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Ma J, Chu TK, Polo Prieto M, Park Y, Li Y, Chen R, Mardon G, Frankfort BJ, Tran NM. Sample multiplexing for retinal single-cell RNA-sequencing. bioRxiv 2024:2024.04.23.589797. [PMID: 38712294 PMCID: PMC11071429 DOI: 10.1101/2024.04.23.589797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Rare cell populations can be challenging to characterize using microfluidic single-cell RNA sequencing (scRNA-seq) platforms. Typically, the population of interest must be enriched and pooled from multiple biological specimens for efficient collection. However, these practices preclude the resolution of sample origin together with phenotypic data and are problematic in experiments in which biological or technical variation is expected to be high (e.g., disease models, genetic perturbation screens, or human samples). One solution is sample multiplexing whereby each sample is tagged with a unique sequence barcode that is resolved bioinformatically. We have established a scRNA-seq sample multiplexing pipeline for mouse retinal ganglion cells using cholesterol-modified-oligos and utilized the enhanced precision to investigate cell type distribution and transcriptomic variance across retinal samples. As single cell transcriptomics are becoming more widely used to research development and disease, sample multiplexing represents a useful method to enhance the precision of scRNA-seq analysis.
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Kyobe S, Kisitu G, Mwesigwa S, Farirai J, Katagirya E, Retshabile G, Williams L, Mirembe A, Ketumile L, Wayengera M, Mukisa J, Sebetso G, Diphoko T, Amujal M, Kigozi E, Katabazi F, Oceng R, Mlotshwa B, Morapedi K, Nsangi B, Wampande E, Tsimako M, Brown C, Kasvosve I, Joloba M, Anabwani G, Mpoloka S, Mardon G, Kekitiinwa A, Hanchard NA, Kyosiimire-Lugemwa J, Matshaba M, Kiragga D. Long-term non-progression and risk factors for disease progression among children living with HIV in Botswana and Uganda: A retrospective cohort study. Int J Infect Dis 2024; 139:132-140. [PMID: 38036259 PMCID: PMC10843817 DOI: 10.1016/j.ijid.2023.11.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 11/08/2023] [Accepted: 11/22/2023] [Indexed: 12/02/2023] Open
Abstract
OBJECTIVES We utilize a large retrospective study cohort derived from electronic medical records to estimate the prevalence of long-term non-progression (LTNP) and determine the factors associated with progression among children infected with HIV in Botswana and Uganda. METHODS Electronic medical records from large tertiary HIV clinical centers in Botswana and Uganda were queried to identify LTNP children 0-18 years enrolled between June 2003 and May 2014 and extract demographic and nutritional parameters. Multivariate subdistribution hazard analyses were used to examine demographic factors and nutritional status in progression in the pre-antiretroviral therapy era. RESULTS Between the two countries, 14,246 antiretroviral therapy-naïve children infected with HIV were enrolled into clinical care. The overall proportion of LTNP was 6.3% (9.5% in Botswana vs 5.9% in Uganda). The median progression-free survival for the cohort was 6.3 years, although this was lower in Botswana than in Uganda (6.6 vs 8.8 years; P <0.001). At baseline, the adjusted subdistribution hazard ratio (aHRsd) of progression was increased among underweight children (aHRsd 1.42; 95% confidence interval [CI]: 1.32-1.53), enrolled after 2010 (aHRsd 1.32; 95% CI 1.22-1.42), and those from Botswana (aHRsd 2; 95% CI 1.91-2.10). CONCLUSIONS In our study, the prevalence of pediatric LTNP was lower than that observed among adult populations, but progression-free survival was higher than expected. Underweight, year of enrollment into care, and country of origin are independent predictors of progression among children.
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Affiliation(s)
- Samuel Kyobe
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda.
| | - Grace Kisitu
- Baylor College of Medicine Children's Foundation Uganda, Kampala, Uganda
| | - Savannah Mwesigwa
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - John Farirai
- Botswana-Baylor Children's Clinical Centre of Excellence, Gaborone, Botswana
| | - Eric Katagirya
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Gaone Retshabile
- Department of Biological Sciences, University of Botswana, Gaborone, Botswana
| | - Lesedi Williams
- Department of Biological Sciences, University of Botswana, Gaborone, Botswana
| | - Angela Mirembe
- Baylor College of Medicine Children's Foundation Uganda, Kampala, Uganda
| | - Lesego Ketumile
- Botswana-Baylor Children's Clinical Centre of Excellence, Gaborone, Botswana
| | - Misaki Wayengera
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - John Mukisa
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Gaseene Sebetso
- Department of Biological Sciences, University of Botswana, Gaborone, Botswana
| | - Thabo Diphoko
- Department of Biological Sciences, University of Botswana, Gaborone, Botswana
| | - Marion Amujal
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Edgar Kigozi
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Fred Katabazi
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Ronald Oceng
- Baylor College of Medicine Children's Foundation Uganda, Kampala, Uganda
| | - Busisiwe Mlotshwa
- Department of Biological Sciences, University of Botswana, Gaborone, Botswana
| | - Koketso Morapedi
- Department of Biological Sciences, University of Botswana, Gaborone, Botswana
| | - Betty Nsangi
- Baylor College of Medicine Children's Foundation Uganda, Kampala, Uganda
| | - Edward Wampande
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | | | - Chester Brown
- University of Tennessee Health Science Center, Memphis, USA
| | - Ishmael Kasvosve
- School of Allied Health Professionals, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Moses Joloba
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Gabriel Anabwani
- Baylor College of Medicine Children's Foundation Uganda, Kampala, Uganda
| | - Sununguko Mpoloka
- Department of Biological Sciences, University of Botswana, Gaborone, Botswana
| | - Graeme Mardon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, USA; Department of Pathology and Immunology, Baylor College of Medicine, Houston, USA
| | - Adeodata Kekitiinwa
- Baylor College of Medicine Children's Foundation Uganda, Kampala, Uganda; Pediatric Retrovirology, Department of Pediatrics, Baylor College of Medicine, Houston, USA
| | - Neil A Hanchard
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, USA; USDA/ARS/Children's Nutrition Research Center, Baylor College of Medicine, Houston, USA; Childhood Complex Disease Genomics Section, Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, USA
| | | | - Mogomotsi Matshaba
- Botswana-Baylor Children's Clinical Centre of Excellence, Gaborone, Botswana; Pediatric Retrovirology, Department of Pediatrics, Baylor College of Medicine, Houston, USA
| | - Dithan Kiragga
- Baylor College of Medicine Children's Foundation Uganda, Kampala, Uganda; Pediatric Retrovirology, Department of Pediatrics, Baylor College of Medicine, Houston, USA
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Li J, Choi J, Cheng X, Ma J, Pema S, Sanes JR, Mardon G, Frankfort BJ, Tran NM, Li Y, Chen R. Comprehensive single-cell atlas of the mouse retina. bioRxiv 2024:2024.01.24.577060. [PMID: 38328114 PMCID: PMC10849744 DOI: 10.1101/2024.01.24.577060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Single-cell RNA sequencing (scRNA-seq) has advanced our understanding of cellular heterogeneity at the single-cell resolution by classifying and characterizing cell types in multiple tissues and species. While several mouse retinal scRNA-seq reference datasets have been published, each dataset either has a relatively small number of cells or is focused on specific cell classes, and thus is suboptimal for assessing gene expression patterns across all retina types at the same time. To establish a unified and comprehensive reference for the mouse retina, we first generated the largest retinal scRNA-seq dataset to date, comprising approximately 190,000 single cells from C57BL/6J mouse whole retinas. This dataset was generated through the targeted enrichment of rare population cells via antibody-based magnetic cell sorting. By integrating this new dataset with public datasets, we conducted an integrated analysis to construct the Mouse Retina Cell Atlas (MRCA) for wild-type mice, which encompasses over 330,000 single cells. The MRCA characterizes 12 major classes and 138 cell types. It captured consensus cell type characterization from public datasets and identified additional new cell types. To facilitate the public use of the MRCA, we have deposited it in CELLxGENE, UCSC Cell Browser, and the Broad Single Cell Portal for visualization and gene expression exploration. The comprehensive MRCA serves as an easy-to-use, one-stop data resource for the mouse retina communities.
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Affiliation(s)
- Jin Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Jongsu Choi
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Xuesen Cheng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Justin Ma
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Shahil Pema
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Joshua R. Sanes
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02130, USA
| | - Graeme Mardon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas 77030, USA
- Departments of Ophthalmology and Neuroscience, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Benjamin J. Frankfort
- Departments of Ophthalmology and Neuroscience, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Nicholas M. Tran
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Yumei Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Rui Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
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Bollepogu Raja KK, Yeung K, Shim YK, Mardon G. Integrative genomic analyses reveal putative cell type-specific targets of the Drosophila ets transcription factor Pointed. BMC Genomics 2024; 25:103. [PMID: 38262913 PMCID: PMC10807358 DOI: 10.1186/s12864-024-10017-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 01/15/2024] [Indexed: 01/25/2024] Open
Abstract
The Ets domain transcription factors direct diverse biological processes throughout all metazoans and are implicated in development as well as in tumor initiation, progression and metastasis. The Drosophila Ets transcription factor Pointed (Pnt) is the downstream effector of the Epidermal growth factor receptor (Egfr) pathway and is required for cell cycle progression, specification, and differentiation of most cell types in the larval eye disc. Despite its critical role in development, very few targets of Pnt have been reported previously. Here, we employed an integrated approach by combining genome-wide single cell and bulk data to identify putative cell type-specific Pnt targets. First, we used chromatin immunoprecipitation with high-throughput sequencing (ChIP-seq) to determine the genome-wide occupancy of Pnt in late larval eye discs. We identified enriched regions that mapped to an average of 6,941 genes, the vast majority of which are novel putative Pnt targets. Next, we integrated ChIP-seq data with two other larval eye single cell genomics datasets (scRNA-seq and snATAC-seq) to reveal 157 putative cell type-specific Pnt targets that may help mediate unique cell type responses upon Egfr-induced differentiation. Finally, our integrated data also predicts cell type-specific functional enhancers that were not reported previously. Together, our study provides a greatly expanded list of putative cell type-specific Pnt targets in the eye and is a resource for future studies that will allow mechanistic insights into complex developmental processes regulated by Egfr signaling.
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Affiliation(s)
- Komal Kumar Bollepogu Raja
- Department of Pathology and Immunology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Kelvin Yeung
- Department of Pathology and Immunology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Yoon-Kyung Shim
- Department of Pathology and Immunology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Graeme Mardon
- Department of Pathology and Immunology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
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Bollepogu Raja KK, Yeung K, Shim YK, Li Y, Chen R, Mardon G. A single cell genomics atlas of the Drosophila larval eye reveals distinct photoreceptor developmental timelines. Nat Commun 2023; 14:7205. [PMID: 37938573 PMCID: PMC10632452 DOI: 10.1038/s41467-023-43037-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 10/30/2023] [Indexed: 11/09/2023] Open
Abstract
The Drosophila eye is a powerful model system to study the dynamics of cell differentiation, cell state transitions, cell maturation, and pattern formation. However, a high-resolution single cell genomics resource that accurately profiles all major cell types of the larval eye disc and their spatiotemporal relationships is lacking. Here, we report transcriptomic and chromatin accessibility data for all known cell types in the developing eye. Photoreceptors appear as strands of cells that represent their dynamic developmental timelines. As photoreceptor subtypes mature, they appear to assume a common transcriptomic profile that is dominated by genes involved in axon function. We identify cell type maturation genes, enhancers, and potential regulators, as well as genes with distinct R3 or R4 photoreceptor specific expression. Finally, we observe that the chromatin accessibility between cones and photoreceptors is distinct. These single cell genomics atlases will greatly enhance the power of the Drosophila eye as a model system.
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Affiliation(s)
- Komal Kumar Bollepogu Raja
- Department of Pathology and Immunology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Kelvin Yeung
- Department of Pathology and Immunology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Yoon-Kyung Shim
- Department of Pathology and Immunology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Yumei Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Rui Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Graeme Mardon
- Department of Pathology and Immunology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
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Yeung K, Bollepogu Raja KK, Shim YK, Li Y, Chen R, Mardon G. Single cell RNA sequencing of the adult Drosophila eye reveals distinct clusters and novel marker genes for all major cell types. Commun Biol 2022; 5:1370. [PMID: 36517671 PMCID: PMC9751288 DOI: 10.1038/s42003-022-04337-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 12/02/2022] [Indexed: 12/16/2022] Open
Abstract
The adult Drosophila eye is a powerful model system for phototransduction and neurodegeneration research. However, single cell resolution transcriptomic data are lacking for this tissue. We present single cell RNA-seq data on 1-day male and female, 3-day and 7-day old male adult eyes, covering early to mature adult eyes. All major cell types, including photoreceptors, cone and pigment cells in the adult eye were captured and identified. Our data sets identified novel cell type specific marker genes, some of which were validated in vivo. R7 and R8 photoreceptors form clusters that reflect their specific Rhodopsin expression and the specific Rhodopsin expression by each R7 and R8 cluster is the major determinant to their clustering. The transcriptomic data presented in this report will facilitate a deeper mechanistic understanding of the adult fly eye as a model system.
