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Hernandez-Moran BA, Papanastasiou AS, Parry D, Meynert A, Gautier P, Grimes G, Adams IR, Trejo-Reveles V, Bengani H, Keighren M, Jackson IJ, Adams DJ, FitzPatrick DR, Rainger J. Robust Genetic Analysis of the X-Linked Anophthalmic ( Ie) Mouse. Genes (Basel) 2022; 13:1797. [PMID: 36292683 PMCID: PMC9601528 DOI: 10.3390/genes13101797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/25/2022] [Accepted: 09/29/2022] [Indexed: 11/24/2022] Open
Abstract
Anophthalmia (missing eye) describes a failure of early embryonic ocular development. Mutations in a relatively small set of genes account for 75% of bilateral anophthalmia cases, yet 25% of families currently are left without a molecular diagnosis. Here, we report our experimental work that aimed to uncover the developmental and genetic basis of the anophthalmia characterising the X-linked Ie (eye-ear reduction) X-ray-induced allele in mouse that was first identified in 1947. Histological analysis of the embryonic phenotype showed failure of normal eye development after the optic vesicle stage with particularly severe malformation of the ventral retina. Linkage analysis mapped this mutation to a ~6 Mb region on the X chromosome. Short- and long-read whole-genome sequencing (WGS) of affected and unaffected male littermates confirmed the Ie linkage but identified no plausible causative variants or structural rearrangements. These analyses did reduce the critical candidate interval and revealed evidence of multiple variants within the ancestral DNA, although none were found that altered coding sequences or that were unique to Ie. To investigate early embryonic events at a genetic level, we then generated mouse ES cells derived from male Ie embryos and wild type littermates. RNA-seq and accessible chromatin sequencing (ATAC-seq) data generated from cultured optic vesicle organoids did not reveal any large differences in gene expression or accessibility of putative cis-regulatory elements between Ie and wild type. However, an unbiased TF-footprinting analysis of accessible chromatin regions did provide evidence of a genome-wide reduction in binding of transcription factors associated with ventral eye development in Ie, and evidence of an increase in binding of the Zic-family of transcription factors, including Zic3, which is located within the Ie-refined critical interval. We conclude that the refined Ie critical region at chrX: 56,145,000-58,385,000 contains multiple genetic variants that may be linked to altered cis regulation but does not contain a convincing causative mutation. Changes in the binding of key transcription factors to chromatin causing altered gene expression during development, possibly through a subtle mis-regulation of Zic3, presents a plausible cause for the anophthalmia phenotype observed in Ie, but further work is required to determine the precise causative allele and its genetic mechanism.
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Affiliation(s)
- Brianda A. Hernandez-Moran
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Rd South, Edinburgh EH4 2XU, UK
| | - Andrew S. Papanastasiou
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Rd South, Edinburgh EH4 2XU, UK
| | - David Parry
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Rd South, Edinburgh EH4 2XU, UK
| | - Alison Meynert
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Rd South, Edinburgh EH4 2XU, UK
| | - Philippe Gautier
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Rd South, Edinburgh EH4 2XU, UK
| | - Graeme Grimes
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Rd South, Edinburgh EH4 2XU, UK
| | - Ian R. Adams
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Rd South, Edinburgh EH4 2XU, UK
| | - Violeta Trejo-Reveles
- The Division of Functional Genetics and Development, The Roslin Institute, Midlothian EH25 9RG, UK
| | - Hemant Bengani
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Rd South, Edinburgh EH4 2XU, UK
| | - Margaret Keighren
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Rd South, Edinburgh EH4 2XU, UK
| | - Ian J. Jackson
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Rd South, Edinburgh EH4 2XU, UK
| | - David J. Adams
- Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - David R. FitzPatrick
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Rd South, Edinburgh EH4 2XU, UK
| | - Joe Rainger
- The Division of Functional Genetics and Development, The Roslin Institute, Midlothian EH25 9RG, UK
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Xu F, Guo D, Jiang Q, Zhang R, Yu T, Yin X, Wu S, Liu D, Wen Y, Wu J, Bi A, Jiang W, Bi H. Association between anti-fibrillin-2 protein induced retinal degeneration via intravitreous delivery and activated TGF-β signaling in mice. Clin Exp Pharmacol Physiol 2022; 49:586-595. [PMID: 35108420 DOI: 10.1111/1440-1681.13631] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 01/04/2022] [Accepted: 01/24/2022] [Indexed: 02/05/2023]
Abstract
