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Kader MA, Devarajan B, Vijayan S, Ramakrishnan R, Sundaresan P, Uduman MS, Krishnadas SR, Kuppamuthu D. Myocilin Mutation N480K Leads to Early Onset Juvenile and Adult-onset Primary Open Angle Glaucoma in a Six Generation Family. J Glaucoma 2024; 33:218-224. [PMID: 37670504 DOI: 10.1097/ijg.0000000000002286] [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: 05/25/2023] [Accepted: 07/29/2023] [Indexed: 09/07/2023]
Abstract
PRCIS A pathogenic autosomal dominant MYOC mutation N480K detected in 6 generations of an Indian family is primarily responsible for juvenile open angle glaucoma (JOAG) and adult-onset primary open angle glaucoma (POAG), emphasizing the importance of screening this mutation at a younger age. PURPOSE To screen myocilin mutations in a large South Indian family with early-onset JOAG and adult-onset POAG. METHODS In a large South Indian family with 20 members, 8 members diagnosed as JOAG, 7 members as POAG, 4 members as JOAG suspect, and 1 member as POAG suspect were screened for myocilin ( MYOC) mutations using Sanger sequencing. Whole exome sequencing was performed on clinically suspected JOAG/POAG individuals. RESULTS Myocilin gene mutation N480K (c.1440C>G) was detected in 20 family members, including proband, of whom 8 were JOAG and 7 were POAG patients, 3 were JOAG suspects, and 2 were unaffected. Among the unaffected carriers, 1 was less than 5 years old, and another was 25 years old. The earliest to develop the disease was a 10-year-old child. The penetrance of the mutation was 95% over 10 years of age. This family had JOAG/POAG suspects with no N480K MYOC mutation, and they were further screened for other mutations using whole-exome sequencing. Polymorphisms CYP1B1 L432V and MYOC R76K were detected in 3 JOAG/POAG suspects, and among these 3, one had another CYP1B1 polymorphic variant R368H. The presence of the CYP1B1 polymorphism along with an MYOC polymorphic variant among the JOAG/POAG suspects needs additional studies to explore their combined role in the onset of glaucoma. CONCLUSIONS This study reveals that MYOC mutation is primarily responsible for JOAG and adult-onset POAG in a family, emphasizing the importance of screening for this mutation at a younger age for early treatment.
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Affiliation(s)
| | | | - Saravanan Vijayan
- Department of Genetics, Aravind Medical Research Foundation, Madurai
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Chadalawada S, Rathinam SR, Lalitha P, Kannan NB, Devarajan B. Detection of microRNAs expression signatures in vitreous humor of intraocular tuberculosis. Mol Biol Rep 2023; 50:10061-10072. [PMID: 37906423 DOI: 10.1007/s11033-023-08819-1] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 09/12/2023] [Indexed: 11/02/2023]
Abstract
BACKGROUND MicroRNA (miRNA) expression analysis has been shown to provide them as biomarkers in several eye diseases and has a regulatory role in pathogenesis. However, miRNA expression analysis in the vitreous humor (VH) of intraocular tuberculosis (IOTB) is not studied. Thus, we aim to find miRNA expression signatures in the VH of IOTB patients to identify their regulatory role in disease pathogenesis and to find them as potential biomarkers for IOTB. METHODS AND RESULTS First, we profiled miRNAs in VH of three IOTB and three Macular hole (MH) samples as controls through small-RNA deep sequencing using Illumina Platform. In-house bioinformatics analysis identified 81 dysregulated miRNAs in IOTB. Further validation in VH of IOTB (n = 15) compared to MH (n = 15) using Real-Time quantitative PCR (RT-qPCR) identified three significantly upregulated miRNAs, hsa-miR-150-5p, hsa-miR-26b-5p, and hsa-miR-21-5p. Based on the miRNA target prediction, functional network analysis, and RT-qPCR analysis of target genes, the three miRNAs downregulating WNT5A, PRKCA, MAP3K7, IL7, TGFB2, IL1A, PRKCB, TNFA, and TP53 genes involving MAPK signaling pathway, PI3K-AKT signaling pathway, WNT signaling pathway, Cell cycle, TGF-beta signaling pathway, Long-term potentiation, and Sphingolipid signaling pathways, have a potential role in disease pathogenesis. The ROC analysis of RT-qPCR data showed that hsa-miR-150-5p with AUC = 0.715, hsa-miR-21-5p with AUC = 0.789, and hsa-miR-26b-5p with AUC = 0.738; however, the combination of hsa-miR-21-5p and hsa-miR-26b-5p with AUC = 0.796 could serve as a potential biomarker for IOTB. CONCLUSIONS This study provides the first report on miRNA expression signatures detected in VH for IOTB pathogenesis and also provides a potential biomarker for IOTB.
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Affiliation(s)
- Swathi Chadalawada
- Department of Microbiology and Bioinformatics, Aravind Medical Research Foundation, 1, Anna Nagar, Madurai, India
- Biomedical Sciences, Madurai Kamaraj University, Madurai, 625021, Tamil Nadu, India
| | - S R Rathinam
- Uveitis Service, Aravind Eye Hospital and PG Institute of Ophthalmology, Madurai, Tamil Nadu, India
| | - Prajna Lalitha
- Department of Microbiology, Aravind Eye Hospital, Madurai, Tamil Nadu, India
| | - Naresh Babu Kannan
- Chief, Retina Vitreous Services, Aravind Eye Hospital, Madurai, Tamil Nadu, India
| | - Bharanidharan Devarajan
- Department of Microbiology and Bioinformatics, Aravind Medical Research Foundation, 1, Anna Nagar, Madurai, India.
