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Peng X, Jia X, Shang G, Xue M, Jiang M, Chen D, Zhang F, Hu Y. The generation and characterization of a transgenic zebrafish line with lens-specific Cre expression. Mol Vis 2024; 30:123-136. [PMID: 38601019 PMCID: PMC11006009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 03/17/2024] [Indexed: 04/12/2024] Open
Abstract
Purpose Danio rerio zebrafish constitute a popular model for studying lens development and congenital cataracts. However, the specific deletion of a gene with a Cre/LoxP system in the zebrafish lens is unavailable because of the lack of a lens-Cre-transgenic zebrafish. This study aimed to generate a transgenic zebrafish line in which Cre recombinase was specifically expressed in the lens. Methods The pTol2 cryaa:Cre-polyA-cryaa:EGFP (enhanced green fluorescent protein) plasmid was constructed and co-injected with Tol2-transposase into one-to-two-cell-stage wild-type (WT) zebrafish embryos. Whole-mount in situ hybridization (ISH), tissue section, hematoxylin and eosin staining, a Western blot, a split-lamp observation, and a grid transmission assay were used to analyze the Cre expression, lens structure, and lens transparency of the transgenic zebrafish. Results In this study, we generated a transgenic zebrafish line, zTg(cryaa:Cre-cryaa:EGFP), in which Cre recombinase and EGFP were driven by the lens-specific cryaa promoter. zTg(cryaa:Cre-cryaa:EGFP) began to express Cre and EGFP specifically in the lens at the 22 hpf stage, and this ectopic Cre could efficiently and specifically delete the red fluorescent protein (RFP) signal from the lens when zTg(cryaa:Cre-cryaa:EGFP) embryos were injected with the loxP-flanked RFP plasmid. The overexpression of Cre and EGFP did not impair zebrafish development or lens transparency. Accordingly, this zTg(cryaa:Cre-cryaa:EGFP) zebrafish line is a useful tool for gene editing, specifically with zebrafish lenses. Conclusions We established a zTg(cryaa:Cre-cryaa:EGFP) zebrafish line that can specifically express an active Cre recombinase in lens tissues. This transgenic zebrafish line can be used as a tool to specifically manipulate a gene in zebrafish lenses.
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Affiliation(s)
- Xuyan Peng
- The Laboratory of Ophthalmology and Vision Science, Department of Ophthalmology, The First Affiliated Hospital of Zhengzhou University, Zheng Zhou, China
| | - Xiaolin Jia
- The Laboratory of Ophthalmology and Vision Science, Department of Ophthalmology, The First Affiliated Hospital of Zhengzhou University, Zheng Zhou, China
| | - Guohui Shang
- Department of Medical Genetics and Cell Biology, School of Basic Medical Sciences, Zhengzhou University, Zheng Zhou, China
| | - Mengjiao Xue
- The Laboratory of Ophthalmology and Vision Science, Department of Ophthalmology, The First Affiliated Hospital of Zhengzhou University, Zheng Zhou, China
| | - Mingjun Jiang
- The Laboratory of Ophthalmology and Vision Science, Department of Ophthalmology, The First Affiliated Hospital of Zhengzhou University, Zheng Zhou, China
| | - Dandan Chen
- The Laboratory of Ophthalmology and Vision Science, Department of Ophthalmology, The First Affiliated Hospital of Zhengzhou University, Zheng Zhou, China
| | - Fengyan Zhang
- The Laboratory of Ophthalmology and Vision Science, Department of Ophthalmology, The First Affiliated Hospital of Zhengzhou University, Zheng Zhou, China
| | - Yanzhong Hu
- The Laboratory of Ophthalmology and Vision Science, Department of Ophthalmology, The First Affiliated Hospital of Zhengzhou University, Zheng Zhou, China
- Joint National Laboratory for Antibody Drug Engineering, Henan University School of Basic Medical Sciences. Kaifeng, China
- Kaifeng Key Lab for Cataract and Myopia, Institute of Eye Disease, Kaifeng Central Hospital, Kaifeng, China
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2
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Panda A, Judycka S, Palińska-Żarska K, Debernardis R, Jarmołowicz S, Jastrzębski JP, Rocha de Almeida T, Błażejewski M, Hliwa P, Krejszeff S, Żarski D. Paternal-effect-genes revealed through sperm cryopreservation in Perca fluviatilis. Sci Rep 2024; 14:6396. [PMID: 38493223 PMCID: PMC10944473 DOI: 10.1038/s41598-024-56971-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 03/13/2024] [Indexed: 03/18/2024] Open
Abstract
Knowledge about paternal-effect-genes (PEGs) (genes whose expression in the progeny is influenced by paternal factors present in the sperm) in fish is very limited. To explore this issue, we used milt cryopreservation as a specific challenge test for sperm cells, thus enabling selection amidst cryo-sensitivity. We created two groups of Eurasian perch (Perca fluviatilis) as a model - eggs fertilized either with fresh (Fresh group) or cryopreserved (Cryo group) milt from the same male followed by phenotypic-transcriptomic examination of consequences of cryopreservation in obtained progeny (at larval stages). Most of the phenotypical observations were similar in both groups, except the final weight which was higher in the Cryo group. Milt cryopreservation appeared to act as a "positive selection" factor, upregulating most PEGs in the Cryo group. Transcriptomic profile of freshly hatched larvae sourced genes involved in the development of visual perception and we identified them as PEGs. Consequently, larvae from the Cryo group exhibited enhanced eyesight, potentially contributing to more efficient foraging and weight gain compared to the Fresh group. This study unveils, for the first time, the significant influence of the paternal genome on the development of the visual system in fish, highlighting pde6g, opn1lw1, and rbp4l as novel PEGs.
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Affiliation(s)
- Abhipsa Panda
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Tuwima 10, 10-748, Olsztyn, Poland
| | - Sylwia Judycka
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Tuwima 10, 10-748, Olsztyn, Poland
| | - Katarzyna Palińska-Żarska
- Department of Ichthyology, Hydrobiology and Aquatic Ecology, National Inland Fisheries Research Institute, Oczapowskiego 10, 10-719, Olsztyn, Poland
| | - Rossella Debernardis
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Tuwima 10, 10-748, Olsztyn, Poland
| | - Sylwia Jarmołowicz
- Department of Ichthyology, Hydrobiology and Aquatic Ecology, National Inland Fisheries Research Institute, Oczapowskiego 10, 10-719, Olsztyn, Poland
| | - Jan Paweł Jastrzębski
- Department of Plant Physiology, Genetics, and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-719, Olsztyn, Poland
| | - Taina Rocha de Almeida
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Tuwima 10, 10-748, Olsztyn, Poland
| | - Maciej Błażejewski
- Department of Ichthyology and Aquaculture, University of Warmia and Mazury in Olsztyn, Oczapowskiego 5, 10-719, Olsztyn, Poland
| | - Piotr Hliwa
- Department of Ichthyology and Aquaculture, University of Warmia and Mazury in Olsztyn, Oczapowskiego 5, 10-719, Olsztyn, Poland
| | - Sławomir Krejszeff
- Department of Aquaculture, National Inland Fisheries Research Institute, Oczapowskiego 10, 10-719, Olsztyn, Poland
| | - Daniel Żarski
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Tuwima 10, 10-748, Olsztyn, Poland.
