1
|
Wan R, Chen Y, Feng X, Luo Z, Peng Z, Qi B, Qin H, Lin J, Chen S, Xu L, Tang J, Zhang T. Exercise potentially prevents colorectal cancer liver metastases by suppressing tumor epithelial cell stemness via RPS4X downregulation. Heliyon 2024; 10:e26604. [PMID: 38439884 PMCID: PMC10909670 DOI: 10.1016/j.heliyon.2024.e26604] [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: 02/05/2024] [Accepted: 02/15/2024] [Indexed: 03/06/2024] Open
Abstract
Background Colorectal cancer (CRC) is the third most prevalent tumor globally. The liver is the most common site for CRC metastasis, and the involvement of the liver is a common cause of death in patients with late-stage CRC. Consequently, mitigating CRC liver metastasis (CRLM) is key to improving CRC prognosis and increasing survival. Exercise has been shown to be an effective method of improving the prognosis of many tumor types. However, the ability of exercise to inhibit CRLM is yet to be thoroughly investigated. Methods The GSE157600 and GSE97084 datasets were used for analysis. A pan-cancer dataset which was uniformly normalized was downloaded and analyzed from the UCSC database: TCGA, TARGET, GTEx (PANCAN, n = 19,131, G = 60,499). Several advanced bioinformatics analyses were conducted, including single-cell sequencing analysis, correlation algorithm, and prognostic screen. CRC tumor microarray (TMA) as well as cell/animal experiments are used to further validate the results of the analysis. Results The greatest variability was found in epithelial cells from the tumor group. RPS4X was generally upregulated in all types of CRC, while exercise downregulated RPS4X expression. A lowered expression of RPS4X may prolong tumor survival and reduce CRC metastasis. RPS4X and tumor stemness marker-CD44 were highly positively correlated and knockdown of RPS4X expression reduced tumor stemness both in vitro and in vivo. Conclusion RPS4X upregulation may enhance CRC stemness and increase the odds of metastasis. Exercise may reduce CRC metastasis through the regulation of RPS4X.
Collapse
Affiliation(s)
- Renwen Wan
- Department of Sports Medicine, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Yisheng Chen
- Department of Sports Medicine, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Xinting Feng
- Department of Sports Medicine, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Zhiwen Luo
- Department of Sports Medicine, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Zhen Peng
- Department of Sports Medicine, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Beijie Qi
- Department of Orthopedics, Shanghai Pudong Hospital, Fudan University Affiliated Pudong Medical Center, Shanghai 201399, China
| | - Haocheng Qin
- Department of Rehabilitation Medicine, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Jinrong Lin
- Department of Sports Medicine, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Shiyi Chen
- Department of Sports Medicine, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Liangfeng Xu
- Department of Gastroenterology, Sheyang County People's Hospital, Yancheng 224300, Jiangsu, China
| | - Jiayin Tang
- Department of Gastrointestinal Surgery, Renji Hospital, Shanghai 200127, China
| | - Ting Zhang
- Department of Integrative Medicine, Huashan Hospital, Fudan University, Shanghai, China
| |
Collapse
|
2
|
Chen L, Chang D, Tandukar B, Deivendran D, Pozniak J, Cruz-Pacheco N, Cho RJ, Cheng J, Yeh I, Marine C, Bastian BC, Ji AL, Shain AH. STmut: a framework for visualizing somatic alterations in spatial transcriptomics data of cancer. Genome Biol 2023; 24:273. [PMID: 38037084 PMCID: PMC10688493 DOI: 10.1186/s13059-023-03121-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 11/22/2023] [Indexed: 12/02/2023] Open
Abstract
Spatial transcriptomic technologies, such as the Visium platform, measure gene expression in different regions of tissues. Here, we describe new software, STmut, to visualize somatic point mutations, allelic imbalance, and copy number alterations in Visium data. STmut is tested on fresh-frozen Visium data, formalin-fixed paraffin-embedded (FFPE) Visium data, and tumors with and without matching DNA sequencing data. Copy number is inferred on all conditions, but the chemistry of the FFPE platform does not permit analyses of single nucleotide variants. Taken together, we propose solutions to add the genetic dimension to spatial transcriptomic data and describe the limitations of different datatypes.
Collapse
Affiliation(s)
- Limin Chen
- Department of Dermatology, University of California, San Francisco, San Francisco, USA
| | - Darwin Chang
- Department of Immunology, H. Lee Moffitt Cancer Center, Tampa, USA
| | - Bishal Tandukar
- Department of Dermatology, University of California, San Francisco, San Francisco, USA
| | - Delahny Deivendran
- Department of Dermatology, University of California, San Francisco, San Francisco, USA
| | - Joanna Pozniak
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Louvain, Belgium
- Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, Louvain, Belgium
| | - Noel Cruz-Pacheco
- Department of Dermatology, University of California, San Francisco, San Francisco, USA
| | - Raymond J Cho
- Department of Dermatology, University of California, San Francisco, San Francisco, USA
| | - Jeffrey Cheng
- Department of Dermatology, University of California, San Francisco, San Francisco, USA
| | - Iwei Yeh
- Department of Dermatology, University of California, San Francisco, San Francisco, USA
- Department of Pathology, University of California, San Francisco, San Francisco, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, USA
| | - Chris Marine
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Louvain, Belgium
- Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, Louvain, Belgium
| | - Boris C Bastian
- Department of Dermatology, University of California, San Francisco, San Francisco, USA
- Department of Pathology, University of California, San Francisco, San Francisco, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, USA
| | - Andrew L Ji
- Department of Dermatology, Department of Oncological Sciences, Black Family Stem Cell Institute, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York City, USA
| | - A Hunter Shain
- Department of Dermatology, University of California, San Francisco, San Francisco, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, USA.
| |
Collapse
|
3
|
Miller SC, MacDonald CC, Kellogg MK, Karamysheva ZN, Karamyshev AL. Specialized Ribosomes in Health and Disease. Int J Mol Sci 2023; 24:ijms24076334. [PMID: 37047306 PMCID: PMC10093926 DOI: 10.3390/ijms24076334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/21/2023] [Accepted: 03/23/2023] [Indexed: 03/30/2023] Open
Abstract
Ribosomal heterogeneity exists within cells and between different cell types, at specific developmental stages, and occurs in response to environmental stimuli. Mounting evidence supports the existence of specialized ribosomes, or specific changes to the ribosome that regulate the translation of a specific group of transcripts. These alterations have been shown to affect the affinity of ribosomes for certain mRNAs or change the cotranslational folding of nascent polypeptides at the exit tunnel. The identification of specialized ribosomes requires evidence of the incorporation of different ribosomal proteins or of modifications to rRNA and/or protein that lead(s) to physiologically relevant changes in translation. In this review, we summarize ribosomal heterogeneity and specialization in mammals and discuss their relevance to several human diseases.
Collapse
Affiliation(s)
- Sarah C. Miller
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Clinton C. MacDonald
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Morgana K. Kellogg
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | | | - Andrey L. Karamyshev
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
- Correspondence: ; Tel.: +1-806-743-4102
| |
Collapse
|
4
|
Gravholt CH, Viuff M, Just J, Sandahl K, Brun S, van der Velden J, Andersen NH, Skakkebaek A. The Changing Face of Turner Syndrome. Endocr Rev 2023; 44:33-69. [PMID: 35695701 DOI: 10.1210/endrev/bnac016] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Indexed: 01/20/2023]
Abstract
Turner syndrome (TS) is a condition in females missing the second sex chromosome (45,X) or parts thereof. It is considered a rare genetic condition and is associated with a wide range of clinical stigmata, such as short stature, ovarian dysgenesis, delayed puberty and infertility, congenital malformations, endocrine disorders, including a range of autoimmune conditions and type 2 diabetes, and neurocognitive deficits. Morbidity and mortality are clearly increased compared with the general population and the average age at diagnosis is quite delayed. During recent years it has become clear that a multidisciplinary approach is necessary toward the patient with TS. A number of clinical advances has been implemented, and these are reviewed. Our understanding of the genomic architecture of TS is advancing rapidly, and these latest developments are reviewed and discussed. Several candidate genes, genomic pathways and mechanisms, including an altered transcriptome and epigenome, are also presented.
Collapse
Affiliation(s)
- Claus H Gravholt
- Department of Endocrinology and Internal Medicine, Aarhus University Hospital, Aarhus 8200 N, Denmark.,Department of Molecular Medicine, Aarhus University Hospital, Aarhus 8200 N, Denmark
| | - Mette Viuff
- Department of Endocrinology and Internal Medicine, Aarhus University Hospital, Aarhus 8200 N, Denmark.,Department of Molecular Medicine, Aarhus University Hospital, Aarhus 8200 N, Denmark
| | - Jesper Just
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus 8200 N, Denmark
| | - Kristian Sandahl
- Department of Endocrinology and Internal Medicine, Aarhus University Hospital, Aarhus 8200 N, Denmark
| | - Sara Brun
- Department of Endocrinology and Internal Medicine, Aarhus University Hospital, Aarhus 8200 N, Denmark
| | - Janielle van der Velden
- Department of Pediatrics, Radboud University Medical Centre, Amalia Children's Hospital, 6525 Nijmegen, the Netherlands
| | - Niels H Andersen
- Department of Cardiology, Aalborg University Hospital, Aalborg 9000, Denmark
| | - Anne Skakkebaek
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus 8200 N, Denmark.,Department of Clinical Genetics, Aarhus University Hospital, Aarhus 8200 N, Denmark
| |
Collapse
|
5
|
Bondhus L, Wei A, Arboleda VA. DMRscaler: a scale-aware method to identify regions of differential DNA methylation spanning basepair to multi-megabase features. BMC Bioinformatics 2022; 23:364. [PMID: 36064314 PMCID: PMC9447346 DOI: 10.1186/s12859-022-04899-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 08/22/2022] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Pathogenic mutations in genes that control chromatin function have been implicated in rare genetic syndromes. These chromatin modifiers exhibit extraordinary diversity in the scale of the epigenetic changes they affect, from single basepair modifications by DNMT1 to whole genome structural changes by PRM1/2. Patterns of DNA methylation are related to a diverse set of epigenetic features across this full range of epigenetic scale, making DNA methylation valuable for mapping regions of general epigenetic dysregulation. However, existing methods are unable to accurately identify regions of differential methylation across this full range of epigenetic scale directly from DNA methylation data. RESULTS To address this, we developed DMRscaler, a novel method that uses an iterative windowing procedure to capture regions of differential DNA methylation (DMRs) ranging in size from single basepairs to whole chromosomes. We benchmarked DMRscaler against several DMR callers in simulated and natural data comparing XX and XY peripheral blood samples. DMRscaler was the only method that accurately called DMRs ranging in size from 100 bp to 1 Mb (pearson's r = 0.94) and up to 152 Mb on the X-chromosome. We then analyzed methylation data from rare-disease cohorts that harbor chromatin modifier gene mutations in NSD1, EZH2, and KAT6A where DMRscaler identified novel DMRs spanning gene clusters involved in development. CONCLUSION Taken together, our results show DMRscaler is uniquely able to capture the size of DMR features across the full range of epigenetic scale and identify novel, co-regulated regions that drive epigenetic dysregulation in human disease.