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Gokulakrishnan K, Nikhil J, Viswanath B, Thirumoorthy C, Narasimhan S, Devarajan B, Joseph E, David AKD, Sharma S, Vasudevan K, Sreeraj VS, Holla B, Shivakumar V, Debnath M, Venkatasubramanian G, Varambally S. Comparison of gut microbiome profile in patients with schizophrenia and healthy controls - A plausible non-invasive biomarker? J Psychiatr Res 2023; 162:140-149. [PMID: 37156128 DOI: 10.1016/j.jpsychires.2023.05.021] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/26/2023] [Accepted: 05/01/2023] [Indexed: 05/10/2023]
Abstract
The human gut microbiome regulates brain function through the microbiome-gut-brain axis and is implicated in several neuropsychiatric disorders. However, the relationship between the gut microbiome and the pathogenesis of schizophrenia (SCZ) is poorly defined, and very few studies have examined the effect of antipsychotic treatment response. We aim to study the differences in the gut microbiota among drug-naïve (DN SCZ) and risperidone-treated SCZ patients (RISP SCZ), compared to healthy controls (HCs). We recruited a total of 60 participants, from the clinical services of a large neuropsychiatric hospital, which included DN SCZ, RISP SCZ and HCs (n = 20 each). Fecal samples were analyzed using 16s rRNA sequencing in this cross-sectional study. No significant differences were found in taxa richness (alpha diversity) but microbial composition differed between SCZ patients (both DN and RISP) and HCs (PERMANOVA, p = 0.02). Linear Discriminant Analysis Effect Size (LEfSe) and Random Forest model identified the top six genera, which significantly differed in abundance between the study groups. A specific genus-level microbial panel of Ruminococcus, UCG005, Clostridium_sensu_stricto_1 and Bifidobacterium could discriminate SCZ patients from HCs with an area under the curve (AUC) of 0.79, HCs vs DN SCZ (AUC: 0.68), HCs vs RISP SCZ (AUC: 0.93) and DN SCZ vs RISP SCZ (AUC: 0.87). Our study identified distinct microbial signatures that could aid in the differentiation of DN SCZ, RISP SCZ, and HCs. Our findings contribute to a better understanding of the role of the gut microbiome in SCZ pathophysiology and suggest potential targeted interventions.
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Affiliation(s)
- Kuppan Gokulakrishnan
- Department of Neurochemistry, National Institute of Mental Health and Neuro Sciences (NIMHANS), Hosur Road, Bengaluru, Karnataka, 560029, India.
| | - Joyappa Nikhil
- Department of Neurochemistry, National Institute of Mental Health and Neuro Sciences (NIMHANS), Hosur Road, Bengaluru, Karnataka, 560029, India
| | - Biju Viswanath
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences (NIMHANS), Hosur Road, Bengaluru, Karnataka, 560029, India
| | - Chinnasamy Thirumoorthy
- Department of Neurochemistry, National Institute of Mental Health and Neuro Sciences (NIMHANS), Hosur Road, Bengaluru, Karnataka, 560029, India
| | - Sandhya Narasimhan
- Department of Neurochemistry, National Institute of Mental Health and Neuro Sciences (NIMHANS), Hosur Road, Bengaluru, Karnataka, 560029, India
| | - Bharanidharan Devarajan
- Department of Bioinformatics, Aravind Medical Research Foundation, Madurai, Tamil Nadu, India
| | - Ebin Joseph
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences (NIMHANS), Hosur Road, Bengaluru, Karnataka, 560029, India
| | - Arul Kevin Daniel David
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences (NIMHANS), Hosur Road, Bengaluru, Karnataka, 560029, India
| | - Sapna Sharma
- Chair of Food Chemistry and Molecular Sensory Science, Technische Universität München, Lise-Meitner-Str. 34, 85354, Freising, Germany
| | - Kavitha Vasudevan
- Department of Foods, Nutrition & Dietetics Research, Madras Diabetes Research Foundation, Chennai, Tamil Nadu, India
| | - Vanteemar S Sreeraj
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences (NIMHANS), Hosur Road, Bengaluru, Karnataka, 560029, India
| | - Bharath Holla
- Department of Integrative Medicine, National Institute of Mental Health and Neuro Sciences (NIMHANS), Hosur Road, Bengaluru, Karnataka, 560029, India
| | - Venkataram Shivakumar
- Department of Integrative Medicine, National Institute of Mental Health and Neuro Sciences (NIMHANS), Hosur Road, Bengaluru, Karnataka, 560029, India
| | - Monojit Debnath
- Department of Human Genetics, National Institute of Mental Health and Neuro Sciences (NIMHANS), Hosur Road, Bengaluru, Karnataka, 560029, India
| | - Ganesan Venkatasubramanian
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences (NIMHANS), Hosur Road, Bengaluru, Karnataka, 560029, India
| | - Shivarama Varambally
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences (NIMHANS), Hosur Road, Bengaluru, Karnataka, 560029, India; Department of Integrative Medicine, National Institute of Mental Health and Neuro Sciences (NIMHANS), Hosur Road, Bengaluru, Karnataka, 560029, India
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Kumaran M, Devarajan B. eyeVarP: a computational framework for the identification of pathogenic variants specific to eye disease. Genet Med 2023:100862. [PMID: 37092535 DOI: 10.1016/j.gim.2023.100862] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 04/11/2023] [Accepted: 04/13/2023] [Indexed: 04/25/2023] Open
Abstract
PURPOSE Disease-specific pathogenic variants prediction tools that predict pathogenic variants from benign have been improved through disease specificity recently. However, they have not been evaluated on disease-specific pathogenic variants compared to other diseases, which would help to prioritize disease-specific variants from several genes or novel genes. Thus, we hypothesize that features of pathogenic variants alone would provide a better model. METHODS We developed eyeVarP, an eye disease-specific variant prioritization tool, which applied the Random Forest (RF) algorithm to the dataset of pathogenic variants of eye diseases and other diseases. We also developed the VarP tool and generalized pipeline to filter missense and InDels and predict their pathogenicity from Exome or genome sequencing data, which provides a complete computational procedure. RESULTS eyeVarP outperformed pan-disease-specific tools in identifying eye disease-specific pathogenic variants under the top ten. VarP outperformed twelve pathogenicity prediction tools with an accuracy of 95% in correctly identifying the pathogenicity of missense and InDels. The complete pipeline would help to develop disease-specific tools for other genetic disorders. CONCLUSION eyeVarP performs better in identifying eye disease-specific pathogenic variants using pathogenic variant features and gene features. Implementing such complete computational procedures would significantly improve the clinical variant interpretation for specific diseases.