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3
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Brennan L, Disatham J, Menko AS, Kantorow M. Multiomic analysis implicates FOXO4 in genetic regulation of chick lens fiber cell differentiation. Dev Biol 2023; 504:25-37. [PMID: 37722500 PMCID: PMC10843493 DOI: 10.1016/j.ydbio.2023.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 09/06/2023] [Accepted: 09/14/2023] [Indexed: 09/20/2023]
Abstract
A classic model for identification of novel differentiation mechanisms and pathways is the eye lens that consists of a monolayer of quiescent epithelial cells that are the progenitors of a core of mature fully differentiated fiber cells. The differentiation of lens epithelial cells into fiber cells follows a coordinated program involving cell cycle exit, expression of key structural proteins and the hallmark elimination of organelles to achieve transparency. Although multiple mechanisms and pathways have been identified to play key roles in lens differentiation, the entirety of mechanisms governing lens differentiation remain to be discovered. A previous study established that specific chromatin accessibility changes were directly associated with the expression of essential lens fiber cell genes, suggesting that the activity of transcription factors needed for expression of these genes could be regulated through binding access to the identified chromatin regions. Sequence analysis of the identified chromatin accessible regions revealed enhanced representation of the binding sequence for the transcription factor FOXO4 suggesting a direct role for FOXO4 in expression of these genes. FOXO4 is known to regulate a variety of cellular processes including cellular response to metabolic and oxidative stress, cell cycle withdrawal, and homeostasis, suggesting a previously unidentified role for FOXO4 in the regulation of lens cell differentiation. To further evaluate the role of FOXO4 we employed a multiomics approach to analyze the relationship between genome-wide FOXO4 binding, the differentiation-specific expression of key genes, and chromatin accessibility. To better identify active promoters and enhancers we also examined histone modification through analysis of H3K27ac. Specific methods included CUT&RUN (FOXO4 binding and H3K27ac modification), RNA-seq (differentiation state specific gene expression), and ATAC-seq (chromatin accessibility). CUT&RUN identified 20,966 FOXO4 binding sites and 33,921 H3K27ac marked regions across the lens fiber cell genome. RNA-seq identified 956 genes with significantly greater expression levels in fiber cells compared to epithelial cells (log2FC > 0.7, q < 0.05) and 2548 genes with significantly lower expression levels (log2FC < -0.7, q < 0.05). Integrated analysis identified 1727 differentiation-state specific genes that were nearest neighbors to at least one FOXO4 binding site, including genes encoding lens gap junctions (GJA1, GJA3), lens structural proteins (BFSP1, CRYBB1, ASL1), and genes required for lens transparency (HSF4, NRCAM). Multiomics analysis comparing the identified FOXO4 binding sites in published ATAC-seq data revealed that chromatin accessibility was associated with FOXO4-dependent gene expression during lens differentiation. The results provide evidence for an important requirement for FOXO4 in the regulated expression of key genes required for lens differentiation and link epigenetic regulation of chromatin accessibility and H3K27ac histone modification with the function of FOXO4 in controlling lens gene expression during lens fiber cell differentiation.
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Affiliation(s)
- Lisa Brennan
- Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL, USA
| | - Joshua Disatham
- Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL, USA
| | - A Sue Menko
- Department of Pathology and Genomic Medicine, Thomas Jefferson University, Philadelphia, PA, USA
| | - Marc Kantorow
- Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL, USA.
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Aryal S, Anand D, Huang H, Reddy AP, Wilmarth PA, David LL, Lachke SA. Proteomic profiling of retina and retinal pigment epithelium combined embryonic tissue to facilitate ocular disease gene discovery. Hum Genet 2023; 142:927-947. [PMID: 37191732 PMCID: PMC10680127 DOI: 10.1007/s00439-023-02570-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/04/2023] [Indexed: 05/17/2023]
Abstract
To expedite gene discovery in eye development and its associated defects, we previously developed a bioinformatics resource-tool iSyTE (integrated Systems Tool for Eye gene discovery). However, iSyTE is presently limited to lens tissue and is predominantly based on transcriptomics datasets. Therefore, to extend iSyTE to other eye tissues on the proteome level, we performed high-throughput tandem mass spectrometry (MS/MS) on mouse embryonic day (E)14.5 retina and retinal pigment epithelium combined tissue and identified an average of 3300 proteins per sample (n = 5). High-throughput expression profiling-based gene discovery approaches-involving either transcriptomics or proteomics-pose a key challenge of prioritizing candidates from thousands of RNA/proteins expressed. To address this, we used MS/MS proteome data from mouse whole embryonic body (WB) as a reference dataset and performed comparative analysis-termed "in silico WB-subtraction"-with the retina proteome dataset. In silico WB-subtraction identified 90 high-priority proteins with retina-enriched expression at stringency criteria of ≥ 2.5 average spectral counts, ≥ 2.0 fold-enrichment, false discovery rate < 0.01. These top candidates represent a pool of retina-enriched proteins, several of which are associated with retinal biology and/or defects (e.g., Aldh1a1, Ank2, Ank3, Dcn, Dync2h1, Egfr, Ephb2, Fbln5, Fbn2, Hras, Igf2bp1, Msi1, Rbp1, Rlbp1, Tenm3, Yap1, etc.), indicating the effectiveness of this approach. Importantly, in silico WB-subtraction also identified several new high-priority candidates with potential regulatory function in retina development. Finally, proteins exhibiting expression or enriched-expression in the retina are made accessible in a user-friendly manner at iSyTE ( https://research.bioinformatics.udel.edu/iSyTE/ ), to allow effective visualization of this information and facilitate eye gene discovery.
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Affiliation(s)
- Sandeep Aryal
- Department of Biological Sciences, University of Delaware, Newark, DE, 19716, USA
| | - Deepti Anand
- Department of Biological Sciences, University of Delaware, Newark, DE, 19716, USA
| | - Hongzhan Huang
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19713, USA
| | - Ashok P Reddy
- Proteomics Shared Resource, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Phillip A Wilmarth
- Proteomics Shared Resource, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Larry L David
- Proteomics Shared Resource, Oregon Health and Science University, Portland, OR, 97239, USA
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Salil A Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE, 19716, USA.
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19713, USA.
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5
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Disatham J, Brennan L, Cvekl A, Kantorow M. Multiomics Analysis Reveals Novel Genetic Determinants for Lens Differentiation, Structure, and Transparency. Biomolecules 2023; 13:693. [PMID: 37189439 PMCID: PMC10136076 DOI: 10.3390/biom13040693] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/13/2023] [Accepted: 04/16/2023] [Indexed: 05/17/2023] Open
Abstract
Recent advances in next-generation sequencing and data analysis have provided new gateways for identification of novel genome-wide genetic determinants governing tissue development and disease. These advances have revolutionized our understanding of cellular differentiation, homeostasis, and specialized function in multiple tissues. Bioinformatic and functional analysis of these genetic determinants and the pathways they regulate have provided a novel basis for the design of functional experiments to answer a wide range of long-sought biological questions. A well-characterized model for the application of these emerging technologies is the development and differentiation of the ocular lens and how individual pathways regulate lens morphogenesis, gene expression, transparency, and refraction. Recent applications of next-generation sequencing analysis on well-characterized chicken and mouse lens differentiation models using a variety of omics techniques including RNA-seq, ATAC-seq, whole-genome bisulfite sequencing (WGBS), chip-seq, and CUT&RUN have revealed a wide range of essential biological pathways and chromatin features governing lens structure and function. Multiomics integration of these data has established new gene functions and cellular processes essential for lens formation, homeostasis, and transparency including the identification of novel transcription control pathways, autophagy remodeling pathways, and signal transduction pathways, among others. This review summarizes recent omics technologies applied to the lens, methods for integrating multiomics data, and how these recent technologies have advanced our understanding ocular biology and function. The approach and analysis are relevant to identifying the features and functional requirements of more complex tissues and disease states.
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Affiliation(s)
- Joshua Disatham
- Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL 33431, USA; (J.D.); (L.B.)
| | - Lisa Brennan
- Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL 33431, USA; (J.D.); (L.B.)
| | - Ales Cvekl
- Departments of Ophthalmology and Visual Sciences and Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA;
| | - Marc Kantorow
- Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL 33431, USA; (J.D.); (L.B.)