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Affiliation(s)
- Kelvin Yeung
- Department of Pathology and Immunology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Komal Kumar Bollepogu Raja
- Department of Pathology and Immunology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Yoon-Kyung Shim
- Department of Pathology and Immunology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Yumei Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Structural and Computation Biology and Molecular Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Rui Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Structural and Computation Biology and Molecular Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Graeme Mardon
- Department of Pathology and Immunology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
- Program in Developmental Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
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Lu J, Xiong K, Qian X, Choi J, Shim YK, Burnett J, Mardon G, Chen R. Spata7 is required for maintenance of the retinal connecting cilium. Sci Rep 2022; 12:5575. [PMID: 35368022 PMCID: PMC8976851 DOI: 10.1038/s41598-022-09530-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 03/22/2022] [Indexed: 11/09/2022] Open
Abstract
SPATA7, an early onset LCA3 retinal disease gene, encodes a putative scaffold protein that is essential for the proper assembly of the connecting cilium (CC) complex in photoreceptors. Previous studies have shown that SPATA7 interacts with other photoreceptor-specific ciliary proteins, such as RPGR and RPGRIP1, and maintains the integrity of CC integrity. However, although it is known that Spata7 is required for early formation of the CC, it is unclear if Spata7 is also required for the maintenance of the CC. To investigate Spata7 function in the retina at the adult stage, loss of function was induced in the adult retina upon tamoxifen induction of an inducible Spata7 knockout allele (Spata7flox/-; UbcCreERT2/+). The phenotype of mutant retina was characterized by a combination of histology, immunobiochemistry, and electroretinography (ERG). Our results demonstrated that Spata7 is also essential for maintaining the integrity of the mature retinal CC. Loss of Spata7 in adults caused phenotypes similar to those seen in germline mutant mice, including photoreceptor cell degeneration and defective ERG responses. Close examination of the CC revealed significantly shortened NPHP1 length as a result of Spata7 deletion. Furthermore, mislocalization of rhodopsin, leading to ER stress-mediated apoptosis, was observed in the retinal layers. Our results indicate that Spata7 is required not only for the establishment but also for the maintenance of the CC of photoreceptors.
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Affiliation(s)
- Jiaxiong Lu
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Kaitlyn Xiong
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Xinye Qian
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Jongsu Choi
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Yoon-Kyung Shim
- Department of Pathology, Baylor College of Medicine, Houston, TX, USA
| | - Jacob Burnett
- Department of Pathology, Baylor College of Medicine, Houston, TX, USA
| | - Graeme Mardon
- Department of Pathology, Baylor College of Medicine, Houston, TX, USA
| | - Rui Chen
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
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Kyobe S, Mwesigwa S, Kisitu GP, Farirai J, Katagirya E, Mirembe AN, Ketumile L, Wayengera M, Katabazi FA, Kigozi E, Wampande EM, Retshabile G, Mlotshwa BC, Williams L, Morapedi K, Kasvosve I, Kyosiimire-Lugemwa J, Nsangi B, Tsimako-Johnstone M, Brown CW, Joloba M, Anabwani G, Bhekumusa L, Mpoloka SW, Mardon G, Matshaba M, Kekitiinwa A, Hanchard NA. Exome Sequencing Reveals a Putative Role for HLA-C*03:02 in Control of HIV-1 in African Pediatric Populations. Front Genet 2021; 12:720213. [PMID: 34512729 PMCID: PMC8428176 DOI: 10.3389/fgene.2021.720213] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 08/05/2021] [Indexed: 12/28/2022] Open
Abstract
Human leucocyte antigen (HLA) class I molecules present endogenously processed antigens to T-cells and have been linked to differences in HIV-1 disease progression. HLA allelotypes show considerable geographical and inter-individual variation, as does the rate of progression of HIV-1 disease, with long-term non-progression (LTNP) of disease having most evidence of an underlying genetic contribution. However, most genetic analyses of LTNP have occurred in adults of European ancestry, limiting the potential transferability of observed associations to diverse populations who carry the burden of disease. This is particularly true of HIV-1 infected children. Here, using exome sequencing (ES) to infer HLA allelotypes, we determine associations with HIV-1 LTNP in two diverse African pediatric populations. We performed a case-control association study of 394 LTNPs and 420 rapid progressors retrospectively identified from electronic medical records of pediatric HIV-1 populations in Uganda and Botswana. We utilized high-depth ES to perform high-resolution HLA allelotyping and assessed evidence of association between HLA class I alleles and LTNP. Sixteen HLA alleles and haplotypes had significantly different frequencies between Uganda and Botswana, with allelic differences being more prominent in HLA-A compared to HLA-B and C allelotypes. Three HLA allelotypes showed association with LTNP, including a novel association in HLA-C (HLA-B∗57:03, aOR 3.21, Pc = 0.0259; B∗58:01, aOR 1.89, Pc = 0.033; C∗03:02, aOR 4.74, Pc = 0.033). Together, these alleles convey an estimated population attributable risk (PAR) of non-progression of 16.5%. We also observed novel haplotype associations with HLA-B∗57:03-C∗07:01 (aOR 5.40, Pc = 0.025) and HLA-B∗58:01-C∗03:02 (aOR 4.88, Pc = 0.011) with a PAR of 9.8%, as well as a previously unreported independent additive effect and heterozygote advantage of HLA-C∗03:02 with B∗58:01 (aOR 4.15, Pc = 0.005) that appears to limit disease progression, despite weak LD (r 2 = 0.18) between these alleles. These associations remained irrespective of gender or country. In one of the largest studies of HIV in Africa, we find evidence of a protective effect of canonical HLA-B alleles and a novel HLA-C association that appears to augment existing HIV-1 control alleles in pediatric populations. Our findings outline the value of using multi-ethnic populations in genetic studies and offer a novel HIV-1 association of relevance to ongoing vaccine studies.
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Affiliation(s)
- Samuel Kyobe
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Savannah Mwesigwa
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Grace P. Kisitu
- Baylor College of Medicine Children’s Foundation, Kampala, Uganda
| | - John Farirai
- Botswana-Baylor Children’s Clinical Centre of Excellence, Gaborone, Botswana
| | - Eric Katagirya
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | | | - Lesego Ketumile
- Botswana-Baylor Children’s Clinical Centre of Excellence, Gaborone, Botswana
| | - Misaki Wayengera
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Fred Ashaba Katabazi
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Edgar Kigozi
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Edward M. Wampande
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Gaone Retshabile
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Busisiwe C. Mlotshwa
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Lesedi Williams
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Koketso Morapedi
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Ishmael Kasvosve
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | | | - Betty Nsangi
- Baylor College of Medicine Children’s Foundation, Kampala, Uganda
| | | | - Chester W. Brown
- University of Tennessee Health Science Center, Memphis, TN, United States
| | - Moses Joloba
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Gabriel Anabwani
- Botswana-Baylor Children’s Clinical Centre of Excellence, Gaborone, Botswana
| | - Lukhele Bhekumusa
- Eswatini - Baylor College of Medicine Children’s Foundation, Mbabane, Eswatini
| | - Sununguko W. Mpoloka
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Graeme Mardon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, United States
| | - Mogomotsi Matshaba
- Botswana-Baylor Children’s Clinical Centre of Excellence, Gaborone, Botswana
- Pediatric Retrovirology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States
| | - Adeodata Kekitiinwa
- Baylor College of Medicine Children’s Foundation, Kampala, Uganda
- Pediatric Retrovirology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States
| | - Neil A. Hanchard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
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9
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Mwesigwa S, Williams L, Retshabile G, Katagirya E, Mboowa G, Mlotshwa B, Kyobe S, Kateete DP, Wampande EM, Wayengera M, Mpoloka SW, Mirembe AN, Kasvosve I, Morapedi K, Kisitu GP, Kekitiinwa AR, Anabwani G, Joloba ML, Matovu E, Mulindwa J, Noyes H, Botha G, Brown CW, Mardon G, Matshaba M, Hanchard NA. Unmapped exome reads implicate a role for Anelloviridae in childhood HIV-1 long-term non-progression. NPJ Genom Med 2021; 6:24. [PMID: 33741997 PMCID: PMC7979878 DOI: 10.1038/s41525-021-00185-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 01/25/2021] [Indexed: 01/31/2023] Open
Abstract
Human immunodeficiency virus (HIV) infection remains a significant public health burden globally. The role of viral co-infection in the rate of progression of HIV infection has been suggested but not empirically tested, particularly among children. We extracted and classified 42 viral species from whole-exome sequencing (WES) data of 813 HIV-infected children in Botswana and Uganda categorised as either long-term non-progressors (LTNPs) or rapid progressors (RPs). The Ugandan participants had a higher viral community diversity index compared to Batswana (p = 4.6 × 10-13), and viral sequences were more frequently detected among LTNPs than RPs (24% vs 16%; p = 0.008; OR, 1.9; 95% CI, 1.6-2.3), with Anelloviridae showing strong association with LTNP status (p = 3 × 10-4; q = 0.004, OR, 3.99; 95% CI, 1.74-10.25). This trend was still evident when stratified by country, sex, and sequencing platform, and after a logistic regression analysis adjusting for age, sex, country, and the sequencing platform (p = 0.02; q = 0.03; OR, 7.3; 95% CI, 1.6-40.5). Torque teno virus (TTV), which made up 95% of the Anelloviridae reads, has been associated with reduced immune activation. We identify an association between viral co-infection and prolonged AIDs-free survival status that may have utility as a biomarker of LTNP and could provide mechanistic insights to HIV progression in children, demonstrating the added value of interrogating off-target WES reads in cohort studies.
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Affiliation(s)
| | | | | | - Eric Katagirya
- College of Health Sciences, Makerere University, Kampala, Uganda
| | - Gerald Mboowa
- College of Health Sciences, Makerere University, Kampala, Uganda
| | | | - Samuel Kyobe
- College of Health Sciences, Makerere University, Kampala, Uganda
| | - David P Kateete
- College of Health Sciences, Makerere University, Kampala, Uganda
| | | | - Misaki Wayengera
- College of Health Sciences, Makerere University, Kampala, Uganda
| | | | - Angella N Mirembe
- Baylor College of Medicine Children's Foundation Uganda (Baylor Uganda), Kampala, Uganda
| | | | | | - Grace P Kisitu
- Baylor College of Medicine Children's Foundation Uganda (Baylor Uganda), Kampala, Uganda
| | - Adeodata R Kekitiinwa
- Baylor College of Medicine Children's Foundation Uganda (Baylor Uganda), Kampala, Uganda
| | - Gabriel Anabwani
- Botswana-Baylor Children's Clinical Centre of Excellence, Gaborone, Botswana
| | - Moses L Joloba
- College of Health Sciences, Makerere University, Kampala, Uganda
| | - Enock Matovu
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Julius Mulindwa
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Harry Noyes
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Gerrit Botha
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Chester W Brown
- University of Tennessee Health Science Center, Le Bonheur Children's Hospital, Memphis, TN, USA
| | - Graeme Mardon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Mogomotsi Matshaba
- Botswana-Baylor Children's Clinical Centre of Excellence, Gaborone, Botswana
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Neil A Hanchard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
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10
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Yeung K, Wang F, Li Y, Wang K, Mardon G, Chen R. Integrative genomic analysis reveals novel regulatory mechanisms of eyeless during Drosophila eye development. Nucleic Acids Res 2019; 46:11743-11758. [PMID: 30295802 PMCID: PMC6294497 DOI: 10.1093/nar/gky892] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 10/02/2018] [Indexed: 01/22/2023] Open
Abstract
Eyeless (ey) is one of the most critical transcription factors for initiating the entire eye development in Drosophila. However, the molecular mechanisms through which Ey regulates target genes and pathways have not been characterized at the genomic level. Using ChIP-Seq, we generated an endogenous Ey-binding profile in Drosophila developing eyes. We found that Ey binding occurred more frequently at promoter compared to non-promoter regions. Ey promoter binding was correlated with the active transcription of genes involved in development and transcription regulation. An integrative analysis revealed that Ey directly regulated a broad and highly connected genetic network, including many essential patterning pathways, and known and novel eye genes. Interestingly, we observed that Ey could target multiple components of the same pathway, which might enhance its control of these pathways during eye development. In addition to protein-coding genes, we discovered Ey also targeted non-coding RNAs, which represents a new regulatory mechanism employed by Ey. These findings suggest that Ey could use multiple molecular mechanisms to regulate target gene expression and pathway function, which might enable Ey to exhibit a greater flexibility in controlling different processes during eye development.
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Affiliation(s)
- Kelvin Yeung
- Department of Pathology and Immunology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Feng Wang
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Yumei Li
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Keqing Wang
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Graeme Mardon
- Department of Pathology and Immunology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.,Program in Developmental Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Rui Chen
- Department of Pathology and Immunology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.,Program in Developmental Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.,Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
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11
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Dharmat R, Eblimit A, Robichaux MA, Zhang Z, Nguyen TMT, Jung SY, He F, Jain A, Li Y, Qin J, Overbeek P, Roepman R, Mardon G, Wensel TG, Chen R. SPATA7 maintains a novel photoreceptor-specific zone in the distal connecting cilium. J Cell Biol 2018; 217:2851-2865. [PMID: 29899041 PMCID: PMC6080925 DOI: 10.1083/jcb.201712117] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 05/09/2018] [Accepted: 05/23/2018] [Indexed: 12/25/2022] Open
Abstract
Photoreceptor-specific ciliopathies often affect a structure that is considered functionally homologous to the ciliary transition zone (TZ) called the connecting cilium (CC). However, it is unclear how mutations in certain ciliary genes disrupt the photoreceptor CC without impacting the primary cilia systemically. By applying stochastic optical reconstruction microscopy technology in different genetic models, we show that the CC can be partitioned into two regions: the proximal CC (PCC), which is homologous to the TZ of primary cilia, and the distal CC (DCC), a photoreceptor-specific extension of the ciliary TZ. This specialized distal zone of the CC in photoreceptors is maintained by SPATA7, which interacts with other photoreceptor-specific ciliary proteins such as RPGR and RPGRIP1. The absence of Spata7 results in the mislocalization of DCC proteins without affecting the PCC protein complexes. This collapse results in destabilization of the axonemal microtubules, which consequently results in photoreceptor degeneration. These data provide a novel mechanism to explain how genetic disruption of ubiquitously present ciliary proteins exerts tissue-specific ciliopathy phenotypes.