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Affiliation(s)
- Manojkumar Kumaran
- Department of Bioinformatics, Aravind Medical Research Foundation, Madurai - 625020, Tamil Nadu, India; School of Chemical and Biotechnology, SASTRA (Deemed to be a university), Thanjavur - 613401, Tamil Nadu, India, Madurai - 625020, Tamil Nadu, India.
| | - Bharanidharan Devarajan
- Department of Bioinformatics, Aravind Medical Research Foundation, Madurai - 625020, Tamil Nadu, India.
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Kalaimani L, Devarajan B, Namperumalsamy VP, Veerappan M, Daniels JT, Chidambaranathan GP. Hsa-miR-143-3p inhibits Wnt-β-catenin and MAPK signaling in human corneal epithelial stem cells. Sci Rep 2022; 12:11432. [PMID: 35794158 PMCID: PMC9259643 DOI: 10.1038/s41598-022-15263-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 02/18/2022] [Accepted: 06/21/2022] [Indexed: 11/09/2022] Open
Abstract
Our previous study demonstrated hsa-miR-143-3p as one of the highly expressed miRNAs in enriched corneal epithelial stem cells (CESCs). Hence this study aims to elucidate the regulatory role of hsa-miR-143-3p in the maintenance of stemness in CESCs. The target genes of hsa-miR-143-3p were predicted and subjected to pathway analysis to select the targets for functional studies. Primary cultured limbal epithelial cells were transfected with hsa-miR-143-3p mimic, inhibitor or scrambled sequence using Lipofectamine 3000. The transfected cells were analysed for (i) colony forming potential, (ii) expression of stem cell (SC) markers/ transcription factors (ABCG2, NANOG, OCT4, KLF4, ΔNp63), (iii) differentiation marker (Cx43), (iv) predicted five targets of hsa-miR-143-3p (DVL3, MAPK1, MAPK14, KRAS and KAT6A), (v) MAPK signaling regulators and (vi) Wnt-β-catenin signaling regulators by qPCR, immunofluorescence staining and/or Western blotting. High expression of hsa-miR-143-3p increased the colony forming potential (10.04 ± 1.35%, p < 0.001) with the ability to form holoclone-like colonies in comparison to control (3.33 ± 0.71%). The mimic treated cells had increased expression of SC markers but reduced expression of Cx43 and hsa-miR-143-3p targets involved in Wnt-β-catenin and MAPK signaling pathways. The expression of β-catenin, active β-catenin and ERK2 in hsa-miR-143-3p inhibitor transfected cells were higher than the control cells and the localized nuclear expression indicated the activation of Wnt and MAPK signaling. Thus, the probable association of hsa-miR-143-3p in the maintenance of CESCs through inhibition of Wnt and MAPK signaling pathways was thus indicated.
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Affiliation(s)
- Lavanya Kalaimani
- Department of Immunology and Stem Cell Biology, Aravind Medical Research Foundation, Madurai, Tamil Nadu, 625020, India.,Department of Biotechnology, Aravind Medical Research Foundation-Affiliated to Alagappa University, Karaikudi, Tamil Nadu, India.,Institute of Ophthalmology, University College London, London, UK
| | - Bharanidharan Devarajan
- Department of Bioinformatics, Aravind Medical Research Foundation, Madurai, Tamil Nadu, India
| | | | - Muthukkaruppan Veerappan
- Department of Immunology and Stem Cell Biology, Aravind Medical Research Foundation, Madurai, Tamil Nadu, 625020, India
| | - Julie T Daniels
- Institute of Ophthalmology, University College London, London, UK
| | - Gowri Priya Chidambaranathan
- Department of Immunology and Stem Cell Biology, Aravind Medical Research Foundation, Madurai, Tamil Nadu, 625020, India. .,Department of Biotechnology, Aravind Medical Research Foundation-Affiliated to Alagappa University, Karaikudi, Tamil Nadu, India.