Fibrillin-2 (FBN2) is a major component of tissue microfibrils, and the decrease of FBN2 perturbs the signaling events mediated by TGF-β, thereby playing a role in macular degeneration. However, the association between the retinal degeneration resulting from the abnormality of FBN2 and the activation of TGF-β signaling has not been fully addressed. In the present study, the mice were divided into a normal control group (NC group), a phosphate-buffered saline (PBS) injection group (PBS group), and an anti-FBN2 protein injection group (anti-FBN2 group), and the mice in PBS and anti-FBN2 groups received the relevant treatment via the intravitreal injection once a week for three consecutive weeks. One week later after injection, the retinal morphology and visual function of the fundus were detected. Further, the expression of FBN2, TGF-β1, TGF-β2 and TGF-β3 in retina was measured using quantitative polymerase chain reaction (Q-PCR) and enzyme-linked immunosorbent assay (ELISA), respectively. As a result, fundus examination suggests that after intravitreous injection of anti-FBN2 protein, there were a large patchy yellow white degeneration region and numerous pigmentations in the retina in anti-FBN2-treated mice; by contrast, there was no apparent change in mice from the NC and PBS groups. The retina suffered markedly damage, and the thickness of whole retina and outer nuclear layer markedly thinned. The expression of FBN2 was decreased whereas the levels of TGF-β1, TGF-β2, and TGF-β3 were upregulated. Together, our findings indicate that the intravitreous delivery of anti-FBN2 protein could induce retina degeneration in mice, accompanied by the higher activated TGF-β. The retinal degeneration mouse model established will provide a platform for the investigation of the retinal diseases.
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Affiliation(s)
- Furu Xu
- Affiliated Eye Hospital of Shandong, University of Traditional Chinese Medicine, Jinan, 250002, China
| | - Dadong Guo
- Shandong Provincial Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Therapy of Ocular Disease, Eye Institute of Shandong University of Traditional Chinese Medicine, Jinan, 250002, China
| | - Qian Jiang
- Department of Ophthalmology and Optometry, Shandong University of Traditional Chinese Medicine, Jinan, 250014, China
| | - Ruixue Zhang
- Department of Ophthalmology and Optometry, Shandong University of Traditional Chinese Medicine, Jinan, 250014, China
| | - Ting Yu
- Department of Ophthalmology and Optometry, Shandong University of Traditional Chinese Medicine, Jinan, 250014, China
| | - Xuewei Yin
- The First Clinical Medical College, Shandong University of Traditional Chinese Medicine, Jinan, 250014, China
| | - Shanshan Wu
- Department of Ophthalmology, West China Hospital of Sichuan University, Sichuan Province, No. 37 Guoxue Xiang, Wuhou District, Chengdu, 610041, China
| | - Dezheng Liu
- Department of Ophthalmology and Optometry, Shandong University of Traditional Chinese Medicine, Jinan, 250014, China
| | - Ying Wen
- Affiliated Eye Hospital of Shandong, University of Traditional Chinese Medicine, Jinan, 250002, China
| | - Jianfeng Wu
- Affiliated Eye Hospital of Shandong, University of Traditional Chinese Medicine, Jinan, 250002, China
| | - Ailing Bi
- Shandong Provincial Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Therapy of Ocular Disease, Eye Institute of Shandong University of Traditional Chinese Medicine, Jinan, 250002, China
| | - Wenjun Jiang
- Shandong Provincial Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Therapy of Ocular Disease, Eye Institute of Shandong University of Traditional Chinese Medicine, Jinan, 250002, China
| | - Hongsheng Bi
- Department of Ophthalmology and Optometry, Shandong University of Traditional Chinese Medicine, Jinan, 250014, China
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Murine allele and transgene symbols: ensuring unique, concise, and informative nomenclature. Mamm Genome 2021; 33:108-119. [PMID: 34389871 PMCID: PMC8913455 DOI: 10.1007/s00335-021-09902-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 08/03/2021] [Indexed: 11/15/2022]
Abstract
In addition to naturally occurring sequence variation and spontaneous mutations, a wide array of technologies exist for modifying the mouse genome. Standardized nomenclature, including allele, transgene, and other mutation nomenclature, as well as persistent unique identifiers (PUID) are critical for effective scientific communication, comparison of results, and integration of data into knowledgebases such as Mouse Genome Informatics (MGI), Alliance for Genome Resources, and International Mouse Strain Resource (IMSR). As well as being the authoritative source for mouse gene, allele, and strain nomenclature, MGI integrates published and unpublished genomic, phenotypic, and expression data while linking to other online resources for a complete view of the mouse as a valuable model organism. The International Committee on Standardized Genetic Nomenclature for Mice has developed allele nomenclature rules and guidelines that take into account the number of genes impacted, the method of allele generation, and the nature of the sequence alteration. To capture details that cannot be included in allele symbols, MGI has further developed allele to gene relationships using sequence ontology (SO) definitions for mutations that provide links between alleles and the genes affected. MGI is also using (HGVS) variant nomenclature for variants associated with alleles that will enhance searching for mutations and will improve cross-species comparison. With the ability to assign unique and informative symbols as well as to link alleles with more than one gene, allele and transgene nomenclature rules and guidelines provide an unambiguous way to represent alterations in the mouse genome and facilitate data integration among multiple resources such the Alliance of Genome Resources and International Mouse Strain Resource.