Collapse
Affiliation(s)
- Leroy Bondhus
- grid.19006.3e0000 0000 9632 6718Department of Human Genetics, David Geffen School of Medicine, UCLA, 615 Charles E. Young Drive South, Los Angeles, CA 90095 USA ,grid.19006.3e0000 0000 9632 6718Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095 USA ,grid.19006.3e0000 0000 9632 6718Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095 USA
| | - Angela Wei
- grid.19006.3e0000 0000 9632 6718Department of Human Genetics, David Geffen School of Medicine, UCLA, 615 Charles E. Young Drive South, Los Angeles, CA 90095 USA ,grid.19006.3e0000 0000 9632 6718Bioinformatics Interdepartmental PhD Program, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095 USA ,grid.19006.3e0000 0000 9632 6718Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095 USA ,grid.19006.3e0000 0000 9632 6718Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095 USA
| | - Valerie A. Arboleda
- grid.19006.3e0000 0000 9632 6718Department of Human Genetics, David Geffen School of Medicine, UCLA, 615 Charles E. Young Drive South, Los Angeles, CA 90095 USA ,grid.19006.3e0000 0000 9632 6718Bioinformatics Interdepartmental PhD Program, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095 USA ,grid.19006.3e0000 0000 9632 6718Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095 USA ,grid.19006.3e0000 0000 9632 6718Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095 USA ,grid.19006.3e0000 0000 9632 6718Molecular Biology Institute, UCLA, Los Angeles, CA 90095 USA ,grid.19006.3e0000 0000 9632 6718Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA 90095 USA
| |
Collapse
|
6
|
Khani F, Nafian S, Mollamohammadi S, Nemati S, Shokoohian B, Hassani SN, Baharvand H, Soleimanpour-Lichaei HR, Salekdeh GH. Y Chromosome Genes May Play Roles in the Development of Neural Rosettes from Human Embryonic Stem Cells. Stem Cell Rev Rep 2022; 18:3008-3020. [PMID: 35661078 DOI: 10.1007/s12015-022-10392-2] [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] [Accepted: 05/15/2022] [Indexed: 01/24/2024]
Abstract
BACKGROUND The human Y chromosome harbors genes that are mainly involved in the growth, development, sexual dimorphism, and spermatogenesis process. Despite many studies, the function of the male-specific region of the Y chromosome (MSY) awaits further clarification, and a cell-based approach can help in this regard. RESULTS In this study, we have developed four stable transgenic male embryonic stem cell (ESCs) lines that can overexpress male-specific genes HSFY1, RBMY1A1, RPS4Y1, and SRY. As a proof of principle, we differentiated one of these cell lines (RPS4Y1 over-expressing ESCs) to the neural stem cell (rosette structure) and characterized them based on the expression level of lineage markers. RPS4Y1 expression in the Doxycycline-treated group was significantly higher than control groups at transcript and protein levels. Furthermore, we found Doxycycline-treated group had a higher differentiation efficiency than the untreated control groups. CONCLUSIONS Our results suggest that the RPS4Y1 gene may play a critical role in neurogenesis. Also, the generated transgenic ESC lines can be widely employed in basic and preclinical studies, such as sexual dimorphism of neural and cardiac functions, the development of cancerous and non-cancerous disease models, and drug screening.
Collapse
Affiliation(s)
- Farzaneh Khani
- Department of Stem Cells and Regenerative Medicine, Institute of Medical Biotechnology, National Institute of Genetic Engineering & Biotechnology (NIGEB), P.O.Box: 14965-161, Tehran, Iran.,Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, 16656-59911, Tehran, Iran
| | - Simin Nafian
- Department of Stem Cells and Regenerative Medicine, Institute of Medical Biotechnology, National Institute of Genetic Engineering & Biotechnology (NIGEB), P.O.Box: 14965-161, Tehran, Iran.,Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, 16656-59911, Tehran, Iran
| | - Sepideh Mollamohammadi
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, 16656-59911, Tehran, Iran
| | - Shiva Nemati
- Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, 16656-59911, Tehran, Iran
| | - Bahare Shokoohian
- Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, 16656-59911, Tehran, Iran
| | - Seyedeh Nafiseh Hassani
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, 16656-59911, Tehran, Iran
| | - Hossein Baharvand
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, 16656-59911, Tehran, Iran.,Department of Developmental Biology, University of Science and Culture, 13145-871, Tehran, Iran
| | - Hamid Reza Soleimanpour-Lichaei
- Department of Stem Cells and Regenerative Medicine, Institute of Medical Biotechnology, National Institute of Genetic Engineering & Biotechnology (NIGEB), P.O.Box: 14965-161, Tehran, Iran.
| | - Ghasem Hosseini Salekdeh
- Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, 16656-59911, Tehran, Iran. .,Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia.
| |
Collapse
|
7
|
Yamazaki W, Tan SL, Taketo T. Role of the X and Y Chromosomes in the Female Germ Cell Line Development in the Mouse (Mus musculus). Sex Dev 2022:1-10. [PMID: 35235936 DOI: 10.1159/000521151] [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: 08/02/2021] [Accepted: 11/18/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND In eutherian mammals, the sex chromosome complement, XX and XY, determines sexual differentiation of gonadal primordia into testes and ovaries, which in turn direct differentiation of germ cells into haploid sperm and oocytes, respectively. When gonadal sex is reversed, however, the germ cell sex becomes discordant with the chromosomal sex. XY females in humans are infertile, while XY females in the mouse (Mus musculus) are subfertile or infertile dependent on the cause of sex reversal and the genetic background. This article reviews publications to understand how the sex chromosome complement affects the fertility of XY oocytes by comparing with XX and monosomy X (XO) oocytes. SUMMARY The results highlight 2 folds disadvantage of XY oocytes over XX oocytes: (1) the X and Y chromosomes fail to pair during the meiotic prophase I, resulting in sex chromosome aneuploidy at the first meiotic division and (2) expression of the Y-linked genes during oocyte growth affects the transcriptome landscape and renders the ooplasmic component incompetent for embryonic development. Key Message: The XX chromosome complement gives the oocyte the highest competence for embryonic development.
Collapse
Affiliation(s)
- Wataru Yamazaki
- Department of Surgery, McGill University, Montreal, Québec, Canada.,Research Institute of McGill University Health Centre, Montreal, Québec, Canada
| | - Seang Lin Tan
- Department of Obstetrics and Gynecology, McGill University, Montreal, Québec, Canada.,Research Institute of McGill University Health Centre, Montreal, Québec, Canada.,OriginElle Fertility Clinic and Women's Health Centre, Montreal, Québec, Canada
| | - Teruko Taketo
- Department of Surgery, McGill University, Montreal, Québec, Canada.,Department of Obstetrics and Gynecology, McGill University, Montreal, Québec, Canada.,Department of Biology, McGill University, Montreal, Québec, Canada.,Research Institute of McGill University Health Centre, Montreal, Québec, Canada
| |
Collapse
|
8
|
Mercer M, Jang S, Ni C, Buszczak M. The Dynamic Regulation of mRNA Translation and Ribosome Biogenesis During Germ Cell Development and Reproductive Aging. Front Cell Dev Biol 2021; 9:710186. [PMID: 34805139 PMCID: PMC8595405 DOI: 10.3389/fcell.2021.710186] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 10/07/2021] [Indexed: 01/21/2023] Open
Abstract
The regulation of mRNA translation, both globally and at the level of individual transcripts, plays a central role in the development and function of germ cells across species. Genetic studies using flies, worms, zebrafish and mice have highlighted the importance of specific RNA binding proteins in driving various aspects of germ cell formation and function. Many of these mRNA binding proteins, including Pumilio, Nanos, Vasa and Dazl have been conserved through evolution, specifically mark germ cells, and carry out similar functions across species. These proteins typically influence mRNA translation by binding to specific elements within the 3′ untranslated region (UTR) of target messages. Emerging evidence indicates that the global regulation of mRNA translation also plays an important role in germ cell development. For example, ribosome biogenesis is often regulated in a stage specific manner during gametogenesis. Moreover, oocytes need to produce and store a sufficient number of ribosomes to support the development of the early embryo until the initiation of zygotic transcription. Accumulating evidence indicates that disruption of mRNA translation regulatory mechanisms likely contributes to infertility and reproductive aging in humans. These findings highlight the importance of gaining further insights into the mechanisms that control mRNA translation within germ cells. Future work in this area will likely have important impacts beyond germ cell biology.
Collapse
Affiliation(s)
- Marianne Mercer
- Department of Molecular Biology, The University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Seoyeon Jang
- Department of Molecular Biology, The University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Chunyang Ni
- Department of Molecular Biology, The University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Michael Buszczak
- Department of Molecular Biology, The University of Texas Southwestern Medical Center, Dallas, TX, United States
| |
Collapse
|
9
|
Chunduri NK, Menges P, Zhang X, Wieland A, Gotsmann VL, Mardin BR, Buccitelli C, Korbel JO, Willmund F, Kschischo M, Raeschle M, Storchova Z. Systems approaches identify the consequences of monosomy in somatic human cells. Nat Commun 2021; 12:5576. [PMID: 34552071 PMCID: PMC8458293 DOI: 10.1038/s41467-021-25288-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 07/30/2021] [Indexed: 01/22/2023] Open
Abstract
Chromosome loss that results in monosomy is detrimental to viability, yet it is frequently observed in cancers. How cancers survive with monosomy is unknown. Using p53-deficient monosomic cell lines, we find that chromosome loss impairs proliferation and genomic stability. Transcriptome and proteome analysis demonstrates reduced expression of genes encoded on the monosomes, which is partially compensated in some cases. Monosomy also induces global changes in gene expression. Pathway enrichment analysis reveals that genes involved in ribosome biogenesis and translation are downregulated in all monosomic cells analyzed. Consistently, monosomies display defects in protein synthesis and ribosome assembly. We further show that monosomies are incompatible with p53 expression, likely due to defects in ribosome biogenesis. Accordingly, impaired ribosome biogenesis and p53 inactivation are associated with monosomy in cancer. Our systematic study of monosomy in human cells explains why monosomy is so detrimental and reveals the importance of p53 for monosomy occurrence in cancer. The mechanisms that allow cancer cells to survive with monosomies are poorly understood. Here the authors analyse p53-deficient monosomic cell lines using transcriptomics and proteomics, and find that impaired ribosome biogenesis and p53 downregulation are associated with sustained monosomies.
