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Meyfour A, Pooyan P, Pahlavan S, Rezaei-Tavirani M, Gourabi H, Baharvand H, Salekdeh GH. Chromosome-Centric Human Proteome Project Allies with Developmental Biology: A Case Study of the Role of Y Chromosome Genes in Organ Development. J Proteome Res 2017; 16:4259-4272. [PMID: 28914051 DOI: 10.1021/acs.jproteome.7b00446] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
One of the main goals of Chromosome-Centric Human Proteome Project is to identify protein evidence for missing proteins (MPs). Here, we present a case study of the role of Y chromosome genes in organ development and how to overcome the challenges facing MPs identification by employing human pluripotent stem cell differentiation into cells of different organs yielding unprecedented biological insight into adult silenced proteins. Y chromosome is a male-specific sex chromosome which escapes meiotic recombination. From an evolutionary perspective, Y chromosome has preserved 3% of ancestral genes compared to 98% preservation of the X chromosome based on Ohno's law. Male specific region of Y chromosome (MSY) contains genes that contribute to central dogma and govern the expression of various targets throughout the genome. One of the most well-known functions of MSY genes is to decide the male-specific characteristics including sex, testis formation, and spermatogenesis, which are majorly formed by ampliconic gene families. Beyond its role in sex-specific gonad development, MSY genes in coexpression with their X counterparts, as single copy and broadly expressed genes, inhibit haplolethality and play a key role in embryogenesis. The role of X-Y related gene mutations in the development of hereditary syndromes suggests an essential contribution of sex chromosome genes to development. MSY genes, solely and independent of their X counterparts and/or in association with sex hormones, have a considerable impact on organ development. In this Review, we present major recent findings on the contribution of MSY genes to gonad formation, spermatogenesis, and the brain, heart, and kidney development and discuss how Y chromosome proteome project may exploit developmental biology to find missing proteins.
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Affiliation(s)
- Anna Meyfour
- Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, Academic Center for Education, Culture and Research , 81589-68433 Tehran, Iran.,Proteomics Research Center, Department of Basic Science, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences , 19839-63113 Tehran, Iran
| | - Paria Pooyan
- Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, Academic Center for Education, Culture and Research , 81589-68433 Tehran, Iran
| | - Sara Pahlavan
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, Academic Center for Education, Culture and Research , 81589-68433 Tehran, Iran
| | - Mostafa Rezaei-Tavirani
- Proteomics Research Center, Department of Basic Science, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences , 19839-63113 Tehran, Iran
| | - Hamid Gourabi
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute , 19395-4644 Tehran, Iran
| | - Hossein Baharvand
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, Academic Center for Education, Culture and Research , 81589-68433 Tehran, Iran.,Department of Developmental Biology, University of Science and Culture , 19395-4644 Tehran, Iran
| | - Ghasem Hosseini Salekdeh
- Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, Academic Center for Education, Culture and Research , 81589-68433 Tehran, Iran.,Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran , 31535-1897 Karaj, Iran
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Ullah E, Wu D, Madireddy L, Lao R, Ling-Fung Tang P, Wan E, Bardakjian T, Kopinsky S, Kwok PY, Schneider A, Baranzini S, Ansar M, Slavotinek A. Two missense mutations in SALL4 in a patient with microphthalmia, coloboma, and optic nerve hypoplasia. Ophthalmic Genet 2017; 38:371-375. [PMID: 27661448 PMCID: PMC6238016 DOI: 10.1080/13816810.2016.1217550] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 07/22/2016] [Indexed: 12/16/2022]
Abstract
To investigate the genetic etiology of anophthalmia and microphthalmia, we used exome sequencing in a Caucasian female with unilateral microphthalmia and coloboma, bilateral optic nerve hypoplasia, ventricular and atrial septal defects, and growth delays. We found two sequence variants in SALL4 - c.[575C>A], predicting p.(Ala192Glu), that was paternally inherited, and c.[2053G>C], predicting p.(Asp685His), that was maternally inherited. Haploinsufficiency for SALL4 due to nonsense or frameshift mutations has been associated with acro-renal ocular syndrome that is characterized by eye defects including Duane anomaly and coloboma, in addition to radial ray malformations and renal abnormalities. Our report is the first description of structural eye defects associated with two missense variants in SALL4 inherited in trans; the absence of reported findings in both parents suggests that both sequence variants are hypomorphic mutations and that both are needed for the ocular phenotype. SALL4 is expressed in the developing lens and regulates BMP4, leading us to speculate that altered BMP4 expression was responsible for the eye defects, but we could not demonstrate altered BMP4 expression in vitro after using small interfering RNAs (siRNAs) to reduce SALL4 expression. We conclude that SALL4 hypomorphic variants may influence eye development.