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Shi J, Yang F, Zhou N, Jiang Y, Zhao Y, Zhu J, Prelaj A, Malhotra J, Normanno N, Danese E, Cardona AF, Hong X, Jiang G, Song X. Isochorismatase domain-containing protein 1 (ISOC1) participates in DNA damage repair and inflammation-related pathways to promote lung cancer development. Transl Lung Cancer Res 2021; 10:1444-1456. [PMID: 33889521 PMCID: PMC8044495 DOI: 10.21037/tlcr-21-219] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
BACKGROUND The advent of novel molecular targets has dramatically changed the treatment landscape of lung cancer in recent years. Isochorismatase domain-containing protein 1 (ISOC1) has been reported as a potential biomarker in gastrointestinal cancer, while its function in lung cancer has not been determined. METHODS The expression levels and prognostic significance of ISOC1 were assessed using bioinformatic analysis. Overexpression of ISOC1 and miR-4633, and knockdown of ISOC1 in non-small cell lung cancer (NSCLC) cell lines were generated by lentiviral infection with overexpressed or shRNA plasmids. CRISPR/Cas9 system was applied to knockout ISOC1 in A549 cells. The functions of ISOC1 and miR-4633 in lung cancer development were investigated using cell proliferation, migration, and invasion assays. Xenograft tumor growth assays in nude mice were further assessed the effect of ISOC1 in the tumorigenesis of NSCLC in vivo. Cell cycle distribution analysis was performed to uncover the underlying mechanism of ISOC1 and miR-4633 in promoting NSCLC cell proliferation. Co-immunoprecipitation combined with mass spectrometry and RNA sequencing were performed to uncover the potential mechanism of ISOC1 in lung cancer development. RESULTS Our results found that ISOC1 expression was upregulated in NSCLC tissues and that increased expression of ISOC1 was significantly associated with worse disease-free survival in NSCLC patients. Overexpression of ISOC1 could increase the proliferation, viability, migration, and invasion of NSCLC cells. Furthermore, miR-4633, located in the first intron of ISOC1, could also promote tumor cell progression and metastasis. Mice xenograft tumor assay showed that knockout of ISOC1 could significantly inhibit tumor growth in vivo. Besides, co-immunoprecipitation combined with mass spectrometry assay revealed that ISOC1 interacted with the proteins of DNA damage repair pathways and that upregulated ISOC1 expression could significantly increase the number of DNA damage lesions. RNA sequencing analysis showed that the downstream signaling pathways mediated by ISOC1 were mainly inflammation-related. CONCLUSIONS We demonstrated that ISOC1 and its intronic miR-4633, both of them could promote NSCLC cell proliferation, migration, invasion, and cell cycle progression. ISOC1 participates in DNA damage repair and inflammation to promote lung cancer development.