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6
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Aryal S, Anand D, Huang H, Reddy AP, Wilmarth PA, David LL, Lachke SA. Proteomic profiling of retina and retinal pigment epithelium combined embryonic tissue to facilitate ocular disease gene discovery. RESEARCH SQUARE 2023:rs.3.rs-2652395. [PMID: 36993571 PMCID: PMC10055508 DOI: 10.21203/rs.3.rs-2652395/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
To expedite gene discovery in eye development and its associated defects, we previously developed a bioinformatics resource-tool iSyTE (integrated Systems Tool for Eye gene discovery). However, iSyTE is presently limited to lens tissue and is predominantly based on transcriptomics datasets. Therefore, to extend iSyTE to other eye tissues on the proteome level, we performed high-throughput tandem mass spectrometry (MS/MS) on mouse embryonic day (E)14.5 retina and retinal pigment epithelium combined tissue and identified an average of 3,300 proteins per sample (n=5). High-throughput expression profiling-based gene discovery approaches-involving either transcriptomics or proteomics-pose a key challenge of prioritizing candidates from thousands of RNA/proteins expressed. To address this, we used MS/MS proteome data from mouse whole embryonic body (WB) as a reference dataset and performed comparative analysis-termed "in silico WB-subtraction"-with the retina proteome dataset. In silico WB-subtraction identified 90 high-priority proteins with retina-enriched expression at stringency criteria of ³2.5 average spectral counts, ³2.0 fold-enrichment, False Discovery Rate <0.01. These top candidates represent a pool of retina-enriched proteins, several of which are associated with retinal biology and/or defects (e.g., Aldh1a1, Ank2, Ank3, Dcn, Dync2h1, Egfr, Ephb2, Fbln5, Fbn2, Hras, Igf2bp1, Msi1, Rbp1, Rlbp1, Tenm3, Yap1, etc.), indicating the effectiveness of this approach. Importantly, in silico WB-subtraction also identified several new high-priority candidates with potential regulatory function in retina development. Finally, proteins exhibiting expression or enriched-expression in the retina are made accessible in a user-friendly manner at iSyTE (https://research.bioinformatics.udel.edu/iSyTE/), to allow effective visualization of this information and facilitate eye gene discovery.
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Affiliation(s)
- Sandeep Aryal
- Department of Biological Sciences, University of Delaware, Newark, DE 19716 USA
| | - Deepti Anand
- Department of Biological Sciences, University of Delaware, Newark, DE 19716 USA
| | - Hongzhan Huang
- Center for Bioinformatics & Computational Biology, University of Delaware, Newark, DE 19713 USA
| | - Ashok P. Reddy
- Proteomics Shared Resource, Oregon Health & Science University, Portland, OR 97239, USA
| | - Phillip A. Wilmarth
- Proteomics Shared Resource, Oregon Health & Science University, Portland, OR 97239, USA
| | - Larry L. David
- Proteomics Shared Resource, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Chemical Physiology & Biochemistry, Oregon Health & Science University, Portland, OR 97239, USA
| | - Salil A. Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE 19716 USA
- Center for Bioinformatics & Computational Biology, University of Delaware, Newark, DE 19713 USA
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7
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Posner M, Murray KL, Andrew B, Brdicka S, Roberts A, Franklin K, Hussen A, Kaye T, Kepp E, McDonald MS, Snodgrass T, Zientek K, David LL. Impact of α-crystallin protein loss on zebrafish lens development. Exp Eye Res 2023; 227:109358. [PMID: 36572168 PMCID: PMC9918708 DOI: 10.1016/j.exer.2022.109358] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/27/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022]
Abstract
The α-crystallin small heat shock proteins contribute to the transparency and refractive properties of the vertebrate eye lens and prevent the protein aggregation that would otherwise produce lens cataracts, the leading cause of human blindness. There are conflicting data in the literature as to what role the α-crystallins may play in early lens development. In this study, we used CRISPR gene editing to produce zebrafish lines with mutations in each of the three α-crystallin genes (cryaa, cryaba and cryabb) to prevent protein production. The absence of each α-crystallin protein was analyzed by mass spectrometry, and lens phenotypes were assessed with differential interference contrast microscopy and histology. Loss of αA-crystallin produced a variety of lens defects with varying severity in larvae at 3 and 4 dpf but little substantial change in normal fiber cell denucleation. Loss of αBa-crystallin produced no substantial lens defects. Our cryabb mutant produced a truncated αBb-crystallin protein and showed no substantial change in lens development. Mutation of each α-crystallin gene did not alter the mRNA levels of the remaining two, suggesting a lack of genetic compensation. These data suggest that αA-crystallin plays some role in lens development, but the range of phenotype severity in null mutants indicates its loss simply increases the chance for defects and that the protein is not essential. Our finding that cryaba and cryabb mutants lack noticeable lens defects is congruent with insubstantial transcript levels for these genes in lens epithelial and fiber cells through five days of development. Future experiments can explore the molecular mechanisms leading to lens defects in cryaa null mutants and the impact of αA-crystallin loss during zebrafish lens aging.
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Affiliation(s)
- Mason Posner
- Department of Biology and Toxicology, Ashland University, Ashland, OH, USA.
| | - Kelly L Murray
- Department of Biology and Toxicology, Ashland University, Ashland, OH, USA
| | - Brandon Andrew
- Department of Biology and Toxicology, Ashland University, Ashland, OH, USA
| | - Stuart Brdicka
- Department of Biology and Toxicology, Ashland University, Ashland, OH, USA
| | - Alexis Roberts
- Department of Biology and Toxicology, Ashland University, Ashland, OH, USA
| | - Kirstan Franklin
- Department of Biology and Toxicology, Ashland University, Ashland, OH, USA
| | - Adil Hussen
- Department of Biology and Toxicology, Ashland University, Ashland, OH, USA
| | - Taylor Kaye
- Department of Biology and Toxicology, Ashland University, Ashland, OH, USA
| | - Emmaline Kepp
- Department of Biology and Toxicology, Ashland University, Ashland, OH, USA
| | - Mathew S McDonald
- Department of Biology and Toxicology, Ashland University, Ashland, OH, USA
| | - Tyler Snodgrass
- Department of Biology and Toxicology, Ashland University, Ashland, OH, USA
| | - Keith Zientek
- Department of Chemical Physiology & Biochemistry, Oregon Health and Science University, USA
| | - Larry L David
- Department of Chemical Physiology & Biochemistry, Oregon Health and Science University, USA
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Zhang SR, Pan M, Gao YB, Fan RY, Bin XN, Qian ST, Tang CL, Ying HJ, Wu JQ, He MF. Efficacy and mechanism study of cordycepin against brain metastases of small cell lung cancer based on zebrafish. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2023; 109:154613. [PMID: 36610112 DOI: 10.1016/j.phymed.2022.154613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 12/03/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Small cell lung cancer (SCLC) is an aggressive tumor with high brain metastasis (BM) potential. There has been no significant progress in the treatment of SCLC for more than 30 years. Cordycepin has shown the therapeutic potential for cancer by modulating multiple cellular signaling pathways. However, the effect and mechanism of cordycepin on anti-SCLC BM remain unknown. PURPOSE In this study, we focused on the anti-SCLC BM effect of cordycepin in the zebrafish model and its potential mechanism. STUDY DESIGN AND METHODS A SCLC xenograft model based on zebrafish embryos and in vitro cell migration assay were established. Cordycepin was administrated by soaking and microinjection in the zebrafish model. RNA-seq assay was performed to analyze transcriptomes of different groups. Geno Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment were performed to reveal the underlying mechanism. Real-time qPCR was used to verify the effects of cordycepin on the key genes. RESULTS Cordycepin showed lower cytotoxicity in vitro compared with cisplatin, anlotinib and etoposide, but showed comparable anti-proliferation and anti-BM effects in zebrafish SCLC xenograft model. Cordycepin showed significant anti-SCLC BM effects when administrated by both soaking and microinjection. RNA-seq demonstrated that cordycepin was involved in vitamin D metabolism, lipid transport, and proteolysis in cellular protein catabolic process pathways in SCLC BM microenvironment in zebrafish, and was involved in regulating the expressions of key genes such as cyp24a1, apoa1a, ctsl. The anti-BM effect of cordycepin in SCLC was mediated by reversing the expression of these genes. CONCLUSION Our work is the first to describe the mechanism of cordycepin against SCLC BM from the perspective of regulating the brain microenvironment, providing new evidence for the anti-tumor effect of cordycepin.