Collapse
Affiliation(s)
| | - Paul Menges
- Department of Molecular Genetics, TU Kaiserslautern, Kaiserslautern, Germany
| | - Xiaoxiao Zhang
- University of Applied Sciences Koblenz, Remagen, Germany
| | - Angela Wieland
- Department of Molecular Genetics, TU Kaiserslautern, Kaiserslautern, Germany
| | | | - Balca R Mardin
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | | | - Jan O Korbel
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Felix Willmund
- Group Genetics of Eukaryotes, TU Kaiserslautern, Kaiserslautern, Germany
| | - Maik Kschischo
- University of Applied Sciences Koblenz, Remagen, Germany
| | - Markus Raeschle
- Department of Molecular Genetics, TU Kaiserslautern, Kaiserslautern, Germany
| | - Zuzana Storchova
- Department of Molecular Genetics, TU Kaiserslautern, Kaiserslautern, Germany.
| |
Collapse
|
10
|
Sim EUH, Lee CW, Narayanan K. The roles of ribosomal proteins in nasopharyngeal cancer: culprits, sentinels or both. Biomark Res 2021; 9:51. [PMID: 34193301 PMCID: PMC8247250 DOI: 10.1186/s40364-021-00311-x] [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] [Received: 02/26/2021] [Accepted: 06/20/2021] [Indexed: 12/15/2022] Open
Abstract
Ribosomal protein genes encode products that are essential for cellular protein biosynthesis and are major components of ribosomes. Canonically, they are involved in the complex system of ribosome biogenesis pivotal to the catalysis of protein translation. Amid this tightly organised process, some ribosomal proteins have unique spatial and temporal physiological activity giving rise to their extra-ribosomal functions. Many of these extra-ribosomal roles pertain to cellular growth and differentiation, thus implicating the involvement of some ribosomal proteins in organogenesis. Consequently, dysregulated functions of these ribosomal proteins could be linked to oncogenesis or neoplastic transformation of human cells. Their suspected roles in carcinogenesis have been reported but not specifically explained for malignancy of the nasopharynx. This is despite the fact that literature since one and half decade ago have documented the association of ribosomal proteins to nasopharyngeal cancer. In this review, we explain the association and contribution of dysregulated expression among a subset of ribosomal proteins to nasopharyngeal oncogenesis. The relationship of these ribosomal proteins with the cancer are explained. We provide information to indicate that the dysfunctional extra-ribosomal activities of specific ribosomal proteins are tightly involved with the molecular pathogenesis of nasopharyngeal cancer albeit mechanisms yet to be precisely defined. The complete knowledge of this will impact future applications in the effective management of nasopharyngeal cancer.
Collapse
Affiliation(s)
- Edmund Ui-Hang Sim
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia.
| | - Choon-Weng Lee
- Institute of Biological Sciences, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Kumaran Narayanan
- School of Science, Monash University, 46150, Bandar Sunway, Selangor, Malaysia.,Department of Genetics and Genomics Sciences, Mount Sinai School of Medicine, New York, NY, 10029, USA
| |
Collapse
|
11
|
Xiong W, Zhang J, Lan T, Kong W, Wang X, Liu L, Chen X, Mo B. High resolution RNA-seq profiling of genes encoding ribosomal proteins across different organs and developmental stages in Arabidopsis thaliana. PLANT DIRECT 2021; 5:e00320. [PMID: 34095740 PMCID: PMC8156134 DOI: 10.1002/pld3.320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 03/16/2021] [Accepted: 03/18/2021] [Indexed: 05/12/2023]
Abstract
In Arabidopsis thaliana, each ribosomal protein (RP) is encoded by a small gene family consisting of two or more highly homologous paralogues, which results in ribosome heterogeneity. It is largely unknown that how genes from multiple member containing RP families are regulated at transcriptional level to accommodate the needs of different plant organs and developmental stages. In this study, we investigated the transcript accumulation profiles of RP genes and found that the expression levels of RP genes are varied dramatically in different organs and developmental stages. Although most RP genes are found to be ubiquitously transcribed, some are obviously transcribed with spatiotemporal specificity. The hierarchical clustering trees of transcript accumulation intensity of RP genes revealed that different organs and developmental stages have different population of RP gene transcripts. By interrogating of the expression fluctuation trend of RP genes, we found that in spite of the fact that most groups of paralogous RP genes are transcribed in concerted manners, some RPs gene have contrasting expression patterns. When transcripts of paralogous RP genes from the same family are considered together, the expression level of most RP genes are well-matched but some are obviously higher or lower, therefore we speculate that some superfluous RPs may act outside the ribosome and a portion of ribosomes may lack one or even more RP(s). Altogether, our analysis results suggested that functional divergence may exist among heterogeneous ribosomes that resulted from different combination of RP paralogues, and substoichiometry of several RP gene families may lead to another layer of heterogeneous ribosomes which also have divergent functions in plants.
Collapse
Affiliation(s)
- Wei Xiong
- Guangdong Provincial Key Laboratory for Plant EpigeneticsLonghua Bioindustry and Innovation Research InstituteCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenChina
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong ProvinceCollege of Optoelectronic EngineeringShenzhen UniversityShenzhenChina
| | - Jiancong Zhang
- Guangdong Provincial Key Laboratory for Plant EpigeneticsLonghua Bioindustry and Innovation Research InstituteCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenChina
| | - Ting Lan
- Guangdong Provincial Key Laboratory for Plant EpigeneticsLonghua Bioindustry and Innovation Research InstituteCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenChina
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong ProvinceCollege of Optoelectronic EngineeringShenzhen UniversityShenzhenChina
| | - Wenwen Kong
- Guangdong Provincial Key Laboratory for Plant EpigeneticsLonghua Bioindustry and Innovation Research InstituteCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenChina
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong ProvinceCollege of Optoelectronic EngineeringShenzhen UniversityShenzhenChina
| | - Xiaoyan Wang
- Guangdong Provincial Key Laboratory for Plant EpigeneticsLonghua Bioindustry and Innovation Research InstituteCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenChina
| | - Lin Liu
- Guangdong Provincial Key Laboratory for Plant EpigeneticsLonghua Bioindustry and Innovation Research InstituteCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenChina
| | - Xuemei Chen
- Department of Botany and Plant SciencesInstitute of Integrative Genome BiologyUniversity of CaliforniaRiversideCAUSA
| | - Beixin Mo
- Guangdong Provincial Key Laboratory for Plant EpigeneticsLonghua Bioindustry and Innovation Research InstituteCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenChina
| |
Collapse
|
12
|
Lee MY, Kim EJ, Shin A, Kim YS. [How to Study the Sex and Gender Effect in Biomedical Research?]. THE KOREAN JOURNAL OF GASTROENTEROLOGY 2021; 77:104-114. [PMID: 33758108 DOI: 10.4166/kjg.2021.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/19/2021] [Accepted: 02/19/2021] [Indexed: 12/16/2022]
Abstract
Men and women are different, but this difference has not been well reflected in clinical trials and preclinical studies of biomedical science. Gender medicine, which systematically analyzes research results according to sex and gender, has been emphasized to overcome this problem. On the other hand, researchers still have difficulty in applying gender medicine to their research. To perform rigorous gender medicine, using correct terms, a thorough literature review during research planning, appropriate statistical analysis and reporting, and cautious interpretation of the results are necessary. Applying gender medicine will increase the reproducibility of studies, promote discoveries, expand the study relevance, and ultimately improve patient care in both men and women. Here, this study reviewed the practical issues on applying gender medicine to both preclinical and clinical studies in the field of biomedical science.
Collapse
Affiliation(s)
- Moon Young Lee
- Department of Physiology, Wonkwang Digestive Disease Research Institute, Wonkwang University School of Medicine, Iksan, Korea
| | - Eui Joong Kim
- Department of Physiology, Wonkwang Digestive Disease Research Institute, Wonkwang University School of Medicine, Iksan, Korea
| | - Aesun Shin
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Korea.,Integrated Major in Innovative Medical Science, Seoul National University Graduate School, Seoul, Korea
| | - Yong Sung Kim
- Department of Physiology, Wonkwang Digestive Disease Research Institute, Wonkwang University School of Medicine, Iksan, Korea.,Sanbon Good Breath Clinic, Gunpo, Korea.,Diversity Committee of the Korean Society of Gastroenterology, Seoul, Korea
| |
Collapse
|
13
|
Almsned F, Lipsky RH, Jafri MS. Transcriptomic analysis of Multiple Sclerosis patient-derived monocytes by RNA-Sequencing for candidate gene discovery. INFORMATICS IN MEDICINE UNLOCKED 2021. [DOI: 10.1016/j.imu.2021.100563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
|
14
|
Vaz B, El Mansouri F, Liu X, Taketo T. Premature ovarian insufficiency in the XO female mouse on the C57BL/6J genetic background. Mol Hum Reprod 2020; 26:678-688. [PMID: 32634219 PMCID: PMC7473787 DOI: 10.1093/molehr/gaaa049] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 06/17/2020] [Indexed: 12/15/2022] Open
Abstract
In humans, all but 1% of monosomy 45.X embryos die in utero and those who reach term suffer from congenital abnormalities and infertility termed Turner's syndrome (TS). By contrast, XO female mice on various genetic backgrounds show much milder physical defects and normal fertility, diminishing their value as an animal model for studying the infertility of TS patients. In this article, we report that XO mice on the C57BL/6J (B6) genetic background showed early oocyte loss, infertility or subfertility and high embryonic lethality, suggesting that the effect of monosomy X in the female germline may be shared between mice and humans. First, we generated XO mice on either a mixed N2(C3H.B6) or B6 genetic background and compared the number of oocytes in neonatal ovaries; N2.XO females retained 45% of the number of oocytes in N2.XX females, whereas B6.XO females retained only 15% of that in B6.XX females. Second, while N2.XO females were as fertile as N2.XX females, both the frequency of delivery and the total number of pups delivered by B6.XO females were significantly lower than those by B6.XX females. Third, after mating with B6 males, both N2.XO and B6.XO females rarely produced XO pups carrying paternal X chromosomes, although a larger percentage of embryos was found to be XO before implantation. Furthermore, B6.XO females delivered 20% XO pups among female progeny after mating with C3H males. We conclude that the impact of monosomy X on female mouse fertility depends on the genetic background.