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Affiliation(s)
- E Ullah
- a Department of Pediatrics , University of California, San Francisco , San Francisco , California , USA
- b Department of Biochemistry, Faculty of Biological Sciences , Quaid-i-Azam University , Islamabad , Pakistan
| | - D Wu
- a Department of Pediatrics , University of California, San Francisco , San Francisco , California , USA
| | - L Madireddy
- c Department of Neurology , University of California, San Francisco , San Francisco , California , USA
| | - R Lao
- d Cardiovascular Research Institute , University of California, San Francisco , San Francisco , California , USA
| | - P Ling-Fung Tang
- d Cardiovascular Research Institute , University of California, San Francisco , San Francisco , California , USA
| | - E Wan
- d Cardiovascular Research Institute , University of California, San Francisco , San Francisco , California , USA
| | - T Bardakjian
- e Division of Medical Genetics , Einstein Healthcare Network , Philadelphia , Pennsylvania , USA
| | - S Kopinsky
- e Division of Medical Genetics , Einstein Healthcare Network , Philadelphia , Pennsylvania , USA
| | - P-Y Kwok
- d Cardiovascular Research Institute , University of California, San Francisco , San Francisco , California , USA
| | - A Schneider
- e Division of Medical Genetics , Einstein Healthcare Network , Philadelphia , Pennsylvania , USA
| | - S Baranzini
- c Department of Neurology , University of California, San Francisco , San Francisco , California , USA
| | - M Ansar
- b Department of Biochemistry, Faculty of Biological Sciences , Quaid-i-Azam University , Islamabad , Pakistan
| | - A Slavotinek
- a Department of Pediatrics , University of California, San Francisco , San Francisco , California , USA
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Kelly GM, Gatie MI. Mechanisms Regulating Stemness and Differentiation in Embryonal Carcinoma Cells. Stem Cells Int 2017; 2017:3684178. [PMID: 28373885 PMCID: PMC5360977 DOI: 10.1155/2017/3684178] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Revised: 01/10/2017] [Accepted: 02/08/2017] [Indexed: 02/06/2023] Open
Abstract
Just over ten years have passed since the seminal Takahashi-Yamanaka paper, and while most attention nowadays is on induced, embryonic, and cancer stem cells, much of the pioneering work arose from studies with embryonal carcinoma cells (ECCs) derived from teratocarcinomas. This original work was broad in scope, but eventually led the way for us to focus on the components involved in the gene regulation of stemness and differentiation. As the name implies, ECCs are malignant in nature, yet maintain the ability to differentiate into the 3 germ layers and extraembryonic tissues, as well as behave normally when reintroduced into a healthy blastocyst. Retinoic acid signaling has been thoroughly interrogated in ECCs, especially in the F9 and P19 murine cell models, and while we have touched on this aspect, this review purposely highlights how some key transcription factors regulate pluripotency and cell stemness prior to this signaling. Another major focus is on the epigenetic regulation of ECCs and stem cells, and, towards that end, this review closes on what we see as a new frontier in combating aging and human disease, namely, how cellular metabolism shapes the epigenetic landscape and hence the pluripotency of all stem cells.
