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Rudrabhatla PK, Divya KP, Fasaludeen A, Menon RN, Cherian A, Urulangodi M, Sundaram S. Generalized Stiffness in Hereditary Hyperekplexia Responsive to Trihexyphenidyl: A Novel Finding. Clin Pediatr (Phila) 2024; 63:885-888. [PMID: 37899614 DOI: 10.1177/00099228231203300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/31/2023]
Affiliation(s)
- Pavan Kumar Rudrabhatla
- R Madhavan Nayar Centre for Comprehensive Epilepsy Care, Department of Neurology, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Trivandrum, India
| | - K P Divya
- Comprehensive Care Centre for Movement Disorders, Department of Neurology, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Trivandrum, India
| | - Alfiya Fasaludeen
- Pediatric Neurology and Neurodevelopmental Disorders, Department of Neurology, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Trivandrum, India
| | - Ramshekhar N Menon
- Pediatric Neurology and Neurodevelopmental Disorders, Department of Neurology, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Trivandrum, India
| | - Ajith Cherian
- R Madhavan Nayar Centre for Comprehensive Epilepsy Care, Department of Neurology, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Trivandrum, India
| | - Madhusoodanan Urulangodi
- Department of Biochemistry, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Trivandrum, India
| | - Soumya Sundaram
- Pediatric Neurology and Neurodevelopmental Disorders, Department of Neurology, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Trivandrum, India
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2
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Kishore A, Sturm M, Soman Pillai K, Hakkaart C, Kalikavil Puthanveedu D, Urulangodi M, Krishnan S, Ashok Kumar Sreelatha A, Rajan R, Pal PK, Yadav R, Sarma G, Casadei N, Gasser T, Bauer P, Riess O, Sharma M. Resequencing the complete SNCA locus in Indian patients with Parkinson's disease. NPJ Parkinsons Dis 2024; 10:85. [PMID: 38622158 PMCID: PMC11018851 DOI: 10.1038/s41531-024-00676-4] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 02/29/2024] [Indexed: 04/17/2024] Open
Abstract
The genetic loci implicated in familial Parkinson's disease (PD) have limited generalizability to the Indian PD population. We tested mutations and the frequency of known mutations in the SNCA gene in a PD cohort from India. We selected 298 PD cases and 301 age-matched controls for targeted resequencing (before QC), along with 363 PD genomes of Indian ancestry and 1029 publicly available whole genomes from India as healthy controls (IndiGenomes), to determine the frequency of monogenic SNCA mutations. The raw sequence reads were analyzed using an in-house analysis pipeline, allowing the detection of small variants and structural variants using Manta. The in-depth analysis of the SNCA locus did not identify missense or structural variants, including previously identified SNCA mutations, in the Indian population. The familial forms of SNCA gene variants do not play a major role in the Indian PD population and this warrants further research in the under-represented population.
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Affiliation(s)
- Asha Kishore
- Comprehensive Care Centre for Movement Disorders, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Kochi, Kerala, India
- Parkinson and Movement Disorder Centre, Centre for Excellence in Neurosciences, Aster Medcity, Kochi, Kerala, India
| | - Marc Sturm
- Institute for Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Kanchana Soman Pillai
- Parkinson and Movement Disorder Centre, Centre for Excellence in Neurosciences, Aster Medcity, Kochi, Kerala, India
| | - Christopher Hakkaart
- Institute for Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Divya Kalikavil Puthanveedu
- Comprehensive Care Centre for Movement Disorders, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Kochi, Kerala, India
| | - Madhusoodanan Urulangodi
- Comprehensive Care Centre for Movement Disorders, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Kochi, Kerala, India
| | - Syam Krishnan
- Comprehensive Care Centre for Movement Disorders, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Kochi, Kerala, India
| | - Ashwin Ashok Kumar Sreelatha
- Centre for Genetic Epidemiology, Institute for Clinical Epidemiology and Applied Biometry, University of Tübingen, Tübingen, Germany
| | - Roopa Rajan
- Department of Neurology, All India Institute for Medical Sciences, New Delhi, India
| | - Pramod Kumar Pal
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, Karnataka, India
| | - Ravi Yadav
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, Karnataka, India
| | - Gangadhara Sarma
- Comprehensive Care Centre for Movement Disorders, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Kochi, Kerala, India
| | - Nicolas Casadei
- Institute for Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Thomas Gasser
- Department for Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Peter Bauer
- Institute for Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- Centogene GmbH, Rostock, Germany
- University Medicine Rostock, Internal Medicine III, Hematology, Rostock, Germany
| | - Olaf Riess
- Institute for Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Manu Sharma
- Centre for Genetic Epidemiology, Institute for Clinical Epidemiology and Applied Biometry, University of Tübingen, Tübingen, Germany.