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Affiliation(s)
- Jinghan Shi
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Fujun Yang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Nanfeng Zhou
- Department of Radiation Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yan Jiang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yanfeng Zhao
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Junjie Zhu
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Arsela Prelaj
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy;,Department of Electronics, Information, and Bioengineering, Polytechnic University of Milan, Milano, Italy
| | - Jyoti Malhotra
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori—IRCCS—“Fondazione G. Pascale”, Naples, Italy
| | - Elisa Danese
- Section of Clinical Biochemistry, University of Verona, Verona, Italy
| | - Andrés F. Cardona
- Foundation for Clinical and Applied Cancer Research-FICMAC/Clinical and Translational Oncology Group, Clínica del Country/Molecular Oncology and Biology Systems Research Group (Fox-G), El Bosque University, Bogotá, Colombia
| | - Xuan Hong
- Department of Thoracic Surgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Gening Jiang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xiao Song
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
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5
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Identification of Possible Risk Variants of Familial Strabismus Using Exome Sequencing Analysis. Genes (Basel) 2021; 12:genes12010075. [PMID: 33435129 PMCID: PMC7827096 DOI: 10.3390/genes12010075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/31/2020] [Accepted: 01/06/2021] [Indexed: 11/16/2022] Open
Abstract
PURPOSE To investigate candidate genes associated with familial strabismus and propose a theory of their interaction in familial strabismus associated with early neurodevelopment. METHODS Eighteen families, including 53 patients diagnosed with strabismus and 34 unaffected family members, were analyzed. All patients with strabismus and available unaffected family members were evaluated using whole exome sequencing. The primary outcome was to identify rare occurring variants among affected individuals and investigate the evidence of their genetic heterogeneity. These results were compared with exome sequencing analysis to build a comprehensive genetic profile of the study families. RESULTS We observed 60 variants from 58 genes in 53 patients diagnosed with strabismus. We prioritized the most credible risk variants, which showed clear segregation in family members affected by strabismus. As a result, we found risk variants in four genes (FAT3, KCNH2, CELSR1, and TTYH1) in five families, suggesting their role in development of familial strabismus. In other families, there were several rare genetic variants in affected cases, but we did not find clear segregation pattern across family members. CONCLUSION Genomic sequencing holds great promise in elucidating the genetic causes of strabismus; further research with larger cohorts or other related approaches are warranted.
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6
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Choquet H, Melles RB, Yin J, Hoffmann TJ, Thai KK, Kvale MN, Banda Y, Hardcastle AJ, Tuft SJ, Glymour MM, Schaefer C, Risch N, Nair KS, Hysi PG, Jorgenson E. A multiethnic genome-wide analysis of 44,039 individuals identifies 41 new loci associated with central corneal thickness. Commun Biol 2020; 3:301. [PMID: 32528159 PMCID: PMC7289804 DOI: 10.1038/s42003-020-1037-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 05/22/2020] [Indexed: 02/08/2023] Open
Abstract
Central corneal thickness (CCT) is one of the most heritable human traits, with broad-sense heritability estimates ranging between 0.68 to 0.95. Despite the high heritability and numerous previous association studies, only 8.5% of CCT variance is currently explained. Here, we report the results of a multiethnic meta-analysis of available genome-wide association studies in which we find association between CCT and 98 genomic loci, of which 41 are novel. Among these loci, 20 were significantly associated with keratoconus, and one (RAPSN rs3740685) was significantly associated with glaucoma after Bonferroni correction. Two-sample Mendelian randomization analysis suggests that thinner CCT does not causally increase the risk of primary open-angle glaucoma. This large CCT study explains up to 14.2% of CCT variance and increases substantially our understanding of the etiology of CCT variation. This may open new avenues of investigation into human ocular traits and their relationship to the risk of vision disorders.
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Affiliation(s)
- Hélène Choquet
- Kaiser Permanente Northern California (KPNC), Division of Research, Oakland, CA, 94612, USA.