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Affiliation(s)
- Rachayata Dharmat
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Aiden Eblimit
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Michael A Robichaux
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX
| | - Zhixian Zhang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX
| | - Thanh-Minh T Nguyen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Sung Yun Jung
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX
| | - Feng He
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX
| | - Antrix Jain
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX
| | - Yumei Li
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Jun Qin
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX
| | - Paul Overbeek
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Ronald Roepman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Graeme Mardon
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
- Pathology and Immunology, Baylor College of Medicine, Houston, TX
| | - Theodore G Wensel
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX
| | - Rui Chen
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX
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12
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Yin W, Kim HT, Wang S, Gunawan F, Wang L, Kishimoto K, Zhong H, Roman D, Preussner J, Guenther S, Graef V, Buettner C, Grohmann B, Looso M, Morimoto M, Mardon G, Offermanns S, Stainier DYR. The potassium channel KCNJ13 is essential for smooth muscle cytoskeletal organization during mouse tracheal tubulogenesis. Nat Commun 2018; 9:2815. [PMID: 30022023 PMCID: PMC6052067 DOI: 10.1038/s41467-018-05043-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 05/25/2018] [Indexed: 12/22/2022] Open
Abstract
Tubulogenesis is essential for the formation and function of internal organs. One such organ is the trachea, which allows gas exchange between the external environment and the lungs. However, the cellular and molecular mechanisms underlying tracheal tube development remain poorly understood. Here, we show that the potassium channel KCNJ13 is a critical modulator of tracheal tubulogenesis. We identify Kcnj13 in an ethylnitrosourea forward genetic screen for regulators of mouse respiratory organ development. Kcnj13 mutants exhibit a shorter trachea as well as defective smooth muscle (SM) cell alignment and polarity. KCNJ13 is essential to maintain ion homeostasis in tracheal SM cells, which is required for actin polymerization. This process appears to be mediated, at least in part, through activation of the actin regulator AKT, as pharmacological increase of AKT phosphorylation ameliorates the Kcnj13-mutant trachea phenotypes. These results provide insight into the role of ion homeostasis in cytoskeletal organization during tubulogenesis.
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Affiliation(s)
- Wenguang Yin
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, 61231, Germany.
| | - Hyun-Taek Kim
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, 61231, Germany
| | - ShengPeng Wang
- Department of Pharmacology, Max Planck Institute for Heart and Lung Research, Bad Nauheim, 61231, Germany
- Cardiovascular Research Center, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Felix Gunawan
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, 61231, Germany
| | - Lei Wang
- Department of Pharmacology, Max Planck Institute for Heart and Lung Research, Bad Nauheim, 61231, Germany
| | - Keishi Kishimoto
- Laboratory for Lung Development, RIKEN Center for Developmental Biology, Kobe, 650-0047, Japan
| | - Hua Zhong
- Departments of Pathology and Immunology and Molecular and Human Genetics, Integrative Molecular and Biomedical Sciences Program, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Dany Roman
- Departments of Pathology and Immunology and Molecular and Human Genetics, Integrative Molecular and Biomedical Sciences Program, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jens Preussner
- Max Planck Institute for Heart and Lung Research, ECCPS Bioinformatics and Deep Sequencing Platform, Bad Nauheim, 61231, Germany
| | - Stefan Guenther
- Max Planck Institute for Heart and Lung Research, ECCPS Bioinformatics and Deep Sequencing Platform, Bad Nauheim, 61231, Germany
| | - Viola Graef
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, 61231, Germany
| | - Carmen Buettner
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, 61231, Germany
| | - Beate Grohmann
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, 61231, Germany
| | - Mario Looso
- Max Planck Institute for Heart and Lung Research, ECCPS Bioinformatics and Deep Sequencing Platform, Bad Nauheim, 61231, Germany
| | - Mitsuru Morimoto
- Laboratory for Lung Development, RIKEN Center for Developmental Biology, Kobe, 650-0047, Japan
| | - Graeme Mardon
- Departments of Pathology and Immunology and Molecular and Human Genetics, Integrative Molecular and Biomedical Sciences Program, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Stefan Offermanns
- Department of Pharmacology, Max Planck Institute for Heart and Lung Research, Bad Nauheim, 61231, Germany
- Center for Molecular Medicine, Goethe University, Frankfurt, 60590, Germany
| | - Didier Y R Stainier
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, 61231, Germany.
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13
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Mboowa G, Mwesigwa S, Katagirya E, Retshabile G, Mlotshwa BC, Williams L, Kekitiinwa A, Kateete D, Wampande E, Wayengera M, Kintu BN, Kisitu GP, Kyobe S, Brown CW, Hanchard NA, Mardon G, Joloba M, Anabwani G, Pettitt E, Tsimako-Johnstone M, Kasvosve I, Maplanka K, Mpoloka SW, Hlatshwayo M, Matshaba M. The Collaborative African Genomics Network (CAfGEN): Applying Genomic technologies to probe host factors important to the progression of HIV and HIV-tuberculosis infection in sub-Saharan Africa. AAS Open Res 2018; 1:3. [PMID: 30714022 PMCID: PMC6358002 DOI: 10.12688/aasopenres.12832.2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2018] [Indexed: 01/25/2023] Open
Abstract
Background: Here, we describe how the Collaborative African Genomics Network ( CAfGEN) of the Human Heredity and Health in Africa (H3Africa) consortium is using genomics to probe host genetic factors important to the progression of HIV and HIV-tuberculosis (TB) coinfection in sub-Saharan Africa. The H3Africa was conceived to facilitate the application of genomics technologies to improve health across Africa.. Methods: CAfGEN is an H3Africa collaborative centre comprising expertise from the University of Botswana; Makerere University; Baylor College of Medicine Children's Clinical Centers of Excellence (COEs) in Botswana, Uganda, and Swaziland; as well as Baylor College of Medicine, Texas. The COEs provide clinical expertise for community engagement, participant recruitment and sample collection while the three University settings facilitate processing and management of genomic samples and provide infrastructure and training opportunities to sustain genomics research. Results: The project has focused on utilizing whole-exome sequencing to identify genetic variants contributing to extreme HIV disease progression phenotypes in children, as well as RNA sequencing and integrated genomics to identify host genetic factors associated with TB disease progression among HIV-positive children. These cohorts, developed using the COEs' electronic medical records, are exceptionally well-phenotyped and present an unprecedented opportunity to assess genetic factors in individuals whose HIV was acquired by a different route than their adult counterparts in the context of a unique clinical course and disease pathophysiology. Conclusions: Our approach offers the prospect of developing a critical mass of well-trained, highly-skilled, continent-based African genomic scientists. To ensure long term genomics research sustainability in Africa, CAfGEN contributes to a wide range of genomics capacity and infrastructure development on the continent, has laid a foundation for genomics graduate programs at its institutions, and continues to actively promote genomics research through innovative forms of community engagement brokered by partnerships with governments and academia to support genomics policy formulation.
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Affiliation(s)
- Gerald Mboowa
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda.,Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Savannah Mwesigwa
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda.,Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Eric Katagirya
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda.,Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Gaone Retshabile
- Department of Biological Sciences, Faculty of Sciences, University of Botswana, Gaborone, Botswana
| | - Busisiwe C Mlotshwa
- Department of Biological Sciences, Faculty of Sciences, University of Botswana, Gaborone, Botswana
| | - Lesedi Williams
- Department of Biological Sciences, Faculty of Sciences, University of Botswana, Gaborone, Botswana
| | | | - David Kateete
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda.,Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Eddie Wampande
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda.,Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda.,Department of Bio-molecular Resources, College of Veterinary Medicine, Makerere University, Kampala, Uganda
| | - Misaki Wayengera
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda.,Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Betty Nsangi Kintu
- Baylor College of Medicine Children's Foundation-Uganda, Kampala, Uganda
| | - Grace P Kisitu
- Baylor College of Medicine Children's Foundation-Uganda, Kampala, Uganda
| | - Samuel Kyobe
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Chester W Brown
- Genetics Division, Department of Pediatrics , University of Tennessee Health Science Center, Memphis, Memphis, TN, USA.,Le Bonheur Children's Hospital, Memphis, Memphis, TN, USA.,St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Neil A Hanchard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.,ARS/USDA/Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine , Houston, TX, USA
| | - Graeme Mardon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
| | - Moses Joloba
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda.,Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Gabriel Anabwani
- Botswana-Baylor Children's Clinical Centre of Excellence, Gaborone, Botswana.,Baylor College of Medicine Children's Foundation-Swaziland, Mbabane, Swaziland
| | - Ed Pettitt
- Botswana-Baylor Children's Clinical Centre of Excellence, Gaborone, Botswana
| | - Masego Tsimako-Johnstone
- Department of Biological Sciences, Faculty of Sciences, University of Botswana, Gaborone, Botswana
| | - Ishmael Kasvosve
- Department of Medical Laboratory Sciences, University of Botswana, Gaborone, Botswana
| | - Koketso Maplanka
- Department of Biological Sciences, Faculty of Sciences, University of Botswana, Gaborone, Botswana
| | - Sununguko W Mpoloka
- Department of Biological Sciences, Faculty of Sciences, University of Botswana, Gaborone, Botswana
| | | | - Mogomotsi Matshaba
- Botswana-Baylor Children's Clinical Centre of Excellence, Gaborone, Botswana.,Pediatric Retrovirology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
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14
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Eblimit A, Agrawal SA, Thomas K, Anastassov IA, Abulikemu T, Moayedi Y, Mardon G, Chen R. Corrigendum to "Conditional loss of Spata7 in photoreceptors causes progressive retinal degeneration in mice" [Exp. Eye Res. 166 (2018) 120-130]. Exp Eye Res 2018; 171:119. [PMID: 29579643 DOI: 10.1016/j.exer.2018.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- A Eblimit
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030-3411, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030-3411, USA
| | - S A Agrawal
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030-3411, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030-3411, USA
| | - K Thomas
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030-3411, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030-3411, USA
| | - I A Anastassov
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030-3411, USA
| | - T Abulikemu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030-3411, USA; The Key Laboratory of Plant Resources and Chemistry of Arid Zone, Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Urumqi, Xinjiang, 830011, China
| | - Y Moayedi
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030-3411, USA
| | - G Mardon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030-3411, USA; Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030-3411, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030-3411, USA.
| | - R Chen
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030-3411, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030-3411, USA.
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15
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Retshabile G, Mlotshwa BC, Williams L, Mwesigwa S, Mboowa G, Huang Z, Rustagi N, Swaminathan S, Katagirya E, Kyobe S, Wayengera M, Kisitu GP, Kateete DP, Wampande EM, Maplanka K, Kasvosve I, Pettitt ED, Matshaba M, Nsangi B, Marape M, Tsimako-Johnstone M, Brown CW, Yu F, Kekitiinwa A, Joloba M, Mpoloka SW, Mardon G, Anabwani G, Hanchard NA. Whole-Exome Sequencing Reveals Uncaptured Variation and Distinct Ancestry in the Southern African Population of Botswana. Am J Hum Genet 2018; 102:731-743. [PMID: 29706352 DOI: 10.1016/j.ajhg.2018.03.010] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 02/26/2018] [Indexed: 01/08/2023] Open
Abstract
Large-scale, population-based genomic studies have provided a context for modern medical genetics. Among such studies, however, African populations have remained relatively underrepresented. The breadth of genetic diversity across the African continent argues for an exploration of local genomic context to facilitate burgeoning disease mapping studies in Africa. We sought to characterize genetic variation and to assess population substructure within a cohort of HIV-positive children from Botswana-a Southern African country that is regionally underrepresented in genomic databases. Using whole-exome sequencing data from 164 Batswana and comparisons with 150 similarly sequenced HIV-positive Ugandan children, we found that 13%-25% of variation observed among Batswana was not captured by public databases. Uncaptured variants were significantly enriched (p = 2.2 × 10-16) for coding variants with minor allele frequencies between 1% and 5% and included predicted-damaging non-synonymous variants. Among variants found in public databases, corresponding allele frequencies varied widely, with Botswana having significantly higher allele frequencies among rare (<1%) pathogenic and damaging variants. Batswana clustered with other Southern African populations, but distinctly from 1000 Genomes African populations, and had limited evidence for admixture with extra-continental ancestries. We also observed a surprising lack of genetic substructure in Botswana, despite multiple tribal ethnicities and language groups, alongside a higher degree of relatedness than purported founder populations from the 1000 Genomes project. Our observations reveal a complex, but distinct, ancestral history and genomic architecture among Batswana and suggest that disease mapping within similar Southern African populations will require a deeper repository of genetic variation and allelic dependencies than presently exists.