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Chandran D, Krishnan S, Urulangodi M, Gopala S. Exosomal microRNAs in Parkinson's disease: insights into biomarker potential and disease pathology. Neurol Sci 2024:10.1007/s10072-024-07439-2. [PMID: 38532190 DOI: 10.1007/s10072-024-07439-2] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 02/29/2024] [Indexed: 03/28/2024]
Abstract
Parkinson's disease (PD) is a prevalent neurodegenerative condition primarily affecting the elderly population. Despite its high incidence in aged individuals, there are no reliable blood-based biomarkers for clinical diagnosis of PD and early screening of susceptible individuals. Recent studies have revealed the significance of exosomes in mediating cell-to-cell communications by transferring bioactive molecules, such as proteins, nucleic acids (including miRNAs), lipids, and metabolites, between cells. Due to their ability to carry diverse molecular cargo and their involvement in various physiological and pathological processes, exosomes have gained significant attention as potential disease biomarkers. Notably, exosomes have the ability to cross the blood-brain barrier, and as a result, they can be found in circulating body fluids, including cerebrospinal fluid (CSF), serum, and plasma. Therefore, the identification of PD-specific exosomes in blood samples could be a promising avenue with biomarker potential for advancing clinical diagnosis and planning therapeutic strategies. This review highlights the current understanding of exosomal miRNAs in PD pathology, emphasising their potential for clinical utility as biomarkers even though several challenges may have to be overcome to precisely utilize exosomal miRNAs as biomarkers specific to PD.
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Affiliation(s)
- Deepthy Chandran
- Department of Biochemistry, Sree Chitra Tirunal Institute for Medical Sciences and Technology (SCTIMST), Medical College POST, Trivandrum, Kerala, 695011, India
| | - Syam Krishnan
- Department of Neurology, Sree Chitra Tirunal Institute for Medical Sciences and Technology (SCTIMST), Medical College POST, Trivandrum, Kerala, 695011, India
| | - Madhusoodanan Urulangodi
- Department of Biochemistry, Sree Chitra Tirunal Institute for Medical Sciences and Technology (SCTIMST), Medical College POST, Trivandrum, Kerala, 695011, India.
| | - Srinivas Gopala
- Department of Biochemistry, Sree Chitra Tirunal Institute for Medical Sciences and Technology (SCTIMST), Medical College POST, Trivandrum, Kerala, 695011, India.
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4
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Vasu MM, Koshy L, Ganapathi S, Jeemon P, Urulangodi M, Gopala S, Greeva P, Anitha A, Reethu S, Divya P, Shamla S, Sumitha K, Madhavan M, Vineeth CP, Kochumoni R, Harikrishnan S. Identification of novel endogenous control miRNAs in heart failure for normalization of qPCR data. Int J Biol Macromol 2024; 261:129714. [PMID: 38286377 DOI: 10.1016/j.ijbiomac.2024.129714] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 12/22/2023] [Accepted: 01/12/2024] [Indexed: 01/31/2024]
Abstract
MicroRNAs (miRNAs), a class of non-coding RNAs, are utilized as biomarkers for a wide range of disorders. Circulating miRNAs are proposed as potential markers in the clinical identification of heart failure (HF). However, identifying miRNA biomarkers in HF requires identification of robust endogenous control miRNAs for normalization in differential expression analysis. Hence, this study aimed to identify circulating miRNAs that can be utilized as endogenous controls in HF. We evaluated the expression of eight miRNAs, which were previously reported as endogenous controls in different pathological conditions. Total RNA, including miRNA, was extracted from the serum samples of 30 HF patients (15 HFrEF and 15 HFpEF) and their matched controls (n = 15). We used quantitative PCR to determine the miRNA expression. The stability of the selected endogenous miRNAs was assessed and compared using a standard set of criteria with the RefFinder software. Six of the eight miRNAs analyzed showed consistent expression among all sample groups. Stability analysis ranked hsa-let-7i-5p, hsa-miR-148b-3p, and hsa-miR-484 as the most stable miRNAs, indicating their potential as reliable endogenous controls.
