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Article: The Role of Gene Expression Regulation on Genetic Risk of Age-Related Macular Degeneration.

Ratnapriya, Rinki

Advances in experimental medicine and biology

2023 Volume 1415, Page(s) 61–66

Abstract: Age-related macular degeneration (AMD) is a major cause of irreversible vision loss in the elderly. It is a complex multifactorial disease that is caused by the cumulative impact of genetic predisposition, environmental stress, and advanced aging. ... ...

Abstract	Age-related macular degeneration (AMD) is a major cause of irreversible vision loss in the elderly. It is a complex multifactorial disease that is caused by the cumulative impact of genetic predisposition, environmental stress, and advanced aging. Knowledge of genetic risk factors underlying AMD susceptibility has advanced rapidly in the past decade that can be largely credited to genome-wide association studies (GWAS) and next-generation sequencing (NGS) efforts. GWAS have identified 34 genetic risk loci for AMD; the majority of which are in the noncoding genome. Several lines of evidence suggest that a complex trait-associated variant is likely to regulate the gene expression (acting as expression quantitative trait loci (eQTLs)), and there is a significant enrichment of GWAS-associated variants within eQTLs. In the last two years, eQTL studies in AMD-relevant tissues have provided functional interpretation of several AMD-GWAS loci. This review highlights the knowledge gained to date and discusses future directions to bridge the gap between genetic predisposition and biological mechanisms to reap the full benefits of GWAS findings.
MeSH term(s)	Humans ; Aged ; Genetic Predisposition to Disease ; Genome-Wide Association Study ; Gene Expression Regulation ; Quantitative Trait Loci ; Macular Degeneration/genetics ; Macular Degeneration/metabolism ; Risk Factors ; Polymorphism, Single Nucleotide
Language	English
Publishing date	2023-07-13
Publishing country	United States
Document type	Review ; Journal Article
ZDB-ID	410187-X
ISSN	0065-2598
ISSN	0065-2598
DOI	10.1007/978-3-031-27681-1_10
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Article: Applications of Genomic Technologies in Retinal Degenerative Diseases.

Ratnapriya, Rinki

Advances in experimental medicine and biology

2019 Volume 1185, Page(s) 281–285

Abstract: Next-generation sequencing (NGS)-based technologies are ideal for genomic analyses owing to their cost-effectiveness, unprecedented speed, and accuracy. Acceleration in examining genome, transcriptome, and epigenome has made significant impact in ... ...

Abstract	Next-generation sequencing (NGS)-based technologies are ideal for genomic analyses owing to their cost-effectiveness, unprecedented speed, and accuracy. Acceleration in examining genome, transcriptome, and epigenome has made significant impact in biomedical sciences. This review highlights the applications of high-throughput NGS technologies in improving the molecular understanding of retinal degenerative diseases (RDDs). I focus on NGS-based methods and strategies that are allowing expedited disease gene identifications, improved diagnosis, and deeper understanding of the mechanisms through which genetic variations lead to diseases.
MeSH term(s)	Genomics ; High-Throughput Nucleotide Sequencing ; Humans ; Retinal Degeneration/genetics ; Sequence Analysis, DNA
Language	English
Publishing date	2019-12-28
Publishing country	United States
Document type	Journal Article ; Review
ISSN	2214-8019 ; 0065-2598
ISSN (online)	2214-8019
ISSN	0065-2598
DOI	10.1007/978-3-030-27378-1_46
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Article: Making Biological Sense of Genetic Studies of Age-Related Macular Degeneration.

Singh, Nivedita / Swaroop, Anand / Ratnapriya, Rinki

Advances in experimental medicine and biology

2021 Volume 1256, Page(s) 201–219

Abstract: Age-related macular degeneration (AMD) is a major cause of blindness in older individuals worldwide. The disease is characterized by deposition of drusen between the retinal pigment epithelium (RPE) and Bruch's membrane, RPE atrophy and death of ... ...

