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Huynh PN, Cheng C. Spatial-temporal comparison of Eph/Ephrin gene expression in ocular lenses from aging and knockout mice. FRONTIERS IN OPHTHALMOLOGY 2024; 4:1410860. [PMID: 38984128 PMCID: PMC11182306 DOI: 10.3389/fopht.2024.1410860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 05/06/2024] [Indexed: 07/11/2024]
Abstract
Cataracts, defined as any opacity in the transparent ocular lens, remain the leading cause of blindness and visual impairment in the world; however, the etiology of this pathology is not fully understood. Studies in mice and humans have found that the EphA2 receptor and the ephrin-A5 ligand play important roles in maintaining lens homeostasis and transparency. However, due to the diversity of the family of Eph receptors and ephrin ligands and their promiscuous binding, identifying functional interacting partners remains a challenge. Previously, 12 of the 14 Ephs and 8 of 8 ephrins in mice were characterized to be expressed in the mouse lens. To further narrow down possible genes of interest in life-long lens homeostasis, we collected and separated the lens epithelium from the fiber cell mass and isolated RNA from each compartment in samples from young adult and middle-aged mice that were either wild-type, EphA2-/- (knockout), or ephrin-A5 -/- . Reverse transcription quantitative polymerase chain reaction (RT-qPCR) was implemented to compare transcript levels of 33 Eph and ephrin gene variants in each tissue compartment. Our results show that, of the Eph and ephrin variants screened, 5 of 33 showed age-related changes, and 2 of 33 showed genotype-related changes in lens epithelium. In the isolated fibers, more dynamic gene expression changes were observed, in which 12 of 33 variants showed age-related changes, and 6 of 33 showed genotype-related changes. These data allow for a more informed decision in determining mechanistic leads in Eph-ephrin-mediated signaling in the lens.
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Affiliation(s)
- Peter N Huynh
- School of Optometry and Vision Science Program, Indiana University, Bloomington, IN, United States
| | - Catherine Cheng
- School of Optometry and Vision Science Program, Indiana University, Bloomington, IN, United States
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2
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Köster KA, Dethlefs M, Duque Escobar J, Oetjen E. Regulation of the Activity of the Dual Leucine Zipper Kinase by Distinct Mechanisms. Cells 2024; 13:333. [PMID: 38391946 PMCID: PMC10886912 DOI: 10.3390/cells13040333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/05/2024] [Accepted: 02/07/2024] [Indexed: 02/24/2024] Open
Abstract
The dual leucine zipper kinase (DLK) alias mitogen-activated protein 3 kinase 12 (MAP3K12) has gained much attention in recent years. DLK belongs to the mixed lineage kinases, characterized by homology to serine/threonine and tyrosine kinase, but exerts serine/threonine kinase activity. DLK has been implicated in many diseases, including several neurodegenerative diseases, glaucoma, and diabetes mellitus. As a MAP3K, it is generally assumed that DLK becomes phosphorylated and activated by upstream signals and phosphorylates and activates itself, the downstream serine/threonine MAP2K, and, ultimately, MAPK. In addition, other mechanisms such as protein-protein interactions, proteasomal degradation, dephosphorylation by various phosphatases, palmitoylation, and subcellular localization have been shown to be involved in the regulation of DLK activity or its fine-tuning. In the present review, the diverse mechanisms regulating DLK activity will be summarized to provide better insights into DLK action and, possibly, new targets to modulate DLK function.
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Affiliation(s)
- Kyra-Alexandra Köster
- Department of Clinical Pharmacology and Toxicology, University Medical Centre Hamburg-Eppendorf, 20246 Hamburg, Germany; (K.-A.K.); (M.D.)
- DZHK Standort Hamburg, Kiel, Lübeck, Germany;
| | - Marten Dethlefs
- Department of Clinical Pharmacology and Toxicology, University Medical Centre Hamburg-Eppendorf, 20246 Hamburg, Germany; (K.-A.K.); (M.D.)
- DZHK Standort Hamburg, Kiel, Lübeck, Germany;
| | - Jorge Duque Escobar
- DZHK Standort Hamburg, Kiel, Lübeck, Germany;
- University Center of Cardiovascular Science, Department of Cardiology, University Heart & Vascular Center Hamburg, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Elke Oetjen
- Department of Clinical Pharmacology and Toxicology, University Medical Centre Hamburg-Eppendorf, 20246 Hamburg, Germany; (K.-A.K.); (M.D.)