| | - Ronald B Melles
- KPNC, Department of Ophthalmology, Redwood City, CA, 94063, USA
| | - Jie Yin
- Kaiser Permanente Northern California (KPNC), Division of Research, Oakland, CA, 94612, USA
| | - Thomas J Hoffmann
- Institute for Human Genetics, University of California San Francisco (UCSF), San Francisco, CA, 94143, USA
- Department of Epidemiology and Biostatistics, UCSF, San Francisco, CA, 94158, USA
| | - Khanh K Thai
- Kaiser Permanente Northern California (KPNC), Division of Research, Oakland, CA, 94612, USA
| | - Mark N Kvale
- Institute for Human Genetics, University of California San Francisco (UCSF), San Francisco, CA, 94143, USA
| | - Yambazi Banda
- Institute for Human Genetics, University of California San Francisco (UCSF), San Francisco, CA, 94143, USA
| | - Alison J Hardcastle
- UCL Institute of Ophthalmology, University College London, London, UK
- National Institute of Health Research Biomedical Research Centre for Ophthalmology, and UCL Institute of Ophthalmology, London, UK
| | | | - M Maria Glymour
- Department of Epidemiology and Biostatistics, UCSF, San Francisco, CA, 94158, USA
| | - Catherine Schaefer
- Kaiser Permanente Northern California (KPNC), Division of Research, Oakland, CA, 94612, USA
| | - Neil Risch
- Kaiser Permanente Northern California (KPNC), Division of Research, Oakland, CA, 94612, USA
- Institute for Human Genetics, University of California San Francisco (UCSF), San Francisco, CA, 94143, USA
- Department of Epidemiology and Biostatistics, UCSF, San Francisco, CA, 94158, USA
| | - K Saidas Nair
- Departments of Ophthalmology and Anatomy, School of Medicine, UCSF, San Francisco, CA, 94143, USA
| | - Pirro G Hysi
- King's College London, Section of Ophthalmology, School of Life Course Sciences, London, UK
- King's College London, Department of Twin Research and Genetic Epidemiology, London, UK
- University College London, Great Ormond Street Hospital Institute of Child Health, London, UK
| | - Eric Jorgenson
- Kaiser Permanente Northern California (KPNC), Division of Research, Oakland, CA, 94612, USA.
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Canovas S, Ivanova E, Romar R, García-Martínez S, Soriano-Úbeda C, García-Vázquez FA, Saadeh H, Andrews S, Kelsey G, Coy P. DNA methylation and gene expression changes derived from assisted reproductive technologies can be decreased by reproductive fluids. eLife 2017; 6. [PMID: 28134613 PMCID: PMC5340525 DOI: 10.7554/elife.23670] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Accepted: 01/28/2017] [Indexed: 12/14/2022] Open
Abstract
The number of children born since the origin of Assisted Reproductive Technologies (ART) exceeds 5 million. The majority seem healthy, but a higher frequency of defects has been reported among ART-conceived infants, suggesting an epigenetic cost. We report the first whole-genome DNA methylation datasets from single pig blastocysts showing differences between in vivo and in vitro produced embryos. Blastocysts were produced in vitro either without (C-IVF) or in the presence of natural reproductive fluids (Natur-IVF). Natur-IVF embryos were of higher quality than C-IVF in terms of cell number and hatching ability. RNA-Seq and DNA methylation analyses showed that Natur-IVF embryos have expression and methylation patterns closer to in vivo blastocysts. Genes involved in reprogramming, imprinting and development were affected by culture, with fewer aberrations in Natur-IVF embryos. Methylation analysis detected methylated changes in C-IVF, but not in Natur-IVF, at genes whose methylation could be critical, such as IGF2R and NNAT. DOI:http://dx.doi.org/10.7554/eLife.23670.001 Infertility has become more common in many countries, particularly those where many people delay having children until later in life. To help individuals experiencing infertility conceive a child, scientists have developed treatments called assisted reproductive technologies (or ARTs for short). So far, more than 5 million children have been born with the help of these treatments. Most of the children seem healthy; however, birth defects are more common in ART-conceived babies than those conceived without treatment. The cause of these birth defects is not known, though scientists suspect it may have something to do with techniques used in ART. One possible culprit is the liquid that is used in the laboratory to help the parents’ sperm and egg come together for fertilization. This same liquid is also used to bathe the developing embryo for the first few days after fertilization before it is implanted into its mother’s womb. Some scientists wonder whether adding the fluids normally found in the reproductive tract of their mother to this liquid could reduce defects in children conceived via ART. Now, Canovas et al. have shown that fertilizing and growing pig embryos in liquids supplemented with fluid from the wombs of female pigs results in embryos that are closer to naturally conceived pig embryos than in non-supplemented liquids. In the experiments, naturally conceived embryos were compared to ART embryos exposed to the usual liquids and with ART embryos grown in liquids with fluid collected from the pig’s reproductive tract added. Cutting edge technologies were used to sequence the entire genomes of all of the embryos and compare which genes were active in each case. Canovas et al. also looked at chemical markers on the DNA – called epigenetic changes – that turn on or off the