Collapse
Affiliation(s)
- B Vaz
- Department of Biology, McGill University, Montreal, QC H3A 1B1, Canada
| | - F El Mansouri
- Department of Surgery, McGill University, Montreal, QC H4A3J1, Canada
- Research Institute of the McGill University Health Centre, Montreal, QC H4A3J1, Canada
| | - X Liu
- Department of Surgery, McGill University, Montreal, QC H4A3J1, Canada
- Research Institute of the McGill University Health Centre, Montreal, QC H4A3J1, Canada
| | - T Taketo
- Department of Biology, McGill University, Montreal, QC H3A 1B1, Canada
- Department of Surgery, McGill University, Montreal, QC H4A3J1, Canada
- Research Institute of the McGill University Health Centre, Montreal, QC H4A3J1, Canada
- Department of Obstetrics & Gynecology, McGill University, Montreal, QC H4A3J1, Canada
| |
Collapse
|
15
|
Nielsen MM, Trolle C, Vang S, Hornshøj H, Skakkebaek A, Hedegaard J, Nordentoft I, Pedersen JS, Gravholt CH. Epigenetic and transcriptomic consequences of excess X-chromosome material in 47,XXX syndrome-A comparison with Turner syndrome and 46,XX females. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2020; 184:279-293. [PMID: 32489015 DOI: 10.1002/ajmg.c.31799] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 04/30/2020] [Accepted: 05/01/2020] [Indexed: 01/21/2023]
Abstract
47,XXX (triple X) and Turner syndrome (45,X) are sex chromosomal abnormalities with detrimental effects on health with increased mortality and morbidity. In karyotypical normal females, X-chromosome inactivation balances gene expression between sexes and upregulation of the X chromosome in both sexes maintain stoichiometry with the autosomes. In 47,XXX and Turner syndrome a gene dosage imbalance may ensue from increased or decreased expression from the genes that escape X inactivation, as well as from incomplete X chromosome inactivation in 47,XXX. We aim to study genome-wide DNA-methylation and RNA-expression changes can explain phenotypic traits in 47,XXX syndrome. We compare DNA-methylation and RNA-expression data derived from white blood cells of seven women with 47,XXX syndrome, with data from seven female controls, as well as with seven women with Turner syndrome (45,X). To address these questions, we explored genome-wide DNA-methylation and transcriptome data in blood from seven females with 47,XXX syndrome, seven females with Turner syndrome, and seven karyotypically normal females (46,XX). Based on promoter methylation, we describe a demethylation of six X-chromosomal genes (AMOT, HTR2C, IL1RAPL2, STAG2, TCEANC, ZNF673), increased methylation for GEMIN8, and four differentially methylated autosomal regions related to four genes (SPEG, MUC4, SP6, and ZNF492). We illustrate how these changes seem compensated at the transcriptome level although several genes show differential exon usage. In conclusion, our results suggest an impact of the supernumerary X chromosome in 47,XXX syndrome on the methylation status of selected genes despite an overall comparable expression profile.
Collapse
Affiliation(s)
| | - Christian Trolle
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Endocrinology and Internal Medicine and Medical Research Laboratories, Aarhus University Hospital, Aarhus, Denmark
| | - Søren Vang
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Henrik Hornshøj
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Anne Skakkebaek
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Jakob Hedegaard
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Iver Nordentoft
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Jakob Skou Pedersen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Claus Højbjerg Gravholt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Endocrinology and Internal Medicine and Medical Research Laboratories, Aarhus University Hospital, Aarhus, Denmark
| |
Collapse
|
16
|
Li D, Wang J. Ribosome heterogeneity in stem cells and development. J Cell Biol 2020; 219:e202001108. [PMID: 32330234 PMCID: PMC7265316 DOI: 10.1083/jcb.202001108] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 04/03/2020] [Accepted: 04/06/2020] [Indexed: 02/08/2023] Open
Abstract
Translation control is critical to regulate protein expression. By directly adjusting protein levels, cells can quickly respond to dynamic transitions during stem cell differentiation and embryonic development. Ribosomes are multisubunit cellular assemblies that mediate translation. Previously seen as invariant machines with the same composition of components in all conditions, recent studies indicate that ribosomes are heterogeneous and that different ribosome types can preferentially translate specific subsets of mRNAs. Such heterogeneity and specialized translation functions are very important in stem cells and development, as they allow cells to quickly respond to stimuli through direct changes of protein abundance. In this review, we discuss ribosome heterogeneity that arises from multiple features of rRNAs, including rRNA variants and rRNA modifications, and ribosomal proteins, including their stoichiometry, compositions, paralogues, and posttranslational modifications. We also discuss alterations of ribosome-associated proteins (RAPs), with a particular focus on their consequent specialized translational control in stem cells and development.
Collapse
Affiliation(s)
- Dan Li
- Department of Cell, Developmental and Regenerative Biology, The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY
- The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Jianlong Wang
- Department of Cell, Developmental and Regenerative Biology, The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY
- The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Medicine, Columbia Center for Human Development, Columbia University Irving Medical Center, New York, NY
| |
Collapse
|
17
|
Bie P, Debrabant B. Gonadal sex and animal experimentation: Perfection vs. 3R principle? Basic Clin Pharmacol Toxicol 2020; 127:111-119. [DOI: 10.1111/bcpt.13411] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 03/26/2020] [Accepted: 03/30/2020] [Indexed: 12/17/2022]
Affiliation(s)
- Peter Bie
- Department of Cardiovascular and Renal Research Institute of Molecular Medicine University of Southern Denmark Odense Denmark
| | - Birgit Debrabant
- Epidemiology, Biostatistics and Biodemography Department of Public Health University of Southern Denmark Odense Denmark
| |
Collapse
|
18
|
Mezera MA, Li W, Edwards AJ, Koch DJ, Beard AD, Wiltbank MC. Identification of stable genes in the corpus luteum of lactating Holstein cows in pregnancy and luteolysis: Implications for selection of reverse-transcription quantitative PCR reference genes. J Dairy Sci 2020; 103:4846-4857. [PMID: 32229123 DOI: 10.3168/jds.2019-17526] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 01/10/2020] [Indexed: 12/20/2022]
Abstract
In lactating dairy cattle, the corpus luteum (CL) is a dynamic endocrine tissue vital for pregnancy maintenance, fertility, and cyclicity. Understanding processes underlying luteal physiology is therefore necessary to increase reproductive efficiency in cattle. A common technique for investigating luteal physiology is reverse-transcription quantitative PCR (RT-qPCR), a valuable tool for quantifying gene expression. However, reference-gene-based RT-qPCR quantification methods require utilization of stably expressed genes to accurately assess mRNA expression. Historically, selection of reference genes in cattle has relied on subjective selection of a small pool of reference genes, many of which may have significant expression variation among different tissues or physiologic states. This is particularly concerning in dynamic tissues such as the CL, with its capacity for rapid physiologic changes during luteolysis, and likely in the less characterized period of CL maintenance during pregnancy. Thus, there is a clear need to identify reference genes well suited for the bovine CL over a wide range of physiological states. Whole-transcriptome RNA sequencing stands as an effective method to identify new reference genes by enabling the assessment of the expression profile of the entire pool of mRNA transcripts. We report the identification of 13 novel putative reference genes using RNA sequencing in the bovine CL throughout early pregnancy and luteolysis: RPL4, UQCRFS1, COX4I1, RPS4X, SSR3, CST3, ZNF266, CDC42, CD63, HIF1A, YWHAE, EIF3E, and PPIB. Independent RT-qPCR analyses were conducted confirming expression stability in another set of CL tissues from pregnancy and regression, with analyses performed for 3 groups of samples: (1) all samples, (2) samples from pregnancy alone, and (3) samples throughout the process of CL regression. Seven genes were found to be more stable in all states than 2 traditional reference genes (ACTB and GAPDH): RPS4X, COX4I1, PPIB, SSR3, RPL4, YWHAE, and CDC42. When CL tissues from pregnant animals alone were analyzed, CST3, HIF1A, and CD63 were also identified as more stable than ACTB and GAPDH. Identification of these new reference genes will aid in accurate normalization of RT-qPCR results, contributing to proper interpretation of gene expression relevant to luteal physiology. Furthermore, our analysis sheds light on the effects of luteolysis and pregnancy on the stability of gene expression in the bovine CL.
Collapse
Affiliation(s)
- M A Mezera
- Department of Dairy Science, University of Wisconsin, Madison 53706; Endocrinology and Reproductive Physiology Program, University of Wisconsin, Madison 53706
| | - W Li
- USDA Dairy Forage Research Center, Madison, WI 53706.
| | - A J Edwards
- USDA Dairy Forage Research Center, Madison, WI 53706
| | - D J Koch
- USDA Dairy Forage Research Center, Madison, WI 53706
| | - A D Beard
- Department of Dairy Science, University of Wisconsin, Madison 53706; Endocrinology and Reproductive Physiology Program, University of Wisconsin, Madison 53706
| | - M C Wiltbank
- Department of Dairy Science, University of Wisconsin, Madison 53706
| |
Collapse
|
19
|
On the Neurocircuitry of Grasping: The influence of action intent on kinematic asymmetries in reach-to-grasp actions. Atten Percept Psychophys 2020; 81:2217-2236. [PMID: 31290131 DOI: 10.3758/s13414-019-01805-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Evidence from electrophysiology suggests that nonhuman primates produce reach-to-grasp movements based on their functional end goal rather than on the biomechanical requirements of the movement. However, the invasiveness of direct-electrical stimulation and single-neuron recording largely precludes analogous investigations in humans. In this review, we present behavioural evidence in the form of kinematic analyses suggesting that the cortical circuits responsible for reach-to-grasp actions in humans are organized in a similar fashion. Grasp-to-eat movements are produced with significantly smaller and more precise maximum grip apertures (MGAs) than are grasp-to-place movements directed toward the same objects, despite near identical mechanical requirements of the two subsequent (i.e., grasp-to-eat and grasp-to-place) movements. Furthermore, the fact that this distinction is limited to right-handed movements suggests that the system governing reach-to-grasp movements is asymmetric. We contend that this asymmetry may be responsible, at least in part, for the preponderance of right-hand dominance among the global population.
Collapse
|
20
|
Park TH, Kim D, Lee YS, Kim SY. A meta-analysis to identify novel diagnostic and therapeutic targets for Dupuytren's disease. Wound Repair Regen 2019; 28:202-210. [PMID: 31688987 DOI: 10.1111/wrr.12774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 10/08/2019] [Accepted: 10/15/2019] [Indexed: 01/20/2023]
Abstract
The aim of this study was to determine novel candidate genes for Dupuytren's disease by performing a meta-analysis. We identified 261 genes (111 up-regulated and 150 down-regulated) that were consistently expressed differentially in Dupuytren's disease across the studies. We performed functional enrichment on total sets of the identified 261 genes and confirmed that most of the genes were closely related to common processes of diseases in general. From the integrated studies of the gene-correlation network and the protein-protein interaction network, we identified three functional modules in the gene co-expression network and four hub gene clusters in the protein-protein interaction network that shared the same genes and represented similar biological functions, implying that the seven groups identified in the systematic analysis of these two networks might be involved in the pathogenesis of Dupuytren's disease. This work demonstrates potential in developing experimental and clinical strategies for understanding and treating Dupuytren's disease.
