and ten normal human brain tissues. Results Immunohistochemical analysis revealed that AVM vessels co-express both artery and vein differentiation genes. H-score analysis revealed that there is statistically significant (P < 0.0001) increase in expression of these proteins in AVM vessels compared to control vessels. These findings were further confirmed by western blot analysis and found to be statistically significant (P < 0.0001 and P < 0.001) for all proteins except Hey2. Both immunostaining and western blot analysis revealed that AVM vessels express GGTP and GLUT1, markers specific to brain capillaries. Immunofluorescent staining demonstrated that expression of KLF2, a vascular maturation marker is significantly (P <0.001) decreased in AVM vessels and was further confirmed by western blot analysis (P < 0.001). Immunohistochemical and western blot analysis demonstrated that another vascular maturation protein Endoglin had high expression in AVM vessels compared to control vessels. The results were found to be statistically significant (P < 0.0001). Summary Our findings suggest that vascular structures of AVMs co-express markers specific for arteries, veins and capillaries. We conclude that AVM nidus constitutes of aberrant vessels which are not terminally differentiated and inadequately matured.
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Affiliation(s)
- Jaya Mary Thomas
- Cardio Vascular Diseases and Diabetes Biology Program, Rajiv Gandhi Centre for Biotechnology, Poojapura, Thycaud, Thiruvananthapuram, Kerala, India
- Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Sumi Surendran
- Cardio Vascular Diseases and Diabetes Biology Program, Rajiv Gandhi Centre for Biotechnology, Poojapura, Thycaud, Thiruvananthapuram, Kerala, India
| | - Mathew Abraham
- Department of Neurosurgery, Sree Chitra Tirunal Institute for Medical Sciences & Technology, Thiruvananthapuram, Kerala, India
| | - Dhakshmi Sasankan
- Cardio Vascular Diseases and Diabetes Biology Program, Rajiv Gandhi Centre for Biotechnology, Poojapura, Thycaud, Thiruvananthapuram, Kerala, India
| | - Sridutt Bhaadri
- Department of Neurosurgery, Sree Chitra Tirunal Institute for Medical Sciences & Technology, Thiruvananthapuram, Kerala, India
| | - Arumugam Rajavelu
- Cardio Vascular Diseases and Diabetes Biology Program, Rajiv Gandhi Centre for Biotechnology, Poojapura, Thycaud, Thiruvananthapuram, Kerala, India
- Tropical Disease Biology Program, Rajiv Gandhi Centre for Biotechnology, Poojapura, Thycaud, Thiruvananthapuram, Kerala, India
- * E-mail: (AR); (CCK)
| | - Chandrasekharan C. Kartha
- Cardio Vascular Diseases and Diabetes Biology Program, Rajiv Gandhi Centre for Biotechnology, Poojapura, Thycaud, Thiruvananthapuram, Kerala, India
- * E-mail: (AR); (CCK)
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