expression of genes without changing the DNA code itself. The analysis showed that ART-conceived embryos grown in the usual liquid had different patterns of gene expression and epigenetic changes compared to naturally conceived embryos. Gene expression and epigenetic changes in the ART embryos grown with the pig reproductive fluid was more similar to the naturally conceived embryos. These findings suggest that abnormal gene expression in the ART-liquid exposed embryos may lead to birth defects, and that using natural reproductive fluids may be safer. To confirm this, scientists will have to implant embryos conceived in these three different conditions into mother pigs and assess the health and gene expression patterns of the resulting piglets. If successful, these new insights might one day lead to improvements in ART techniques used to treat infertility in people. DOI:http://dx.doi.org/10.7554/eLife.23670.002
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Affiliation(s)
- Sebastian Canovas
- Physiology of Reproduction Group, Departamento de Fisiología, Facultad de Veterinaria, Universidad de Murcia-Campus Mare Nostrum, Murcia, Spain.,Instituto Murciano de Investigación Biosanitaria, Murcia, Spain
| | - Elena Ivanova
- Epigenetics Programme, The Babraham Institute, Cambridge, United Kingdom
| | - Raquel Romar
- Physiology of Reproduction Group, Departamento de Fisiología, Facultad de Veterinaria, Universidad de Murcia-Campus Mare Nostrum, Murcia, Spain.,Instituto Murciano de Investigación Biosanitaria, Murcia, Spain
| | - Soledad García-Martínez
- Physiology of Reproduction Group, Departamento de Fisiología, Facultad de Veterinaria, Universidad de Murcia-Campus Mare Nostrum, Murcia, Spain.,Instituto Murciano de Investigación Biosanitaria, Murcia, Spain
| | - Cristina Soriano-Úbeda
- Physiology of Reproduction Group, Departamento de Fisiología, Facultad de Veterinaria, Universidad de Murcia-Campus Mare Nostrum, Murcia, Spain.,Instituto Murciano de Investigación Biosanitaria, Murcia, Spain
| | - Francisco A García-Vázquez
- Physiology of Reproduction Group, Departamento de Fisiología, Facultad de Veterinaria, Universidad de Murcia-Campus Mare Nostrum, Murcia, Spain.,Instituto Murciano de Investigación Biosanitaria, Murcia, Spain
| | - Heba Saadeh
- Epigenetics Programme, The Babraham Institute, Cambridge, United Kingdom.,Bioinformatics Group, The Babraham Institute, Cambridge, United Kingdom
| | - Simon Andrews
- Bioinformatics Group, The Babraham Institute, Cambridge, United Kingdom
| | - Gavin Kelsey
- Epigenetics Programme, The Babraham Institute, Cambridge, United Kingdom.,Centre for Trophoblast Research, University of Cambridge, Cambridge, United Kingdom
| | - Pilar Coy
- Physiology of Reproduction Group, Departamento de Fisiología, Facultad de Veterinaria, Universidad de Murcia-Campus Mare Nostrum, Murcia, Spain.,Instituto Murciano de Investigación Biosanitaria, Murcia, Spain
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8
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Douvaras P, Dorà NJ, Mort RL, Lodge EJ, Hill RE, West JD. Abnormal corneal epithelial maintenance in mice heterozygous for the micropinna microphthalmia mutation Mp. Exp Eye Res 2016; 149:26-39. [PMID: 27235794 PMCID: PMC4974241 DOI: 10.1016/j.exer.2016.05.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 04/26/2016] [Accepted: 05/23/2016] [Indexed: 01/06/2023]
Abstract
We investigated the corneal morphology of adult Mp/+ mice, which are heterozygous for the micropinna microphthalmia mutation, and identified several abnormalities, which implied that corneal epithelial maintenance was abnormal. The Mp/+ corneal epithelium was thin, loosely packed and contained goblet cells in older mice. Evidence also suggested that the barrier function was compromised. However, there was no major effect on corneal epithelial cell turnover and mosaic patterns of radial stripes indicated that radial cell movement was normal. Limbal blood vessels formed an abnormally wide limbal vasculature ring, K19-positive cells were distributed more widely than normal and K12 was weakly expressed in the peripheral cornea. This raises the possibilities that the limbal-corneal boundary was poorly defined or the limbus was wider than normal. BrdU label-retaining cell numbers and quantitative clonal analysis suggested that limbal epithelial stem cell numbers were not depleted and might be higher than normal. However, as corneal epithelial homeostasis was abnormal, it is possible that Mp/+ stem cell function was impaired. It has been shown recently that the Mp mutation involves a chromosome 18 inversion that disrupts the Fbn2 and Isoc1 genes and produces an abnormal, truncated fibrillin-2MP protein. This abnormal protein accumulates in the endoplasmic reticulum (ER) of cells that normally express Fbn2 and causes ER stress. It was also shown that Fbn2 is expressed in the corneal stroma but not the corneal epithelium, suggesting that the presence of truncated fibrillin-2MP protein in the corneal stroma disrupts corneal epithelial homeostasis in Mp/+ mice. Heterozygous mutant Mp/+ mice have small, abnormal eyes. The corneal epithelium is thin, loosely packed and has goblet cells. Corneal epithelial cell turnover and radial cell movement appear normal. The cornea-limbal border is poorly defined and the limbus appears wider than normal. Indirect tests suggest stem cells are not depleted and numbers might be increased.