Collapse
Affiliation(s)
- Tae Hwan Park
- Department of Plastic and Reconstructive Surgery, CHA Bundang Medical Center, School of Medicine, CHA University, Seongnam, Korea.,KCRN Research, Germantown, Maryland, 20874
| | - Dongha Kim
- Department of Biochemistry, School of Medicine, Konkuk University, Seoul, Korea
| | - Young-Seok Lee
- Department of Biochemistry, School of Medicine, Konkuk University, Seoul, Korea
| | - Sung Young Kim
- Department of Biochemistry, School of Medicine, Konkuk University, Seoul, Korea
| |
Collapse
|
21
|
Zhou Q, Wang T, Leng L, Zheng W, Huang J, Fang F, Yang L, Chen F, Lin G, Wang WJ, Kristiansen K. Single-cell RNA-seq reveals distinct dynamic behavior of sex chromosomes during early human embryogenesis. Mol Reprod Dev 2019; 86:871-882. [PMID: 31094050 DOI: 10.1002/mrd.23162] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 03/21/2019] [Accepted: 04/11/2019] [Indexed: 12/20/2022]
Abstract
Several animal and human studies have demonstrated that sex affects kinetics and metabolism during early embryo development. However, the mechanism governing these differences at the molecular level before the expression of the sex-determining gene SRY is unknown. We performed a systematic profiling of gene expression comparing male and female embryos using available single-cell RNA-sequencing data of 1607 individual cells from 99 human preimplantation embryos, covering development stages from 4-cell to late blastocyst. We observed consistent chromosome-wide transcription of autosomes, whereas expression from sex chromosomes exhibits significant differences after embryonic genome activation (EGA). Activation of the Y chromosome is initiated by expression of two genes, RPS4Y1 and DDX3Y, whereas the X chromosome is widely activated, with both copies in females being activated after EGA. In contrast to the stable activation of the Y chromosome, expression of X-linked genes in females declines at the late blastocyst stage, especially in trophectoderm cells, revealing a rapid process of dosage compensation. This dynamic behavior results in a dosage imbalance between male and female embryos, which influences genes involved in cell cycle, protein translation and metabolism. Our results reveal the dynamics of sex chromosomes expression and silencing during early embryogenesis. Studying sex differences during human embryogenesis, as well as understanding the process of X chromosome inactivation and their effects on the sex bias development of in vitro fertilized embryos, will expand the capabilities of assisted reproductive technology and possibly improve the treatment of infertility and enhance reproductive health.
Collapse
Affiliation(s)
- Qing Zhou
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Taifu Wang
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Lizhi Leng
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China.,Key Laboratory of Reproductive and Stem Cells Engineering, Ministry of Health, Changsha, China
| | - Wei Zheng
- Reproductive & Genetic Hospital of CITIC-Xiangya, Changsha, China
| | - Jinrong Huang
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Fang Fang
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Ling Yang
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Fang Chen
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Ge Lin
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China.,Key Laboratory of Reproductive and Stem Cells Engineering, Ministry of Health, Changsha, China.,Reproductive & Genetic Hospital of CITIC-Xiangya, Changsha, China.,National Engineering and Research Center of Human Stem Cell, Changsha, China
| | - Wen-Jing Wang
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Karsten Kristiansen
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
22
|
Andreyeva EN, Ogienko AA, Yushkova AA, Popova JV, Pavlova GA, Kozhevnikova EN, Ivankin AV, Gatti M, Pindyurin AV. Non3 is an essential Drosophila gene required for proper nucleolus assembly. Vavilovskii Zhurnal Genet Selektsii 2019. [DOI: 10.18699/vj19.481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The nucleolus is a dynamic non-membrane-bound nuclear organelle, which plays key roles not only in ribosome biogenesis but also in many other cellular processes. Consistent with its multiple functions, the nucleolus has been implicated in many human diseases, including cancer and degenerative pathologies of the nervous system and heart. Here, we report the characterization of the Drosophila Non3 (Novel nucleolar protein 3) gene, which encodes a protein homologous to the human Brix domain-containing Rpf2 that has been shown to control ribosomal RNA (rRNA) processing. We used imprecise P-element excision to generate four new mutant alleles in the Non3 gene. Complementation and phenotypic analyses showed that these Non3 mutations can be arranged in an allelic series that includes both viable and lethal alleles. The strongest lethal allele (Non3∆600) is a genetically null allele that carries a large deletion of the gene and exhibits early lethality when homozygous. Flies heterozygous for Non3∆600 occasionally exhibit a mild reduction in the bristle size, but develop normally and are fertile. However, heteroallelic combinations of viable Non3 mutations (Non3197, Non3310 and Non3259) display a Minute-like phenotype, consisting in delayed development and short and thin bristles, suggesting that they are defective in ribosome biogenesis. We also demonstrate that the Non3 protein localizes to the nucleolus of larval brain cells and it is required for proper nucleolar localization of Fibrillarin, a protein important for post-translational modification and processing of rRNAs. In summary, we generated a number of genetic and biochemical tools that were exploited for an initial characterization of Non3, and will be instrumental for future functional studies on this gene and its protein product.
Collapse
Affiliation(s)
| | - A. A. Ogienko
- Institute of Molecular and Cellular Biology, SB RAS; Novosibirsk State University
| | - A. A. Yushkova
- Institute of Molecular and Cellular Biology, SB RAS; Novosibirsk State University
| | - J. V. Popova
- Institute of Molecular and Cellular Biology, SB RAS; Institute of Cytology and Genetics, SB RAS
| | | | - E. N. Kozhevnikova
- Institute of Molecular and Cellular Biology, SB RAS; Institute of Cytology and Genetics, SB RAS
| | | | - M. Gatti
- Institute of Molecular and Cellular Biology, SB RAS; IBPM CNR and Department of Biology and Biotechnology, Sapienza University of Rome
| | - A. V. Pindyurin
- Institute of Molecular and Cellular Biology, SB RAS; Novosibirsk State University; Institute of Cytology and Genetics, SB RAS
| |
Collapse
|
23
|
Wainer Katsir K, Linial M. Human genes escaping X-inactivation revealed by single cell expression data. BMC Genomics 2019; 20:201. [PMID: 30871455 PMCID: PMC6419355 DOI: 10.1186/s12864-019-5507-6] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 02/04/2019] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND In mammals, sex chromosomes pose an inherent imbalance of gene expression between sexes. In each female somatic cell, random inactivation of one of the X-chromosomes restores this balance. While most genes from the inactivated X-chromosome are silenced, 15-25% are known to escape X-inactivation (termed escapees). The expression levels of these genes are attributed to sex-dependent phenotypic variability. RESULTS We used single-cell RNA-Seq to detect escapees in somatic cells. As only one X-chromosome is inactivated in each cell, the origin of expression from the active or inactive chromosome can be determined from the variation of sequenced RNAs. We analyzed primary, healthy fibroblasts (n = 104), and clonal lymphoblasts with sequenced parental genomes (n = 25) by measuring the degree of allelic-specific expression (ASE) from heterozygous sites. We identified 24 and 49 candidate escapees, at varying degree of confidence, from the fibroblast and lymphoblast transcriptomes, respectively. We critically test the validity of escapee annotations by comparing our findings with a large collection of independent studies. We find that most genes (66%) from the unified set were previously reported as escapees. Furthermore, out of the overlooked escapees, 11 are long noncoding RNA (lncRNAs). CONCLUSIONS X-chromosome inactivation and escaping from it are robust, permanent phenomena that are best studies at a single-cell resolution. The cumulative information from individual cells increases the potential of identifying escapees. Moreover, despite the use of a limited number of cells, clonal cells (i.e., same X- chromosomes are coordinately inhibited) with genomic phasing are valuable for detecting escapees at high confidence. Generalizing the method to uncharacterized genomic loci resulted in lncRNAs escapees which account for 20% of the listed candidates. By confirming genes as escapees and propose others as candidates from two different cell types, we contribute to the cumulative knowledge and reliability of human escapees.
Collapse
Affiliation(s)
- Kerem Wainer Katsir
- Department of Biological Chemistry, The Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190400, Jerusalem, Israel
| | - Michal Linial
- Department of Biological Chemistry, The Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190400, Jerusalem, Israel.
| |
Collapse
|
24
|
Arambula SE, Reinl EL, El Demerdash N, McCarthy MM, Robertson CL. Sex differences in pediatric traumatic brain injury. Exp Neurol 2019; 317:168-179. [PMID: 30831070 DOI: 10.1016/j.expneurol.2019.02.016] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 02/21/2019] [Accepted: 02/28/2019] [Indexed: 02/08/2023]
Abstract
The response of the developing brain to traumatic injury is different from the response of the mature, adult brain. There are critical developmental trajectories in the young brain, whereby injury can lead to long term functional abnormalities. Emerging preclinical and clinical literature supports the presence of significant sex differences in both the response to and the recovery from pediatric traumatic brain injury (TBI). These sex differences are seen at all pediatric ages, including neonates/infants, pre-pubertal children, and adolescents. As importantly, the response to neuroprotective therapies or treatments can differ between male and females subjects. These sex differences can result from several biologic origins, and may manifest differently during the various phases of brain and body development. Recognizing and understanding these potential sex differences is crucial, and should be considered in both preclinical and clinical studies of pediatric TBI.
Collapse
Affiliation(s)
- Sheryl E Arambula
- Department of Pharmacology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Erin L Reinl
- Department of Pharmacology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Nagat El Demerdash
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Margaret M McCarthy
- Department of Pharmacology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Courtney L Robertson
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
| |
Collapse
|
25
|
Viuff M, Skakkebaek A, Nielsen MM, Chang S, Gravholt CH. Epigenetics and genomics in Turner syndrome. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2019; 181:68-75. [PMID: 30811826 DOI: 10.1002/ajmg.c.31683] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Accepted: 01/10/2019] [Indexed: 12/20/2022]
Abstract
The pathogenesis of Turner syndrome (TS) and the genotype-phenotype relationship has been thoroughly investigated during the last decade. It has become evident that the phenotype seen in TS does not only depend on simple gene dosage as a result of X chromosome monosomy. The origin of TS specific comorbidities such as infertility, cardiac malformations, bone dysgenesis, and autoimmune diseases may depend on a complex relationship between genes as well as transcriptional and epigenetic factors affecting gene expression across the genome. Furthermore, two individuals with TS with the exact same karyotype may exhibit completely different traits, suggesting that no conventional genotype-phenotype relationship exists. Here, we review the different genetic mechanisms behind differential gene expression, and highlight potential key-genes essential to the comorbidities seen in TS and other X chromosome aneuploidy syndromes. KDM6A, important for germ cell development, has shown to be differentially expressed and methylated in Turner and Klinefelter syndrome across studies. Furthermore, TIMP1/TIMP3 genes seem to affect the prevalence of bicuspid aortic valve. KDM5C could play a role in the neurocognitive development of Turner and Klinefelter syndrome. However, further research is needed to elucidate the genetic mechanism behind the phenotypic variability and the different phenotypic traits seen in TS.
Collapse
Affiliation(s)
- Mette Viuff
- Department of Endocrinology and Internal Medicine (MEA), Aarhus University Hospital, Aarhus, Denmark.,Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Anne Skakkebaek
- Department of Endocrinology and Internal Medicine (MEA), Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Morten M Nielsen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Simon Chang
- Department of Endocrinology and Internal Medicine (MEA), Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Biochemistry, Esbjerg Sygehus, Denmark
| | - Claus H Gravholt
- Department of Endocrinology and Internal Medicine (MEA), Aarhus University Hospital, Aarhus, Denmark.,Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| |
Collapse
|
26
|
Combination of Gonadal Dysgenesis and Monosomy X with a Novo Translocation (13,14). Case Rep Endocrinol 2019; 2018:3796415. [PMID: 30647978 PMCID: PMC6311845 DOI: 10.1155/2018/3796415] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 11/29/2018] [Indexed: 11/17/2022] Open
Abstract
Turner syndrome is a common sex chromosome disorder characterized by complete or partial absence of an X chromosome. The spectrum of its clinical features and cytogenetics are various. We report new chromosomal formula revealed by DSD and associated with translocation (13,14). To our knowledge, this is the first case of 45X, t(13;14) de novo translocation as a variation of Turner syndrome in a patient with this clinical presentation.