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Affiliation(s)
- Gaone Retshabile
- Department of Biological Sciences, University of Botswana, Gaborone, Botswana
| | - Busisiwe C Mlotshwa
- Department of Biological Sciences, University of Botswana, Gaborone, Botswana
| | - Lesedi Williams
- Department of Biological Sciences, University of Botswana, Gaborone, Botswana
| | - Savannah Mwesigwa
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Gerald Mboowa
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda; Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Zhuoyi Huang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Navin Rustagi
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shanker Swaminathan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; USDA/ARS/Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Eric Katagirya
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Samuel Kyobe
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Misaki Wayengera
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Grace P Kisitu
- Baylor College of Medicine Children's Foundation, Kampala, Uganda
| | - David P Kateete
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda; Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Eddie M Wampande
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda; Department of Bio-molecular Resources, College of Veterinary Medicine, Makerere University, Kampala, Uganda
| | - Koketso Maplanka
- Department of Biological Sciences, University of Botswana, Gaborone, Botswana
| | - Ishmael Kasvosve
- Department of Medical Laboratory Sciences, University of Botswana, Gaborone, Botswana
| | - Edward D Pettitt
- Botswana-Baylor Children's Clinical Centre of Excellence, Gaborone, Botswana
| | - Mogomotsi Matshaba
- Botswana-Baylor Children's Clinical Centre of Excellence, Gaborone, Botswana; Pediatric Retrovirology, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Betty Nsangi
- Baylor College of Medicine Children's Foundation, Kampala, Uganda
| | - Marape Marape
- Botswana-Baylor Children's Clinical Centre of Excellence, Gaborone, Botswana
| | | | - Chester W Brown
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; University of Tennessee Health Science Center, Memphis, TN 38105, USA
| | - Fuli Yu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Adeodata Kekitiinwa
- Baylor College of Medicine Children's Foundation, Kampala, Uganda; Pediatric Retrovirology, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Moses Joloba
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Sununguko W Mpoloka
- Department of Biological Sciences, University of Botswana, Gaborone, Botswana
| | - Graeme Mardon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Gabriel Anabwani
- Botswana-Baylor Children's Clinical Centre of Excellence, Gaborone, Botswana; Pediatric Retrovirology, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Neil A Hanchard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; USDA/ARS/Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX 77030, USA.
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Mboowa G, Mwesigwa S, Katagirya E, Retshabile G, Mlotshwa BC, Williams L, Kekitiinwa A, Kateete D, Wampande E, Wayengera M, Kintu BN, Kisitu GP, Kyobe S, Brown CW, Hanchard NA, Mardon G, Joloba M, Anabwani G, Pettitt E, Tsimako-Johnstone M, Kasvosve I, Maplanka K, Mpoloka SW, Hlatshwayo M, Matshaba M. The Collaborative African Genomics Network (CAfGEN): Applying Genomic technologies to probe host factors important to the progression of HIV and HIV-tuberculosis infection in sub-Saharan Africa. AAS Open Res 2018; 1:3. [DOI: 10.12688/aasopenres.12832.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Background: The Human Heredity and Health in Africa consortium (H3Africa) was conceived to facilitate the application of genomics technologies to improve health across Africa. Here, we describe how the Collaborative African Genomics Network (CAfGEN) of the H3Africa consortium is using genomics to probe host genetic factors important to the progression of HIV and HIV-tuberculosis (TB) coinfection in sub-Saharan Africa. Methods: CAfGEN is an H3Africa collaborative centre comprising expertise from the University of Botswana; Makerere University; Baylor College of Medicine Children’s Clinical Centers of Excellence (COEs) in Botswana, Uganda, and Swaziland; as well as Baylor College of Medicine, Texas. The COEs provide clinical expertise for community engagement, participant recruitment and sample collection while the three University settings facilitate processing and management of genomic samples and provide infrastructure and training opportunities to sustain genomics research. Results: The project has focused on utilizing whole-exome sequencing to identify genetic variants contributing to extreme HIV disease progression phenotypes in children, as well as RNA sequencing and integrated genomics to identify host genetic factors associated with TB disease progression among HIV-positive children. These cohorts, developed using the COEs’ electronic medical records, are exceptionally well-phenotyped and present an unprecedented opportunity to assess genetic factors in individuals whose HIV was acquired by a different route than their adult counterparts in the context of a unique clinical course and disease pathophysiology. Conclusions: Our approach offers the prospect of developing a critical mass of well-trained, highly-skilled, continent-based African genomic scientists. To ensure long term genomics research sustainability in Africa, CAfGEN contributes to a wide range of genomics capacity and infrastructure development on the continent, has laid a foundation for genomics graduate programs at its institutions, and continues to actively promote genomics research through innovative forms of community engagement brokered by partnerships with governments and academia to support genomics policy formulation.
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Eblimit A, Agrawal SA, Thomas K, Anastassov IA, Abulikemu T, Moayedi Y, Mardon G, Chen R. Conditional loss of Spata7 in photoreceptors causes progressive retinal degeneration in mice. Exp Eye Res 2017; 166:120-130. [PMID: 29100828 DOI: 10.1016/j.exer.2017.10.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 10/10/2017] [Accepted: 10/13/2017] [Indexed: 12/31/2022]
Abstract
The mammalian retina consists of multiple cell layers including photoreceptor cells, which are light sensing neurons that play essential functions in the visual process. Previously, we identified mutations in SPATA7, encoding spermatogenesis associated protein 7, in families with Leber Congenital Amaurosis (LCA) and juvenile Retinitis Pigmentosa (RP), and showed that Spata7 null mice recapitulate the human disease phenotype of retinal degeneration. SPATA7 is expressed in the connecting cilium of photoreceptor (PR) cells in the mouse retina, as well as in retinal pigment epithelium (RPE) cells, but the functional role of Spata7 in the RPE remains unknown. To investigate whether Spata7 is required in PRs, the RPE, or both, we conditionally knocked out Spata7 in photoreceptors and RPE cells using Crx-Cre and Best1-Cre transgenic mouse lines, respectively. In Spata7 photoreceptor-specific conditional (cKO) mice, both rod and cone photoreceptor dysfunction and degeneration is observed, characterized by progressive thinning of the outer nuclear layer and reduced response to light; however, RPE-specific deletion of Spata7 does not impair retinal function or cell survival. Furthermore, our findings show that both Rhodopsin and RPGRIP1 are mislocalized in the Spata7Flox/-; Crx-Cre cKO mice, suggesting that loss of Spata7 in photoreceptors alone can result in altered trafficking of these proteins in the connecting cilium. Together, our findings suggest that loss of Spata7 in photoreceptors alone is sufficient to cause photoreceptor degeneration, but its function in the RPE is not required for photoreceptor survival; therefore, loss of Spata7 in photoreceptors alters both rod and cone function and survival, consistent with the clinical phenotypes observed in LCA and RP patients with mutations in SPATA7.
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Affiliation(s)
- Aiden Eblimit
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030-3411, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030-3411, USA
| | - Smriti Akshay Agrawal
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030-3411, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030-3411, USA
| | - Kandace Thomas
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030-3411, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030-3411, USA
| | - Ivan Assenov Anastassov
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030-3411, USA
| | - Tajiguli Abulikemu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030-3411, USA; The Key Laboratory of Plant Resources and Chemistry of Arid Zone, Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Urumqi, Xinjiang, 830011, China
| | | | - Graeme Mardon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030-3411, USA; Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030-3411, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030-3411, USA.
| | - Rui Chen
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030-3411, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030-3411, USA.
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18
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Mlotshwa BC, Mwesigwa S, Mboowa G, Williams L, Retshabile G, Kekitiinwa A, Wayengera M, Kyobe S, Brown CW, Hanchard NA, Mardon G, Joloba M, Anabwani G, Mpoloka SW. The collaborative African genomics network training program: a trainee perspective on training the next generation of African scientists. Genet Med 2017; 19:826-833. [PMID: 28383545 PMCID: PMC5509501 DOI: 10.1038/gim.2016.177] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 09/19/2016] [Indexed: 11/09/2022] Open
Abstract
Purpose: The Collaborative African Genomics Network (CAfGEN) aims to establish sustainable genomics research programs in Botswana and Uganda through long-term training of PhD students from these countries at Baylor College of Medicine. Here, we present an overview of the CAfGEN PhD training program alongside trainees’ perspectives on their involvement. Background: Historically, collaborations between high-income countries (HICs) and low- and middle-income countries (LMICs), or North–South collaborations, have been criticized for the lack of a mutually beneficial distribution of resources and research findings, often undermining LMICs. CAfGEN plans to address this imbalance in the genomics field through a program of technology and expertise transfer to the participating LMICs. Methods: An overview of the training program is presented. Trainees from the CAfGEN project summarized their experiences, looking specifically at the training model, benefits of the program, challenges encountered relating to the cultural transition, and program outcomes after the first 2 years. Conclusion: Collaborative training programs like CAfGEN will not only help establish sustainable long-term research initiatives in LMICs but also foster stronger North–South and South–South networks. The CAfGEN model offers a framework for the development of training programs aimed at genomics education for those for whom genomics is not their “first language.” Genet Med advance online publication 06 April 2017
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Affiliation(s)
- Busisiwe C Mlotshwa
- Department of Biological Sciences, Faculty of Sciences, University of Botswana, Gaborone, Botswana
| | - Savannah Mwesigwa
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Gerald Mboowa
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Lesedi Williams
- Department of Biological Sciences, Faculty of Sciences, University of Botswana, Gaborone, Botswana
| | - Gaone Retshabile
- Department of Biological Sciences, Faculty of Sciences, University of Botswana, Gaborone, Botswana
| | | | - Misaki Wayengera
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Samuel Kyobe
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Chester W Brown
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA.,Current affiliation: Genetics Division, Department of Pediatrics, University of Tennessee Health Science Center, Le Bonheur Children's Hospital, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Neil A Hanchard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA.,ARS/USDA/Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Graeme Mardon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030
| | - Moses Joloba
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Gabriel Anabwani
- Botswana-Baylor Children's Clinical Centre of Excellence, Gaborone
| | - Sununguko W Mpoloka
- Department of Biological Sciences, Faculty of Sciences, University of Botswana, Gaborone, Botswana
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19
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Jin M, Eblimit A, Pulikkathara M, Corr S, Chen R, Mardon G. Conditional knockout of retinal determination genes in differentiating cells in Drosophila. FEBS J 2016; 283:2754-66. [PMID: 27257739 DOI: 10.1111/febs.13772] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Revised: 05/18/2016] [Accepted: 06/02/2016] [Indexed: 12/13/2022]
Abstract
Conditional gene knockout in postmitotic cells is a valuable technique which allows the study of gene function with spatiotemporal control. Surprisingly, in contrast to its long-term and extensive use in mouse studies, this technology is lacking in Drosophila. Here, we use a novel method for generating complete loss of eyes absent (eya) or sine oculis (so) function in postmitotic cells posterior to the morphogenetic furrow (MF). Specifically, genomic rescue constructs with flippase recognition target (FRT) sequences flanking essential exons are used to generate conditional null alleles. By removing gene function in differentiating cells, we show that eya and so are dispensable for larval photoreceptor differentiation, but are required for differentiation during pupal development. Both eya and so are necessary for photoreceptor survival and the apoptosis caused by loss of eya or so function is likely a secondary consequence of inappropriate differentiation. We also confirm their requirement for cone cell development and reveal a novel role in interommatidial bristle (IOB) formation. In addition, so is required for normal eye disc morphology. This is the first report of a knockout method to study eya and so function in postmitotic cells. This technology will open the door to a large array of new functional studies in virtually any tissue and at any stage of development or in adults.
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Affiliation(s)
- Meng Jin
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
| | - Aiden Eblimit
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Stuart Corr
- Department of Surgery, Baylor College of Medicine, Houston, TX, USA.,Department of Chemistry, Rice University, Houston, TX, USA.,Department of Biomedical Engineering, University of Houston, TX, USA
| | - Rui Chen
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Program in Developmental Biology, Baylor College of Medicine, Houston, TX, USA
| | - Graeme Mardon
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Program in Developmental Biology, Baylor College of Medicine, Houston, TX, USA.,Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA.,Department of Ophthalmology, Baylor College of Medicine, Houston, TX, USA.,Program in Cell and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
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20
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Yang Z, Zhong H, Chen J, Zhang X, Zhang H, Luo X, Xu S, Chen H, Lu D, Han Y, Li J, Fu L, Qi X, Peng Y, Xiang K, Lin Q, Guo Y, Li M, Cao X, Zhang Y, Liao S, Peng Y, Zhang L, Guo X, Dong S, Liang F, Wang J, Willden A, Seang Aun H, Serey B, Sovannary T, Bunnath L, Samnom H, Mardon G, Li Q, Meng A, Shi H, Su B. A Genetic Mechanism for Convergent Skin Lightening during Recent Human Evolution. Mol Biol Evol 2016; 33:1177-87. [PMID: 26744415 PMCID: PMC4839214 DOI: 10.1093/molbev/msw003] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Skin lightening among Eurasians is thought to have been a convergence occurring independently in Europe and East Asia as an adaptation to high latitude environments. Among Europeans, several genes responsible for such lightening have been found, but the information available for East Asians is much more limited. Here, a genome-wide comparison between dark-skinned Africans and Austro-Asiatic speaking aborigines and light-skinned northern Han Chinese identified the pigmentation gene OCA2, showing unusually deep allelic divergence between these groups. An amino acid substitution (His615Arg) of OCA2 prevalent in most East Asian populations—but absent in Africans and Europeans—was significantly associated with skin lightening among northern Han Chinese. Further transgenic and targeted gene modification analyses of zebrafish and mouse both exhibited the phenotypic effect of the OCA2 variant manifesting decreased melanin production. These results indicate that OCA2 plays an important role in the convergent skin lightening of East Asians during recent human evolution.