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Chowdhury S, Duvesh R, Kumaran M, Anjanamurthy R, Kumar J, Vanniarajan A, Devarajan B, Sundaresan P. Clinical reassessments and whole-exome sequencing uncover novel BEST1 mutation associated with bestrophinopathy phenotype. Ophthalmic Genet 2021; 43:191-200. [PMID: 34751623 DOI: 10.1080/13816810.2021.1998553] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
BACKGROUND The diagnosis of retinal dystrophies can be challenging due to the spectrum of protean phenotypic manifestations. This study employed trio-whole-exome sequencing (trio-WES) to unveil the genetic cause of an inherited retinal disorder in a south Indian family. MATERIALS AND METHODS Proband's initial ophthalmic examinations was performed in the year 2016. WES was performed on a proband-parent trio to identify causative mutation followed by Sanger validation, segregation analysis, sequence and structure-based computational analysis to assess its pathogenicity. Based on the genetic findings, detailed clinical reassessments were performed in year 2020 for the proband and available family members. RESULTS WES revealed a novel homozygous BEST1 mutation c.G310A (p.D104N) in the proband and heterozygous for the parents, indicating autosomal recessive inheritance. Segregation analysis showed heterozygous mutation in maternal grandfather and normal genotype for younger brother and maternal grandmother. Moreover, the structure-based analysis revealed the mutation p.D104N in the cytoplasmic domain, causing structural hindrance by altering hydrogen bonds and destabilizing the BEST1 protein structure. Proband's clinical assessments were consistent with autosomal recessive bestrophinopathy (ARB) phenotype. Additionally, characteristic absent light rise and decreased light peak-to-dark trough ratio (LP:DT) was observed bilaterally in EOG. CONCLUSIONS Our study demonstrates the utility of WES and clinical re-evaluations in establishing the precise diagnosis of autosomal recessive bestrophinopathy associated with a novel mutation, thus expanding the BEST1-related mutation spectrum.
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Affiliation(s)
- Susmita Chowdhury
- Department of Genetics, Aravind Medical Research Foundation, Madurai, India.,Department of Molecular Biology, Aravind Medical Research Foundation - Affiliated to Alagappa University, Karaikudi, India
| | - Roopam Duvesh
- Department of Genetics, Aravind Medical Research Foundation, Madurai, India
| | - Manojkumar Kumaran
- Department of Bioinformatics, Aravind Medical Research Foundation, Madurai, India.,School of Chemical and Biotechnology, SASTRA (Deemed to Be University), Thanjavur, India
| | - Rupa Anjanamurthy
- Department of Paediatric Ophthalmology & Adult Strabismus Services, Aravind Eye Hospital, Madurai, India
| | - Jayant Kumar
- Department of Vitreo-Retina Services, Aravind Eye Hospital, Madurai, India
| | - Ayyasamy Vanniarajan
- Department of Molecular Genetics, Aravind Medical Research Foundation, Madurai, India
| | | | - Periasamy Sundaresan
- Department of Genetics, Aravind Medical Research Foundation, Madurai, India.,Department of Molecular Biology, Aravind Medical Research Foundation - Affiliated to Alagappa University, Karaikudi, India
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Shah MH, Kumaran M, Chermakani P, Kader MA, Ramakrishnan R, Krishnadas SR, Devarajan B, Sundaresan P. Whole-exome sequencing identifies multiple pathogenic variants in a large South Indian family with primary open-angle glaucoma. Indian J Ophthalmol 2021; 69:2461-2468. [PMID: 34427245 PMCID: PMC8544095 DOI: 10.4103/ijo.ijo_3301_20] [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] [Indexed: 11/22/2022] Open
Abstract
Purpose: To identify the pathogenic variants associated with primary open-angle glaucoma (POAG) using whole-exome sequencing (WES) data of a large South Indian family. Methods: We recruited a large five-generation South Indian family (n = 84) with a positive family history of POAG (n = 19). All study participants had a comprehensive ocular evaluation. We performed WES for 16 samples (nine POAG and seven unaffected controls) since Sanger sequencing of the POAG candidate genes (MYOC, OPTN, and TBK1) showed no genetic variation. We used an in-house pipeline for prioritizing the pathogenic variants based on their segregation among the POAG individual. Results: We identified one novel and five low-frequency pathogenic variants with consistent co-segregation in all affected individuals. The variant c.G3719A in RPGR-interacting domain of RPGRIP1 that segregated heterozygously with the six POAG cases is distinct from variants causing photoreceptor dystrophies, reported affecting the RPGR protein complex signaling in primary cilia. The cilia in trabecular meshwork (TM) cells has been reported to mediate the intraocular pressure (IOP) sensation. Furthermore, we identified a novel c.A1295G variant in Rho guanine nucleotide exchange factors Gene 40 (ARHGEF40) and a likely pathogenic variant in the RPGR gene, suggesting that they may alter the RhoA activity essential for IOP regulation. Conclusion: Our study supports that low-frequency pathogenic variants in multiple genes and pathways probably affect Primary Open Angle Glaucoma’s pathogenesis in the large South Indian family. Furthermore, it requires larger case-controls to perform family-based association tests and to strengthen our analysis.