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Affiliation(s)
- Gregory M. Kelly
- Department of Biology, Molecular Genetics Unit, Western University, London, ON, Canada
- Collaborative Program in Developmental Biology, Western University, London, ON, Canada
- Department of Paediatrics and Department of Physiology and Pharmacology, Western University, London, ON, Canada
- Child Health Research Institute, London, ON, Canada
- Ontario Institute for Regenerative Medicine, Toronto, ON, Canada
- The Hospital for Sick Children, Toronto, ON, Canada
| | - Mohamed I. Gatie
- Department of Biology, Molecular Genetics Unit, Western University, London, ON, Canada
- Collaborative Program in Developmental Biology, Western University, London, ON, Canada
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Falahzadeh K, Shahhoseini M, Afsharian P. Differential Incorporation of β-actin as A Component of RNA Polymerase II into Regulatory Regions of Stemness/Differentiation Genes in Retinoic Acid-Induced Differentiated Human Embryonic Carcinoma Cells. CELL JOURNAL 2016; 18:214-20. [PMID: 27540526 PMCID: PMC4988420 DOI: 10.22074/cellj.2016.4316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Accepted: 11/22/2015] [Indexed: 12/14/2022]
Abstract
Objective Nuclear actin is involved in transcription regulation by recruitment of histone
modifiers and chromatin remodelers to the regulatory regions of active genes. In recent
years, further attention has been focused on the role of actin as a nuclear protein in
transcriptional processes. In the current study, the epigenetic role of nuclear actin on
transcription regulation of two stemness (OCT4 and NANOG)
and two differentiation) NESTIN and PAX6) marker genes was evaluated in a human embryonal carcinoma cell line (NT2)
before and after differentiation induction. Materials and Methods In this experimental study, differentiation of embryonal cells was
induced by retinoic acid (RA), and quantitative real-time polymerase chain reaction (PCR)
was used to evaluate differential expression of marker genes before and 3 days after RA-
induced differentiation. Chromatin immunoprecipitation (ChIP) coupled with real-time PCR
was then undertaken to monitor the incorporation of β-actin, as a functional component of
RNA polymerase II, in the regulatory regions of marker genes. Results Data showed significant change in nuclear actin incorporation into the promoter
regions of NESTIN and PAX6 after RA-induction.
Conclusion We emphasize the dynamic functional role of nuclear actin in differentiation
of embryonal cells and its role as a subunit of RNA polymerase II.
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Affiliation(s)
- Khadijeh Falahzadeh
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran; Department of Cell and Molecular Biology, Faculty of Biological Sciences, Kharazmi University (TMU), Tehran, Iran
| | - Maryam Shahhoseini
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - Parvaneh Afsharian
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
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Bayarri-Olmos R, Hansen S, Henriksen ML, Storm L, Thiel S, Garred P, Munthe-Fog L. Genetic variation of COLEC10 and COLEC11 and association with serum levels of collectin liver 1 (CL-L1) and collectin kidney 1 (CL-K1). PLoS One 2015; 10:e0114883. [PMID: 25710878 PMCID: PMC4339841 DOI: 10.1371/journal.pone.0114883] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 11/14/2014] [Indexed: 11/18/2022] Open
Abstract
Collectin liver 1 (CL-L1, alias CL-10) and collectin kidney 1 (CL-K1, alias CL-11), encoded by the COLEC10 and COLEC11 genes, respectively, are highly homologous soluble pattern recognition molecules in the lectin pathway of complement. These proteins may be involved in anti-microbial activity and in tissue development as mutations in COLEC11 are one of the causes of the developmental defect syndrome 3MC. We studied variations in COLEC10 and COLEC11, the impact on serum concentration and to what extent CL-L1 and CL-K1 serum concentrations are correlated. We sequenced the promoter regions, exons and exon-intron boundaries of COLEC10 and COLEC11 in samples from Danish Caucasians and measured the corresponding serum levels of CL-L1 and CL-K1. The median concentration of CL-L1 and CL-K1 was 1.87 μg/ml (1.00-4.14 μg/ml) and 0.32 μg/ml (0.11-0.69 μg/ml), respectively. The level of CL-L1 strongly correlated with CL-K1 (ρ = 0.7405, P <0.0001). Both genes were highly conserved with the majority of variations in the non-coding regions. Three non-synonymous variations were tested: COLEC10 Glu78Asp (rs150828850, minor allele frequency (MAF): 0.003), COLEC10 Arg125Trp (rs149331285, MAF: 0.007) and COLEC11 His219Arg (rs7567833, MAF: 0.033). Carriers of COLEC10 Arg125Trp had increased CL-L1 serum levels (P = 0.0478), whereas promoter polymorphism COLEC11-9570C>T (rs3820897) was associated with decreased levels of CL-K1 (P = 0.044). In conclusion, COLEC10 and COLEC11 are highly conserved, which may reflect biological importance of CL-L1 and CL-K1. Moreover, the strong inter individual correlation between the two proteins suggests that a major proportion are found as heterooligomers or subjected to the same regulatory mechanisms.