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Affiliation(s)
- Panagiotis Douvaras
- Genes and Development Group, Centre for Integrative Physiology, Clinical Sciences, University of Edinburgh Medical School, Hugh Robson Building, George Square, Edinburgh, EH8 9XD, UK
| | - Natalie J Dorà
- Genes and Development Group, Centre for Integrative Physiology, Biomedical Sciences, University of Edinburgh Medical School, Hugh Robson Building, George Square, Edinburgh, EH8 9XD, UK
| | - Richard L Mort
- Genes and Development Group, Centre for Integrative Physiology, Clinical Sciences, University of Edinburgh Medical School, Hugh Robson Building, George Square, Edinburgh, EH8 9XD, UK
| | - Emily J Lodge
- Genes and Development Group, Centre for Integrative Physiology, Clinical Sciences, University of Edinburgh Medical School, Hugh Robson Building, George Square, Edinburgh, EH8 9XD, UK
| | - Robert E Hill
- Medical and Developmental Genetics Section, MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
| | - John D West
- Genes and Development Group, Centre for Integrative Physiology, Clinical Sciences, University of Edinburgh Medical School, Hugh Robson Building, George Square, Edinburgh, EH8 9XD, UK.
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Chen ZT, Li L, Guo Y, Qu S, Zhao W, Chen H, Su F, Yin J, Mo QY, Zhu XD. Analysis of the differential secretome of nasopharyngeal carcinoma cell lines CNE-2R and CNE-2. Oncol Rep 2015; 34:2477-88. [PMID: 26352878 DOI: 10.3892/or.2015.4255] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2015] [Accepted: 07/23/2015] [Indexed: 11/05/2022] Open
Abstract
Radioresistance is the major cause of poor prognosis in nasopharyngeal carcinoma (NPC). To identify and characterize the secretome associated with NPC radioresistance, we compared the conditioned serum-free medium of radioresistant CNE-2R cells with that of the parental radiosensitive CNE-2 cells using isobaric tags for relative and absolute quantitation (iTRAQ) with liquid chromatography-electrospray tandem mass spectrometry (LC-ESI-MS/MS) quantitative proteomics. Before proceeding to quantitative proteomics, we investigated the survival curves of CNE-2R and CNE-2 cells by colony formation assay, and the CNE-2R survival curves were significantly higher than those for CNE-2. In total, 3,581 proteins were identified in the quantitative proteomics experiments, and 40 proteins exhibited significant differences between the CNE-2R and CNE-2 cells. Twenty-six of the 40 proteins were secreted by classical, non-classical, or exosomal secretion pathways. To verify the reliability of iTRAQ quantitative proteomics, we applied western blotting (WB) to study the secretory protein expression of fibrillin-2, CD166, sulfhydryl oxidase 1 and cofilin-2, which are involved in cell adhesion, migration and invasion. The WB results showed that fibrillin-2 (p=0.017) and sulfhydryl oxidase 1 (p=0.000) were highly expressed in the CNE-2 cells, while CD166 (p=0.012) and cofilin-2 (p=0.003) were highly expressed in the CNE-2R cells, which was in accordance with iTRAQ quantitative proteomics. Finally, a phenotypic subset of CD166-positive NPC cells was verified by immunocytochemistry. In summary, we defined a collection of secretory proteins that may be relevant to the radioresistance in NPC cells, and we determined that CD166, which is widely used as a positive marker of cancer stem cells, is expressed in NPC cells.