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Affiliation(s)
- Mohd Hussain Shah
- Department of Genetics, Aravind Medical Research Foundation, Madurai, India
| | - Manojkumar Kumaran
- Department of Bioinformatics, Aravind Medical Research Foundation, Madurai; School of Chemical and Biotechnology, SASTRA (Deemed to be University), Thanjavur, India
| | - Prakash Chermakani
- Department of Genetics, Aravind Medical Research Foundation; Department of Molecular Biology, Alagappa University, Karaikudi, Tamil Nadu, India
| | | | - R Ramakrishnan
- Glaucoma Clinic, Aravind Eye Hospital, Tirunelveli, India
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Kandasamy K, Thirumalmuthu K, Prajna NV, Lalitha P, Mohankumar V, Devarajan B. Comparative genomics of ocular Pseudomonas aeruginosa strains from keratitis patients with different clinical outcomes. Genomics 2020; 112:4769-4776. [DOI: 10.1016/j.ygeno.2020.08.032] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 08/19/2020] [Accepted: 08/27/2020] [Indexed: 12/21/2022]
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9
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Kalaimani L, Devarajan B, Subramanian U, Ayyasamy V, Namperumalsamy VP, Veerappan M, Chidambaranathan GP. MicroRNA Profiling of Highly Enriched Human Corneal Epithelial Stem Cells by Small RNA Sequencing. Sci Rep 2020; 10:7418. [PMID: 32366885 PMCID: PMC7198595 DOI: 10.1038/s41598-020-64273-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 01/21/2020] [Accepted: 03/31/2020] [Indexed: 12/18/2022] Open
Abstract
The objective of the study was to elucidate the microRNA (miRNA) profile of an enriched human corneal epithelial stem cell (CESC) population in comparison to differentiated central corneal epithelial cells (CCECs) by small RNA sequencing. The CESCs were enriched by differential enzymatic treatment to isolate the basal limbal epithelial cells followed by laser capture microdissection of cells with nucleus to cytoplasm ratio ≥0.7, from donor tissues. Small RNA sequencing was carried out using Illumina NextSeq. 500 platform and the validation of differentially expressed miRNAs by quantitative real-time PCR (qPCR) and locked nucleic acid miRNA in-situ hybridization (LNA-ISH). The sequencing identified 62 miRNAs in CESCs and 611 in CCECs. Six miRNAs: hsa-miR-21-5p, 3168, 143-3p, 10a-5p, 150-5p and 1910-5p were found to be significantly upregulated in enriched CESCs, which was further confirmed by qPCR and LNA-ISH. The expression of hsa-miR-143-3p was exclusive to clusters of limbal basal epithelial cells. The targets of the upregulated miRNAs were predicted to be associated with signaling pathways -Wnt, PI3K-AKT, MAPK and pathways that regulate pluripotency of stem cells, cell migration, growth and proliferation. Further studies are essential to elucidate their functional role in maintenance of stemness. The findings of the study also hypothesize the inherent potential of hsa-miR-143-3p to serve as a biomarker for identifying CESCs.
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Affiliation(s)
- Lavanya Kalaimani
- Department of Immunology and Stem Cell Biology, Aravind Medical Research Foundation, Madurai, Tamil Nadu, India
- Department of Biotechnology, Aravind Medical Research Foundation -Affiliated to Alagappa University, Karaikudi, Tamil Nadu, India
| | - Bharanidharan Devarajan
- Department of Bioinformatics, Aravind Medical Research Foundation, Madurai, Tamil Nadu, India
| | - Umadevi Subramanian
- Department of Bioinformatics, Aravind Medical Research Foundation, Madurai, Tamil Nadu, India
| | - Vanniarajan Ayyasamy
- Department of Molecular Genetics, Aravind Medical Research Foundation, Madurai, Tamil Nadu, India
| | | | - Muthukkaruppan Veerappan
- Department of Immunology and Stem Cell Biology, Aravind Medical Research Foundation, Madurai, Tamil Nadu, India
| | - Gowri Priya Chidambaranathan
- Department of Immunology and Stem Cell Biology, Aravind Medical Research Foundation, Madurai, Tamil Nadu, India.
- Department of Biotechnology, Aravind Medical Research Foundation -Affiliated to Alagappa University, Karaikudi, Tamil Nadu, India.
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Raj RK, Dhoble P, Anjanamurthy R, Chermakani P, Kumaran M, Devarajan B, Sundaresan P. Genetic characterization of Stargardt clinical phenotype in South Indian patients using sanger and targeted sequencing. Eye Vis (Lond) 2020; 7:3. [PMID: 31934596 PMCID: PMC6950877 DOI: 10.1186/s40662-019-0168-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 12/07/2019] [Indexed: 11/10/2022]
Abstract
Background Stargardt disease 1 (STGD1; MIM 248200) is a monogenic form of autosomal recessive genetic disease caused by mutation in ABCA4. This gene has a major role in hydrolyzing N-retinylidene-phosphatidylethanolamine to all-trans-retinal and phosphatidylethanolamine. The purpose of this study is to identify the frequency of putative disease-causing mutations associated with Stargardt disease in a South Indian population. Methods A total of 28 clinically diagnosed Stargardt-like phenotype patients were recruited from south India. Ophthalmic examination of all patients was carefully carried out by a retina specialist based on the stages of fundus imaging and ERG grouping. Genetic analysis of ABCA4 was performed for all patients using Sanger sequencing and clinical exome sequencing. Results This study identified disease-causing mutations in ABCA4 in 75% (21/28) of patients, 7% (2/28) exhibited benign variants and 18% (5/28) were negative for the disease-causing mutation. Conclusion This is the first study describing the genetic association of ABCA4 disease-causing mutation in South Indian Stargardt 1 patients (STGD1). Our findings highlighted the presence of two novel missense mutations and an (in/del, single base pair deletion & splice variant) in ABCA4. However, genetic heterogeneity in ABCA4 mutants requires a larger sample size to establish a true correlation with clinical phenotype.