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Affiliation(s)
- Shi-Ru Zhang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 Puzhu South Road, Nanjing 211816, China
| | - Miao Pan
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 Puzhu South Road, Nanjing 211816, China
| | - Ying-Bin Gao
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 Puzhu South Road, Nanjing 211816, China
| | - Ruo-Yue Fan
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 Puzhu South Road, Nanjing 211816, China
| | - Xin-Ni Bin
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 Puzhu South Road, Nanjing 211816, China
| | - Si-Tong Qian
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, No. 24 Tongjia Lane, Nanjing 210009, China
| | - Cheng-Lun Tang
- Luzhou Pinchuang Technology Co. Ltd., Nanjing Sheng Ming Yuan Health Technology Co. Ltd., Nanjing 210032, China
| | - Han-Jie Ying
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 Puzhu South Road, Nanjing 211816, China
| | - Jia-Qi Wu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 Puzhu South Road, Nanjing 211816, China.
| | - Ming-Fang He
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 Puzhu South Road, Nanjing 211816, China.
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9
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Patel SD, Anand D, Motohashi H, Katsuoka F, Yamamoto M, Lachke SA. Deficiency of the bZIP transcription factors Mafg and Mafk causes misexpression of genes in distinct pathways and results in lens embryonic developmental defects. Front Cell Dev Biol 2022; 10:981893. [PMID: 36092713 PMCID: PMC9459095 DOI: 10.3389/fcell.2022.981893] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 07/28/2022] [Indexed: 01/11/2023] Open
Abstract
Deficiency of the small Maf proteins Mafg and Mafk cause multiple defects, namely, progressive neuronal degeneration, cataract, thrombocytopenia and mid-gestational/perinatal lethality. Previous data shows Mafg -/-:Mafk +/- compound knockout (KO) mice exhibit cataracts age 4-months onward. Strikingly, Mafg -/-:Mafk -/- double KO mice develop lens defects significantly early in life, during embryogenesis, but the pathobiology of these defects is unknown, and is addressed here. At embryonic day (E)16.5, the epithelium of lens in Mafg -/-:Mafk -/- animals appears abnormally multilayered as demonstrated by E-cadherin and nuclear staining. Additionally, Mafg -/-:Mafk -/- lenses exhibit abnormal distribution of F-actin near the "fulcrum" region where epithelial cells undergo apical constriction prior to elongation and reorientation as early differentiating fiber cells. To identify the underlying molecular changes, we performed high-throughput RNA-sequencing of E16.5 Mafg -/-:Mafk -/- lenses and identified a cohort of differentially expressed genes that were further prioritized using stringent filtering criteria and validated by RT-qPCR. Several key factors associated with the cytoskeleton, cell cycle or extracellular matrix (e.g., Cdk1, Cdkn1c, Camsap1, Col3a1, Map3k12, Sipa1l1) were mis-expressed in Mafg -/-:Mafk -/- lenses. Further, the congenital cataract-linked extracellular matrix peroxidase Pxdn was significantly overexpressed in Mafg -/-:Mafk -/- lenses, which may cause abnormal cell morphology. These data also identified the ephrin signaling receptor Epha5 to be reduced in Mafg -/-:Mafk -/- lenses. This likely contributes to the Mafg -/-:Mafk -/- multilayered lens epithelium pathology, as loss of an ephrin ligand, Efna5 (ephrin-A5), causes similar lens defects. Together, these findings uncover a novel early function of Mafg and Mafk in lens development and identify their new downstream regulatory relationships with key cellular factors.
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Affiliation(s)
- Shaili D. Patel
- Department of Biological Sciences, University of Delaware, Newark, DE, United States
| | - Deepti Anand
- Department of Biological Sciences, University of Delaware, Newark, DE, United States
| | - Hozumi Motohashi
- Department of Gene Expression Regulation, Institute of Development, Aging, and Cancer, Tohoku University, Sendai, Japan
| | - Fumiki Katsuoka
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, Sendai, Japan
| | - Masayuki Yamamoto
- Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Salil A. Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE, United States,Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, United States,*Correspondence: Salil A. Lachke,
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10
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Lachke SA. RNA-binding proteins and post-transcriptional regulation in lens biology and cataract: Mediating spatiotemporal expression of key factors that control the cell cycle, transcription, cytoskeleton and transparency. Exp Eye Res 2022; 214:108889. [PMID: 34906599 PMCID: PMC8792301 DOI: 10.1016/j.exer.2021.108889] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 11/29/2021] [Accepted: 12/05/2021] [Indexed: 01/03/2023]
Abstract
Development of the ocular lens - a transparent tissue capable of sustaining frequent shape changes for optimal focusing power - pushes the boundaries of what cells can achieve using the molecular toolkit encoded by their genomes. The mammalian lens contains broadly two types of cells, the anteriorly located monolayer of epithelial cells which, at the equatorial region of the lens, initiate differentiation into fiber cells that contribute to the bulk of the tissue. This differentiation program involves massive upregulation of select fiber cell-expressed RNAs and their subsequent translation into high amounts of proteins, such as crystallins. But intriguingly, fiber cells achieve this while also simultaneously undergoing significant morphological changes such as elongation - involving about 1000-fold length-wise increase - and migration, which requires modulation of cytoskeletal and cell adhesion factors. Adding further to the challenges, these molecular and cellular events have to be coordinated as fiber cells progress toward loss of their nuclei and organelles, which irreversibly compromises their potential for harnessing genetically hardwired information. A long-standing question is how processes downstream of signaling and transcription, which may also participate in feedback regulation, contribute toward orchestrating these cellular differentiation events in the lens. It is now becoming clear from findings over the past decade that post-transcriptional gene expression regulatory mechanisms are critical in controlling cellular proteomes and coordinating key processes in lens development and fiber cell differentiation. Indeed, RNA-binding proteins (RBPs) such as Caprin2, Celf1, Rbm24 and Tdrd7 have now been described in mediating post-transcriptional control over key factors (e.g. Actn2, Cdkn1a (p21Cip1), Cdkn1b (p27Kip1), various crystallins, Dnase2b, Hspb1, Pax6, Prox1, Sox2) that are variously involved in cell cycle, transcription, cytoskeleton maintenance and differentiation in the lens. Furthermore, deficiencies of these RBPs have been shown to result in various eye and lens defects and/or cataract. Because fiber cell differentiation in the lens occurs throughout life, the underlying regulatory mechanisms operational in development are expected to also be recruited for the maintenance of transparency in aged lenses. Indeed, in support of this, TDRD7 and CAPRIN2 loci have been linked to age-related cataract in humans. Here, I will review the role of key RBPs in the lens and their importance in understanding the pathology of lens defects. I will discuss advances in RBP-based gene expression control, in general, and the important challenges that need to be addressed in the lens to define the mechanisms that determine the epithelial and fiber cell proteome. Finally, I will also discuss in detail several key future directions including the application of bioinformatics approaches such as iSyTE to study RBP-based post-transcriptional gene expression control in the aging lens and in the context of age-related cataract.