- DZHK Standort Hamburg, Kiel, Lübeck, Germany;
- Institute of Pharmacy, University of Hamburg, 20146 Hamburg, Germany
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3
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Tangeman JA, Rebull SM, Grajales-Esquivel E, Weaver JM, Bendezu-Sayas S, Robinson ML, Lachke SA, Del Rio-Tsonis K. Integrated single-cell multiomics uncovers foundational regulatory mechanisms of lens development and pathology. Development 2024; 151:dev202249. [PMID: 38180241 PMCID: PMC10906490 DOI: 10.1242/dev.202249] [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: 08/09/2023] [Accepted: 11/28/2023] [Indexed: 01/06/2024]
Abstract
Ocular lens development entails epithelial to fiber cell differentiation, defects in which cause congenital cataracts. We report the first single-cell multiomic atlas of lens development, leveraging snRNA-seq, snATAC-seq and CUT&RUN-seq to discover previously unreported mechanisms of cell fate determination and cataract-linked regulatory networks. A comprehensive profile of cis- and trans-regulatory interactions, including for the cataract-linked transcription factor MAF, is established across a temporal trajectory of fiber cell differentiation. Furthermore, we identify an epigenetic paradigm of cellular differentiation, defined by progressive loss of the H3K27 methylation writer Polycomb repressive complex 2 (PRC2). PRC2 localizes to heterochromatin domains across master-regulator transcription factor gene bodies, suggesting it safeguards epithelial cell fate. Moreover, we demonstrate that FGF hyper-stimulation in vivo leads to MAF network activation and the emergence of novel lens cell states. Collectively, these data depict a comprehensive portrait of lens fiber cell differentiation, while defining regulatory effectors of cell identity and cataract formation.
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Affiliation(s)
- Jared A. Tangeman
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056, USA
- Cell, Molecular, and Structural Biology Program, Miami University, Oxford, OH 45056, USA
| | - Sofia M. Rebull
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056, USA
| | - Erika Grajales-Esquivel
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056, USA
| | - Jacob M. Weaver
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056, USA
- Cell, Molecular, and Structural Biology Program, Miami University, Oxford, OH 45056, USA
| | - Stacy Bendezu-Sayas
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056, USA
- Cell, Molecular, and Structural Biology Program, Miami University, Oxford, OH 45056, USA
| | - Michael L. Robinson
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056, USA
- Cell, Molecular, and Structural Biology Program, Miami University, Oxford, OH 45056, 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
| | - Katia Del Rio-Tsonis
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056, USA
- Cell, Molecular, and Structural Biology Program, Miami University, Oxford, OH 45056, USA
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4
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Wang X, Sun Q, Wang W, Liu B, Gu Y, Chen L. Decoding key cell sub-populations and molecular alterations in glioblastoma at recurrence by single-cell analysis. Acta Neuropathol Commun 2023; 11:125. [PMID: 37525259 PMCID: PMC10391841 DOI: 10.1186/s40478-023-01613-x] [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: 04/27/2023] [Accepted: 07/01/2023] [Indexed: 08/02/2023] Open
Abstract
Glioblastoma (GBM) is the most frequent malignant brain tumor, the relapse of which is unavoidable following standard treatment. However, the effective treatment for recurrent GBM is lacking, necessitating the understanding of key mechanisms driving tumor recurrence and the identification of new targets for intervention. Here, we integrated single-cell RNA-sequencing data spanning 36 patient-matched primary and recurrent GBM (pGBM and rGBM) specimens, with 6 longitudinal GBM spatial transcriptomics to explore molecular alterations at recurrence, with each cell type characterized in parallel. Genes involved in extracellular matrix (ECM) organization are preferentially enriched in rGBM cells, and MAFK is highlighted as a potential regulator. Notably, we uncover a unique subpopulation of GBM cells that is much less detected in pGBM and highly expresses ECM and mesenchyme related genes, suggesting it may contribute to the molecular transition of rGBM. Further regulatory network analysis reveals that transcription factors, such as NFATC4 and activator protein 1 members, may function as hub regulators. All non-tumor cells alter their specific sets of genes as well and certain subgroups of myeloid cells appear to be physically associated with the mesenchyme-like GBM subpopulation. Altogether, our study provides new insights into the molecular understanding of GBM relapse and candidate targets for rGBM treatment.