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Affiliation(s)
- Rajendran Kadarkarai Raj
- 1Department of Genetics, Aravind Medical Research Foundation-Madurai, No.1 Anna Nagar, Madurai, Tamil Nadu 625 020 India
| | - Pankaja Dhoble
- 2Retina Consultant, Department of Vitreo Retinal services, Aravind Eye Hospital-Pondicherry, Puducherry, India
| | - Rupa Anjanamurthy
- 3Department of Paediatrics and Adult strabismus, Aravind Eye Hospital-Madurai, Madurai, Tamil Nadu India
| | - Prakash Chermakani
- 1Department of Genetics, Aravind Medical Research Foundation-Madurai, No.1 Anna Nagar, Madurai, Tamil Nadu 625 020 India
| | - Manojkumar Kumaran
- 4Department of Bioinformatics, Aravind Medical Research Foundation-Madurai, Madurai, Tamil Nadu India
| | - Bharanidharan Devarajan
- 4Department of Bioinformatics, Aravind Medical Research Foundation-Madurai, Madurai, Tamil Nadu India
| | - Periasamy Sundaresan
- 1Department of Genetics, Aravind Medical Research Foundation-Madurai, No.1 Anna Nagar, Madurai, Tamil Nadu 625 020 India
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Kalaimani L, Devarajan B, Prajna Namperumalsamy V, Veerappan M, Daniels JT, Priya Chidambaranathan G. Hsa‐miR‐150‐5p regulates human corneal epithelial stem cells through Wnt signaling. Acta Ophthalmol 2019. [DOI: 10.1111/j.1755-3768.2019.5202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lavanya Kalaimani
- Institute of Ophthalmology University College London London United Kingdom
| | | | | | - Muthukkaruppan Veerappan
- Department of Immunology and Stem Cell Biology Aravind Medical Research Foundation Madurai India
| | - Julie T. Daniels
- Institute of Ophthalmology University College London London United Kingdom
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Thirumalmuthu K, Devarajan B, Prajna L, Mohankumar V. Mechanisms of Fluoroquinolone and Aminoglycoside Resistance in Keratitis-AssociatedPseudomonas aeruginosa. Microb Drug Resist 2019; 25:813-823. [DOI: 10.1089/mdr.2018.0218] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Affiliation(s)
- Kannan Thirumalmuthu
- Department of Ocular Microbiology and Aravind Medical Research Foundation, Madurai, India
| | | | - Lalitha Prajna
- Department of Ocular Microbiology and Aravind Medical Research Foundation, Madurai, India
| | - Vidyarani Mohankumar
- Department of Ocular Microbiology and Aravind Medical Research Foundation, Madurai, India
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Kumaran M, Subramanian U, Devarajan B. Performance assessment of variant calling pipelines using human whole exome sequencing and simulated data. BMC Bioinformatics 2019; 20:342. [PMID: 31208315 PMCID: PMC6580603 DOI: 10.1186/s12859-019-2928-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [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: 07/14/2018] [Accepted: 05/31/2019] [Indexed: 12/30/2022] Open
Abstract
Background Whole exome sequencing (WES) is a cost-effective method that identifies clinical variants but it demands accurate variant caller tools. Currently available tools have variable accuracy in predicting specific clinical variants. But it may be possible to find the best combination of aligner-variant caller tools for detecting accurate single nucleotide variants (SNVs) and small insertion and deletion (InDels) separately. Moreover, many important aspects of InDel detection are overlooked while comparing the performance of tools, particularly its base pair length. Results We assessed the performance of variant calling pipelines using the combinations of four variant callers and five aligners on human NA12878 and simulated exome data. We used high confidence variant calls from Genome in a Bottle (GiaB) consortium for validation, and GRCh37 and GRCh38 as the human reference genome. Based on the performance metrics, both BWA and Novoalign aligners performed better with DeepVariant and SAMtools callers for detecting SNVs, and with DeepVariant and GATK for InDels. Furthermore, we obtained similar results on human NA24385 and NA24631 exome data from GiaB. Conclusion In this study, DeepVariant with BWA and Novoalign performed best for detecting accurate SNVs and InDels. The accuracy of variant calling was improved by merging the top performing pipelines. The results of our study provide useful recommendations for analysis of WES data in clinical genomics. Electronic supplementary material The online version of this article (10.1186/s12859-019-2928-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Manojkumar Kumaran
- Department of Bioinformatics, Aravind Medical Research Foundation, Madurai, Tamil Nadu, 625020, India.,School of Chemical and Biotechnology, SASTRA (Deemed to be University), Thanjavur, Tamil Nadu, 613401, India
| | - Umadevi Subramanian
- Department of Bioinformatics, Aravind Medical Research Foundation, Madurai, Tamil Nadu, 625020, India
| | - Bharanidharan Devarajan
- Department of Bioinformatics, Aravind Medical Research Foundation, Madurai, Tamil Nadu, 625020, India.