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Affiliation(s)
- Zhaohui Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Hua Zhong
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX
| | - Jing Chen
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Xiaoming Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Hui Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Xin Luo
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Shuhua Xu
- Max Planck Independent Research Group on Population Genomics, Chinese Academy of Sciences and Max Planck Society (CAS-MPG) Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Hua Chen
- Center for Computational Genomics, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Dongsheng Lu
- Max Planck Independent Research Group on Population Genomics, Chinese Academy of Sciences and Max Planck Society (CAS-MPG) Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yinglun Han
- College of Life Science, Liaoning Normal University, Dalian, China
| | - Jinkun Li
- Department of Urology, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Lijie Fu
- Department of Urology, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Xuebin Qi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yi Peng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Kun Xiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Qiang Lin
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Yan Guo
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Ming Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Xiangyu Cao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yanfeng Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Shiyu Liao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yingmei Peng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Lin Zhang
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Xiaosen Guo
- BGI-Shenzhen, Shenzhen, China Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Jun Wang
- BGI-Shenzhen, Shenzhen, China Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Andrew Willden
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Hong Seang Aun
- Geography and Land Management, Royal University of Phnom Penh, Phnom Penh, Kingdom of Cambodia
| | - Bun Serey
- Geography and Land Management, Royal University of Phnom Penh, Phnom Penh, Kingdom of Cambodia
| | - Tuot Sovannary
- Geography and Land Management, Royal University of Phnom Penh, Phnom Penh, Kingdom of Cambodia
| | - Long Bunnath
- Geography and Land Management, Royal University of Phnom Penh, Phnom Penh, Kingdom of Cambodia
| | - Ham Samnom
- Capacity Development Facilitator for Handicap International Federation and Freelance Researcher, Battambang, Kingdom of Cambodia
| | - Graeme Mardon
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX
| | - Qingwei Li
- College of Life Science, Liaoning Normal University, Dalian, China
| | - Anming Meng
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Hong Shi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
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Zhong H, Chen Y, Li Y, Chen R, Mardon G. Erratum: CRISPR-engineered mosaicism rapidly reveals that loss of Kcnj13 function in mice mimics human disease phenotypes. Sci Rep 2015; 5:9731. [PMID: 26177189 PMCID: PMC4502830 DOI: 10.1038/srep09731] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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22
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Zhong H, Eblimit A, Moayedi Y, Boye SL, Chiodo VA, Chen Y, Li Y, Nichols RM, Hauswirth WW, Chen R, Mardon G. AAV8(Y733F)-mediated gene therapy in a Spata7 knockout mouse model of Leber congenital amaurosis and retinitis pigmentosa. Gene Ther 2015; 22:619-27. [PMID: 25965394 DOI: 10.1038/gt.2015.42] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 03/14/2015] [Accepted: 03/23/2015] [Indexed: 12/27/2022]
Abstract
Loss of SPATA7 function causes the pathogenesis of Leber congenital amaurosis and retinitis pigmentosa. Spata7 knockout mice mimic human SPATA7-related retinal disease with apparent photoreceptor degeneration observed as early as postnatal day 15 (P15). To test the efficacy of adeno-associated virus (AAV)-mediated gene therapy for rescue of photoreceptor survival and function in Spata7 mutant mice, we employed the AAV8(Y733F) vector carrying hGRK1-driven full-length FLAG-tagged Spata7 cDNA to target both rod and cone photoreceptors. Following subretinal injection of this vector, FLAG-tagged SPATA7 was found to colocalize with endogenous SPATA7 in wild-type mice. In Spata7 mutant mice initially treated at P15, we observed improvement of photoresponse, photoreceptor ultrastructure and significant alleviation of photoreceptor degeneration. Furthermore, we performed treatments at P28 and P56 and found that all treatments (P15-P56) can ameliorate rod and cone loss in the long term (1 year); however, none efficiently protect photoreceptors from degeneration by 86 weeks of age as only a small amount of treated photoreceptors can survive to this time. This study demonstrates long-term improvement of photoreceptor function by AAV8(Y733F)-introduced Spata7 expression in a mouse model as potential treatment of the human disease, but also suggests that treated mutant photoreceptors still undergo progressive degeneration.
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Affiliation(s)
- H Zhong
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
| | - A Eblimit
- 1] HGSC, Baylor College of Medicine, Houston, TX, USA [2] Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Y Moayedi
- 1] Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA [2] Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - S L Boye
- Department of Ophthalmology, College of Medicine, University of Florida, Gainesville, FL, USA
| | - V A Chiodo
- Department of Ophthalmology, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Y Chen
- 1] HGSC, Baylor College of Medicine, Houston, TX, USA [2] Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Y Li
- 1] HGSC, Baylor College of Medicine, Houston, TX, USA [2] Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - R M Nichols
- Department of Ophthalmology, Baylor College of Medicine, Houston, TX, USA
| | - W W Hauswirth
- Department of Ophthalmology, College of Medicine, University of Florida, Gainesville, FL, USA
| | - R Chen
- 1] HGSC, Baylor College of Medicine, Houston, TX, USA [2] Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA [3] Program in Developmental Biology, Baylor College of Medicine, Houston, TX, USA
| | - G Mardon
- 1] Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA [2] Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA [3] Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA [4] Department of Ophthalmology, Baylor College of Medicine, Houston, TX, USA [5] Program in Developmental Biology, Baylor College of Medicine, Houston, TX, USA
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23
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Chen K, Wu K, Jiao X, Wang L, Ju X, Wang M, Di Sante G, Xu S, Wang Q, Li K, Sun X, Xu C, Li Z, Casimiro MC, Ertel A, Addya S, McCue PA, Lisanti MP, Wang C, Davis RJ, Mardon G, Pestell RG. The endogenous cell-fate factor dachshund restrains prostate epithelial cell migration via repression of cytokine secretion via a cxcl signaling module. Cancer Res 2015; 75:1992-2004. [PMID: 25769723 DOI: 10.1158/0008-5472.can-14-0611] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 02/24/2015] [Indexed: 01/01/2023]
Abstract
Prostate cancer is the second leading form of cancer-related death in men. In a subset of prostate cancer patients, increased chemokine signaling IL8 and IL6 correlates with castrate-resistant prostate cancer (CRPC). IL8 and IL6 are produced by prostate epithelial cells and promote prostate cancer cell invasion; however, the mechanisms restraining prostate epithelial cell cytokine secretion are poorly understood. Herein, the cell-fate determinant factor DACH1 inhibited CRPC tumor growth in mice. Using Dach1(fl/fl)/Probasin-Cre bitransgenic mice, we show IL8 and IL6 secretion was altered by approximately 1,000-fold by endogenous Dach1. Endogenous Dach1 is shown to serve as a key endogenous restraint to prostate epithelial cell growth and restrains migration via CXCL signaling. DACH1 inhibited expression, transcription, and secretion of the CXCL genes (IL8 and IL6) by binding to their promoter regulatory regions in chromatin. DACH1 is thus a newly defined determinant of benign and malignant prostate epithelium cellular growth, migration, and cytokine abundance in vivo.
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Affiliation(s)
- Ke Chen
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania. Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Kongming Wu
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania. Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania. Tongji Hospital, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, China.
| | - Xuanmao Jiao
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania. Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Liping Wang
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania. Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Xiaoming Ju
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania. Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Min Wang
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania. Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Gabriele Di Sante
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania. Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Shaohua Xu
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania. Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Qiong Wang
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania. Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Kevin Li
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania. Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Xin Sun
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania. Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Congwen Xu
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania. Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Zhiping Li
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania. Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Mathew C Casimiro
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania. Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Adam Ertel
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Sankar Addya
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Peter A McCue
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Michael P Lisanti
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Chenguang Wang
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania. Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | | | - Graeme Mardon
- Departments of Pathology and Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Richard G Pestell
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania. Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania. Kazan Federal University, Kazan, Republic of Tatarstan, Russian Federation.
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24
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Jusiak B, Wang F, Karandikar UC, Kwak SJ, Wang H, Chen R, Mardon G. Genome-wide DNA binding pattern of the homeodomain transcription factor Sine oculis (So) in the developing eye of Drosophila melanogaster.. Genom Data 2014; 2:153-155. [PMID: 25126519 PMCID: PMC4128500 DOI: 10.1016/j.gdata.2014.06.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The eye of the fruit fly Drosophila melanogaster provides a highly tractable genetic model system for the study of animal development, and many genes that regulate Drosophila eye formation have homologs implicated in human development and disease. Among these is the homeobox gene sine oculis (so), which encodes a homeodomain transcription factor (TF) that is both necessary for eye development and sufficient to reprogram a subset of cells outside the normal eye field toward an eye fate. We have performed a genome-wide analysis of So binding to DNA prepared from developing Drosophila eye tissue in order to identify candidate direct targets of So-mediated transcriptional regulation, as described in our recent article [20]. The data are available from NCBI Gene Expression Omnibus (GEO) with the accession number GSE52943. Here we describe the methods, data analysis, and quality control of our So ChIP-seq dataset.
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Affiliation(s)
- Barbara Jusiak
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Feng Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America ; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Umesh C Karandikar
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Su-Jin Kwak
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Hui Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America ; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Rui Chen
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, United States of America ; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America ; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Graeme Mardon
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, United States of America ; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America ; Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, United States of America ; Department of Neuroscience, Baylor College of Medicine, Houston, Texas, United States of America ; Department of Ophthalmology, Baylor College of Medicine, Houston, Texas, United States of America ; Program in Cell and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America
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25
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Eblimit A, Nguyen TMT, Chen Y, Esteve-Rudd J, Zhong H, Letteboer S, Van Reeuwijk J, Simons DL, Ding Q, Wu KM, Li Y, Van Beersum S, Moayedi Y, Xu H, Pickard P, Wang K, Gan L, Wu SM, Williams DS, Mardon G, Roepman R, Chen R. Spata7 is a retinal ciliopathy gene critical for correct RPGRIP1 localization and protein trafficking in the retina. Hum Mol Genet 2014; 24:1584-601. [PMID: 25398945 DOI: 10.1093/hmg/ddu573] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Leber congenital amaurosis (LCA) and juvenile retinitis pigmentosa (RP) are severe hereditary diseases that causes visual impairment in infants and children. SPATA7 has recently been identified as the LCA3 and juvenile RP gene in humans, whose function in the retina remains elusive. Here, we show that SPATA7 localizes at the primary cilium of cells and at the connecting cilium (CC) of photoreceptor cells, indicating that SPATA7 is a ciliary protein. In addition, SPATA7 directly interacts with the retinitis pigmentosa GTPase regulator interacting protein 1 (RPGRIP1), a key connecting cilium protein that has also been linked to LCA. In the retina of Spata7 null mutant mice, a substantial reduction of RPGRIP1 levels at the CC of photoreceptor cells is observed, suggesting that SPATA7 is required for the stable assembly and localization of the ciliary RPGRIP1 protein complex. Furthermore, our results pinpoint a role of this complex in protein trafficking across the CC to the outer segments, as we identified that rhodopsin accumulates in the inner segments and around the nucleus of photoreceptors. This accumulation then likely triggers the apoptosis of rod photoreceptors that was observed. Loss of Spata7 function in mice indeed results in a juvenile RP-like phenotype, characterized by progressive degeneration of photoreceptor cells and a strongly decreased light response. Together, these results indicate that SPATA7 functions as a key member of a retinal ciliopathy-associated protein complex, and that apoptosis of rod photoreceptor cells triggered by protein mislocalization is likely the mechanism of disease progression in LCA3/ juvenile RP patients.
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Affiliation(s)
| | - Thanh-Minh T Nguyen
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen 6525, The Netherlands
| | - Yiyun Chen
- HGSC, Department of Molecular and Human Genetics
| | - Julian Esteve-Rudd
- Jules Stein Eye Institute, UCLA David Geffen School of Medicine, Los Angeles, CA 90095, USA
| | - Hua Zhong
- Department of Pathology and Immunology
| | - Stef Letteboer
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen 6525, The Netherlands
| | - Jeroen Van Reeuwijk
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen 6525, The Netherlands
| | - David L Simons
- Department of Neuroscience and Department of Ophthalmology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Qian Ding
- Department of Ophthalmology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Ka Man Wu
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen 6525, The Netherlands
| | - Yumei Li
- HGSC, Department of Molecular and Human Genetics
| | - Sylvia Van Beersum
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen 6525, The Netherlands
| | | | - Huidan Xu
- HGSC, Department of Molecular and Human Genetics
| | | | - Keqing Wang
- HGSC, Department of Molecular and Human Genetics
| | - Lin Gan
- Department of Ophthalmology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Samuel M Wu
- Department of Neuroscience and Department of Ophthalmology, Baylor College of Medicine, Houston, TX 77030, USA
| | - David S Williams
- Jules Stein Eye Institute, UCLA David Geffen School of Medicine, Los Angeles, CA 90095, USA
| | - Graeme Mardon
- Department of Molecular and Human Genetics, Department of Pathology and Immunology, Department of Neuroscience and Department of Ophthalmology, Baylor College of Medicine, Houston, TX 77030, USA,
| | - Ronald Roepman
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen 6525, The Netherlands,
| | - Rui Chen
- HGSC, Department of Molecular and Human Genetics,
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26
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Jusiak B, Karandikar UC, Kwak SJ, Wang F, Wang H, Chen R, Mardon G. Regulation of Drosophila eye development by the transcription factor Sine oculis. PLoS One 2014; 9:e89695. [PMID: 24586968 PMCID: PMC3934907 DOI: 10.1371/journal.pone.0089695] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 01/21/2014] [Indexed: 11/18/2022] Open
Abstract
Homeodomain transcription factors of the Sine oculis (SIX) family direct multiple regulatory processes throughout the metazoans. Sine oculis (So) was first characterized in the fruit fly Drosophila melanogaster, where it is both necessary and sufficient for eye development, regulating cell survival, proliferation, and differentiation. Despite its key role in development, only a few direct targets of So have been described previously. In the current study, we aim to expand our knowledge of So-mediated transcriptional regulation in the developing Drosophila eye using ChIP-seq to map So binding regions throughout the genome. We find 7,566 So enriched regions (peaks), estimated to map to 5,952 genes. Using overlap between the So ChIP-seq peak set and genes that are differentially regulated in response to loss or gain of so, we identify putative direct targets of So. We find So binding enrichment in genes not previously known to be regulated by So, including genes that encode cell junction proteins and signaling pathway components. In addition, we analyze a subset of So-bound novel genes in the eye, and find eight genes that have previously uncharacterized eye phenotypes and may be novel direct targets of So. Our study presents a greatly expanded list of candidate So targets and serves as basis for future studies of So-mediated gene regulation in the eye.