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Affiliation(s)
- Mahesh Mundalil Vasu
- Centre for Advanced Research and Excellence in Heart Failure (CARE-HF), Sree Chitra Tirunal Institute for Medical Sciences and Technology (SCTIMST), Trivandrum 695011, Kerala, India
| | - Linda Koshy
- Centre for Advanced Research and Excellence in Heart Failure (CARE-HF), Sree Chitra Tirunal Institute for Medical Sciences and Technology (SCTIMST), Trivandrum 695011, Kerala, India
| | - Sanjay Ganapathi
- Centre for Advanced Research and Excellence in Heart Failure (CARE-HF), Sree Chitra Tirunal Institute for Medical Sciences and Technology (SCTIMST), Trivandrum 695011, Kerala, India; Department of Cardiology, Sree Chitra Tirunal Institute for Medical Sciences and Technology (SCTIMST), Trivandrum 695011, Kerala, India
| | - Panniyammakal Jeemon
- Centre for Advanced Research and Excellence in Heart Failure (CARE-HF), Sree Chitra Tirunal Institute for Medical Sciences and Technology (SCTIMST), Trivandrum 695011, Kerala, India; Achutha Menon Centre for Health Science Studies, Sree Chitra Tirunal Institute for Medical Sciences and Technology (SCTIMST), Trivandrum 695011, Kerala, India
| | - Madhusoodanan Urulangodi
- Department of Biochemistry, Sree Chitra Tirunal Institute for Medical Sciences and Technology (SCTIMST), Trivandrum 695011, Kerala, India
| | - Srinivas Gopala
- Department of Biochemistry, Sree Chitra Tirunal Institute for Medical Sciences and Technology (SCTIMST), Trivandrum 695011, Kerala, India
| | - Philip Greeva
- Centre for Advanced Research and Excellence in Heart Failure (CARE-HF), Sree Chitra Tirunal Institute for Medical Sciences and Technology (SCTIMST), Trivandrum 695011, Kerala, India
| | - Ayyappan Anitha
- Department of Neurogenetics, Institute for Communicative and Cognitive Neurosciences (ICCONS), Kavalappara, Shoranur, Palakkad 679 523, Kerala, India
| | - Salim Reethu
- Centre for Advanced Research and Excellence in Heart Failure (CARE-HF), Sree Chitra Tirunal Institute for Medical Sciences and Technology (SCTIMST), Trivandrum 695011, Kerala, India
| | - Prasad Divya
- Centre for Advanced Research and Excellence in Heart Failure (CARE-HF), Sree Chitra Tirunal Institute for Medical Sciences and Technology (SCTIMST), Trivandrum 695011, Kerala, India
| | - Shajahan Shamla
- Centre for Advanced Research and Excellence in Heart Failure (CARE-HF), Sree Chitra Tirunal Institute for Medical Sciences and Technology (SCTIMST), Trivandrum 695011, Kerala, India
| | - Kumar Sumitha
- Department of Cardiology, Sree Chitra Tirunal Institute for Medical Sciences and Technology (SCTIMST), Trivandrum 695011, Kerala, India
| | - Madhuma Madhavan
- Centre for Advanced Research and Excellence in Heart Failure (CARE-HF), Sree Chitra Tirunal Institute for Medical Sciences and Technology (SCTIMST), Trivandrum 695011, Kerala, India
| | - C Purushothaman Vineeth
- Department of Cardiology, Sree Chitra Tirunal Institute for Medical Sciences and Technology (SCTIMST), Trivandrum 695011, Kerala, India
| | - Rajamoni Kochumoni
- Department of Cardiology, Sree Chitra Tirunal Institute for Medical Sciences and Technology (SCTIMST), Trivandrum 695011, Kerala, India
| | - Sivadasanpillai Harikrishnan
- Centre for Advanced Research and Excellence in Heart Failure (CARE-HF), Sree Chitra Tirunal Institute for Medical Sciences and Technology (SCTIMST), Trivandrum 695011, Kerala, India; Department of Cardiology, Sree Chitra Tirunal Institute for Medical Sciences and Technology (SCTIMST), Trivandrum 695011, Kerala, India.
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5
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Vidyadharan P, Ckv S, Sethumadhavan A, Gopala S, T Raghavan C, Urulangodi M. Functional assessment of DNA extraction methods from frozen human blood samples for Sanger sequencing analysis. Cell Mol Biol (Noisy-le-grand) 2023; 69:25-33. [PMID: 37715434 DOI: 10.14715/cmb/2023.69.8.4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Indexed: 09/17/2023]
Abstract
The quality of input DNA is crucial for obtaining significant inferences from molecular techniques like Sanger sequencing and Next Generation Sequencing experiments. Many of the extraction methods are suitable for retrieving quality DNA from fresh blood and tissue samples, regardless of the isolation principle. However, while isolating DNA from frozen blood samples, processed tissue samples or low-quality samples, careful selection of suitable extraction methods is extremely important. Moreover, there is no standard protocol recommended for genomic DNA extraction from stored blood samples, particularly those stored in a Biobank, for applications like Sanger sequencing. Consequently, we have systematically compared different commercial DNA isolation kits with a modified manual extraction method for blood samples frozen for up to three years and assessed their quality, yield and suitability for PCR, Real-Time PCR and Sanger sequencing. The manual DNA extraction method was improved by incorporating a few modifications: a lower NaCl concentration was used for precipitating DNA and excluded the use of phenol. The modified method provided the maximum DNA yield from stored blood. Although all the methods tested were suitable for recovering DNA from stored blood, the modified method described here may be preferred for large-scale applications as it provides cost-effective ways to obtain large quantities of quality DNA. Most importantly, the DNA isolated by the modified method appears to be more stable in long-term storage at -80°C.