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Affiliation(s)
- Salil A Lachke
- Department of Biological Sciences, University of Delaware, 105 The Green, Delaware Avenue, 236 Wolf Hall, Newark, DE, USA; Center for Bioinformatics & Computational Biology, University of Delaware, Newark, DE, 19716, USA.
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11
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Slavotinek A, Misceo D, Htun S, Mathisen L, Frengen E, Foreman M, Hurtig JE, Enyenihi L, Sterrett MC, Leung SW, Schneidman-Duhovny D, Estrada-Veras J, Duncan JL, Haaxma CA, Kamsteeg EJ, Xia V, Beleford D, Si Y, Douglas G, Treidene HE, van Hoof A, Fasken MB, Corbett AH. Biallelic variants in the RNA exosome gene EXOSC5 are associated with developmental delays, short stature, cerebellar hypoplasia and motor weakness. Hum Mol Genet 2021; 29:2218-2239. [PMID: 32504085 DOI: 10.1093/hmg/ddaa108] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 05/10/2020] [Accepted: 05/28/2020] [Indexed: 12/15/2022] Open
Abstract
The RNA exosome is an essential ribonuclease complex required for processing and/or degradation of both coding and non-coding RNAs. We identified five patients with biallelic variants in EXOSC5, which encodes a structural subunit of the RNA exosome. The clinical features of these patients include failure to thrive, short stature, feeding difficulties, developmental delays that affect motor skills, hypotonia and esotropia. Brain MRI revealed cerebellar hypoplasia and ventriculomegaly. While we ascertained five patients, three patients with distinct variants of EXOSC5 were studied in detail. The first patient had a deletion involving exons 5-6 of EXOSC5 and a missense variant, p.Thr114Ile, that were inherited in trans, the second patient was homozygous for p.Leu206His and the third patient had paternal isodisomy for chromosome 19 and was homozygous for p.Met148Thr. The additional two patients ascertained are siblings who had an early frameshift mutation in EXOSC5 and the p.Thr114Ile missense variant that were inherited in trans. We employed three complementary approaches to explore the requirement for EXOSC5 in brain development and assess consequences of pathogenic EXOSC5 variants. Loss of function for exosc5 in zebrafish results in shortened and curved tails/bodies, reduced eye/head size and edema. We modeled pathogenic EXOSC5 variants in both budding yeast and mammalian cells. Some of these variants cause defects in RNA exosome function as well as altered interactions with other RNA exosome subunits. These findings expand the number of genes encoding RNA exosome subunits linked to human disease while also suggesting that disease mechanism varies depending on the specific pathogenic variant.
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Affiliation(s)
- Anne Slavotinek
- Department of Pediatrics, University of California, San Francisco, CA 94143, USA
| | - Doriana Misceo
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo 0450, Norway
| | - Stephanie Htun
- Department of Pediatrics, University of California, San Francisco, CA 94143, USA
| | - Linda Mathisen
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo 0450, Norway
| | - Eirik Frengen
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo 0450, Norway
| | - Michelle Foreman
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center-Houston, Houston, TX 77030, USA
| | - Jennifer E Hurtig
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center-Houston, Houston, TX 77030, USA
| | - Liz Enyenihi
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | | | - Sara W Leung
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Dina Schneidman-Duhovny
- School of Computer Science and Engineering and the Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Juvianee Estrada-Veras
- Department of Pediatrics-Medical Genetics and Metabolism, Uniformed Services University/Walter Reed NMMC Bethesda, MD 20889, USA
| | - Jacque L Duncan
- Department of Ophthalmology, University of California, San Francisco, CA 94143, USA
| | - Charlotte A Haaxma
- Department of Pediatric Neurology, Amalia Children's Hospital and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen 6500 HB, The Netherlands
| | - Erik-Jan Kamsteeg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500 HB, The Netherlands
| | - Vivian Xia
- Department of Pediatrics, University of California, San Francisco, CA 94143, USA
| | - Daniah Beleford
- Department of Pediatrics, University of California, San Francisco, CA 94143, USA
| | - Yue Si
- GeneDx Inc., MD 20877, USA
| | | | - Hans Einar Treidene
- Department of Radiology and Nuclear Medicine, Oslo University Hospital, Oslo 0450, Norway
| | - Ambro van Hoof
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center-Houston, Houston, TX 77030, USA
| | - Milo B Fasken
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Anita H Corbett
- Department of Biology, Emory University, Atlanta, GA 30322, USA
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12
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Hong Y, Luo Y. Zebrafish Model in Ophthalmology to Study Disease Mechanism and Drug Discovery. Pharmaceuticals (Basel) 2021; 14:ph14080716. [PMID: 34451814 PMCID: PMC8400593 DOI: 10.3390/ph14080716] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/16/2021] [Accepted: 07/21/2021] [Indexed: 12/14/2022] Open
Abstract
Visual impairment and blindness are common and seriously affect people’s work and quality of life in the world. Therefore, the effective therapies for eye diseases are of high priority. Zebrafish (Danio rerio) is an alternative vertebrate model as a useful tool for the mechanism elucidation and drug discovery of various eye disorders, such as cataracts, glaucoma, diabetic retinopathy, age-related macular degeneration, photoreceptor degeneration, etc. The genetic and embryonic accessibility of zebrafish in combination with a behavioral assessment of visual function has made it a very popular model in ophthalmology. Zebrafish has also been widely used in ocular drug discovery, such as the screening of new anti-angiogenic compounds or neuroprotective drugs, and the oculotoxicity test. In this review, we summarized the applications of zebrafish as the models of eye disorders to study disease mechanism and investigate novel drug treatments.
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Affiliation(s)
| | - Yan Luo
- Correspondence: ; Tel.: +86-020-87335931
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13
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Choquet H, Melles RB, Anand D, Yin J, Cuellar-Partida G, Wang W, Hoffmann TJ, Nair KS, Hysi PG, Lachke SA, Jorgenson E. A large multiethnic GWAS meta-analysis of cataract identifies new risk loci and sex-specific effects. Nat Commun 2021; 12:3595. [PMID: 34127677 PMCID: PMC8203611 DOI: 10.1038/s41467-021-23873-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 05/17/2021] [Indexed: 01/16/2023] Open
Abstract
Cataract is the leading cause of blindness among the elderly worldwide and cataract surgery is one of the most common operations performed in the United States. As the genetic etiology of cataract formation remains unclear, we conducted a multiethnic genome-wide association meta-analysis, combining results from the GERA and UK Biobank cohorts, and tested for replication in the 23andMe research cohort. We report 54 genome-wide significant loci, 37 of which were novel. Sex-stratified analyses identified CASP7 as an additional novel locus specific to women. We show that genes within or near 80% of the cataract-associated loci are significantly expressed and/or enriched-expressed in the mouse lens across various spatiotemporal stages as per iSyTE analysis. Furthermore, iSyTE shows 32 candidate genes in the associated loci have altered gene expression in 9 different gene perturbation mouse models of lens defects/cataract, suggesting their relevance to lens biology. Our work provides further insight into the complex genetic architecture of cataract susceptibility.