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Affiliation(s)
- Barbara Jusiak
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Umesh C. Karandikar
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Su-Jin Kwak
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Feng Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Hui Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Rui Chen
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Graeme Mardon
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Ophthalmology, Baylor College of Medicine, Houston, Texas, United States of America
- Program in Cell and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America
- * E-mail:
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27
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Atkins M, Jiang Y, Sansores-Garcia L, Jusiak B, Halder G, Mardon G. Dynamic rewiring of the Drosophila retinal determination network switches its function from selector to differentiation. PLoS Genet 2013; 9:e1003731. [PMID: 24009524 PMCID: PMC3757064 DOI: 10.1371/journal.pgen.1003731] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Accepted: 07/05/2013] [Indexed: 01/15/2023] Open
Abstract
Organ development is directed by selector gene networks. Eye development in the fruit fly Drosophila melanogaster is driven by the highly conserved selector gene network referred to as the “retinal determination gene network,” composed of approximately 20 factors, whose core comprises twin of eyeless (toy), eyeless (ey), sine oculis (so), dachshund (dac), and eyes absent (eya). These genes encode transcriptional regulators that are each necessary for normal eye development, and sufficient to direct ectopic eye development when misexpressed. While it is well documented that the downstream genes so, eya, and dac are necessary not only during early growth and determination stages but also during the differentiation phase of retinal development, it remains unknown how the retinal determination gene network terminates its functions in determination and begins to promote differentiation. Here, we identify a switch in the regulation of ey by the downstream retinal determination genes, which is essential for the transition from determination to differentiation. We found that central to the transition is a switch from positive regulation of ey transcription to negative regulation and that both types of regulation require so. Our results suggest a model in which the retinal determination gene network is rewired to end the growth and determination stage of eye development and trigger terminal differentiation. We conclude that changes in the regulatory relationships among members of the retinal determination gene network are a driving force for key transitions in retinal development. Animals develop by using different combinations of simple instructions. The highly conserved retinal determination (RD) network is an ancient set of instructions that evolved when multicellular animals first developed primitive eyes. Evidence suggests that this network is re-used throughout evolution to direct the development of organs that communicate with the brain, providing information about our internal and external world. This includes our eyes, ears, kidneys, and pancreas. An upstream member of the network named eyeless must be activated early to initiate eye development. Eyeless then activates the expression of downstream genes that maintain eyeless expression and define the eye field. Here, we show that eyeless must also be turned off for final steps of eye development. We investigated the mechanism by which eyeless is turned off and we find that feedback regulation by the downstream RD genes changes to repress Eyeless expression during late stages of development. This study shows that tight regulation of eyeless is important for normal development and provides a mechanism for its repression.
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Affiliation(s)
- Mardelle Atkins
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, United States of America
- VIB Center for the Biology of Disease, KU Leuven Center for Human Genetics, University of Leuven, Leuven Belgium
| | - Yuwei Jiang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Developmental Biology, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States of America
| | - Leticia Sansores-Garcia
- VIB Center for the Biology of Disease, KU Leuven Center for Human Genetics, University of Leuven, Leuven Belgium
| | - Barbara Jusiak
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Georg Halder
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, United States of America
- VIB Center for the Biology of Disease, KU Leuven Center for Human Genetics, University of Leuven, Leuven Belgium
| | - Graeme Mardon
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Pathology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Ophthalmology, Baylor College of Medicine, Houston, Texas, United States of America
- * E-mail:
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Li Y, Jiang Y, Chen Y, Karandikar U, Hoffman K, Chattopadhyay A, Mardon G, Chen R. optix functions as a link between the retinal determination network and the dpp pathway to control morphogenetic furrow progression in Drosophila. Dev Biol 2013; 381:50-61. [PMID: 23792115 DOI: 10.1016/j.ydbio.2013.06.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Revised: 06/10/2013] [Accepted: 06/11/2013] [Indexed: 10/26/2022]
Abstract
optix, the Drosophila ortholog of the SIX3/6 gene family in vertebrate, encodes a homeodomain protein with a SIX protein-protein interaction domain. In vertebrates, Six3/6 genes are required for normal eye as well as brain development. However, the normal function of optix in Drosophila remains unknown due to lack of loss-of-function mutation. Previous studies suggest that optix is likely to play an important role as part of the retinal determination (RD) network. To elucidate normal optix function during retinal development, multiple null alleles for optix have been generated. Loss-of-function mutations in optix result in lethality at the pupae stage. Surprisingly, close examination of its function during eye development reveals that, unlike other members of the RD network, optix is required only for morphogenetic furrow (MF) progression, but not initiation. The mechanisms by which optix regulates MF progression is likely through regulation of signaling molecules in the furrow. Specifically, although unaffected during MF initiation, expression of dpp in the MF is dramatically reduced in optix mutant clones. In parallel, we find that optix is regulated by sine oculis and eyes absent, key members of the RD network. Furthermore, positive feedback between optix and sine oculis and eyes absent is observed, which is likely mediated through dpp signaling pathway. Together with the observation that optix expression does not depend on hh or dpp, we propose that optix functions together with hh to regulate dpp in the MF, serving as a link between the RD network and the patterning pathways controlling normal retinal development.
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Affiliation(s)
- Yumei Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77303, USA
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29
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Haase Gilbert E, Kwak SJ, Chen R, Mardon G. Drosophila signal peptidase complex member Spase12 is required for development and cell differentiation. PLoS One 2013; 8:e60908. [PMID: 23573290 PMCID: PMC3616019 DOI: 10.1371/journal.pone.0060908] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Accepted: 03/05/2013] [Indexed: 01/22/2023] Open
Abstract
It is estimated that half of all proteins expressed in eukaryotic cells are transferred across or into at least one cellular membrane to reach their functional location. Protein translocation into the endoplasmic reticulum (ER) is critical to the subsequent localization of secretory and transmembrane proteins. A vital component of the translocation machinery is the signal peptidase complex (SPC) - which is conserved from yeast to mammals – and functions to cleave the signal peptide sequence (SP) of secretory and membrane proteins entering the ER. Failure to cleave the SP, due to mutations that abolish the cleavage site or reduce SPC function, leads to the accumulation of uncleaved proteins in the ER that cannot be properly localized resulting in a wide range of defects depending on the protein(s) affected. Despite the obvious importance of the SPC, in vivo studies investigating its function in a multicellular organism have not been reported. The Drosophila SPC comprises four proteins: Spase18/21, Spase22/23, Spase25 and Spase12. Spc1p, the S. cerevisiae homolog of Spase12, is not required for SPC function or viability; Drosophila spase12 null alleles, however, are embryonic lethal. The data presented herein show that spase12 LOF clones disrupt development of all tissues tested including the eye, wing, leg, and antenna. In the eye, spase12 LOF clones result in a disorganized eye, defective cell differentiation, ectopic interommatidial bristles, and variations in support cell size, shape, number, and distribution. In addition, spase12 mosaic tissue is susceptible to melanotic mass formation suggesting that spase12 LOF activates immune response pathways. Together these data demonstrate that spase12 is an essential gene in Drosophila where it functions to mediate cell differentiation and development. This work represents the first reported in vivo analysis of a SPC component in a multicellular organism.
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Affiliation(s)
- Erin Haase Gilbert
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Su-Jin Kwak
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Rui Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, United States of America
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Graeme Mardon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, United States of America
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Ophthalmology, Baylor College of Medicine, Houston, Texas, United States of America
- * E-mail:
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30
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Jin M, Jusiak B, Bai Z, Mardon G. Eyes absent tyrosine phosphatase activity is not required for Drosophila development or survival. PLoS One 2013; 8:e58818. [PMID: 23554934 PMCID: PMC3595212 DOI: 10.1371/journal.pone.0058818] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Accepted: 02/06/2013] [Indexed: 12/15/2022] Open
Abstract
Eyes absent (Eya) is an evolutionarily conserved transcriptional coactivator and protein phosphatase that regulates multiple developmental processes throughout the metazoans. Drosophila eya is necessary for survival as well as for the formation of the adult eye. Eya contains a tyrosine phosphatase domain, and mutations altering presumptive active-site residues lead to strongly reduced activities in ectopic eye induction, in vivo genetic rescue using the Gal4-UAS system, and in vitro phosphatase assays. However, these mutations have not been analyzed during normal development with the correct levels, timing, and patterns of endogenous eya expression. To investigate whether the tyrosine phosphatase activity of Eya plays a role in Drosophila survival or normal eye formation, we generated three eya genomic rescue (eyaGR) constructs that alter key active-site residues and tested them in vivo. In striking contrast to previous studies, all eyaGR constructs fully restore eye formation as well as viability in an eya null mutant background. We conclude that the tyrosine phosphatase activity of Eya is not required for normal eye development or survival in Drosophila. Our study suggests the need for a re-evaluation of the mechanism of Eya action and underscores the importance of studying genes in their native context.
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Affiliation(s)
- Meng Jin
- Laboratory of Developmental Immunology, School of Life Science, Shandong University, Jinan, Shandong, People’s Republic of China
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Barbara Jusiak
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Zengliang Bai
- Laboratory of Developmental Immunology, School of Life Science, Shandong University, Jinan, Shandong, People’s Republic of China
- * E-mail: (GM); (ZB)
| | - Graeme Mardon
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Ophthalmology, Baylor College of Medicine, Houston, Texas, United States of America
- Program in Cell and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America
- * E-mail: (GM); (ZB)
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Jusiak B, Abulimiti A, Haelterman N, Chen R, Mardon G. MAPK target sites of eyes absent are not required for eye development or survival in Drosophila. PLoS One 2012; 7:e50776. [PMID: 23251383 PMCID: PMC3520925 DOI: 10.1371/journal.pone.0050776] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Accepted: 10/24/2012] [Indexed: 11/18/2022] Open
Abstract
Eyes absent (Eya) is a highly conserved transcription cofactor and protein phosphatase that plays an essential role in eye development and survival in Drosophila. Ectopic eye induction assays using cDNA transgenes have suggested that mitogen activated protein kinase (MAPK) activates Eya by phosphorylating it on two consensus target sites, S402 and S407, and that this activation potentiates the ability of Eya to drive eye formation. However, this mechanism has never been tested in normal eye development. In the current study, we generated a series of genomic rescue transgenes to investigate how loss- and gain-of-function mutations at these two MAPK target sites within Eya affect Drosophila survival and normal eye formation: eya+GR, the wild-type control; eyaSAGR, which lacks phosphorylation at the two target residues; and eyaSDEGR, which contains phosphomimetic amino acids at the same two residues. Contrary to the previous studies in ectopic eye development, all eya genomic transgenes tested rescue both eye formation and survival equally effectively. We conclude that, in contrast to ectopic eye formation, MAPK-mediated phosphorylation of Eya on S402 and S407 does not play a role in normal development. This is the first study in Drosophila to evaluate the difference in outcomes between genomic rescue and ectopic cDNA-based overexpression of the same gene. These findings indicate similar genomic rescue strategies may prove useful for re-evaluating other long-standing Drosophila developmental models.
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Affiliation(s)
- Barbara Jusiak
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Abuduaini Abulimiti
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Nele Haelterman
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Rui Chen
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, United States of America
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Graeme Mardon
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Pathology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Ophthalmology, Baylor College of Medicine, Houston, Texas, United States of America
- Program in Cell and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America
- * E-mail:
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Wang H, Chen X, Dudinsky L, Patenia C, Chen Y, Li Y, Wei Y, Abboud EB, Al-Rajhi AA, Lewis RA, Lupski JR, Mardon G, Gibbs RA, Perkins BD, Chen R. Exome capture sequencing identifies a novel mutation in BBS4. Mol Vis 2011; 17:3529-40. [PMID: 22219648 PMCID: PMC3250376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2011] [Accepted: 12/26/2011] [Indexed: 11/02/2022] Open
Abstract
PURPOSE Leber congenital amaurosis (LCA) is one of the most severe eye dystrophies characterized by severe vision loss at an early stage and accounts for approximately 5% of all retinal dystrophies. The purpose of this study was to identify a novel LCA disease allele or gene and to develop an approach combining genetic mapping with whole exome sequencing. METHODS Three patients from King Khaled Eye Specialist Hospital (KKESH205) underwent whole genome single nucleotide polymorphism genotyping, and a single candidate region was identified. Taking advantage of next-generation high-throughput DNA sequencing technologies, whole exome capture sequencing was performed on patient KKESH205#7. Sanger direct sequencing was used during the validation step. The zebrafish model was used to examine the function of the mutant allele. RESULTS A novel missense mutation in Bardet-Biedl syndrome 4 protein (BBS4) was identified in a consanguineous family from Saudi Arabia. This missense mutation in the fifth exon (c.253G>C;p.E85Q) of BBS4 is likely a disease-causing mutation as it segregates with the disease. The mutation is not found in the single nucleotide polymorphism (SNP) database, the 1000 Genomes Project, or matching normal controls. Functional analysis of this mutation in zebrafish indicates that the G253C allele is pathogenic. Coinjection of the G253C allele cannot rescue the mislocalization of rhodopsin in the retina when BBS4 is knocked down by morpholino injection. Immunofluorescence analysis in cell culture shows that this missense mutation in BBS4 does not cause obvious defects in protein expression or pericentriolar localization. CONCLUSIONS This mutation likely mainly reduces or abolishes BBS4 function in the retina. Further studies of this allele will provide important insights concerning the pleiotropic nature of BBS4 function.