Abstract	Age-related macular degeneration (AMD) is a major cause of blindness in older individuals worldwide. The disease is characterized by deposition of drusen between the retinal pigment epithelium (RPE) and Bruch's membrane, RPE atrophy and death of photoreceptors. AMD is a complex disease with multiple genetic and non-genetic risk factors. Genome-wide association studies (GWAS) have identified 52 variants at 34 genetic loci associated with AMD. A majority of the AMD-GWAS variants are present in non-coding region of the genome and could quantitatively impact distinct human traits [called quantitative trait loci (QTLs)] by affecting regulation of gene expression. The integration of different regulatory features, such as open-chromatin regions, histone marks, transcription factor binding sites, with AMD-GWAS can provide meaningful insights into variant's function. However, functional interpretation of variant-gene relationship in AMD is challenging because of inadequate understanding of cell-type specific and context-dependent information in disease-relevant tissues. Here we focus on the role of sequencing-based omic studies in assigning biological meaning to disease-associated variants and genes. We also discuss the methods and model systems that can be utilized to unravel molecular mechanisms of a complex disorder like AMD.
MeSH term(s)	Aged ; Bruch Membrane ; Genome-Wide Association Study ; Humans ; Macular Degeneration/genetics ; Retina ; Retinal Pigment Epithelium
Language	English
Publishing date	2021-04-13
Publishing country	United States
Document type	Journal Article
ISSN	2214-8019 ; 0065-2598
ISSN (online)	2214-8019
ISSN	0065-2598
DOI	10.1007/978-3-030-66014-7_8
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Article ; Online: Single-cell transcriptional profiling of murine conjunctival immune cells reveals distinct populations expressing homeostatic and regulatory genes.

Alam, Jehan / Yazdanpanah, Ghasem / Ratnapriya, Rinki / Borcherding, Nicholas / de Paiva, Cintia S / Li, DeQuan / Pflugfelder, Stephen C

Mucosal immunology

2022 Volume 15, Issue 4, Page(s) 620–628

Abstract: Immune cells in the exposed conjunctiva mucosa defend against environmental and microbial stresses. Expression profiling by single-cell RNA sequencing was performed to identify conjunctival immune cell populations expressing homeostatic and regulatory ... ...

Abstract	Immune cells in the exposed conjunctiva mucosa defend against environmental and microbial stresses. Expression profiling by single-cell RNA sequencing was performed to identify conjunctival immune cell populations expressing homeostatic and regulatory genes. Fourteen distinct clusters were identified, including myeloid cells (neutrophils, monocytes, macrophages), dendritic cells (DC), and lymphoid cells (B, T, γδT, ILC2, and NK) lineages. Novel neutrophil [lipocalin (Lcn2) high and low), and MHCII
MeSH term(s)	Animals ; Conjunctiva ; Dendritic Cells ; Genes, Regulator ; Immunity, Innate ; Interleukin-13 ; Lymphocytes ; Mice ; Monocytes
Chemical Substances	Interleukin-13
Language	English
Publishing date	2022-03-31
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural
ZDB-ID	2411370-0
ISSN	1935-3456 ; 1933-0219
ISSN (online)	1935-3456
ISSN	1933-0219
DOI	10.1038/s41385-022-00507-w
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Article ; Online: QTL mapping of human retina DNA methylation identifies 87 gene-epigenome interactions in age-related macular degeneration.

Advani, Jayshree / Mehta, Puja A / Hamel, Andrew R / Mehrotra, Sudeep / Kiel, Christina / Strunz, Tobias / Corso-Díaz, Ximena / Kwicklis, Madeline / van Asten, Freekje / Ratnapriya, Rinki / Chew, Emily Y / Hernandez, Dena G / Montezuma, Sandra R / Ferrington, Deborah A / Weber, Bernhard H F / Segrè, Ayellet V / Swaroop, Anand

Nature communications

2024 Volume 15, Issue 1, Page(s) 1972

Abstract: DNA methylation provides a crucial epigenetic mark linking genetic variations to environmental influence. We have analyzed array-based DNA methylation profiles of 160 human retinas with co-measured RNA-seq and >8 million genetic variants, uncovering ... ...

Abstract	DNA methylation provides a crucial epigenetic mark linking genetic variations to environmental influence. We have analyzed array-based DNA methylation profiles of 160 human retinas with co-measured RNA-seq and >8 million genetic variants, uncovering sites of genetic regulation in cis (37,453 methylation quantitative trait loci and 12,505 expression quantitative trait loci) and 13,747 DNA methylation loci affecting gene expression, with over one-third specific to the retina. Methylation and expression quantitative trait loci show non-random distribution and enrichment of biological processes related to synapse, mitochondria, and catabolism. Summary data-based Mendelian randomization and colocalization analyses identify 87 target genes where methylation and gene-expression changes likely mediate the genotype effect on age-related macular degeneration. Integrated pathway analysis reveals epigenetic regulation of immune response and metabolism including the glutathione pathway and glycolysis. Our study thus defines key roles of genetic variations driving methylation changes, prioritizes epigenetic control of gene expression, and suggests frameworks for regulation of macular degeneration pathology by genotype-environment interaction in retina.
MeSH term(s)	Humans ; DNA Methylation/genetics ; Epigenesis, Genetic ; Epigenome ; Macular Degeneration/genetics ; Retina
Language	English
Publishing date	2024-03-04
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-024-46063-8
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Article ; Online: Whole genome sequencing of 4,787 individuals identifies gene-based rare variants in age-related macular degeneration.