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Affiliation(s)
- Hélène Choquet
- Kaiser Permanente Northern California (KPNC), Division of Research, Oakland, CA, USA.
| | | | - Deepti Anand
- Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - Jie Yin
- Kaiser Permanente Northern California (KPNC), Division of Research, Oakland, CA, USA
| | | | | | | | - Thomas J Hoffmann
- Institute for Human Genetics, UCSF, San Francisco, CA, USA.,Department of Epidemiology and Biostatistics, UCSF, San Francisco, CA, USA
| | - K Saidas Nair
- Departments of Ophthalmology and Anatomy, School of Medicine, UCSF, San Francisco, CA, USA
| | - Pirro G Hysi
- King's College London, Section of Ophthalmology, School of Life Course Sciences, London, UK.,King's College London, Department of Twin Research and Genetic Epidemiology, London, UK.,University College London, Great Ormond Street Hospital Institute of Child Health, London, UK
| | - Salil A Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE, USA.,Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA
| | - Eric Jorgenson
- Kaiser Permanente Northern California (KPNC), Division of Research, Oakland, CA, USA
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14
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Farnsworth DR, Posner M, Miller AC. Single cell transcriptomics of the developing zebrafish lens and identification of putative controllers of lens development. Exp Eye Res 2021; 206:108535. [PMID: 33705730 PMCID: PMC8092445 DOI: 10.1016/j.exer.2021.108535] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 01/31/2021] [Accepted: 03/02/2021] [Indexed: 01/10/2023]
Abstract
The vertebrate lens is a valuable model system for investigating the gene expression changes that coordinate tissue differentiation due to its inclusion of two spatially separated cell types, the outer epithelial cells and the deeper denucleated fiber cells that they support. Zebrafish are a useful model system for studying lens development given the organ's rapid development in the first several days of life in an accessible, transparent embryo. While we have strong foundational knowledge of the diverse lens crystallin proteins and the basic gene regulatory networks controlling lens development, no study has detailed gene expression in a vertebrate lens at single cell resolution. Here we report an atlas of lens gene expression in zebrafish embryos and larvae at single cell resolution through five days of development, identifying a number of novel putative regulators of lens development. Our data address open questions about the temperospatial expression of α-crystallins during lens development that will support future studies of their function and provide the first detailed view of β- and γ-crystallin expression in and outside the lens. We describe divergent expression in transcription factor genes that occur as paralog pairs in the zebrafish. Finally, we examine the expression dynamics of cytoskeletal, membrane associated, RNA-binding, and transcription factor genes, identifying a number of novel patterns. Overall these data provide a foundation for identifying and characterizing lens developmental regulatory mechanisms and revealing targets for future functional studies with potential therapeutic impact.
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Affiliation(s)
| | - Mason Posner
- Department of Biology and Toxicology, Ashland University, Ashland, OH, USA.
| | - Adam C Miller
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
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15
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Harding P, Cunha DL, Moosajee M. Animal and cellular models of microphthalmia. THERAPEUTIC ADVANCES IN RARE DISEASE 2021; 2:2633004021997447. [PMID: 37181112 PMCID: PMC10032472 DOI: 10.1177/2633004021997447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 02/02/2021] [Indexed: 05/16/2023]
Abstract
Microphthalmia is a rare developmental eye disorder affecting 1 in 7000 births. It is defined as a small (axial length ⩾2 standard deviations below the age-adjusted mean) underdeveloped eye, caused by disruption of ocular development through genetic or environmental factors in the first trimester of pregnancy. Clinical phenotypic heterogeneity exists amongst patients with varying levels of severity, and associated ocular and systemic features. Up to 11% of blind children are reported to have microphthalmia, yet currently no treatments are available. By identifying the aetiology of microphthalmia and understanding how the mechanisms of eye development are disrupted, we can gain a better understanding of the pathogenesis. Animal models, mainly mouse, zebrafish and Xenopus, have provided extensive information on the genetic regulation of oculogenesis, and how perturbation of these pathways leads to microphthalmia. However, differences exist between species, hence cellular models, such as patient-derived induced pluripotent stem cell (iPSC) optic vesicles, are now being used to provide greater insights into the human disease process. Progress in 3D cellular modelling techniques has enhanced the ability of researchers to study interactions of different cell types during eye development. Through improved molecular knowledge of microphthalmia, preventative or postnatal therapies may be developed, together with establishing genotype-phenotype correlations in order to provide patients with the appropriate prognosis, multidisciplinary care and informed genetic counselling. This review summarises some key discoveries from animal and cellular models of microphthalmia and discusses how innovative new models can be used to further our understanding in the future. Plain language summary Animal and Cellular Models of the Eye Disorder, Microphthalmia (Small Eye) Microphthalmia, meaning a small, underdeveloped eye, is a rare disorder that children are born with. Genetic changes or variations in the environment during the first 3 months of pregnancy can disrupt early development of the eye, resulting in microphthalmia. Up to 11% of blind children have microphthalmia, yet currently no treatments are available. By understanding the genes necessary for eye development, we can determine how disruption by genetic changes or environmental factors can cause this condition. This helps us understand why microphthalmia occurs, and ensure patients are provided with the appropriate clinical care and genetic counselling advice. Additionally, by understanding the causes of microphthalmia, researchers can develop treatments to prevent or reduce the severity of this condition. Animal models, particularly mice, zebrafish and frogs, which can also develop small eyes due to the same genetic/environmental changes, have helped us understand the genes which are important for eye development and can cause birth eye defects when disrupted. Studying a patient's own cells grown in the laboratory can further help researchers understand how changes in genes affect their function. Both animal and cellular models can be used to develop and test new drugs, which could provide treatment options for patients living with microphthalmia. This review summarises the key discoveries from animal and cellular models of microphthalmia and discusses how innovative new models can be used to further our understanding in the future.
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Affiliation(s)
| | | | - Mariya Moosajee
- UCL Institute of Ophthalmology, 11-43 Bath
Street, London, EC1V 9EL, UK
- Moorfields Eye Hospital NHS Foundation Trust,
London, UK
- Great Ormond Street Hospital for Children NHS
Foundation Trust, London, UK
- The Francis Crick Institute, London, UK
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16
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Liu Z, Wang R, Lin H, Liu Y. Lens regeneration in humans: using regenerative potential for tissue repairing. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:1544. [PMID: 33313289 PMCID: PMC7729322 DOI: 10.21037/atm-2019-rcs-03] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The crystalline lens is an important optic element in human eyes. It is transparent and biconvex, refracting light and accommodating to form a clear retinal image. The lens originates from the embryonic ectoderm. The epithelial cells at the lens equator proliferate, elongate and differentiate into highly aligned lens fiber cells, which are the structural basis for maintaining the transparency of the lens. Cataract refers to the opacity of the lens. Currently, the treatment of cataract is to remove the opaque lens and implant an intraocular lens (IOL). This strategy is inappropriate for children younger than 2 years, because a developing eyeball is prone to have severe complications such as inflammatory proliferation and secondary glaucoma. On the other hand, the absence of the crystalline lens greatly affects visual function rehabilitation. The researchers found that mammalian lenses possess regenerative potential. We identified lens stem cells through linear tracking experiments and designed a minimally invasive lens-content removal surgery (MILS) to remove the opaque lens material while preserving the lens capsule, stem cells and microenvironment. In infants with congenital cataract, functional lens regeneration in situ can be observed after MILS, and the prognosis of visual function is better than that of traditional surgery. Because of insufficient regenerative ability in humans, the morphology and volume of the regenerated lens cannot reach the level of a normal lens. The activation, proliferation and differentiation of lens stem cells and the alignment of lens fibers are regulated by epigenetic factors, growth factors, transcription factors, immune system and other signals and their interactions. The construction of appropriate microenvironment can accelerate lens regeneration and improve its morphology. The therapeutic concept of MILS combined with microenvironment manipulation to activate endogenous stem cells for functional regeneration of organs in situ can be extended to other tissues and organs with strong self-renewal and repair ability.
