Differential Gene Expression in Age-Related Macular Degeneration

Morgan, Denise J.; DeAngelis, Margaret M.

doi:10.1101/cshperspect.a017210

Cited by 20 publications

(22 citation statements)

References 72 publications

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“…We additionally demonstrated excellent tissue integrity as measured in our downstream gene expression and epigenetic experiments 7,8,46. Further, tissue expression signatures as measured by single cell nuclei sequencing obtained from tissue processed in the aforementioned manner are consistent with the specific tissue type and the individual cell type 47.…”

Section: Resultsmentioning

confidence: 52%

“…Law enforcement, firefighters, emergency medical services, providers, or emergency rescuers are required by law as soon as reasonably possible to notify the appropriate organ procurement organization, tissue bank, or eye bank of a pending death or a death that occurs in Utah (Section 112). Working with the Utah Lions Eye Bank, our biorepository implements a standardized system for acquisition of eyes and peripheral blood (serum and plasma) and vitreous ≤6 hours of death, as well as retrospective collection of epidemiologic and clinical data from these donors8 (a detailed appendix can be found Supplementary Information). Because there is a short death-to-preservation time, only potential eye donors that reside 1 hour away in travel distance by car from the Utah Lions Eye Bank (at the John A. Moran Eye Center in Salt Lake City, Utah) are approached.…”

Section: Methodsmentioning

confidence: 99%

“…Our understanding of the systemic pathophysiologic disease mechanisms for AMD have, to date, been primarily informed by genetic epidemiologic studies in human populations (for review, please see DeAngelis et al) 3,7–16. Certainly these analyses have led to identification of important environmental exposures, genetic variation, and serum biomarkers associated with AMD.…”

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confidence: 99%

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The Utah Protocol for Postmortem Eye Phenotyping and Molecular Biochemical Analysis

Owen

Shakoor

Morgan

et al. 2019

Invest. Ophthalmol. Vis. Sci.

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PURPOSE. Current understanding of local disease pathophysiology in AMD is limited. Analysis of the human disease-affected tissue is most informative, as gene expression, expressed quantitative trait loci, microenvironmental, and epigenetic changes can be tissue, cell type, and location specific. Development of a novel translational treatment and prevention strategies particularly for earlier forms of AMD are needed, although access to human ocular tissue analysis is challenging. We present a standardized protocol to study rapidly processed postmortem donor eyes for molecular biochemical and genomic studies. METHODS. We partnered with the Utah Lions Eye Bank to obtain donor human eyes, blood, and vitreous, within 6 hours postmortem. Phenotypic analysis was performed using spectraldomain optical coherence tomography (SD-OCT) and color fundus photography. Macular and extramacular tissues were immediately isolated, and the neural retina and retinal pigment epithelium/choroid from each specimen were separated and preserved. Ocular disease phenotype was analyzed using clinically relevant grading criteria by a group of four ophthalmologists incorporating data from SD-OCT retinal images, fundus photographs, and medical records. RESULTS. The use of multimodal imaging leads to greater resolution of retinal pathology, allowing greater phenotypic rigor for both interobserver phenotype and known clinical diagnoses. Further, our analysis resulted in excellent quality RNA, which demonstrated appropriate tissue segregation. CONCLUSIONS. The Utah protocol is a standardized methodology for analysis of disease mechanisms in AMD. It uniquely allows for simultaneous rigorous phenotypic, molecular biochemical, and genomic analysis of both systemic and local tissues. This better enables the development of disease biomarkers and therapeutic interventions.

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Section: Resultsmentioning

confidence: 52%

Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

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The Utah Protocol for Postmortem Eye Phenotyping and Molecular Biochemical Analysis

Owen

Shakoor

Morgan

et al. 2019

Invest. Ophthalmol. Vis. Sci.

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“…Most importantly these images are taken in a manner consistent with the appearance of the analogous images utilized in the clinical setting. Dissections of donor eyes were carried out immediately according to a standardized protocol to reliably isolate the RPE/choroid from the retina and segregate the layers into quadrants 37 (Owen et al, in press). After the eye is flowered and all imaging is complete, macula retina tissue is collected using an 6mm disposable biopsy punch (Integra, Cat # 33-37) centered over the fovea and flash frozen and stored at −80°C.…”

Section: Methodsmentioning

confidence: 99%

Single-nuclei RNA-seq on human retinal tissue provides improved transcriptome profiling