Kwong, Alan / Zawistowski, Matthew / Fritsche, Lars G / Zhan, Xiaowei / Bragg-Gresham, Jennifer / Branham, Kari E / Advani, Jayshree / Othman, Mohammad / Ratnapriya, Rinki / Teslovich, Tanya M / Stambolian, Dwight / Chew, Emily Y / Abecasis, Gonçalo R / Swaroop, Anand

Human molecular genetics

2023 Volume 33, Issue 4, Page(s) 374–385

Abstract: Genome-wide association studies have contributed extensively to the discovery of disease-associated common variants. However, the genetic contribution to complex traits is still largely difficult to interpret. We report a genome-wide association study of ...

Abstract	Genome-wide association studies have contributed extensively to the discovery of disease-associated common variants. However, the genetic contribution to complex traits is still largely difficult to interpret. We report a genome-wide association study of 2394 cases and 2393 controls for age-related macular degeneration (AMD) via whole-genome sequencing, with 46.9 million genetic variants. Our study reveals significant single-variant association signals at four loci and independent gene-based signals in CFH, C2, C3, and NRTN. Using data from the Exome Aggregation Consortium (ExAC) for a gene-based test, we demonstrate an enrichment of predicted rare loss-of-function variants in CFH, CFI, and an as-yet unreported gene in AMD, ORMDL2. Our method of using a large variant list without individual-level genotypes as an external reference provides a flexible and convenient approach to leverage the publicly available variant datasets to augment the search for rare variant associations, which can explain additional disease risk in AMD.
MeSH term(s)	Humans ; Genome-Wide Association Study/methods ; Macular Degeneration/genetics ; Genotype ; Genetic Testing ; Whole Genome Sequencing ; Polymorphism, Single Nucleotide/genetics ; Genetic Predisposition to Disease ; Complement Factor H/genetics
Chemical Substances	Complement Factor H (80295-65-4)
Language	English
Publishing date	2023-11-07
Publishing country	England
Document type	Journal Article
ZDB-ID	1108742-0
ISSN	1460-2083 ; 0964-6906
ISSN (online)	1460-2083
ISSN	0964-6906
DOI	10.1093/hmg/ddad189
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Article: A Novel

Ratnapriya, Rinki / Jacobson, Samuel G / Cideciyan, Artur V / English, Milton A / Roman, Alejandro J / Sumaroka, Alexander / Sheplock, Rebecca / Swaroop, Anand

Frontiers in cell and developmental biology

2021 Volume 9, Page(s) 720782

Abstract: Despite major progress in the discovery of causative genes, many individuals and families with inherited retinal degenerations (IRDs) remain without a molecular diagnosis. We applied whole exome sequencing to identify the genetic cause in a family with ... ...

Abstract	Despite major progress in the discovery of causative genes, many individuals and families with inherited retinal degenerations (IRDs) remain without a molecular diagnosis. We applied whole exome sequencing to identify the genetic cause in a family with an autosomal dominant IRD. Eye examinations were performed and affected patients were studied with electroretinography and kinetic and chromatic static perimetry. Sequence variants were analyzed in genes (
Language	English
Publishing date	2021-08-17
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2737824-X
ISSN	2296-634X
ISSN	2296-634X
DOI	10.3389/fcell.2021.720782
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Article: Genetic architecture of retinal and macular degenerative diseases: the promise and challenges of next-generation sequencing.

Ratnapriya, Rinki / Swaroop, Anand

Genome medicine

2013 Volume 5, Issue 10, Page(s) 84

Abstract: Inherited retinal degenerative diseases (RDDs) display wide variation in their mode of inheritance, underlying genetic defects, age of onset, and phenotypic severity. Molecular mechanisms have not been delineated for many retinal diseases, and treatment ... ...