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Affiliation(s)
- Zhenzhen Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Ruixin Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Haotian Lin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Yizhi Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
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17
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Barnum CE, Al Saai S, Patel SD, Cheng C, Anand D, Xu X, Dash S, Siddam AD, Glazewski L, Paglione E, Polson SW, Chuma S, Mason RW, Wei S, Batish M, Fowler VM, Lachke SA. The Tudor-domain protein TDRD7, mutated in congenital cataract, controls the heat shock protein HSPB1 (HSP27) and lens fiber cell morphology. Hum Mol Genet 2020; 29:2076-2097. [PMID: 32420594 PMCID: PMC7390939 DOI: 10.1093/hmg/ddaa096] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 04/10/2020] [Accepted: 05/12/2020] [Indexed: 12/13/2022] Open
Abstract
Mutations of the RNA granule component TDRD7 (OMIM: 611258) cause pediatric cataract. We applied an integrated approach to uncover the molecular pathology of cataract in Tdrd7-/- mice. Early postnatal Tdrd7-/- animals precipitously develop cataract suggesting a global-level breakdown/misregulation of key cellular processes. High-throughput RNA sequencing integrated with iSyTE-bioinformatics analysis identified the molecular chaperone and cytoskeletal modulator, HSPB1, among high-priority downregulated candidates in Tdrd7-/- lens. A protein fluorescence two-dimensional difference in-gel electrophoresis (2D-DIGE)-coupled mass spectrometry screen also identified HSPB1 downregulation, offering independent support for its importance to Tdrd7-/- cataractogenesis. Lens fiber cells normally undergo nuclear degradation for transparency, posing a challenge: how is their cell morphology, also critical for transparency, controlled post-nuclear degradation? HSPB1 functions in cytoskeletal maintenance, and its reduction in Tdrd7-/- lens precedes cataract, suggesting cytoskeletal defects may contribute to Tdrd7-/- cataract. In agreement, scanning electron microscopy (SEM) revealed abnormal fiber cell morphology in Tdrd7-/- lenses. Further, abnormal phalloidin and wheat germ agglutinin (WGA) staining of Tdrd7-/- fiber cells, particularly those exhibiting nuclear degradation, reveals distinct regulatory mechanisms control F-actin cytoskeletal and/or membrane maintenance in post-organelle degradation maturation stage fiber cells. Indeed, RNA immunoprecipitation identified Hspb1 mRNA in wild-type lens lysate TDRD7-pulldowns, and single-molecule RNA imaging showed co-localization of TDRD7 protein with cytoplasmic Hspb1 mRNA in differentiating fiber cells, suggesting that TDRD7-ribonucleoprotein complexes may be involved in optimal buildup of key factors. Finally, Hspb1 knockdown in Xenopus causes eye/lens defects. Together, these data uncover TDRD7's novel upstream role in elevation of stress-responsive chaperones for cytoskeletal maintenance in post-nuclear degradation lens fiber cells, perturbation of which causes early-onset cataracts.
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Affiliation(s)
- Carrie E Barnum
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Salma Al Saai
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Shaili D Patel
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Catherine Cheng
- School of Optometry, Indiana University, Bloomington, IN 47405, USA
| | - Deepti Anand
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Xiaolu Xu
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Soma Dash
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Archana D Siddam
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Lisa Glazewski
- Nemours Biomedical Research Department, Alfred I duPont Hospital for Children, Wilmington, DE 19803, USA
| | - Emily Paglione
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Shawn W Polson
- Center for Bioinformatics & Computational Biology, University of Delaware, Newark, DE 19716, USA
| | - Shinichiro Chuma
- Institute for Frontier Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Robert W Mason
- Nemours Biomedical Research Department, Alfred I duPont Hospital for Children, Wilmington, DE 19803, USA
| | - Shuo Wei
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Mona Batish
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
- Department of Medical and Molecular Sciences, University of Delaware, Newark, DE 19716, USA
| | - Velia M Fowler
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Salil A Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
- Center for Bioinformatics & Computational Biology, University of Delaware, Newark, DE 19716, USA
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18
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Kujawski S, Crespo C, Luz M, Yuan M, Winkler S, Knust E. Loss of Crb2b-lf leads to anterior segment defects in old zebrafish. Biol Open 2020; 9:bio047555. [PMID: 31988089 PMCID: PMC7044448 DOI: 10.1242/bio.047555] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 01/09/2020] [Indexed: 12/02/2022] Open
Abstract
Defects in the retina or the anterior segment of the eye lead to compromised vision and affect millions of people. Understanding how these ocular structures develop and are maintained is therefore of paramount importance. The maintenance of proper vision depends, among other factors, on the function of genes controlling apico-basal polarity. In fact, mutations in polarity genes are linked to retinal degeneration in several species, including human. Here we describe a novel zebrafish crb2b allele (crb2be40 ), which specifically affects the crb2b long isoform. crb2be40 mutants are viable and display normal ocular development. However, old crb2be40 mutant fish develop multiple defects in structures of the anterior segment, which includes the cornea, the iris and the lens. Phenotypes are characterised by smaller pupils due to expansion of the iris and tissues of the iridocorneal angle, an increased number of corneal stromal keratocytes, an abnormal corneal endothelium and an expanded lens capsule. These findings illustrate a novel role for crb2b in the maintenance of the anterior segment and hence add an important function to this polarity regulator, which may be conserved in other vertebrates including humans.
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Affiliation(s)
- Satu Kujawski
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Cátia Crespo
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Marta Luz
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Michaela Yuan
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Sylke Winkler
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Elisabeth Knust
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
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Aryal S, Anand D, Hernandez FG, Weatherbee BAT, Huang H, Reddy AP, Wilmarth PA, David LL, Lachke SA. MS/MS in silico subtraction-based proteomic profiling as an approach to facilitate disease gene discovery: application to lens development and cataract. Hum Genet 2019; 139:151-184. [PMID: 31797049 DOI: 10.1007/s00439-019-02095-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 11/24/2019] [Indexed: 12/20/2022]
Abstract
While the bioinformatics resource-tool iSyTE (integrated Systems Tool for Eye gene discovery) effectively identifies human cataract-associated genes, it is currently based on just transcriptome data, and thus, it is necessary to include protein-level information to gain greater confidence in gene prioritization. Here, we expand iSyTE through development of a novel proteome-based resource on the lens and demonstrate its utility in cataract gene discovery. We applied high-throughput tandem mass spectrometry (MS/MS) to generate a global protein expression profile of mouse lens at embryonic day (E)14.5, which identified 2371 lens-expressed proteins. A major challenge of high-throughput expression profiling is identification of high-priority candidates among the thousands of expressed proteins. To address this problem, we generated new MS/MS proteome data on mouse whole embryonic body (WB). WB proteome was then used as a reference dataset for performing "in silico WB-subtraction" comparative analysis with the lens proteome, which effectively identified 422 proteins with lens-enriched expression at ≥ 2.5 average spectral counts, ≥ 2.0 fold enrichment (FDR < 0.01) cut-off. These top 20% candidates represent a rich pool of high-priority proteins in the lens including known human cataract-linked genes and many new potential regulators of lens development and homeostasis. This rich information is made publicly accessible through iSyTE (https://research.bioinformatics.udel.edu/iSyTE/), which enables user-friendly visualization of promising candidates, thus making iSyTE a comprehensive tool for cataract gene discovery.
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Affiliation(s)
- Sandeep Aryal
- Department of Biological Sciences, University of Delaware, 105 The Green, Delaware Avenue, 236 Wolf Hall, Newark, DE, USA
| | - Deepti Anand
- Department of Biological Sciences, University of Delaware, 105 The Green, Delaware Avenue, 236 Wolf Hall, Newark, DE, USA
| | - Francisco G Hernandez
- Department of Biological Sciences, University of Delaware, 105 The Green, Delaware Avenue, 236 Wolf Hall, Newark, DE, USA
| | - Bailey A T Weatherbee
- Department of Biological Sciences, University of Delaware, 105 The Green, Delaware Avenue, 236 Wolf Hall, Newark, DE, USA
| | - Hongzhan Huang
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19716, USA
| | - Ashok P Reddy
- Proteomics Shared Resource, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Phillip A Wilmarth
- Proteomics Shared Resource, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Larry L David
- Proteomics Shared Resource, Oregon Health and Science University, Portland, OR, 97239, USA
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Salil A Lachke
- Department of Biological Sciences, University of Delaware, 105 The Green, Delaware Avenue, 236 Wolf Hall, Newark, DE, USA.