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Khedekar A, Devarajan B, Ramasamy K, Muthukkaruppan V, Kim U. Smartphone-based application improves the detection of retinoblastoma. Eye (Lond) 2019; 33:896-901. [PMID: 30635644 DOI: 10.1038/s41433-018-0333-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 11/29/2018] [Accepted: 12/20/2018] [Indexed: 11/09/2022] Open
Abstract
PURPOSE To improve and validate the smartphone-based leukocoria detection application so that non-ophthalmologists could make use of the smartphone for early detection of Retinoblastoma (RB) in young children without anesthesia and pharmacological dilatation of the pupil. METHODS Two apps, MDEyeCare and CRADLE, developed for red reflex based leukocoria detection were used in iPhone 6s. MDEyeCare methodology was modified with respect to ambient lighting, the distance between camera and eye and different gazes for better performance. We analyzed totally 34 eyes of 23 RB patients and four normal children. Each of the RB patients was confirmed with clinical examination and radiological investigations. RESULTS Modification in the methodology of MDEyeCare app could detect the leukocoria in early stages of RB (50% of Group B, 83% of Group C). In late stages (Group D and E), 100% of tumors were detected. The CRADLE app failed to provide adequate leukocoria detection except four late stage RB eyes. Among the 14 normal eyes (6 from unilateral RB and eight from normal children), pseudo-leukocoria was observed in three eyes only at lateral gaze even with MDEyeCare app. CONCLUSION Improved methodology in smartphone-based app enhanced the detection of RB and this may translate into better outcome after treatment with respect to vision salvage.
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Affiliation(s)
- Amit Khedekar
- Department of Orbit, Oculoplasty and Oncology, Aravind Eye Hospital, Madurai, India.,Khedekar's Eye Clinic, Mumbai, India
| | | | - Kim Ramasamy
- Department of Retina, Aravind Eye Hospital, Madurai, India
| | | | - Usha Kim
- Department of Orbit, Oculoplasty and Oncology, Aravind Eye Hospital, Madurai, India
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Abstract
PURPOSE MicroRNAs (miRNAs) are small, stable, noncoding RNA molecules with regulatory function and marked tissue specificity that posttranscriptionally regulate gene expression. However, their role in fungal keratitis remains unknown. The purpose of this study was to identify the miRNA profile and its regulatory role in fungal keratitis. METHODS Normal donor (n = 3) and fungal keratitis (n = 5) corneas were pooled separately, and small RNA deep sequencing was performed using a sequencing platform. A bioinformatics approach was applied to identify differentially-expressed miRNAs and their targets, and select miRNAs were validated by real-time quantitative PCR (qPCR). The regulatory functions of miRNAs were predicted by combining miRNA target genes and pathway analysis. The mRNA expression levels of select target genes were further analyzed by qPCR. RESULTS By deep sequencing, 75 miRNAs were identified as differentially expressed with fold change greater than 2 and probability score greater than 0.9 in fungal keratitis corneas. The highly dysregulated miRNAs (miR-511-5p, miR-142-3p, miR-155-5p, and miR-451a) may regulate wound healing as they were predicted to specifically target wound inflammatory genes. Moreover, the increased expression of miR-451a in keratitis correlated with reduced expression of its target, macrophage migration inhibitory factor, suggesting possible regulatory functions. CONCLUSIONS This is, to our knowledge, the first report on comprehensive human corneal miRNA expression profile in fungal keratitis. Several miRNAs with high expression in fungal keratitis point toward their potential role in regulation of pathogenesis. Further insights in understanding their role in corneal wound inflammation may help design new therapeutic strategies.
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Affiliation(s)
- Hemadevi Boomiraj
- Department of Microbiology Aravind Medical Research Foundation, Madurai, India
| | | | - Prajna Lalitha
- Department of Microbiology Aravind Medical Research Foundation, Madurai, India
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16
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Thirumalairaj K, Abraham A, Devarajan B, Gaikwad N, Kim U, Muthukkaruppan V, Vanniarajan A. A stepwise strategy for rapid and cost-effective RB1 screening in Indian retinoblastoma patients. J Hum Genet 2015; 60:547-52. [PMID: 26084579 DOI: 10.1038/jhg.2015.62] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 04/28/2015] [Accepted: 04/30/2015] [Indexed: 01/02/2023]
Abstract
India has the highest number of retinoblastoma (RB) patients among the developing countries owing to its increasing population. Of the patients with RB, about 40% have the heritable form of the disease, making genetic analysis of the RB1 gene an integral part of disease management. However, given the large size of the RB1 gene with its widely dispersed exons and no reported hotspots, genetic testing can be cumbersome. To overcome this problem, we have developed a rapid screening strategy by prioritizing the order of exons to be analyzed, based on the frequency of nonsense mutations, deletions and duplications reported in the RB1-Leiden Open Variation Database and published literature on Indian patients. Using this strategy for genetic analysis, mutations were identified in 76% of patients in half the actual time and one third of the cost. This reduction in time and cost will allow for better risk prediction for siblings and offspring, thereby facilitating genetic counseling for families, especially in developing countries.