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Affiliation(s)
- Hui Wang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Xianfeng Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Lynn Dudinsky
- Department of Biology, Texas A&M University, College Station, TX
| | - Claire Patenia
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Yiyun Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Yumei Li
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Yue Wei
- Leukemia Department, University of Texas, M. D. Anderson Cancer Center, Houston, TX
| | - Emad B. Abboud
- King Khaled Eye Specialist Hospital, Riyadh, Kingdom of Saudi Arabia
| | - Ali A. Al-Rajhi
- King Khaled Eye Specialist Hospital, Riyadh, Kingdom of Saudi Arabia
| | - Richard Alan Lewis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
- Department of Ophthalmology, Baylor College of Medicine, Houston, TX
- Texas Children’s Hospital, Baylor College of Medicine, Houston, TX
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
- Texas Children’s Hospital, Baylor College of Medicine, Houston, TX
- Department of Neurology, Baylor College of Medicine, Houston, TX
| | - Graeme Mardon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
- Department of Neurology, Baylor College of Medicine, Houston, TX
- Department of Neuroscience, Baylor College of Medicine, Houston, TX
- Department of Pathology, Baylor College of Medicine, Houston, TX
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Brian D. Perkins
- Department of Biology, Texas A&M University, College Station, TX
| | - Rui Chen
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX
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Wang X, Wang H, Cao M, Li Z, Chen X, Patenia C, Gore A, Abboud EB, Al-Rajhi AA, Lewis RA, Lupski JR, Mardon G, Zhang K, Muzny D, Gibbs RA, Chen R. Whole-exome sequencing identifies ALMS1, IQCB1, CNGA3, and MYO7A mutations in patients with Leber congenital amaurosis. Hum Mutat 2011; 32:1450-9. [PMID: 21901789 DOI: 10.1002/humu.21587] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Accepted: 07/28/2011] [Indexed: 12/21/2022]
Abstract
It has been well documented that mutations in the same retinal disease gene can result in different clinical phenotypes due to difference in the mutant allele and/or genetic background. To evaluate this, a set of consanguineous patient families with Leber congenital amaurosis (LCA) that do not carry mutations in known LCA disease genes was characterized through homozygosity mapping followed by targeted exon/whole-exome sequencing to identify genetic variations. Among these families, a total of five putative disease-causing mutations, including four novel alleles, were found for six families. These five mutations are located in four genes, ALMS1, IQCB1, CNGA3, and MYO7A. Therefore, in our LCA collection from Saudi Arabia, three of the 37 unassigned families carry mutations in retinal disease genes ALMS1, CNGA3, and MYO7A, which have not been previously associated with LCA, and 3 of the 37 carry novel mutations in IQCB1, which has been recently associated with LCA. Together with other reports, our results emphasize that the molecular heterogeneity underlying LCA, and likely other retinal diseases, may be highly complex. Thus, to obtain accurate diagnosis and gain a complete picture of the disease, it is essential to sequence a larger set of retinal disease genes and combine the clinical phenotype with molecular diagnosis.
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Affiliation(s)
- Xia Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
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Anderson AE, Karandikar UC, Pepple KL, Chen Z, Bergmann A, Mardon G. The enhancer of trithorax and polycomb gene Caf1/p55 is essential for cell survival and patterning in Drosophila development. Development 2011; 138:1957-66. [PMID: 21490066 DOI: 10.1242/dev.058461] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In vitro data suggest that the human RbAp46 and RbAp48 genes encode proteins involved in multiple chromatin remodeling complexes and are likely to play important roles in development and tumor suppression. However, to date, our understanding of the role of RbAp46/RbAp48 and its homologs in metazoan development and disease has been hampered by a lack of insect and mammalian mutant models, as well as redundancy due to multiple orthologs in most organisms studied. Here, we report the first mutations in the single Drosophila RbAp46/RbAp48 homolog Caf1, identified as strong suppressors of a senseless overexpression phenotype. Reduced levels of Caf1 expression result in flies with phenotypes reminiscent of Hox gene misregulation. Additionally, analysis of Caf1 mutant tissue suggests that Caf1 plays important roles in cell survival and segment identity, and loss of Caf1 is associated with a reduction in the Polycomb Repressive Complex 2 (PRC2)-specific histone methylation mark H3K27me3. Taken together, our results suggest suppression of senseless overexpression by mutations in Caf1 is mediated by participation of Caf1 in PRC2-mediated silencing. More importantly, our mutant phenotypes confirm that Caf1-mediated silencing is vital to Drosophila development. These studies underscore the importance of Caf1 and its mammalian homologs in development and disease.
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Affiliation(s)
- Aimée E Anderson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
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Jiang Y, Scott KL, Kwak SJ, Chen R, Mardon G. Sds22/PP1 links epithelial integrity and tumor suppression via regulation of myosin II and JNK signaling. Oncogene 2011; 30:3248-60. [PMID: 21399659 DOI: 10.1038/onc.2011.46] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Loss of epithelial integrity often correlates with the progression of malignant tumors. Sds22, a regulatory subunit of protein phosphatase 1 (PP1), has recently been linked to regulation of epithelial polarity in Drosophila. However, its role in tumorigenesis remains obscure. In this study, using Drosophila imaginal tissue as an in vivo model system, we show that sds22 is a new potential tumor suppressor gene in Drosophila. Without sds22, cells lose epithelial architecture, and become invasive and tumorigenic when combined with Ras overexpression; conversely, sds22 overexpression can largely suppress tumorigenic growth of Ras(V12)scrib(-/-) mutant cells. Mechanistically, we show that sds22 prevents cell invasion and metastasis by inhibiting myosin II and Jun N-terminal kinase (JNK) activity downstream of PP1. Loss of this inhibition causes cells to lose epithelial organization and promotes cell invasion. Finally, human Sds22 is focally deleted and downregulated in multiple carcinomas, and this downregulation correlates with tumor progression, suggesting that sds22 inactivation may contribute to tumorigenesis and metastatic potential in human cancers via a similar mechanism.
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Affiliation(s)
- Y Jiang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
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Wang H, den Hollander AI, Moayedi Y, Abulimiti A, Li Y, Collin RW, Hoyng CB, Lopez I, Abboud EB, Al-Rajhi AA, Bray M, Lewis RA, Lupski JR, Mardon G, Koenekoop RK, Chen R. Mutations in SPATA7 Cause Leber Congenital Amaurosis and Juvenile Retinitis Pigmentosa. Am J Hum Genet 2010. [DOI: 10.1016/j.ajhg.2010.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Popov VM, Wu K, Powell MJ, Mardon G, Wang C, Pestell RG. The Dachshund gene in development and hormone-responsive tumorigenesis. Trends Endocrinol Metab 2010; 21:41-9. [PMID: 19896866 PMCID: PMC2818438 DOI: 10.1016/j.tem.2009.08.002] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2009] [Revised: 08/04/2009] [Accepted: 08/05/2009] [Indexed: 01/14/2023]
Abstract
The dachshund (dac) gene was initially described as a mutant phenotype in flies featuring extremely short legs relative to their body length. Functioning as a dominant suppressor of the ellipse mutation, a hypermorphic allele of the Epidermal Growth Factor Receptor (EGFR), the dac gene plays a key role in metazoan development, regulating ocular, limb, brain, and gonadal development. In the Drosophila eye, dac is a key component of the Retinal Determination Gene Network (RDGN) governing the normal initiation of the morphogenetic furrow and thereby eye development. Recent studies have demonstrated an important role for human Dachshund homologue (DACH1) in tumorigenesis, in particular, breast, prostate and ovarian cancer. The molecular mechanisms by which DACH1 regulates differentiation and tumorigenesis are discussed herein.
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Affiliation(s)
- Vladimir M. Popov
- Department of Cancer Biology, Kimmel Cancer Center, Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA
| | - Kongming Wu
- Department of Cancer Biology, Kimmel Cancer Center, Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA
| | - Michael J. Powell
- Department of Cancer Biology, Kimmel Cancer Center, Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA
| | - Graeme Mardon
- Departments of Pathology, Neuroscience, Ophthalmology and Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030
| | - Chenguang Wang
- Department of Cancer Biology, Kimmel Cancer Center, Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA
| | - Richard G. Pestell
- Department of Cancer Biology, Kimmel Cancer Center, Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA
- Corresponding Author: Richard G. Pestell, The Kimmel Cancer Center, Department of Cancer Biology, Thomas Jefferson University, 233 South 10 Street, Philadelphia, PA 19107, Tel: 213-503-5692; Fax: 215-503-9334, For Reprints:
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Abstract
The eye-antennal imaginal disc of Drosophila melanogaster has often been described as an epithelial monolayer with complex signaling events playing out in two dimensions. However, the imaginal disc actually comprises two opposing epithelia (the peripodial epithelium, or PE, and the disc proper, or DP) separated by a lumen to form a sac-like structure. Recent studies expose complex molecular interactions between the PE and the DP, and reveal dynamic communication between the two tissues. Further findings suggest the PE makes important contributions to DP development by acting as a source of signaling molecules as well as cells. Here we summarize those findings and highlight implications for further research.
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Affiliation(s)
- Mardelle Atkins
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA
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39
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Wang H, den Hollander AI, Moayedi Y, Abulimiti A, Li Y, Collin RW, Hoyng CB, Lopez I, Bray M, Lewis RA, Lupski JR, Mardon G, Koenekoop RK, Chen R, Koenekoop RK, Chen R. Mutations in SPATA7 cause Leber congenital amaurosis and juvenile retinitis pigmentosa. Am J Hum Genet 2009; 84:380-7. [PMID: 19268277 DOI: 10.1016/j.ajhg.2009.02.005] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2008] [Revised: 02/04/2009] [Accepted: 02/06/2009] [Indexed: 11/25/2022] Open
Abstract
Leber congenital amaurosis (LCA) and juvenile retinitis pigmentosa (RP) are the most common hereditary causes of visual impairment in infants and children. Using homozygosity mapping, we narrowed down the critical region of the LCA3 locus to 3.8 Mb between markers D14S1022 and D14S1005. By direct Sanger sequencing of all genes within this region, we found a homozygous nonsense mutation in the SPATA7 gene in Saudi Arabian family KKESH-060. Three other loss-of-function mutations were subsequently discovered in patients with LCA or juvenile RP from distinct populations. Furthermore, we determined that Spata7 is expressed in the mature mouse retina. Our findings reveal another human visual-disease gene that causes LCA and juvenile RP.
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40
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Pepple KL, Atkins M, Venken K, Wellnitz K, Harding M, Frankfort B, Mardon G. Two-step selection of a single R8 photoreceptor: a bistable loop between senseless and rough locks in R8 fate. Development 2008; 135:4071-9. [PMID: 19004852 DOI: 10.1242/dev.028951] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Patterning of sensory organs requires precise regulation of neural induction and repression. The neurocrystalline pattern of the adult Drosophila compound eye is generated by ordered selection of single founder photoreceptors (R8s) for each unit eye or ommatidium. R8 selection requires mechanisms that restrict R8 potential to a single cell from within a group of cells expressing the proneural gene atonal (ato). One model of R8 selection suggests that R8 precursors are selected from a three-cell ;R8 equivalence group' through repression of ato by the homeodomain transcription factor Rough (Ro). A second model proposes that lateral inhibition is sufficient to select a single R8 from an equipotent group of cells called the intermediate group (IG). Here, we provide new evidence that lateral inhibition, but not ro, is required for the initial selection of a single R8 precursor. We show that in ro mutants, ectopic R8s develop from R2,5 photoreceptor precursors independently of ectopic Ato and hours after normal R8s are specified. We also show that Ro directly represses the R8 specific zinc-finger transcription factor senseless (sens) in the developing R2,5 precursors to block ectopic R8 differentiation. Our results support a new model for R8 selection in which lateral inhibition establishes a transient pattern of selected R8s that is permanently reinforced by a repressive bistable loop between sens and ro. This model provides new insight into the strategies that allow successful integration of a repressive patterning signal, such as lateral inhibition, with continued developmental plasticity during retinal differentiation.
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Affiliation(s)
- Kathryn L Pepple
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
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Li Y, Wang H, Peng J, Gibbs RA, Lewis RA, Lupski JR, Mardon G, Chen R. Mutation survey of known LCA genes and loci in the Saudi Arabian population. Invest Ophthalmol Vis Sci 2008; 50:1336-43. [PMID: 18936139 DOI: 10.1167/iovs.08-2589] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE The purpose of this study was to perform a comprehensive survey of all known Leber congenital amaurosis (LCA) genes and loci in a collection of 37 consanguineous LCA families from Saudi Arabia. METHODS Direct PCR and sequencing were used to screen 13 known LCA genes (GUCY2D, CRX, RPE65, TULP1, AIPL1, CRB1, RPGRIP1, LRAT, RDH12, IMPDH1, CEP290, RD3, LCA5). In addition, families without mutations identified were further screened with STR markers around these 13 known LCA genes and two loci. RESULTS Disease-causing mutations were identified in nine of the 37 families: five in TULP1, two in CRB1, one in RPE65, and one in GUCY2D. Mutations in known genes only accounted for 24% of the Saudi families--much less than what has been observed in the European population (65%). Phenotype-genotype analysis was carried out to investigate the LCA disease penetrance for all families whose mutations identified. All identified mutations were found to segregate perfectly with the disease phenotype. On the other hand, severity of the disease varies for different patients carrying the same mutation and even within the same family. Furthermore, based on homozygosity mapping with both STR and SNP markers, one family is likely to map to the LCA3 locus. CONCLUSIONS These results underscore the importance of studying LCA disease families from different ethnic backgrounds to identify additional novel LCA disease genes. Furthermore, perfect segregation between mutation and disease indicates that LCA is fully penetrant. However, phenotypic variations among patients carrying the same mutation suggest that at least some of the variations in the clinical phenotype is due to modification from the genetic background, environment, or other factors.