Collapse
|
27
|
Davegårdh C, Hall Wedin E, Broholm C, Henriksen TI, Pedersen M, Pedersen BK, Scheele C, Ling C. Sex influences DNA methylation and gene expression in human skeletal muscle myoblasts and myotubes. Stem Cell Res Ther 2019; 10:26. [PMID: 30646953 PMCID: PMC6332625 DOI: 10.1186/s13287-018-1118-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 12/07/2018] [Accepted: 12/20/2018] [Indexed: 12/12/2022] Open
Abstract
Background Sex differences are known to impact muscle phenotypes, metabolism, and disease risk. Skeletal muscle stem cells (satellite cells) are important for muscle repair and to maintain functional skeletal muscle. Here we studied, for the first time, effects of sex on DNA methylation and gene expression in primary human myoblasts (activated satellite cells) before and after differentiation into myotubes. Method We used an array-based approach to analyse genome-wide DNA methylation and gene expression in myoblasts and myotubes from 13 women and 13 men. The results were followed up with a reporter gene assay. Results Genome-wide DNA methylation and gene expression differences between the sexes were detected in both myoblasts and myotubes, on the autosomes as well as the X-chromosome, despite lack of exposure to sex hormones and other factors that differ between sexes. Pathway analysis revealed higher expression of oxidative phosphorylation and other metabolic pathways in myoblasts from women compared to men. Oxidative phosphorylation was also enriched among genes with higher expression in myotubes from women. Forty genes in myoblasts and 9 in myotubes had differences in both DNA methylation and gene expression between the sexes, including LAMP2 and SIRT1 in myoblasts and KDM6A in myotubes. Furthermore, increased DNA methylation of LAMP2 promoter had negative effects on reporter gene expression. Five genes (CREB5, RPS4X, SYAP1, XIST, and ZRSR2) showed differential DNA methylation and gene expression between the sexes in both myoblasts and myotubes. Interestingly, differences in DNA methylation and expression between women and men were also found during differentiation (myoblasts versus myotubes), e.g., in genes involved in energy metabolism. Interestingly, more DNA methylation changes occur in women compared to men on autosomes. Conclusion All together, we show that epigenetic and transcriptional differences exist in human myoblasts and myotubes as well as during differentiation between women and men. We believe that these intrinsic differences might contribute to sex dependent differences in muscular phenotypes. Electronic supplementary material The online version of this article (10.1186/s13287-018-1118-4) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Cajsa Davegårdh
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, 20502, Malmö, Sweden.
| | - Elin Hall Wedin
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, 20502, Malmö, Sweden
| | - Christa Broholm
- Department of Endocrinology, Rigshospitalet, 2100, Copenhagen, Denmark.,The Centre of Inflammation and Metabolism and the Centre for Physical Activity Research, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Tora Ida Henriksen
- Department of Endocrinology, Rigshospitalet, 2100, Copenhagen, Denmark.,The Centre of Inflammation and Metabolism and the Centre for Physical Activity Research, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Maria Pedersen
- The Centre of Inflammation and Metabolism and the Centre for Physical Activity Research, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Bente Klarlund Pedersen
- The Centre of Inflammation and Metabolism and the Centre for Physical Activity Research, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Camilla Scheele
- The Centre of Inflammation and Metabolism and the Centre for Physical Activity Research, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark.,Novo Nordisk Foundation Center, Section for Basic Metabolic Research, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
| | - Charlotte Ling
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, 20502, Malmö, Sweden.
| |
Collapse
|
28
|
Li Y, Zhu M, Huo Y, Zhang X, Liao M. Anti-fibrosis activity of combination therapy with epigallocatechin gallate, taurine and genistein by regulating glycolysis, gluconeogenesis, and ribosomal and lysosomal signaling pathways in HSC-T6 cells. Exp Ther Med 2018; 16:4329-4338. [PMID: 30542382 PMCID: PMC6257822 DOI: 10.3892/etm.2018.6743] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 12/21/2017] [Indexed: 12/24/2022] Open
Abstract
A previous study by our group indicated that combined treatment with taurine, epigallocatechin gallate (EGCG) and genistein protects against liver fibrosis. The aim of the present study was to elucidate the antifibrotic mechanism of this combination treatment using isobaric tag for relative and absolute quantification (iTRAQ)-based proteomics in an activated rat hepatic stellate cell (HSC) line. In the present study, HSC-T6 cells were incubated with taurine, EGCG and genistein, and cellular proteins were extracted and processed for iTRAQ labeling. Quantification and identification of proteins was performed using two-dimensional liquid chromatography coupled with tandem mass spectrometry. Proteomic analysis indicated that the expression of 166 proteins were significantly altered in response to combination treatment with taurine, EGCG and genistein. A total 76 of these proteins were upregulated and 90 were downregulated. Differentially expressed proteins were grouped according to their association with specific Kyoto Encyclopedia of Genes and Genomes pathways. The results indicated that the differentially expressed proteins hexokinase-2 and lysosome-associated membrane glycoprotein 1 were associated with glycolysis, gluconeogenesis and lysosome signaling pathways. The expression of these proteins was validated using western blot analysis; the expression of hexokinase-2 was significantly decreased and the expression of lysosome-associated membrane glycoprotein 1 was significantly increased in HSC-T6 cells treated with taurine, EGCG and genistein compared with the control, respectively (P<0.05). These results were in accordance with the changes in protein expression identified using the iTRAQ approach. Therefore, the antifibrotic effect of combined therapy with taurine, EGCG and genistein may be associated with the activation of several pathways in HSCs, including glycolysis, gluconeogenesis, and the ribosome and lysosome signaling pathways. The differentially expressed proteins identified in the current study may be useful for treatment of liver fibrosis in the future.
Collapse
Affiliation(s)
- Yan Li
- Guangxi University Library, Guangxi University, Nanning, Guangxi 530004, P.R. China
| | - Min Zhu
- Guangxi University Library, Guangxi University, Nanning, Guangxi 530004, P.R. China
| | - Yani Huo
- Medical Scientific Research Centre, Key Laboratory of High-Incidence-Tumor Prevention and Treatment, Guangxi Medical University, Ministry of Education, Nanning, Guangxi 530021, P.R. China
| | - Xuerong Zhang
- Medical Scientific Research Centre, Key Laboratory of High-Incidence-Tumor Prevention and Treatment, Guangxi Medical University, Ministry of Education, Nanning, Guangxi 530021, P.R. China
| | - Ming Liao
- Medical Scientific Research Centre, Key Laboratory of High-Incidence-Tumor Prevention and Treatment, Guangxi Medical University, Ministry of Education, Nanning, Guangxi 530021, P.R. China
| |
Collapse
|
29
|
Specialized ribosomes and the control of translation. Biochem Soc Trans 2018; 46:855-869. [PMID: 29986937 DOI: 10.1042/bst20160426] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 05/21/2018] [Accepted: 05/24/2018] [Indexed: 11/17/2022]
Abstract
The control of translation is increasingly recognized as a major factor in determining protein levels in the cell. The ribosome - the cellular machine that mediates protein synthesis - is typically seen as a key, but invariant, player in this process. This is because translational control is thought to be mediated by other auxiliary factors while ribosome recruitment is seen as the end-point of regulation. However, recent developments have made it clear that heterogeneous ribosome types can exist in different tissues, and more importantly, that these ribosomes can preferentially translate different subsets of mRNAs. In so doing, heterogeneous ribosomes could be key regulatory players in differentiation and development. Here, we examine current evidence for the existence of different ribosome types and how they might arise. In particular, we will take a close look at the mechanisms through which these ribosomes might mediate selective mRNA translation. We also summarize recently developed techniques/approaches that will aid in our understanding of the functions of such specialized ribosomes.
Collapse
|
30
|
Farooqui A, Tazyeen S, Ahmed MM, Alam A, Ali S, Malik MZ, Ali S, Ishrat R. Assessment of the key regulatory genes and their Interologs for Turner Syndrome employing network approach. Sci Rep 2018; 8:10091. [PMID: 29973620 PMCID: PMC6031616 DOI: 10.1038/s41598-018-28375-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 06/15/2018] [Indexed: 12/13/2022] Open
Abstract
Turner Syndrome (TS) is a condition where several genes are affected but the molecular mechanism remains unknown. Identifying the genes that regulate the TS network is one of the main challenges in understanding its aetiology. Here, we studied the regulatory network from manually curated genes reported in the literature and identified essential proteins involved in TS. The power-law distribution analysis showed that TS network carries scale-free hierarchical fractal attributes. This organization of the network maintained the self-ruled constitution of nodes at various levels without having centrality-lethality control systems. Out of twenty-seven genes culminating into leading hubs in the network, we identified two key regulators (KRs) i.e. KDM6A and BDNF. These KRs serve as the backbone for all the network activities. Removal of KRs does not cause its breakdown, rather a change in the topological properties was observed. Since essential proteins are evolutionarily conserved, the orthologs of selected interacting proteins in C. elegans, cat and macaque monkey (lower to higher level organisms) were identified. We deciphered three important interologs i.e. KDM6A-WDR5, KDM6A-ASH2L and WDR5-ASH2L that form a triangular motif. In conclusion, these KRs and identified interologs are expected to regulate the TS network signifying their biological importance.
Collapse
Affiliation(s)
- Anam Farooqui
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Safia Tazyeen
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Mohd Murshad Ahmed
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Aftab Alam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Shahnawaz Ali
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Md Zubbair Malik
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Sher Ali
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Romana Ishrat
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India.
| |
Collapse
|
31
|
Colaco S, Modi D. Genetics of the human Y chromosome and its association with male infertility. Reprod Biol Endocrinol 2018; 16:14. [PMID: 29454353 PMCID: PMC5816366 DOI: 10.1186/s12958-018-0330-5] [Citation(s) in RCA: 125] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 02/06/2018] [Indexed: 12/12/2022] Open
Abstract
The human Y chromosome harbors genes that are responsible for testis development and also for initiation and maintenance of spermatogenesis in adulthood. The long arm of the Y chromosome (Yq) contains many ampliconic and palindromic sequences making it predisposed to self-recombination during spermatogenesis and hence susceptible to intra-chromosomal deletions. Such deletions lead to copy number variation in genes of the Y chromosome resulting in male infertility. Three common Yq deletions that recur in infertile males are termed as AZF (Azoospermia Factor) microdeletions viz. AZFa, AZFb and AZFc. As estimated from data of nearly 40,000 Y chromosomes, the global prevalence of Yq microdeletions is 7.5% in infertile males; however the European infertile men are less susceptible to Yq microdeletions, the highest prevalence is in Americans and East Asian infertile men. In addition, partial deletions of the AZFc locus have been associated with infertility but the effect seems to be ethnicity dependent. Analysis of > 17,000 Y chromosomes from fertile and infertile men has revealed an association of gr/gr deletion with male infertility in Caucasians and Mongolian men, while the b2/b3 deletion is associated with male infertility in African and Dravidian men. Clinically, the screening for Yq microdeletions would aid the clinician in determining the cause of male infertility and decide a rational management strategy for the patient. As these deletions are transmitted to 100% of male offspring born through assisted reproduction, testing of Yq deletions will allow the couples to make an informed choice regarding the perpetuation of male infertility in future generations. With the emerging data on association of Yq deletions with testicular cancers and neuropsychiatric conditions long term follow-up data is urgently needed for infertile men harboring Yq deletions. If found so, the information will change the current the perspective of androgenetics from infertility and might have broad implication in men health.