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Affiliation(s)
- Xin Wang
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, 430072, China
- BGI Research, Hangzhou, 310030 China
| | - Qian Sun
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, 430072, China
| | - Weiwen Wang
- China National GeneBank, BGI Research, Shenzhen, 518120 China
| | - Baohui Liu
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, 430072, China
| | - Ying Gu
- BGI Research, Hangzhou, 310030 China
- BGI Research, Shenzhen, 518083 China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI Research, Shenzhen, 518083 China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Liang Chen
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, 430072, China
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5
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Tangeman JA, Rebull SM, Grajales-Esquivel E, Weaver JM, Bendezu-Sayas S, Robinson ML, Lachke SA, Rio-Tsonis KD. Integrated single-cell multiomics uncovers foundational regulatory mechanisms of lens development and pathology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.10.548451. [PMID: 37502967 PMCID: PMC10369908 DOI: 10.1101/2023.07.10.548451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Ocular lens development entails epithelial to fiber cell differentiation, defects in which cause congenital cataract. We report the first single-cell multiomic atlas of lens development, leveraging snRNA-seq, snATAC-seq, and CUT&RUN-seq to discover novel mechanisms of cell fate determination and cataract-linked regulatory networks. A comprehensive profile of cis- and trans-regulatory interactions, including for the cataract-linked transcription factor MAF, is established across a temporal trajectory of fiber cell differentiation. Further, we divulge a conserved epigenetic paradigm of cellular differentiation, defined by progressive loss of H3K27 methylation writer Polycomb repressive complex 2 (PRC2). PRC2 localizes to heterochromatin domains across master-regulator transcription factor gene bodies, suggesting it safeguards epithelial cell fate. Moreover, we demonstrate that FGF hyper-stimulation in vivo leads to MAF network activation and the emergence of novel lens cell states. Collectively, these data depict a comprehensive portrait of lens fiber cell differentiation, while defining regulatory effectors of cell identity and cataract formation.
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Affiliation(s)
- Jared A Tangeman
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056 USA
- Cell, Molecular, and Structural Biology Program, Miami University, Oxford, OH 45056 USA
| | - Sofia M Rebull
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056 USA
| | - Erika Grajales-Esquivel
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056 USA
| | - Jacob M Weaver
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056 USA
- Cell, Molecular, and Structural Biology Program, Miami University, Oxford, OH 45056 USA
| | - Stacy Bendezu-Sayas
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056 USA
- Cell, Molecular, and Structural Biology Program, Miami University, Oxford, OH 45056 USA
| | - Michael L Robinson
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056 USA
- Cell, Molecular, and Structural Biology Program, Miami University, Oxford, OH 45056 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
| | - Katia Del Rio-Tsonis
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056 USA
- Cell, Molecular, and Structural Biology Program, Miami University, Oxford, OH 45056 USA
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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. 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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7
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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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8
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Hao Z, Zhang M, Chen X, Zhu M, Han B, He Y, Yi H, Tang S. Genetic variants of the nuclear factor erythroid 2-related factor 2/antioxidant reaction element pathway on the risk of antituberculosis drug-induced liver injury: a systematic review. Pharmacogenomics 2023; 24:345-357. [PMID: 37166414 DOI: 10.2217/pgs-2023-0040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
Abstract
Aim: To evaluate the effects of genetic variants in the nuclear factor erythroid 2-related factor 2/antioxidant reaction element signaling pathway on antituberculosis drug-induced liver injury (AT-DILI) susceptibility. Methods: The PubMed, Embase, Cochrane, Web of Science, China National Knowledge Infrastructure and Wanfang databases were searched from inception to April 2022. Results: Seven case-control studies with 4676 patients were included. Six genes with 35 SNPs in the pathway have been reported. Among 17 SNPs reported in two or more studies, the meta-analysis indicated that only one SNP (rs3735656 in MAFK) was significantly associated with a decreased risk for AT-DILI under the dominant model (odds ratio: 0.636; 95% CI: 0.519-0.780; p < 0.001). Conclusion: SNP rs3735656 in the MAFK gene was significantly associated with the risk of AT-DILI.