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Affiliation(s)
- Kannan Thirumalairaj
- Department of Molecular Genetics, Aravind Medical Research Foundation, Madurai, India
| | - Aloysius Abraham
- Department of Molecular Genetics, Aravind Medical Research Foundation, Madurai, India
| | | | - Namrata Gaikwad
- Department of Orbit, Oculoplasty and Oncology, Aravind Eye Hospital, Madurai, India
| | - Usha Kim
- Department of Orbit, Oculoplasty and Oncology, Aravind Eye Hospital, Madurai, India
| | | | - Ayyasamy Vanniarajan
- Department of Molecular Genetics, Aravind Medical Research Foundation, Madurai, India
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Devarajan B, Prakash L, Kannan TR, Abraham AA, Kim U, Muthukkaruppan V, Vanniarajan A. Targeted next generation sequencing of RB1 gene for the molecular diagnosis of Retinoblastoma. BMC Cancer 2015; 15:320. [PMID: 25928201 PMCID: PMC4415345 DOI: 10.1186/s12885-015-1340-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [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: 11/21/2014] [Accepted: 04/22/2015] [Indexed: 12/02/2022] Open
Abstract
Background The spectrum of RB1gene mutations in Retinoblastoma (RB) patients and the necessity of multiple traditional methods for complete variant analysis make the molecular diagnosis a cumbersome, labor-intensive and time-consuming process. Here, we have used targeted next generation sequencing (NGS) approach with in-house analysis pipeline to explore its potential for the molecular diagnosis of RB. Methods Thirty-three patients with RB and their family members were selected randomly. DNA from patient blood and/or tumor was used for RB1 gene targeted sequencing. The raw reads were obtained from Illumina Miseq. An in-house bioinformatics pipeline was developed to detect both single nucleotide variants (SNVs) and small insertions/deletions (InDels) and to distinguish between somatic and germline mutations. In addition, ExomeCNV and Cn. MOPS were used to detect copy number variations (CNVs). The pathogenic variants were identified with stringent criteria, and were further confirmed by conventional methods and cosegregation in families. Results Using our approach, an array of pathogenic variants including SNVs, InDels and CNVs were detected in 85% of patients. Among the variants detected, 63% were germline and 37% were somatic. Interestingly, nine novel pathogenic variants (33%) were also detected in our study. Conclusions We demonstrated for the first time that targeted NGS is an efficient approach for the identification of wide spectrum of pathogenic variants in RB patients. This study is helpful for the molecular diagnosis of RB in a comprehensive and time-efficient manner.
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Affiliation(s)
| | - Logambiga Prakash
- Department of Bioinformatics, Aravind Medical Research Foundation, Madurai, India.
| | - Thirumalai Raj Kannan
- Department of Molecular Genetics, Aravind Medical Research Foundation, Madurai, India.
| | - Aloysius A Abraham
- Department of Molecular Genetics, Aravind Medical Research Foundation, Madurai, India.
| | - Usha Kim
- Department of Orbit, Oculoplasty and Oncology, Aravind Eye Hospital, Madurai, India.
| | | | - Ayyasamy Vanniarajan
- Department of Molecular Genetics, Aravind Medical Research Foundation, Madurai, India.
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Dreaden TM, Devarajan B, Barry BA, Schmidt-Krey I. Structure-function insights of membrane and soluble proteins revealed by electron crystallography. Methods Mol Biol 2013; 955:519-526. [PMID: 23132078 DOI: 10.1007/978-1-62703-176-9_27] [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] [Indexed: 06/01/2023]
Abstract
Electron crystallography is emerging as an important method in solving protein structures. While it has found extensive applications in the understanding of membrane protein structure and function at a wide range of resolutions, from revealing oligomeric arrangements to atomic models, electron crystallography has also provided invaluable information on the soluble α/β-tubulin which could not be obtained by any other method to date. Examples of critical insights from selected structures of membrane proteins as well as α/β-tubulin are described here, demonstrating the vast potential of electron crystallography that is first beginning to unfold.
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Affiliation(s)
- Tina M Dreaden
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
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Mishra A, Devarajan B, Reardon ME, Dwivedi P, Krishnan V, Cisar JO, Das A, Narayana SVL, Ton-That H. Two autonomous structural modules in the fimbrial shaft adhesin FimA mediate Actinomyces interactions with streptococci and host cells during oral biofilm development. Mol Microbiol 2011; 81:1205-20. [PMID: 21696465 DOI: 10.1111/j.1365-2958.2011.07745.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
By combining X-ray crystallography and modelling, we describe here the atomic structure of distinct adhesive moieties of FimA, the shaft fimbrillin of Actinomyces type 2 fimbriae, which uniquely mediates the receptor-dependent intercellular interactions between Actinomyces and oral streptococci as well as host cells during the development of oral biofilms. The FimA adhesin is built with three IgG-like domains, each of which harbours an intramolecular isopeptide bond, previously described in several Gram-positive pilins. Genetic and biochemical studies demonstrate that although these isopeptide bonds are dispensable for fimbrial assembly, cell-cell interactions and biofilm formation, they contribute significantly to the proteolytic stability of FimA. Remarkably, FimA harbours two autonomous adhesive modules, which structurally resemble the Staphylococcus aureus Cna B domain. Each isolated module can bind the plasma glycoprotein asialofetuin as well as the polysaccharide receptors present on the surface of oral streptococci and epithelial cells. Thus, FimA should serve as an excellent paradigm for the development of therapeutic strategies and elucidating the precise molecular mechanisms underlying the interactions between cellular receptors and Gram-positive fimbriae.
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Affiliation(s)
- Arunima Mishra
- Department of Microbiology & Molecular Genetics, University of Texas Health Science Center, Houston, TX, USA
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