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Affiliation(s)
- Pravi Vidyadharan
- Department of Neurology, Sree Chitra Tirunal Institute for Medical Sciences and Technology (SCTIMST), Medical College POST, Trivandrum, Kerala, India-695011.
| | - Santhi Ckv
- Department of Neurology, Sree Chitra Tirunal Institute for Medical Sciences and Technology (SCTIMST), Medical College POST, Trivandrum, Kerala, India-695011.
| | - Anjali Sethumadhavan
- Molecular Genetics Unit, Sree Chitra Tirunal Institute for Medical Sciences and Technology (SCTIMST), Medical College POST, Trivandrum, Kerala, India-695011.
| | - Srinivas Gopala
- Molecular Genetics Unit, Sree Chitra Tirunal Institute for Medical Sciences and Technology (SCTIMST), Medical College POST, Trivandrum, Kerala, India-695011.
| | - Cibin T Raghavan
- Molecular Genetics Unit, Sree Chitra Tirunal Institute for Medical Sciences and Technology (SCTIMST), Medical College POST, Trivandrum, Kerala, India-695011.
| | - Madhusoodanan Urulangodi
- Molecular Genetics Unit, Sree Chitra Tirunal Institute for Medical Sciences and Technology (SCTIMST), Medical College POST, Trivandrum, Kerala, India-695011.
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6
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Vijayaraghavan A, Urulangodi M, Ajit Valaparambil K, Sundaram S, Krishnan S. Movement Disorders in GRIA2-Related Disorder - Expanding the Genetic Spectrum of Developmental Dyskinetic Encephalopathy. Mov Disord Clin Pract 2023; 10:1222-1224. [PMID: 37635778 PMCID: PMC10450229 DOI: 10.1002/mdc3.13797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/28/2023] [Accepted: 05/08/2023] [Indexed: 08/29/2023] Open
Affiliation(s)
- Asish Vijayaraghavan
- Comprehensive Care Centre for Movement Disorders, Department of NeurologySree Chitra Tirunal Institute for Medical Sciences and TechnologyTrivandrumIndia
| | - Madhusoodanan Urulangodi
- Department of BiochemistrySree Chitra Tirunal Institute for Medical Sciences and TechnologyTrivandrumIndia
| | - Karthika Ajit Valaparambil
- Pediatric Neurology and Neurodevelopmental Disorders, Department of NeurologySree Chitra Tirunal Institute for Medical Sciences and TechnologyTrivandrumIndia
| | - Soumya Sundaram
- Pediatric Neurology and Neurodevelopmental Disorders, Department of NeurologySree Chitra Tirunal Institute for Medical Sciences and TechnologyTrivandrumIndia
| | - Syam Krishnan
- Comprehensive Care Centre for Movement Disorders, Department of NeurologySree Chitra Tirunal Institute for Medical Sciences and TechnologyTrivandrumIndia
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7
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Alfiya F, Jose M, Chandrasekharan SV, Sundaram S, Urulangodi M, Thomas B, Radhakrishnan A, Banerjee M, Menon RN. C12orf57 pathogenic variants: a unique cause of developmental encephalopathy in a south Indian child. J Genet 2022; 101:30. [PMID: 35791610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Open reading frame variants which lack stop codons such as C12orf57 variants are known to cause Temtamy syndrome, an extremely rare disorder characterized by intellectual disability, seizures, facial dysmorphism and agenesis of corpus callosum. C12orf57 was initially reported to be required for human corpus callosum development. We report the first child who is of Indian origin with developmental and epileptic encephalopathy (DEE) with a unique phenotypic evolution as focal onset reflex seizures. We performed whole exome sequencing of genomic DNA isolated from peripheral blood samples of proband and his parents. Two pathogenic compound heterozygous variants, a start loss variant (Chr12:7053285:c.1A>G) and a premature stop gain variant (Chr12:7053327:c.43C>T), involving the C12orf57 gene were identified in the proband. Our case report which details genotyping in this rare syndromic developmental encephalopathy, with no prior cases reported from India, expands the ethnic spectrum of patients.
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Affiliation(s)
- F Alfiya
- Department of Neurology, Sree Chitra Tirunal Institute for Medical Sciences and Technology (SCTIMST), Thiruvananthapuram 695 011, India.