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19716, USA.
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20
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Paradis H, Ahmad R, McDonald J, Boyce D, Gendron RL. Ocular tissue changes associated with anterior segment opacity in lumpfish (Cyclopterus lumpus L) eye. JOURNAL OF FISH DISEASES 2019; 42:1401-1408. [PMID: 31393016 DOI: 10.1111/jfd.13065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 07/05/2019] [Accepted: 07/09/2019] [Indexed: 06/10/2023]
Abstract
Lumpfish use their vision to hunt prey or, in the case of aquaculture, to see and eat pelleted diets. A common anterior ocular opacity abnormality designated in the literature as "cataract" described in both farmed and wild lumpfish has not yet been characterized in detail at the pathobiological level. We describe here lens tissue changes associated with cataract in cultured and domesticated lumpfish. Methodology included gross observations, ophthalmoscopy and histology. Young adult cultured animals approaching 400 days post-hatch presented a range of anterior segment opacities associated with lenticular abnormalities observable at a histological level. Wild aged domesticated animals also displayed cataracts characterized mainly by abnormalities of the lens observed by both ophthalmoscopy and histology. Dysplastic lesions of the lens in one aged domesticated lumpfish were accompanied with both retinal and optic nerve degeneration. These novel naturally occurring anatomical changes in lumpfish present both commonalities and unique features associated with cataract in young adult cultured animals versus aged domesticated broodstock animals.
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Affiliation(s)
- Helene Paradis
- Division of Biomedical Sciences, Faculty of Medicine, Memorial University, NL, St. John's, Canada
| | - Raahyma Ahmad
- Division of Biomedical Sciences, Faculty of Medicine, Memorial University, NL, St. John's, Canada
| | - James McDonald
- Division of Biomedical Sciences, Faculty of Medicine, Memorial University, NL, St. John's, Canada
| | - Danny Boyce
- Department of Ocean Sciences, Memorial University, St. John's, NL, Canada
| | - Robert L Gendron
- Division of Biomedical Sciences, Faculty of Medicine, Memorial University, NL, St. John's, Canada
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21
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Zhao Y, Zheng D, Cvekl A. Profiling of chromatin accessibility and identification of general cis-regulatory mechanisms that control two ocular lens differentiation pathways. Epigenetics Chromatin 2019; 12:27. [PMID: 31053165 PMCID: PMC6498704 DOI: 10.1186/s13072-019-0272-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 04/23/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Promoters and enhancers are cis-regulatory DNA sequences that control specificity and quantity of transcription. Both are rich on clusters of cis-acting sites that interact with sequence-specific DNA-binding transcription factors (TFs). At the level of chromatin, these regions display increased nuclease sensitivity, reduced nucleosome density, including nucleosome-free regions, and specific combinations of posttranslational modifications of core histone proteins. Together, "open" and "closed" chromatins represent transcriptionally active and repressed states of individual genes, respectively. Cellular differentiation is marked by changes in local chromatin structure. Lens morphogenesis, regulated by TF Pax6, includes differentiation of epithelial precursor cells into lens fibers in parallel with differentiation of epithelial precursors into the mature lens epithelium. RESULTS Using ATAC-seq, we investigated dynamics of chromatin changes during mouse lens fibers and epithelium differentiation. Tissue-specific features of these processes are demonstrated via comparative studies of embryonic stem cells, forebrain, and liver chromatins. Unbiased analysis reveals cis-regulatory logic of lens differentiation through known (e.g., AP-1, Ets, Hsf4, Maf, and Pax6 sites) and novel (e.g., CTCF, Tead, and NF1) motifs. Twenty-six DNA-binding TFs, recognizing these cis-motifs, are markedly up-regulated in differentiating lens fibers. As specific examples, our ATAC-seq data uncovered both the regulatory regions and TF binding motifs in Foxe3, Prox1, and Mip loci that are consistent with previous, though incomplete, experimental data. A cross-examination of Pax6 binding with ATAC-seq data demonstrated that Pax6 bound to both open (H3K27ac and P300-enriched) and closed chromatin domains in lens and forebrain. CONCLUSIONS Our study has generated the first lens chromatin accessibility maps that support a general model of stage-specific chromatin changes associated with transcriptional activities of batteries of genes required for lens fiber cell formation. Analysis of active (or open) promoters and enhancers reveals important cis-DNA motifs that establish the molecular foundation for temporally and spatially regulated gene expression in lens. Together, our data and models open new avenues for the field to conduct mechanistic studies of transcriptional control regions, reconstruction of gene regulatory networks that govern lens morphogenesis, and identification of cataract-causing mutations in noncoding sequences.
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Affiliation(s)
- Yilin Zhao
- The Departments of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| | - Deyou Zheng
- The Departments of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461 USA
- Neurology and Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| | - Ales Cvekl
- The Departments of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461 USA
- Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY 10461 USA
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Anand D, Kakrana A, Siddam AD, Huang H, Saadi I, Lachke SA. RNA sequencing-based transcriptomic profiles of embryonic lens development for cataract gene discovery. Hum Genet 2018; 137:941-954. [PMID: 30417254 DOI: 10.1007/s00439-018-1958-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 11/07/2018] [Indexed: 12/21/2022]
Abstract
Isolated or syndromic congenital cataracts are heterogeneous developmental defects, making the identification of the associated genes challenging. In the past, mouse lens expression microarrays have been successfully applied in bioinformatics tools (e.g., iSyTE) to facilitate human cataract-associated gene discovery. To develop a new resource for geneticists, we report high-throughput RNA sequencing (RNA-seq) profiles of mouse lens at key embryonic stages (E)10.5 (lens pit), E12.5 (primary fiber cell differentiation), E14.5 and E16.5 (secondary fiber cell differentiation). These stages capture important events as the lens develops from an invaginating placode into a transparent tissue. Previously, in silico whole-embryo body (WB)-subtraction-based "lens-enriched" expression has been effective in prioritizing cataract-linked genes. To apply an analogous approach, we generated new mouse WB RNA-seq datasets and show that in silico WB subtraction of lens RNA-seq datasets successfully identifies key genes based on lens-enriched expression. At ≥2 counts-per-million expression, ≥1.5 log2 fold-enrichment (p < 0.05) cutoff, E10.5 lens exhibits 1401 enriched genes (17% lens-expressed genes), E12.5 lens exhibits 1937 enriched genes (22% lens-expressed genes), E14.5 lens exhibits 2514 enriched genes (31% lens-expressed genes), and E16.5 lens exhibits 2745 enriched genes (34% lens-expressed genes). Biological pathway analysis identified genes associated with lens development, transcription regulation and signaling pathways, among other functional groups. Furthermore, these new RNA-seq data confirmed high expression of established cataract-linked genes and identified new potential regulators in the lens. Finally, we developed new lens stage-specific UCSC Genome Brower annotation tracks and made these publicly accessible through iSyTE ( https://research.bioinformatics.udel.edu/iSyTE/ ) for user-friendly visualization of lens gene expression/enrichment to prioritize genes from high-throughput data from cataract cases.
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Affiliation(s)
- Deepti Anand
- Department of Biological Sciences, University of Delaware, 105 The Green, Delaware Avenue, 236 Wolf Hall, Newark, DE, 19716, USA
| | - Atul Kakrana
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19716, USA
| | - Archana D Siddam
- Department of Biological Sciences, University of Delaware, 105 The Green, Delaware Avenue, 236 Wolf Hall, Newark, DE, 19716, USA
| | - Hongzhan Huang
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19716, USA
| | - Irfan Saadi
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Salil A Lachke
- Department of Biological Sciences, University of Delaware, 105 The Green, Delaware Avenue, 236 Wolf Hall, Newark, DE, 19716, USA. .,Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19716, USA.
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