Collapse
Affiliation(s)
- Stacy Colaco
- Department of Molecular and Cellular Biology, ICMR-National Institute for Research in Reproductive Health, JM Street, Parel, Mumbai, Maharashtra, 400012, India
| | - Deepak Modi
- Department of Molecular and Cellular Biology, ICMR-National Institute for Research in Reproductive Health, JM Street, Parel, Mumbai, Maharashtra, 400012, India.
| |
Collapse
|
32
|
Chen X, Tong C, Li H, Peng W, Li R, Luo X, Ge H, Ran Y, Li Q, Liu Y, Xiong X, Bai Y, Zhang H, Baker PN, Liu X, Qi H. Dysregulated Expression of RPS4Y1 (Ribosomal Protein S4, Y-Linked 1) Impairs STAT3 (Signal Transducer and Activator of Transcription 3) Signaling to Suppress Trophoblast Cell Migration and Invasion in Preeclampsia. Hypertension 2018; 71:481-490. [PMID: 29378854 DOI: 10.1161/hypertensionaha.117.10250] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 09/13/2017] [Accepted: 12/27/2017] [Indexed: 12/15/2022]
Abstract
Normal placentation and a successful pregnancy depend on appropriate trophoblast cell migration and invasion. Inadequate trophoblast invasion and impaired spiral artery remodeling may lead to pregnancy-related disorders, such as preeclampsia. RPS4Y1 (ribosomal protein S4, Y-linked 1) is a member of the S4E family of ribosomal proteins. In this study, we found that RPS4Y1 levels were upregulated in placental samples collected from preeclamptic patients, when compared with the normotensive pregnant women. In vitro, inhibition of RPS4Y1 induced trophoblast cell invasion, promoted placental explant outgrowth, and increased STAT3 (signal transducer and activator of transcription 3) phosphorylation along with elevated expression of N-cadherin and vimentin. Conversely, overexpression of RPS4Y1 results in reduced trophoblast cell invasion and decreased STAT3 phosphorylation. In addition, the suppression of RPS4Y1 promotes trophoblast cell invasion, which could be abolished by the STAT3 knockdown. Meanwhile, we observed reductions of STAT3 phosphorylation expression in preeclampsia patients. Collectively, these results demonstrate that the level of RPS4Y1 expression may be associated with preeclampsia by affecting trophoblast cell migration and invasion via the STAT3/epithelial-mesenchymal transition pathway.
Collapse
Affiliation(s)
- Xuehai Chen
- From the Department of Obstetrics and Gynecology and Canada-China-New Zealand Joint Laboratory of Maternal and Fetal Medicine, First Affiliated Hospital of Chongqing Medical University, China (X.C., C.T., H.L., W.P., R.L., X.L., H.G., Y.R., Q.L., Y.L., X.X., Y.B., H.Z., X.L., H.Q.); and College of Medicine, Biological Sciences and Psychology, University of Leicester, United Kingdom (P.N.B.)
| | - Chao Tong
- From the Department of Obstetrics and Gynecology and Canada-China-New Zealand Joint Laboratory of Maternal and Fetal Medicine, First Affiliated Hospital of Chongqing Medical University, China (X.C., C.T., H.L., W.P., R.L., X.L., H.G., Y.R., Q.L., Y.L., X.X., Y.B., H.Z., X.L., H.Q.); and College of Medicine, Biological Sciences and Psychology, University of Leicester, United Kingdom (P.N.B.)
| | - Haiying Li
- From the Department of Obstetrics and Gynecology and Canada-China-New Zealand Joint Laboratory of Maternal and Fetal Medicine, First Affiliated Hospital of Chongqing Medical University, China (X.C., C.T., H.L., W.P., R.L., X.L., H.G., Y.R., Q.L., Y.L., X.X., Y.B., H.Z., X.L., H.Q.); and College of Medicine, Biological Sciences and Psychology, University of Leicester, United Kingdom (P.N.B.)
| | - Wei Peng
- From the Department of Obstetrics and Gynecology and Canada-China-New Zealand Joint Laboratory of Maternal and Fetal Medicine, First Affiliated Hospital of Chongqing Medical University, China (X.C., C.T., H.L., W.P., R.L., X.L., H.G., Y.R., Q.L., Y.L., X.X., Y.B., H.Z., X.L., H.Q.); and College of Medicine, Biological Sciences and Psychology, University of Leicester, United Kingdom (P.N.B.)
| | - Rong Li
- From the Department of Obstetrics and Gynecology and Canada-China-New Zealand Joint Laboratory of Maternal and Fetal Medicine, First Affiliated Hospital of Chongqing Medical University, China (X.C., C.T., H.L., W.P., R.L., X.L., H.G., Y.R., Q.L., Y.L., X.X., Y.B., H.Z., X.L., H.Q.); and College of Medicine, Biological Sciences and Psychology, University of Leicester, United Kingdom (P.N.B.)
| | - Xin Luo
- From the Department of Obstetrics and Gynecology and Canada-China-New Zealand Joint Laboratory of Maternal and Fetal Medicine, First Affiliated Hospital of Chongqing Medical University, China (X.C., C.T., H.L., W.P., R.L., X.L., H.G., Y.R., Q.L., Y.L., X.X., Y.B., H.Z., X.L., H.Q.); and College of Medicine, Biological Sciences and Psychology, University of Leicester, United Kingdom (P.N.B.)
| | - Huisheng Ge
- From the Department of Obstetrics and Gynecology and Canada-China-New Zealand Joint Laboratory of Maternal and Fetal Medicine, First Affiliated Hospital of Chongqing Medical University, China (X.C., C.T., H.L., W.P., R.L., X.L., H.G., Y.R., Q.L., Y.L., X.X., Y.B., H.Z., X.L., H.Q.); and College of Medicine, Biological Sciences and Psychology, University of Leicester, United Kingdom (P.N.B.)
| | - Yuxin Ran
- From the Department of Obstetrics and Gynecology and Canada-China-New Zealand Joint Laboratory of Maternal and Fetal Medicine, First Affiliated Hospital of Chongqing Medical University, China (X.C., C.T., H.L., W.P., R.L., X.L., H.G., Y.R., Q.L., Y.L., X.X., Y.B., H.Z., X.L., H.Q.); and College of Medicine, Biological Sciences and Psychology, University of Leicester, United Kingdom (P.N.B.)
| | - Qin Li
- From the Department of Obstetrics and Gynecology and Canada-China-New Zealand Joint Laboratory of Maternal and Fetal Medicine, First Affiliated Hospital of Chongqing Medical University, China (X.C., C.T., H.L., W.P., R.L., X.L., H.G., Y.R., Q.L., Y.L., X.X., Y.B., H.Z., X.L., H.Q.); and College of Medicine, Biological Sciences and Psychology, University of Leicester, United Kingdom (P.N.B.)
| | - Yamin Liu
- From the Department of Obstetrics and Gynecology and Canada-China-New Zealand Joint Laboratory of Maternal and Fetal Medicine, First Affiliated Hospital of Chongqing Medical University, China (X.C., C.T., H.L., W.P., R.L., X.L., H.G., Y.R., Q.L., Y.L., X.X., Y.B., H.Z., X.L., H.Q.); and College of Medicine, Biological Sciences and Psychology, University of Leicester, United Kingdom (P.N.B.)
| | - Xi Xiong
- From the Department of Obstetrics and Gynecology and Canada-China-New Zealand Joint Laboratory of Maternal and Fetal Medicine, First Affiliated Hospital of Chongqing Medical University, China (X.C., C.T., H.L., W.P., R.L., X.L., H.G., Y.R., Q.L., Y.L., X.X., Y.B., H.Z., X.L., H.Q.); and College of Medicine, Biological Sciences and Psychology, University of Leicester, United Kingdom (P.N.B.)
| | - Yuxiang Bai
- From the Department of Obstetrics and Gynecology and Canada-China-New Zealand Joint Laboratory of Maternal and Fetal Medicine, First Affiliated Hospital of Chongqing Medical University, China (X.C., C.T., H.L., W.P., R.L., X.L., H.G., Y.R., Q.L., Y.L., X.X., Y.B., H.Z., X.L., H.Q.); and College of Medicine, Biological Sciences and Psychology, University of Leicester, United Kingdom (P.N.B.)
| | - Hua Zhang
- From the Department of Obstetrics and Gynecology and Canada-China-New Zealand Joint Laboratory of Maternal and Fetal Medicine, First Affiliated Hospital of Chongqing Medical University, China (X.C., C.T., H.L., W.P., R.L., X.L., H.G., Y.R., Q.L., Y.L., X.X., Y.B., H.Z., X.L., H.Q.); and College of Medicine, Biological Sciences and Psychology, University of Leicester, United Kingdom (P.N.B.)
| | - Philip N Baker
- From the Department of Obstetrics and Gynecology and Canada-China-New Zealand Joint Laboratory of Maternal and Fetal Medicine, First Affiliated Hospital of Chongqing Medical University, China (X.C., C.T., H.L., W.P., R.L., X.L., H.G., Y.R., Q.L., Y.L., X.X., Y.B., H.Z., X.L., H.Q.); and College of Medicine, Biological Sciences and Psychology, University of Leicester, United Kingdom (P.N.B.)
| | - Xiru Liu
- From the Department of Obstetrics and Gynecology and Canada-China-New Zealand Joint Laboratory of Maternal and Fetal Medicine, First Affiliated Hospital of Chongqing Medical University, China (X.C., C.T., H.L., W.P., R.L., X.L., H.G., Y.R., Q.L., Y.L., X.X., Y.B., H.Z., X.L., H.Q.); and College of Medicine, Biological Sciences and Psychology, University of Leicester, United Kingdom (P.N.B.).
| | - Hongbo Qi
- From the Department of Obstetrics and Gynecology and Canada-China-New Zealand Joint Laboratory of Maternal and Fetal Medicine, First Affiliated Hospital of Chongqing Medical University, China (X.C., C.T., H.L., W.P., R.L., X.L., H.G., Y.R., Q.L., Y.L., X.X., Y.B., H.Z., X.L., H.Q.); and College of Medicine, Biological Sciences and Psychology, University of Leicester, United Kingdom (P.N.B.)
| |
Collapse
|
33
|
Abstract
The properties of the human Y chromosome - namely, male specificity, haploidy and escape from crossing over - make it an unusual component of the genome, and have led to its genetic variation becoming a key part of studies of human evolution, population history, genealogy, forensics and male medical genetics. Next-generation sequencing (NGS) technologies have driven recent progress in these areas. In particular, NGS has yielded direct estimates of mutation rates, and an unbiased and calibrated molecular phylogeny that has unprecedented detail. Moreover, the availability of direct-to-consumer NGS services is fuelling a rise of 'citizen scientists', whose interest in resequencing their own Y chromosomes is generating a wealth of new data.