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Koshy L, Jeemon P, Ganapathi S, Madhavan M, Urulangodi M, Sharma M, Harikrishnan S. Association of South Asian-specific MYBPC3Δ deletion polymorphism and cardiomyopathy: A systematic review and meta-analysis. Meta Gene 2021. [DOI: 10.1016/j.mgene.2021.100883] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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Bhavya B, Easwer HV, Vilanilam GC, Anand CR, Sreelakshmi K, Urulangodi M, Rajalakshmi P, Neena I, Padmakrishnan CJ, Menon GR, Krishnakumar K, Deepti AN, Gopala S. Corrigendum to "MutT Homolog1 has multifaceted role in glioma and is under the apparent orchestration by Hypoxia Inducible factor1 alpha" [Life Sci. Available online 29 October 2020, 118673]. Life Sci 2020; 265:118810. [PMID: 33303203 DOI: 10.1016/j.lfs.2020.118810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Bharathan Bhavya
- Department of Biochemistry, Sree Chitra Tirunal Institute for Medical Sciences & Technology, Thiruvananthapuram 695011, Kerala, India
| | - H V Easwer
- Department of Neurosurgery, Sree Chitra Tirunal Institute for Medical Sciences & Technology, Thiruvananthapuram 695011, Kerala, India
| | - G C Vilanilam
- Department of Neurosurgery, Sree Chitra Tirunal Institute for Medical Sciences & Technology, Thiruvananthapuram 695011, Kerala, India
| | - C R Anand
- Department of Biochemistry, Sree Chitra Tirunal Institute for Medical Sciences & Technology, Thiruvananthapuram 695011, Kerala, India
| | - K Sreelakshmi
- Department of Biochemistry, Sree Chitra Tirunal Institute for Medical Sciences & Technology, Thiruvananthapuram 695011, Kerala, India
| | - Madhusoodanan Urulangodi
- Department of Biochemistry, Sree Chitra Tirunal Institute for Medical Sciences & Technology, Thiruvananthapuram 695011, Kerala, India
| | - P Rajalakshmi
- Department of Pathology, Sree Chitra Tirunal Institute for Medical Sciences & Technology, Thiruvananthapuram 695011, Kerala, India
| | - Issac Neena
- Department of Pathology, Sree Chitra Tirunal Institute for Medical Sciences & Technology, Thiruvananthapuram 695011, Kerala, India
| | - C J Padmakrishnan
- Department of Biochemistry, Sree Chitra Tirunal Institute for Medical Sciences & Technology, Thiruvananthapuram 695011, Kerala, India
| | - Girish R Menon
- Department of Neurosurgery, Sree Chitra Tirunal Institute for Medical Sciences & Technology, Thiruvananthapuram 695011, Kerala, India
| | - K Krishnakumar
- Department of Neurosurgery, Sree Chitra Tirunal Institute for Medical Sciences & Technology, Thiruvananthapuram 695011, Kerala, India
| | - A N Deepti
- Department of Pathology, Sree Chitra Tirunal Institute for Medical Sciences & Technology, Thiruvananthapuram 695011, Kerala, India
| | - Srinivas Gopala
- Department of Biochemistry, Sree Chitra Tirunal Institute for Medical Sciences & Technology, Thiruvananthapuram 695011, Kerala, India.
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10
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Bhavya B, Easwer HV, Vilanilam GC, Anand CR, Sreelakshmi K, Urulangodi M, Rajalakshmi P, Neena I, Padmakrishnan CJ, Menon GR, Krishnakumar K, Deepti AN, Gopala S. MutT Homolog1 has multifaceted role in glioma and is under the apparent orchestration by Hypoxia Inducible factor1 alpha. Life Sci 2020; 264:118673. [PMID: 33130078 DOI: 10.1016/j.lfs.2020.118673] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 10/15/2020] [Accepted: 10/22/2020] [Indexed: 11/17/2022]
Abstract
AIMS The study focused on the expression and role of a recent potential cancer therapeutic target protein, MutT Homolog1 (MTH1). MTH1 gets activated in an increased reactive oxygen species (ROS) environment and removes the oxidized nucleotides from the cell. The study aimed to check the role of MTH1 in DNA damage and apoptosis, migration and angiogenesis and also to examine its regulation in glioma. MAIN METHODS The experiments were carried out in human glioma tissue samples and brain tissues of epilepsy patients (non-tumor control). We used two human glioblastomas cell lines, U87MG and U251MG cells. In order to study the role of MTH1 in glioma and to analyze the relation of MTH1 with Hif1α, we have used MTH1 siRNA and Hif1α siRNA respectively. KEY FINDINGS We found an increased expression of MTH1 in glioma tissues compared to the non-tumor brain tissues. Correlation analysis revealed that those samples showing reduced expression of MTH1 also had high levels of DNA damage and apoptotic markers, while diminished expression of angiogenesis regulators and levels of migration. MTH1 knockdown in vitro by siRNA in tumor cell lines corroborates the above observation. This justifies the emergence of MTH1 inhibitors as potential first-in-class drugs. Mechanistically, our observations suggest that Hif1α may modulate MTH1 expression. SIGNIFICANCE We found elevated MTH1 expression in glioma irrespective of their grades, while its inhibition affects multiple tumor progression pathways, and that targeting Hif1α could simulate the same.