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Affiliation(s)
- Zhuolu Hao
- Department of Epidemiology & Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Meiling Zhang
- Department of Infectious Disease, The Jurong Hospital Affiliated to Jiangsu University, Jurong, 212400, China
| | - Xinyu Chen
- Department of Epidemiology & Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Min Zhu
- Department of Epidemiology & Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Bing Han
- Department of Epidemiology & Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Yiwen He
- Department of Epidemiology & Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Honggang Yi
- Department of Epidemiology & Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Shaowen Tang
- Department of Epidemiology & Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
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9
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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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10
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Chang W, Zhao Y, Rayêe D, Xie Q, Suzuki M, Zheng D, Cvekl A. Dynamic changes in whole genome DNA methylation, chromatin and gene expression during mouse lens differentiation. Epigenetics Chromatin 2023; 16:4. [PMID: 36698218 PMCID: PMC9875507 DOI: 10.1186/s13072-023-00478-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 01/17/2023] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Cellular differentiation is marked by temporally and spatially coordinated gene expression regulated at multiple levels. DNA methylation represents a universal mechanism to control chromatin organization and its accessibility. Cytosine methylation of CpG dinucleotides regulates binding of methylation-sensitive DNA-binding transcription factors within regulatory regions of transcription, including promoters and distal enhancers. Ocular lens differentiation represents an advantageous model system to examine these processes as lens comprises only two cell types, the proliferating lens epithelium and postmitotic lens fiber cells all originating from the epithelium. RESULTS Using whole genome bisulfite sequencing (WGBS) and microdissected lenses, we investigated dynamics of DNA methylation and chromatin changes during mouse lens fiber and epithelium differentiation between embryos (E14.5) and newborns (P0.5). Histone H3.3 variant chromatin landscapes were also generated for both P0.5 lens epithelium and fibers by chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq). Tissue-specific features of DNA methylation patterns are demonstrated via comparative studies with embryonic stem (ES) cells and neural progenitor cells (NPCs) at Nanog, Pou5f1, Sox2, Pax6 and Six3 loci. Comparisons with ATAC-seq and RNA-seq data demonstrate that reduced methylation is associated with increased expression of fiber cell abundant genes, including crystallins, intermediate filament (Bfsp1 and Bfsp2) and gap junction proteins (Gja3 and Gja8), marked by high levels of histone H3.3 within their transcribed regions. Interestingly, Pax6-binding sites exhibited predominantly DNA hypomethylation in lens chromatin. In vitro binding of Pax6 proteins showed Pax6's ability to interact with sites containing one or two methylated CpG dinucleotides. CONCLUSIONS Our study has generated the first data on methylation changes between two different stages of mammalian lens development and linked these data with chromatin accessibility maps, presence of histone H3.3 and gene expression. Reduced DNA methylation correlates with expression of important genes involved in lens morphogenesis and lens fiber cell differentiation.
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Affiliation(s)
- William Chang
- Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Yilin Zhao
- Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Danielle Rayêe
- Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Qing Xie
- Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
- Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
- University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Masako Suzuki
- Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Deyou Zheng
- Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
- Neurology and Neuroscience, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Ales Cvekl
- Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
- Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
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11
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Mapping the Universe of Eph Receptor and Ephrin Ligand Transcripts in Epithelial and Fiber Cells of the Eye Lens. Cells 2022; 11:cells11203291. [PMID: 36291158 PMCID: PMC9600312 DOI: 10.3390/cells11203291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/14/2022] [Accepted: 10/15/2022] [Indexed: 11/17/2022] Open
Abstract
The eye lens is a transparent, ellipsoid organ in the anterior chamber of the eye that is required for fine focusing of light onto the retina to transmit a clear image. Cataracts, defined as any opacity in the lens, remains the leading cause of blindness in the world. Recent studies in humans and mice indicate that Eph–ephrin bidirectional signaling is important for maintaining lens transparency. Specifically, mutations and polymorphisms in the EphA2 receptor and the ephrin-A5 ligand have been linked to congenital and age-related cataracts. It is unclear what other variants of Ephs and ephrins are expressed in the lens or whether there is preferential expression in epithelial vs. fiber cells. We performed a detailed analysis of Eph receptor and ephrin ligand mRNA transcripts in whole mouse lenses, epithelial cell fractions, and fiber cell fractions using a new RNA isolation method. We compared control samples with EphA2 knockout (KO) and ephrin-A5 KO samples. Our results revealed the presence of transcripts for 12 out of 14 Eph receptors and 8 out of 8 ephrin ligands in various fractions of lens cells. Using specific primer sets, RT-PCR, and sequencing, we verified the variant of each gene that is expressed, and we found two epithelial-cell-specific genes. Surprisingly, we also identified one Eph receptor variant that is expressed in KO lens fibers but is absent from control lens fibers. We also identified one low expression ephrin variant that is only expressed in ephrin-A5 control samples. These results indicate that the lens expresses almost all Ephs and ephrins, and there may be many receptor–ligand pairs that play a role in lens homeostasis.
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