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Affiliation(s)
- Rafael Bayarri-Olmos
- Laboratory of Molecular Medicine, Department of Clinical Immunology, Section 7631, Rigshospitalet, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Soren Hansen
- Department of Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Maiken Lumby Henriksen
- Department of Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Line Storm
- Department of Biomedicine, Faculty of Health Sciences, Aarhus University, Aarhus, Denmark
| | - Steffen Thiel
- Department of Biomedicine, Faculty of Health Sciences, Aarhus University, Aarhus, Denmark
| | - Peter Garred
- Laboratory of Molecular Medicine, Department of Clinical Immunology, Section 7631, Rigshospitalet, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lea Munthe-Fog
- Laboratory of Molecular Medicine, Department of Clinical Immunology, Section 7631, Rigshospitalet, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- * E-mail:
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Yiang GT, Tsai HF, Chen JR, Chou PL, Wu TK, Liu HC, Chang WJ, Liu LC, Tseng HH, Yu YL. RC-6 ribonuclease induces caspase activation, cellular senescence and neuron-like morphology in NT2 embryonal carcinoma cells. Oncol Rep 2014; 31:1738-44. [PMID: 24535104 DOI: 10.3892/or.2014.3023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Accepted: 11/25/2013] [Indexed: 11/05/2022] Open
Abstract
Frog ribonucleases have been demonstrated to have anticancer activities. However, whether RC-6 ribonuclease exerts anticancer activity on human embryonal carcinoma cells remains unclear. In the present study, RC-6 induced cytotoxicity in NT2 cells (a human embryonal carcinoma cell line) and our studies showed that RC-6 can exert anticancer effects and induce caspase-9 and -3 activities. Moreover, to date, there is no evidence that frog ribonuclease-induced cytotoxicity effects are related to cellular senescence. Therefore, our studies showed that RC-6 can increase p16 and p21 protein levels and induce cellular senescence in NT2 cells. Notably, similar to retinoic acid-differentiated NT2 cells, neuron-like morphology was found on some remaining live cells after RC-6 treatment. In conclusion, our study is the first to demonstrate that RC-6 can induce cytotoxic effects, caspase-9/-3 activities, cellular senescence and neuron-like morphology in NT2 cells.
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Affiliation(s)
- Giou-Teng Yiang
- Department of Emergency Medicine, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei 231, Taiwan, R.O.C
| | - Hsiu-Feng Tsai
- Department of Emergency Medicine, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei 231, Taiwan, R.O.C
| | - Jer-Rong Chen
- Department of Surgery, China Medical University Hospital, Taichung 404, Taiwan, R.O.C
| | - Pei-Lun Chou
- Division of Allergy-Immunology-Rheumatology, Department of Internal Medicine, Saint Mary's Hospital Luodong, Yilan 265, Taiwan, R.O.C
| | - Tsai-Kun Wu
- Division of Renal Medicine, Tungs' Taichung Metroharbor Hospital, Taichung 435, Taiwan, R.O.C
| | - Hsiao-Chun Liu
- Department of Nursing, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei 231, Taiwan, R.O.C
| | - Wei-Jung Chang
- Graduate Institute of Cancer Biology and Center for Molecular Medicine, China Medical University, Taichung 404, Taiwan, R.O.C
| | - Liang-Chih Liu
- Department of Surgery, China Medical University Hospital, Taichung 404, Taiwan, R.O.C
| | - Hsu-Hung Tseng
- Division of General Surgery, Taichung Hospital, Ministry of Health and Welfare, Taichung 403, Taiwan, R.O.C
| | - Yung-Luen Yu
- Graduate Institute of Cancer Biology and Center for Molecular Medicine, China Medical University, Taichung 404, Taiwan, R.O.C
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