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Affiliation(s)
- Bharathan Bhavya
- Department of Biochemistry, Sree Chitra Tirunal Institute for Medical Sciences & Technology, Thiruvananthapuram 695011, Kerala, India
| | - H V Easwer
- Department of Neurosurgery, Sree Chitra Tirunal Institute for Medical Sciences & Technology, Thiruvananthapuram 695011, Kerala, India
| | - G C Vilanilam
- Department of Neurosurgery, Sree Chitra Tirunal Institute for Medical Sciences & Technology, Thiruvananthapuram 695011, Kerala, India
| | - C R Anand
- Department of Biochemistry, Sree Chitra Tirunal Institute for Medical Sciences & Technology, Thiruvananthapuram 695011, Kerala, India
| | - K Sreelakshmi
- Department of Biochemistry, Sree Chitra Tirunal Institute for Medical Sciences & Technology, Thiruvananthapuram 695011, Kerala, India
| | - Madhusoodanan Urulangodi
- Department of Biochemistry, Sree Chitra Tirunal Institute for Medical Sciences & Technology, Thiruvananthapuram 695011, Kerala, India
| | - P Rajalakshmi
- Department of Pathology, Sree Chitra Tirunal Institute for Medical Sciences & Technology, Thiruvananthapuram 695011, Kerala, India
| | - Issac Neena
- Department of Pathology, Sree Chitra Tirunal Institute for Medical Sciences & Technology, Thiruvananthapuram 695011, Kerala, India
| | - C J Padmakrishnan
- Department of Biochemistry, Sree Chitra Tirunal Institute for Medical Sciences & Technology, Thiruvananthapuram 695011, Kerala, India
| | - Girish R Menon
- Department of Neurosurgery, Sree Chitra Tirunal Institute for Medical Sciences & Technology, Thiruvananthapuram 695011, Kerala, India
| | - K Krishnakumar
- Department of Neurosurgery, Sree Chitra Tirunal Institute for Medical Sciences & Technology, Thiruvananthapuram 695011, Kerala, India
| | - A N Deepti
- Department of Pathology, Sree Chitra Tirunal Institute for Medical Sciences & Technology, Thiruvananthapuram 695011, Kerala, India
| | - Srinivas Gopala
- Department of Biochemistry, Sree Chitra Tirunal Institute for Medical Sciences & Technology, Thiruvananthapuram 695011, Kerala, India.
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Urulangodi M, Mohanty A. Correction to: DNA damage response and repair pathway modulation by non-histone protein methylation: implications in neurodegeneration. J Cell Commun Signal 2020; 15:151. [PMID: 32990932 DOI: 10.1007/s12079-020-00587-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
- Madhusoodanan Urulangodi
- Department of Biochemistry, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala, PIN-695011, India.
| | - Abhishek Mohanty
- Rajiv Gandhi Cancer Institute and Research Centre, New Delhi, PIN-110085, India.
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Urulangodi M, Mohanty A. DNA damage response and repair pathway modulation by non-histone protein methylation: implications in neurodegeneration. J Cell Commun Signal 2019; 14:31-45. [PMID: 31749026 DOI: 10.1007/s12079-019-00538-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 11/14/2019] [Indexed: 12/11/2022] Open
Abstract
Protein post-translational modifications (PTMs) have emerged to be combinatorial, essential mechanisms used by eukaryotic cells to regulate local chromatin structure, diversify and extend their protein functions and dynamically coordinate complex intracellular signalling processes. Most common types of PTMs include enzymatic addition of small chemical groups resulting in phosphorylation, glycosylation, poly(ADP-ribosyl)ation, nitrosylation, methylation, acetylation or covalent attachment of complete proteins such as ubiquitin and SUMO. Protein arginine methyltransferases (PRMTs) and protein lysine methyltransferases (PKMTs) enzymes catalyse the methylation of arginine and lysine residues in target proteins, respectively. Rapid progress in quantitative proteomic analysis and functional assays have not only documented the methylation of histone proteins post-translationally but also identified their occurrence in non-histone proteins which dynamically regulate a plethora of cellular functions including DNA damage response and repair. Emerging advances have now revealed the role of both histone and non-histone methylations in the regulating the DNA damage response (DDR) proteins, thereby modulating the DNA repair pathways both in proliferating and post-mitotic neuronal cells. Defects in many cellular DNA repair processes have been found primarily manifested in neuronal tissues. Moreover, fine tuning of the dynamicity of methylation of non-histone proteins as well as the perturbations in this dynamic methylation processes have recently been implicated in neuronal genomic stability maintenance. Considering the impact of methylation on chromatin associated pathways, in this review we attempt to link the evidences in non-histone protein methylation and DDR with neurodegenerative research.
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Affiliation(s)
- Madhusoodanan Urulangodi
- Department of Biochemistry, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala, PIN-695011, India.
| | - Abhishek Mohanty
- Rajiv Gandhi Cancer Institute and Research Centre, New Delhi, PIN-110085, India.