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Affiliation(s)
- Yumei Li
- Departments of Molecular and Human Genetics
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Abstract
dachshund/Dach gene family members encode transcriptional cofactors with highly conserved protein interaction domains and are expressed in the developing eyes, brains, and limbs in insects and vertebrates. These observations suggest that the developmental roles of dachshund/Dach in these tissues have been conserved since the divergence of arthropods and chordates. However, while Drosophila dachshund mutants have abnormalities in eye, brain, limbs, mouse Dach1 or Dach2 knockout mutants do not exhibit gross anatomical malformations in these tissues. In addition, Dach1/2 double homozygotes have intact eyes and limbs. Here we show that in Dach1/Dach2 double mutants, female reproductive tract (FRT) development is severely disrupted. This defect is associated with the Müllerian duct (MD) and not the Wolffian duct (WD), which normally differentiate into either the FRT or male reproductive tract (MRT), respectively. Dach1 and Dach2 are expressed in the MD, and in Dach1/2 double mutants, MD expression of Lim1 and Wnt7a is abnormal and MD development is disrupted. In contrast, WD and MRT development are not grossly affected. We propose that Dach1 and Dach2 proteins may redundantly control FRT formation by regulating the expression of target genes required for development of the MD. This vertebrate Dach1/2 function may have been conserved during arthropod evolution, as Drosophila dachshund mutants also exhibit an FRT phenotype.
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Affiliation(s)
- Richard J Davis
- Department of Ophthalmology, Columbia University Medical Center, Harkness Eye Institute, New York City, New York
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43
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Pepple KL, Anderson AE, Frankfort BJ, Mardon G. A genetic screen in Drosophila for genes interacting with senseless during neuronal development identifies the importin moleskin. Genetics 2006; 175:125-41. [PMID: 17110483 PMCID: PMC1774993 DOI: 10.1534/genetics.106.065680] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Senseless (Sens) is a conserved transcription factor required for normal development of the Drosophila peripheral nervous system. In the Drosophila retina, sens is necessary and sufficient for differentiation of R8 photoreceptors and interommatidial bristles (IOBs). When Sens is expressed in undifferentiated cells posterior to the morphogenetic furrow, ectopic IOBs are formed. This phenotype was used to identify new members of the sens pathway in a dominant modifier screen. Seven suppressor and three enhancer complementation groups were isolated. Three groups from the screen are the known genes Delta, lilliputian, and moleskin/DIM-7 (msk), while the remaining seven groups represent novel genes with previously undefined functions in neural development. The nuclear import gene msk was identified as a potent suppressor of the ectopic interommatidial bristle phenotype. In addition, msk mutant adult eyes are extremely disrupted with defects in multiple cell types. Reminiscent of the sens mutant phenotype, msk eyes demonstrate reductions in the number of R8 photoreceptors due to an R8 to R2,5 fate switch, providing genetic evidence that Msk is a component of the sens pathway. Interestingly, in msk tissue, the loss of R8 fate occurs earlier than with sens and suggests a previously unidentified stage of R8 development between atonal and sens.
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Affiliation(s)
- Kathryn L Pepple
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
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44
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Abstract
Drosophila dachshund is a critical regulator of eye, brain, and limb formation. Vertebrate homologs, Dach1 and Dach2, are expressed in the developing retina, brain, and limbs, suggesting functional conservation of the dachshund/Dach gene family. Dach1 mutants die postnatally, but exhibit grossly normal development. Here we report the generation of Dach2 mutant mice. Although deletion of Dach2 exon 1 results in abrogation of RNA expression, Dach2 mutants are viable and fertile. Histochemical analysis reveals grossly normal Dach2 mutant eye development. In addition, a battery of neurological assays failed to yield significant differences in behavior between Dach2 mutants and controls. We discuss these findings in the light of published observations of DACH2 mutations in the human population. Finally, to test the functional conservation hypothesis, we generated Dach2; Dach1 double mutant mice. Dach double mutants die after birth, similar to Dach1 homozygotes. However, unlike Drosophila dachshund mutants that lack eyes and exhibit leg truncations, the eyes and limbs of Dach double mutants are present, suggesting differences between Dach and dachshund gene function during embryonic eye and limb formation.
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Affiliation(s)
- Richard J Davis
- Department of Pathology, Baylor College of Medicine, Houston, Texas 77030, USA
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45
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Ostrin EJ, Li Y, Hoffman K, Liu J, Wang K, Zhang L, Mardon G, Chen R. Genome-wide identification of direct targets of the Drosophila retinal determination protein Eyeless. Genome Res 2006; 16:466-76. [PMID: 16533912 PMCID: PMC1457028 DOI: 10.1101/gr.4673006] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The discovery of direct downstream targets of transcription factors (TFs) is necessary for understanding the genetic mechanisms underlying complex, highly regulated processes such as development. In this report, we have used a combinatorial strategy to conduct a genome-wide search for novel direct targets of Eyeless (Ey), a key transcription factor controlling early eye development in Drosophila. To overcome the lack of high-quality consensus binding site sequences, phylogenetic shadowing of known Ey binding sites in sine oculis (so) was used to construct a position weight matrix (PWM) of the Ey protein. This PWM was then used for in silico prediction of potential binding sites in the Drosophila melanogaster genome. To reduce the false positive rate, conservation of these potential binding sites was assessed by comparing the genomic sequences from seven Drosophila species. In parallel, microarray analysis of wild-type versus ectopic ey-expressing tissue, followed by microarray-based epistasis experiments in an atonal (ato) mutant background, identified 188 genes induced by ey. Intersection of in silico predicted conserved Ey binding sites with the candidate gene list produced through expression profiling yields a list of 20 putative ey-induced, eye-enriched, ato-independent, direct targets of Ey. The accuracy of this list of genes was confirmed using both in vitro and in vivo methods. Initial analysis reveals three genes, eyes absent, shifted, and Optix, as novel direct targets of Ey. These results suggest that the integrated strategy of computational biology, genomics, and genetics is a powerful approach to identify direct downstream targets for any transcription factor genome-wide.
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Affiliation(s)
| | - Yumei Li
- Molecular and Human Genetics
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Kristi Hoffman
- Pathology
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Jing Liu
- Molecular and Human Genetics
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Keqing Wang
- Molecular and Human Genetics
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Li Zhang
- Department of Biostatistics, The University of Texas, M.D. Anderson Cancer Center, Houston, Texas 77030, USA
| | - Graeme Mardon
- Molecular and Human Genetics
- Ophthalmology
- Neuroscience
- Pathology
- Program in Developmental Biology
- Corresponding authors.E-mail ; fax (713) 798-5741.E-mail ; fax (713) 798-3359
| | - Rui Chen
- Molecular and Human Genetics
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
- Corresponding authors.E-mail ; fax (713) 798-5741.E-mail ; fax (713) 798-3359
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46
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Purcell P, Oliver G, Mardon G, Donner AL, Maas RL. Pax6-dependence of Six3, Eya1 and Dach1 expression during lens and nasal placode induction. Gene Expr Patterns 2005; 6:110-8. [PMID: 16024294 DOI: 10.1016/j.modgep.2005.04.010] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2005] [Revised: 04/15/2005] [Accepted: 04/18/2005] [Indexed: 11/17/2022]
Abstract
The Drosophila eyeless gene plays a central role in fly eye development and controls a subordinate regulatory network consisting of the so, eya and dac genes. All three genes have highly conserved mammalian homologs, suggesting possible conservation of this eye forming regulatory network. sine oculis (so) belongs to the so/Six gene family, and Six3 is prominently expressed in the developing mammalian eye. Eya1 and Dach1 are mammalian homologs of eya and dac, respectively, and although neither Eya1 nor Dach1 knockout mice express prenatal eye defects, possibilities exist for postnatal ocular phenotypes or for functional redundancy between related family members. To examine whether expression relationships analogous to those between ey, so, eya and dac exist in early mammalian oculogenesis, we investigated Pax6, Six3, Eya1 and Dach1 protein expression in murine lens and nasal placode development. Six3 expression in the pre-placode lens ectoderm is initially Pax6-independent, but subsequently both its expression and nuclear localization become Pax6-dependent. Six3, Dach1 and Eya1 nasal expression in pre-placode ectoderm are also initially Pax6-independent, but thereafter become Pax6-dependent. Pax6, Six3, Dach1 and Eya1 are all co-expressed in the developing ciliary marginal zone, a source of retinal stem cells in some vertebrates. An in vitro protein-protein interaction is detected between Six3 and Eya1. Collectively, these findings suggest that the Pax-Eya-Six-Dach network is at best only partly conserved during lens and nasal placode development. However, the findings do not rule out the possibility that such a regulatory network acts at later stages of oculogenesis.
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Affiliation(s)
- Patricia Purcell
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard, Medical School, New Research Building, Rm. 458H, 77, Avenue Louis Pasteur, Boston, MA 02115, USA
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47
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Pappu KS, Ostrin EJ, Middlebrooks BW, Sili BT, Chen R, Atkins MR, Gibbs R, Mardon G. Dual regulation and redundant function of two eye-specific enhancers of the Drosophila retinal determination gene dachshund. Development 2005; 132:2895-905. [PMID: 15930118 DOI: 10.1242/dev.01869] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Drosophila eye development is controlled by a conserved network of retinal determination (RD) genes. The RD genes encode nuclear proteins that form complexes and function in concert with extracellular signal-regulated transcription factors. Identification of the genomic regulatory elements that govern the eye-specific expression of the RD genes will allow us to better understand how spatial and temporal control of gene expression occurs during early eye development. We compared conserved non-coding sequences (CNCSs) between five Drosophilids along the approximately 40 kb genomic locus of the RD gene dachshund (dac). Our analysis uncovers two separate eye enhancers in intron eight and the 3' non-coding regions of the dac locus defined by clusters of highly conserved sequences. Loss- and gain-of-function analyses suggest that the 3' eye enhancer is synergistically activated by a combination of eya, so and dpp signaling, and only indirectly activated by ey, whereas the 5' eye enhancer is primarily regulated by ey, acting in concert with eya and so. Disrupting conserved So-binding sites in the 3' eye enhancer prevents reporter expression in vivo. Our results suggest that the two eye enhancers act redundantly and in concert with each other to integrate distinct upstream inputs and direct the eye-specific expression of dac.
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Affiliation(s)
- Kartik S Pappu
- Program in Developmental Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
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48
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Pesah Y, Burgess H, Middlebrooks B, Ronningen K, Prosser J, Tirunagaru V, Zysk J, Mardon G. Whole-mount analysis reveals normal numbers of dopaminergic neurons following misexpression of alpha-Synuclein in Drosophila. Genesis 2005; 41:154-9. [PMID: 15789427 DOI: 10.1002/gene.20106] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Previously published reports have suggested that misexpression of alpha-Synuclein in the Drosophila central nervous system causes neurodegeneration and progressive age-dependent locomotor dysfunction similar to pathologic and clinical manifestations of Parkinson's disease. The number of dopaminergic (DA) neurons in these studies was assessed using immunohistochemistry with an anti-tyrosine hydroxylase antibody on sequential paraffin sections of fly brains. In contrast, we do not observe any DA cell loss in alpha-Synuclein expressing fly brains when using whole-mount immunohistochemistry as an assay. Our results suggest that the DA cell loss observed with misexpression of alpha-Synuclein is not fully penetrant under a variety of experimental conditions and that this may complicate interpretation of such experiments.
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Affiliation(s)
- Yakov Pesah
- Division of Neuroscience, Baylor College of Medicine, Houston, Texas 77030, USA
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49
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Abstract
With its unique structure and dynamic development, the Drosophila eye has been a powerful genetic model system for studying molecular mechanisms of cell fate specification and differentiation. Hundreds of genes that function in a complex genetic network controlling this process have been identified during the past two decades. To further advance our understanding of the molecular mechanisms of eye development, it is increasingly important to place the current genetic pathway into a whole-genome perspective. Here, we review emerging technologies and strategies that will help to achieve this goal, including generation of a complete mutant set in Drosophila, genome-wide transcription factor target identification, and systematic studies of gene function aided by computational biology.
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Affiliation(s)
- Rui Chen
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
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50
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Domingos PM, Brown S, Barrio R, Ratnakumar K, Frankfort BJ, Mardon G, Steller H, Mollereau B. Regulation of R7 and R8 differentiation by the spalt genes. Dev Biol 2004; 273:121-33. [PMID: 15302602 DOI: 10.1016/j.ydbio.2004.05.026] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2004] [Revised: 05/19/2004] [Accepted: 05/25/2004] [Indexed: 10/26/2022]
Abstract
Photoreceptor development begins in the larval eye imaginal disc, where eight distinct photoreceptor cells (R1-R8) are sequentially recruited into each of the developing ommatidial clusters. Final photoreceptor differentiation, including rhabdomere formation and rhodopsin expression, is completed during pupal life. During pupation, spalt was previously proposed to promote R7 and R8 terminal differentiation. Here we show that spalt is required for proper R7 differentiation during the third instar larval stage since the expression of several R7 larval markers (prospero, enhancer of split mdelta0.5, and runt) is lost in spalt mutant clones. In R8, spalt is not required for cell specification or differentiation in the larval disc but promotes terminal differentiation during pupation. We show that spalt is necessary for senseless expression in R8 and sufficient to induce ectopic senseless in R1-R6 during pupation. Moreover, misexpression of spalt or senseless is sufficient to induce ectopic rhodopsin 6 expression and partial suppression of rhodopsin 1. We demonstrate that spalt and senseless are part of a genetic network, which regulates rhodopsin 6 and rhodopsin 1. Taken together, our results suggest that while spalt is required for R7 differentiation during larval stages, spalt and senseless promote terminal R8 differentiation during pupal stages, including the regulation of rhodopsin expression.
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Affiliation(s)
- Pedro M Domingos
- Howard Hughes Medical Institute, Strang Laboratory of Cancer Research, The Rockefeller University, New York, NY 10021, USA
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