Liang

Dharmat

Owen

et al. 2018

Preprint

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26Gene expression profiling is an effective way to provide insights into cell function. 27 However, for heterogeneous tissues, bulk RNA-Seq can only provide the average gene 28 expression profile for all cells from the tissue, making the interpretation of the sequencing 29 result challenging. Single-cell RNA-seq, on the other hand, generates transcriptomic 30 profiles of individual cell and cell types, making it a powerful method to decode the 31 heterogeneity in complex tissues. 32 The retina is a heterogeneous tissue composed of multiple cell types with distinct 33 functions. Here we report the first single-nuclei RNA-seq transcriptomic study on human 34 neural retinal tissue to identify transcriptome profile for individual cell types. Six retina 35 samples from three healthy donors were profiled and RNA-seq data with high quality was 36 obtained for 4730 single nuclei. All seven major cell types were observed from the dataset 37 and signature genes for each cell type were identified by differential gene express 38 analysis. The gene expression of the macular and peripheral retina was compared at the 39 cell type level, showing significant improvement from previous bulk RNA-seq studies. 40Furthermore, our dataset showed improved power in prioritizing genes associated with 41 human retinal diseases compared to both mouse single-cell RNA-seq and human bulk 42 RNA-seq results. In conclusion, we demonstrated that feasibility of obtaining single cell 43 transcriptome from human frozen tissues to provide additional insights that is missed by 44 either the human bulk RNA-seq or the animal models. 45 46 48 cell type and state, and investigating human diseases 1-3 . Transcriptome can be more 49 powerful when combined with other 'omics' data to build prediction models on human 50 diseases 4 . For example, by combining transcriptomic data and proteomic data, a list of 51 candidate disease genes can be predicted with high specificity 5 . However, until recently, 52 vast majority transcriptome profiles are generated from profiling tissue samples 53 containing thousands to millions of cells. Thus, gene expression information of individual 54 cells would be lost. For tissues with high cellular heterogeneity, knowing the transcriptome 55 profiles of each cell type would be important for both identification of novel cell types and 56 understanding the functional organization of the tissue. Cell sorting would be required to 57 obtain transcriptome of a single cell type; not only was it not always practical, but also the 58 heterogeneities of many tissues were not fully revealed. This gap was met by the 59 development of the high throughput single-cell RNA-seq technology 6-8 . 60 61 Transcriptomic studies on the single cell level was first performed decades ago 9,10 , while 62 the first single-cell transcriptome study based on Next-Generation Sequencing was 63 reported ten years ago 11 . Since then, technologies have been dramatically improved in 64 scale and sensitivity. Development in single-cell isolation, such as microf...

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“…Therapeutics that can prevent the progression from early to intermediate and/or from intermediate to advanced stages of the disease are greatly needed to alleviate the profound detrimental impacts of vision loss; elucidation of the molecular mechanisms involved in the etiology and progression of AMD, taking into account evidence from gene expression, epigenetic, molecular, and biochemical studies to complement genetic epidemiological studies, will be necessary to accomplish this goal [22–25]. …”

Section: Introductionmentioning

confidence: 99%

Epidemiology of age-related macular degeneration (AMD): associations with cardiovascular disease phenotypes and lipid factors

2016

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Age-related macular degeneration (AMD) is the leading cause of irreversible blindness in adults over 50 years old. Genetic, epidemiological, and molecular studies are beginning to unravel the intricate mechanisms underlying this complex disease, which implicate the lipid-cholesterol pathway in the pathophysiology of disease development and progression. Many of the genetic and environmental risk factors associated with AMD are also associated with other complex degenerative diseases of advanced age, including cardiovascular disease (CVD). In this review, we present epidemiological findings associating AMD with a variety of lipid pathway genes, cardiovascular phenotypes, and relevant environmental exposures. Despite a number of studies showing significant associations between AMD and these lipid/cardiovascular factors, results have been mixed and as such the relationships among these factors and AMD remain controversial. It is imperative that researchers not only tease out the various contributions of such factors to AMD development but also the connections between AMD and CVD to develop optimal precision medical care for aging adults.

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Differential Gene Expression in Age-Related Macular Degeneration

Cited by 20 publications

References 72 publications

The Utah Protocol for Postmortem Eye Phenotyping and Molecular Biochemical Analysis

The Utah Protocol for Postmortem Eye Phenotyping and Molecular Biochemical Analysis

Single-nuclei RNA-seq on human retinal tissue provides improved transcriptome profiling

Epidemiology of age-related macular degeneration (AMD): associations with cardiovascular disease phenotypes and lipid factors

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