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Affiliation(s)
- Ze-Tan Chen
- Department of Radiation Oncology, Cancer Hospital of Guangxi Medical University and Cancer Institute of Guangxi Zhuang Autonomous Region, Nanning, Guangxi 530021, P.R. China
| | - Ling Li
- Department of Radiation Oncology, Cancer Hospital of Guangxi Medical University and Cancer Institute of Guangxi Zhuang Autonomous Region, Nanning, Guangxi 530021, P.R. China
| | - Ya Guo
- Department of Radiation Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710004, P.R. China
| | - Song Qu
- Department of Radiation Oncology, Cancer Hospital of Guangxi Medical University and Cancer Institute of Guangxi Zhuang Autonomous Region, Nanning, Guangxi 530021, P.R. China
| | - Wei Zhao
- Department of Radiation Oncology, Cancer Hospital of Guangxi Medical University and Cancer Institute of Guangxi Zhuang Autonomous Region, Nanning, Guangxi 530021, P.R. China
| | - Hao Chen
- Department of Radiation Oncology, Cancer Hospital of Guangxi Medical University and Cancer Institute of Guangxi Zhuang Autonomous Region, Nanning, Guangxi 530021, P.R. China
| | - Fang Su
- Department of Radiation Oncology, Cancer Hospital of Guangxi Medical University and Cancer Institute of Guangxi Zhuang Autonomous Region, Nanning, Guangxi 530021, P.R. China
| | - Jun Yin
- Department of Radiation Oncology, Cancer Hospital of Guangxi Medical University and Cancer Institute of Guangxi Zhuang Autonomous Region, Nanning, Guangxi 530021, P.R. China
| | - Qi-Yan Mo
- Department of Radiation Oncology, Cancer Hospital of Guangxi Medical University and Cancer Institute of Guangxi Zhuang Autonomous Region, Nanning, Guangxi 530021, P.R. China
| | - Xiao-Dong Zhu
- Department of Radiation Oncology, Cancer Hospital of Guangxi Medical University and Cancer Institute of Guangxi Zhuang Autonomous Region, Nanning, Guangxi 530021, P.R. China
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10
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Heavner WE, Andoniadou CL, Pevny LH. Establishment of the neurogenic boundary of the mouse retina requires cooperation of SOX2 and WNT signaling. Neural Dev 2014; 9:27. [PMID: 25488119 PMCID: PMC4295269 DOI: 10.1186/1749-8104-9-27] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 11/14/2014] [Indexed: 12/03/2022] Open
Abstract
Background Eye development in vertebrates relies on the critical regulation of SOX2 expression. Humans with mutations in SOX2 often suffer from eye defects including anophthalmia (no eye) and microphthalmia (small eye). In mice, deletion of Sox2 in optic cup progenitor cells results in loss of neural competence and cell fate conversion of the neural retina to a non-neurogenic fate, specifically the acquisition of fate associated with progenitors of the ciliary epithelium. This fate is also promoted with constitutive expression of stabilized β-Catenin in the optic cup, where the WNT pathway is up-regulated. We addressed whether SOX2 co-ordinates the neurogenic boundary of the retina through modulating the WNT/β-Catenin pathway by using a genetic approach in the mouse. Results Upon deletion of Sox2 in the optic cup, response to WNT signaling was expanded, correlating with loss of neural competence, cell fate conversion of the neural retina to ciliary epithelium primordium and, in addition, increased cell cycle time of optic cup progenitors. Removal of Ctnnb1 rescued the cell fate conversion; however, the loss of neural competence and the proliferation defect resulting from lack of SOX2 were not overcome. Lastly, central Sox2-deficient optic cup progenitor cells exhibited WNT-independent up-regulation of D-type Cyclins. Conclusion We propose two distinct roles for SOX2 in the developing retina. Our findings suggest that SOX2 antagonizes the WNT pathway to maintain a neurogenic fate and, in contrast, regulates cycling of optic cup progenitors in a WNT-independent manner. Given that WNT signaling acting upstream of SOX2 has been implicated in the tumorigenicity of embryonic stem cell-derived retinal progenitor cells, our results distinguish the endogenous role of WNT signaling in early optic cup patterning and support a WNT-independent role for SOX2 in maintaining retinal progenitor cell proliferation. Electronic supplementary material The online version of this article (doi:10.1186/1749-8104-9-27) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Whitney E Heavner
- UNC Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA.
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