Abstract	Inherited retinal degenerative diseases (RDDs) display wide variation in their mode of inheritance, underlying genetic defects, age of onset, and phenotypic severity. Molecular mechanisms have not been delineated for many retinal diseases, and treatment options are limited. In most instances, genotype-phenotype correlations have not been elucidated because of extensive clinical and genetic heterogeneity. Next-generation sequencing (NGS) methods, including exome, genome, transcriptome and epigenome sequencing, provide novel avenues towards achieving comprehensive understanding of the genetic architecture of RDDs. Whole-exome sequencing (WES) has already revealed several new RDD genes, whereas RNA-Seq and ChIP-Seq analyses are expected to uncover novel aspects of gene regulation and biological networks that are involved in retinal development, aging and disease. In this review, we focus on the genetic characterization of retinal and macular degeneration using NGS technology and discuss the basic framework for further investigations. We also examine the challenges of NGS application in clinical diagnosis and management.
Language	English
Publishing date	2013-10-11
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2484394-5
ISSN	1756-994X
ISSN	1756-994X
DOI	10.1186/gm488
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Article: QTL mapping of human retina DNA methylation identifies 87 gene-epigenome interactions in age-related macular degeneration.

Advani, Jayshree / Corso-Diaz, Ximena / Kwicklis, Madeline / van Asten, Freekje / Ratnapriya, Rinki / Mehta, Puja / Hamel, Andrew / Mahrotra, Sudeep / Segrè, Ayellet / Kiel, Christina / Strunz, Tobias / Weber, Bernhard / Chew, Emily / Hernandez, Dena / Montezuma, Sandra / Ferrington, Deborah / Swaroop, Anand

Research square

2023

Abstract: DNA methylation (DNAm) provides a crucial epigenetic mark linking genetic variations to environmental influence. We analyzed array-based DNAm profiles of 160 human retinas with co-measured RNA-seq and > 8 million genetic variants, uncovering sites of ... ...

Abstract	DNA methylation (DNAm) provides a crucial epigenetic mark linking genetic variations to environmental influence. We analyzed array-based DNAm profiles of 160 human retinas with co-measured RNA-seq and > 8 million genetic variants, uncovering sites of genetic regulation in
Language	English
Publishing date	2023-06-16
Publishing country	United States
Document type	Preprint
DOI	10.21203/rs.3.rs-3011096/v1
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Article: IL-17 Producing Lymphocytes Cause Dry Eye and Corneal Disease With Aging in RXRα Mutant Mouse.

Alam, Jehan / Yazdanpanah, Ghasem / Ratnapriya, Rinki / Borcherding, Nicholas / de Paiva, Cintia S / Li, DeQuan / Guimaraes de Souza, Rodrigo / Yu, Zhiyuan / Pflugfelder, Stephen C

Frontiers in medicine

2022 Volume 9, Page(s) 849990

Abstract: Purpose: To investigate IL-17 related mechanisms for developing dry eye disease in the Pinkie mouse strain with a loss of function RXRα mutation.: Methods: Measures of dry eye disease were assessed in the cornea and conjunctiva. Expression profiling ... ...

Abstract	Purpose: To investigate IL-17 related mechanisms for developing dry eye disease in the Pinkie mouse strain with a loss of function RXRα mutation. Methods: Measures of dry eye disease were assessed in the cornea and conjunctiva. Expression profiling was performed by single-cell RNA sequencing (scRNA-seq) to compare gene expression in conjunctival immune cells. Conjunctival immune cells were immunophenotyped by flow cytometry and confocal microscopy. The activity of RXRα ligand 9-cis retinoic acid (RA) was evaluated in cultured monocytes and γδ T cells. Results: Compared to wild type (WT) C57BL/6, Pinkie has increased signs of dry eye disease, including decreased tear volume, corneal barrier disruption, corneal/conjunctival cornification and goblet cell loss, and corneal vascularization, opacification, and ulceration with aging. ScRNA-seq of conjunctival immune cells identified γδ T cells as the predominant IL-17 expressing population in both strains and there is a 4-fold increased percentage of γδ T cells in Pinkie. Compared to WT, IL-17a, and IL-17f significantly increased in Pinkie with conventional T cells and γδ T cells as the major producers. Flow cytometry revealed an increased number of IL-17 Conclusion: These findings indicate that RXRα suppresses generation of dry eye disease-inducing IL-17 producing lymphocytes s in the conjunctiva and identifies RXRα as a potential therapeutic target in dry eye.
Language	English
Publishing date	2022-03-23
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2775999-4
ISSN	2296-858X
ISSN	2296-858X
DOI	10.3389/fmed.2022.849990
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