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Sebesta M, Urulangodi M, Stefanovie B, Szakal B, Pacesa M, Lisby M, Branzei D, Krejci L. Esc2 promotes Mus81 complex-activity via its SUMO-like and DNA binding domains. Nucleic Acids Res 2016; 45:215-230. [PMID: 27694623 PMCID: PMC5224511 DOI: 10.1093/nar/gkw882] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Revised: 08/30/2016] [Accepted: 09/22/2016] [Indexed: 01/17/2023] Open
Abstract
Replication across damaged DNA templates is accompanied by transient formation of sister chromatid junctions (SCJs). Cells lacking Esc2, an adaptor protein containing no known enzymatic domains, are defective in the metabolism of these SCJs. However, how Esc2 is involved in the metabolism of SCJs remains elusive. Here we show interaction between Esc2 and a structure-specific endonuclease Mus81-Mms4 (the Mus81 complex), their involvement in the metabolism of SCJs, and the effects Esc2 has on the enzymatic activity of the Mus81 complex. We found that Esc2 specifically interacts with the Mus81 complex via its SUMO-like domains, stimulates enzymatic activity of the Mus81 complex in vitro, and is involved in the Mus81 complex-dependent resolution of SCJs in vivo. Collectively, our data point to the possibility that the involvement of Esc2 in the metabolism of SCJs is, in part, via modulation of the activity of the Mus81 complex.
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Affiliation(s)
- Marek Sebesta
- National Centre for Biomolecular Research, Masaryk University, Kamenice 5/A4, CZ-62500 Brno, Czech Republic.,Department of Biology, Masaryk University, Kamenice 5/A7, CZ-62500 Brno, Czech Republic.,IFOM, the FIRC Institute of Molecular Oncology, Via Adamello 16, IT-20139 Milan, Italy
| | | | - Barbora Stefanovie
- National Centre for Biomolecular Research, Masaryk University, Kamenice 5/A4, CZ-62500 Brno, Czech Republic.,Department of Biology, Masaryk University, Kamenice 5/A7, CZ-62500 Brno, Czech Republic.,International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St. Anne's University Hospital Brno, Pekarska 53, CZ-656 91 Brno, Czech Republic
| | - Barnabas Szakal
- IFOM, the FIRC Institute of Molecular Oncology, Via Adamello 16, IT-20139 Milan, Italy
| | - Martin Pacesa
- National Centre for Biomolecular Research, Masaryk University, Kamenice 5/A4, CZ-62500 Brno, Czech Republic
| | - Michael Lisby
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Dana Branzei
- IFOM, the FIRC Institute of Molecular Oncology, Via Adamello 16, IT-20139 Milan, Italy
| | - Lumir Krejci
- National Centre for Biomolecular Research, Masaryk University, Kamenice 5/A4, CZ-62500 Brno, Czech Republic .,Department of Biology, Masaryk University, Kamenice 5/A7, CZ-62500 Brno, Czech Republic.,International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St. Anne's University Hospital Brno, Pekarska 53, CZ-656 91 Brno, Czech Republic
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Urulangodi M, Dhanaraju R, Gupta K, Roy RP, Bujnicki JM, Rao DN. Asymmetric DNA methylation by dimeric EcoP15I DNA methyltransferase. Biochimie 2016; 128-129:70-82. [PMID: 27422119 DOI: 10.1016/j.biochi.2016.07.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 07/11/2016] [Indexed: 11/16/2022]
Abstract
EcoP15I DNA methyltransferase (M.EcoP15I) recognizes short asymmetric sequence, 5'-CAGCAG-3', and methylates the second adenine only on one strand of the double-stranded DNA (dsDNA). In vivo, this methylation is sufficient to protect the host DNA from cleavage by the cognate restriction endonuclease, R.EcoP15I, because of the stringent cleavage specificity requirements. Biochemical and structural characterization support the notion that purified M.EcoP15I exists and functions as dimer. However, the exact role of dimerization in M.EcoP15I reaction mechanism remains elusive. Here we engineered M.EcoP15I to a stable monomeric form and studied the role of dimerization in enzyme catalyzed methylation reaction. While the monomeric form binds single-stranded DNA (ssDNA) containing the recognition sequence it is unable to methylate it. Further we show that, while the monomeric form has AdoMet binding and Mg(2+) binding motifs intact, optimal dsDNA binding required for methylation is dependent on dimerization. Together, our biochemical data supports a unique subunit organization for M.EcoP15I to catalyze the methylation reaction.
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Affiliation(s)
| | - Rajkumar Dhanaraju
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Kanchan Gupta
- National Institute of Immunology, New Delhi 110 067, India
| | - Rajendra P Roy
- National Institute of Immunology, New Delhi 110 067, India
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, PL-02-109 Warsaw, Poland
| | - Desirazu N Rao
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India.
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Urulangodi M, Sebesta M, Menolfi D, Szakal B, Sollier J, Sisakova A, Krejci L, Branzei D. Local regulation of the Srs2 helicase by the SUMO-like domain protein Esc2 promotes recombination at sites of stalled replication. Genes Dev 2016; 29:2067-80. [PMID: 26443850 PMCID: PMC4604347 DOI: 10.1101/gad.265629.115] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [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] [Indexed: 01/16/2023]
Abstract
In this study, Urulangodi et al. demonstrate that a SUMO-mediated regulatory mechanism enables recombination-mediated DNA damage tolerance (DDT) specifically at sites of compromised replication forks. By using a combination of genetic, biochemical, and molecular approaches, they identified a SUMO-like domain (SLD)-containing protein, Esc2, that allows optimal recruitment of the Rad51 recombinase at sites of perturbed replication, thus advancing our understanding of DDT and the pathways that support genome integrity. Accurate completion of replication relies on the ability of cells to activate error-free recombination-mediated DNA damage bypass at sites of perturbed replication. However, as anti-recombinase activities are also recruited to replication forks, how recombination-mediated damage bypass is enabled at replication stress sites remained puzzling. Here we uncovered that the conserved SUMO-like domain-containing Saccharomyces cerevisiae protein Esc2 facilitates recombination-mediated DNA damage tolerance by allowing optimal recruitment of the Rad51 recombinase specifically at sites of perturbed replication. Mechanistically, Esc2 binds stalled replication forks and counteracts the anti-recombinase Srs2 helicase via a two-faceted mechanism involving chromatin recruitment and turnover of Srs2. Importantly, point mutations in the SUMO-like domains of Esc2 that reduce its interaction with Srs2 cause suboptimal levels of Rad51 recruitment at damaged replication forks. In conclusion, our results reveal how recombination-mediated DNA damage tolerance is locally enabled at sites of replication stress and globally prevented at undamaged replicating chromosomes.
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Affiliation(s)
- Madhusoodanan Urulangodi
- FIRC (Fondazione Italiana per la Ricerca sul Cancro) Institute of Molecular Oncology (IFOM), 20139 Milan, Italy
| | - Marek Sebesta
- FIRC (Fondazione Italiana per la Ricerca sul Cancro) Institute of Molecular Oncology (IFOM), 20139 Milan, Italy; National Centre for Biomolecular Research, Masaryk University, CZ-62500 Brno, Czech Republic
| | - Demis Menolfi
- FIRC (Fondazione Italiana per la Ricerca sul Cancro) Institute of Molecular Oncology (IFOM), 20139 Milan, Italy
| | - Barnabas Szakal
- FIRC (Fondazione Italiana per la Ricerca sul Cancro) Institute of Molecular Oncology (IFOM), 20139 Milan, Italy
| | - Julie Sollier
- FIRC (Fondazione Italiana per la Ricerca sul Cancro) Institute of Molecular Oncology (IFOM), 20139 Milan, Italy
| | - Alexandra Sisakova
- Department of Biology, Masaryk University, CZ-62500 Brno, Czech Republic; International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St. Anne's University Hospital Brno, CZ-656 91 Brno, Czech Republic
| | - Lumir Krejci
- National Centre for Biomolecular Research, Masaryk University, CZ-62500 Brno, Czech Republic; Department of Biology, Masaryk University, CZ-62500 Brno, Czech Republic; International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St. Anne's University Hospital Brno, CZ-656 91 Brno, Czech Republic
| | - Dana Branzei
- FIRC (Fondazione Italiana per la Ricerca sul Cancro) Institute of Molecular Oncology (IFOM), 20139 Milan, Italy
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Affiliation(s)
| | - Barnabas Szakal
- a IFOM, the FIRC Institute of Molecular Oncology , Milan , Italy
| | - Dana Branzei
- a IFOM, the FIRC Institute of Molecular Oncology , Milan , Italy
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Gonzalez-Huici V, Szakal B, Urulangodi M, Psakhye I, Castellucci F, Menolfi D, Rajakumara E, Fumasoni M, Bermejo R, Jentsch S, Branzei D. DNA bending facilitates the error-free DNA damage tolerance pathway and upholds genome integrity. EMBO J 2014; 33:327-40. [PMID: 24473148 PMCID: PMC3983681 DOI: 10.1002/embj.201387425] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
DNA replication is sensitive to damage in the template. To bypass lesions and complete replication, cells activate recombination-mediated (error-free) and translesion synthesis-mediated (error-prone) DNA damage tolerance pathways. Crucial for error-free DNA damage tolerance is template switching, which depends on the formation and resolution of damage-bypass intermediates consisting of sister chromatid junctions. Here we show that a chromatin architectural pathway involving the high mobility group box protein Hmo1 channels replication-associated lesions into the error-free DNA damage tolerance pathway mediated by Rad5 and PCNA polyubiquitylation, while preventing mutagenic bypass and toxic recombination. In the process of template switching, Hmo1 also promotes sister chromatid junction formation predominantly during replication. Its C-terminal tail, implicated in chromatin bending, facilitates the formation of catenations/hemicatenations and mediates the roles of Hmo1 in DNA damage tolerance pathway choice and sister chromatid junction formation. Together, the results suggest that replication-associated topological changes involving the molecular DNA bender, Hmo1, set the stage for dedicated repair reactions that limit errors during replication and impact on genome stability.
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