Collapse
|
34
|
Giorgio E, Brussino A, Biamino E, Belligni EF, Bruselles A, Ciolfi A, Caputo V, Pizzi S, Calcia A, Di Gregorio E, Cavalieri S, Mancini C, Pozzi E, Ferrero M, Riberi E, Borelli I, Amoroso A, Ferrero GB, Tartaglia M, Brusco A. Exome sequencing in children of women with skewed X-inactivation identifies atypical cases and complex phenotypes. Eur J Paediatr Neurol 2017; 21:475-484. [PMID: 28027854 DOI: 10.1016/j.ejpn.2016.12.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 11/03/2016] [Accepted: 12/11/2016] [Indexed: 12/30/2022]
Abstract
BACKGROUND More than 100 X-linked intellectual disability (X-LID) genes have been identified to be involved in 10-15% of intellectual disability (ID). METHOD To identify novel possible candidates, we selected 18 families with a male proband affected by isolated or syndromic ID. Pedigree and/or clinical presentation suggested an X-LID disorder. After exclusion of known genetic diseases, we identified seven cases whose mother showed a skewed X-inactivation (>80%) that underwent whole exome sequencing (WES, 50X average depth). RESULTS WES allowed to solve the genetic basis in four cases, two of which (Coffin-Lowry syndrome, RPS6K3 gene; ATRX syndrome, ATRX gene) had been missed by previous clinical/genetics tests. One further ATRX case showed a complex phenotype including pontocerebellar atrophy (PCA), possibly associated to an unidentified PCA gene mutation. In a case with suspected Lujan-Fryns syndrome, a c.649C>T (p.Pro217Ser) MECP2 missense change was identified, likely explaining the neurological impairment, but not the marfanoid features, which were possibly associated to the p.Thr1020Ala variant in fibrillin 1. Finally, a c.707T>G variant (p.Phe236Cys) in the DMD gene was identified in a patient retrospectively recognized to be affected by Becker muscular dystrophy (BMD, OMIM 300376). CONCLUSION Overall, our data show that WES may give hints to solve complex ID phenotypes with a likely X-linked transmission, and that a significant proportion of these orphan conditions might result from concomitant mutations affecting different clinically associated genes.
Collapse
Affiliation(s)
- Elisa Giorgio
- University of Torino, Department of Medical Sciences, 10126, Turin, Italy
| | | | - Elisa Biamino
- University of Torino, Department of Public Health and Pediatrics, 10126, Turin, Italy
| | - Elga Fabia Belligni
- University of Torino, Department of Public Health and Pediatrics, 10126, Turin, Italy
| | - Alessandro Bruselles
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù IRCSS, Rome, Italy
| | - Andrea Ciolfi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù IRCSS, Rome, Italy
| | - Viviana Caputo
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Simone Pizzi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù IRCSS, Rome, Italy
| | - Alessandro Calcia
- University of Torino, Department of Medical Sciences, 10126, Turin, Italy
| | - Eleonora Di Gregorio
- University of Torino, Department of Medical Sciences, 10126, Turin, Italy; Città della Salute e della Scienza University Hospital, Medical Genetics Unit, Turin, Italy
| | - Simona Cavalieri
- University of Torino, Department of Medical Sciences, 10126, Turin, Italy
| | - Cecilia Mancini
- University of Torino, Department of Medical Sciences, 10126, Turin, Italy
| | - Elisa Pozzi
- University of Torino, Department of Medical Sciences, 10126, Turin, Italy
| | - Marta Ferrero
- University of Torino, Department of Medical Sciences, 10126, Turin, Italy
| | - Evelise Riberi
- University of Torino, Department of Public Health and Pediatrics, 10126, Turin, Italy
| | - Iolanda Borelli
- University of Torino, Department of Medical Sciences, 10126, Turin, Italy
| | - Antonio Amoroso
- University of Torino, Department of Medical Sciences, 10126, Turin, Italy
| | | | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù IRCSS, Rome, Italy
| | - Alfredo Brusco
- University of Torino, Department of Medical Sciences, 10126, Turin, Italy; Città della Salute e della Scienza University Hospital, Medical Genetics Unit, Turin, Italy.
| |
Collapse
|
35
|
Sun YX, Zhang YX, Zhang D, Xu CM, Chen SC, Zhang JY, Ruan YC, Chen F, Zhang RJ, Qian YQ, Liu YF, Jin LY, Yu TT, Xu HY, Luo YQ, Liu XM, Sun F, Sheng JZ, Huang HF. XCI-escaping gene KDM5C contributes to ovarian development via downregulating miR-320a. Hum Genet 2016; 136:227-239. [PMID: 27896428 DOI: 10.1007/s00439-016-1752-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2016] [Accepted: 11/22/2016] [Indexed: 01/03/2023]
Abstract
Mechanisms underlying female gonadal dysgenesis remain unclarified and relatively unstudied. Whether X-chromosome inactivation (XCI)-escaping genes and microRNAs (miRNAs) contribute to this condition is currently unknown. We compared 45,X Turner Syndrome women with 46,XX normal women, and investigated differentially expressed miRNAs in Turner Syndrome through plasma miRNA sequencing. We found that miR-320a was consistently upregulated not only in 45,X plasma and peripheral blood mononuclear cells (PBMCs), but also in 45,X fetal gonadal tissues. The levels of miR-320a in PBMCs from 45,X, 46,XX, 46,XY, and 47,XXY human subjects were inversely related to the expression levels of XCI-escaping gene KDM5C in PBMCs. In vitro models indicated that KDM5C suppressed miR-320a transcription by directly binding to the promoter of miR-320a to prevent histone methylation. In addition, we demonstrated that KITLG, an essential gene for ovarian development and primordial germ cell survival, was a direct target of miR-320a and that it was downregulated in 45,X fetal gonadal tissues. In conclusion, we demonstrated that downregulation of miR-320a by the XCI-escaping gene KDM5C contributed to ovarian development by targeting KITLG.
Collapse
Affiliation(s)
- Yi-Xi Sun
- Key Laboratory of Reproductive Genetics, Ministry of Education (Zhejiang University), Hangzhou, 310058, Zhejiang, China.,Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310006, Zhejiang, China
| | - Yi-Xin Zhang
- Key Laboratory of Reproductive Genetics, Ministry of Education (Zhejiang University), Hangzhou, 310058, Zhejiang, China.,Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310006, Zhejiang, China
| | - Dan Zhang
- Key Laboratory of Reproductive Genetics, Ministry of Education (Zhejiang University), Hangzhou, 310058, Zhejiang, China.,Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310006, Zhejiang, China
| | - Chen-Ming Xu
- Key Laboratory of Reproductive Genetics, Ministry of Education (Zhejiang University), Hangzhou, 310058, Zhejiang, China.,International Peace Maternal and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Song-Chang Chen
- Key Laboratory of Reproductive Genetics, Ministry of Education (Zhejiang University), Hangzhou, 310058, Zhejiang, China.,International Peace Maternal and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Jun-Yu Zhang
- International Peace Maternal and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China.,Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education (Shanghai Jiao Tong University), Shanghai, 200030, China
| | - Ye-Chun Ruan
- Epithelial Cell Biology Research Centre, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Feng Chen
- Key Laboratory of Reproductive Genetics, Ministry of Education (Zhejiang University), Hangzhou, 310058, Zhejiang, China.,Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310006, Zhejiang, China
| | - Run-Ju Zhang
- Key Laboratory of Reproductive Genetics, Ministry of Education (Zhejiang University), Hangzhou, 310058, Zhejiang, China.,Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310006, Zhejiang, China
| | - Ye-Qing Qian
- Key Laboratory of Reproductive Genetics, Ministry of Education (Zhejiang University), Hangzhou, 310058, Zhejiang, China.,Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310006, Zhejiang, China
| | - Yi-Feng Liu
- Key Laboratory of Reproductive Genetics, Ministry of Education (Zhejiang University), Hangzhou, 310058, Zhejiang, China.,Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310006, Zhejiang, China
| | - Lu-Yang Jin
- Key Laboratory of Reproductive Genetics, Ministry of Education (Zhejiang University), Hangzhou, 310058, Zhejiang, China.,Department of Pathology and Pathophysiology, School of Medicine, Zhejiang University, Hangzhou, 310000, Zhejiang, China
| | - Tian-Tian Yu
- Key Laboratory of Reproductive Genetics, Ministry of Education (Zhejiang University), Hangzhou, 310058, Zhejiang, China.,Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310006, Zhejiang, China
| | - Hai-Yan Xu
- Key Laboratory of Reproductive Genetics, Ministry of Education (Zhejiang University), Hangzhou, 310058, Zhejiang, China.,Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310006, Zhejiang, China
| | - Yu-Qin Luo
- Key Laboratory of Reproductive Genetics, Ministry of Education (Zhejiang University), Hangzhou, 310058, Zhejiang, China.,Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310006, Zhejiang, China
| | - Xin-Mei Liu
- Key Laboratory of Reproductive Genetics, Ministry of Education (Zhejiang University), Hangzhou, 310058, Zhejiang, China.,International Peace Maternal and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Fei Sun
- International Peace Maternal and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China.,Institute of Embryo-Fetal Original Adult Disease and Shanghai Key Laboratory for Reproductive Medicine, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Jian-Zhong Sheng
- Key Laboratory of Reproductive Genetics, Ministry of Education (Zhejiang University), Hangzhou, 310058, Zhejiang, China.,Department of Pathology and Pathophysiology, School of Medicine, Zhejiang University, Hangzhou, 310000, Zhejiang, China
| | - He-Feng Huang
- Key Laboratory of Reproductive Genetics, Ministry of Education (Zhejiang University), Hangzhou, 310058, Zhejiang, China. .,International Peace Maternal and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China. .,Institute of Embryo-Fetal Original Adult Disease and Shanghai Key Laboratory for Reproductive Medicine, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China. .,Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education (Shanghai Jiao Tong University), Shanghai, 200030, China. .,Key Laboratory of Reproductive Genetics, Ministry of Education (Zhejiang University), Hangzhou, 310006, Zhejiang, China.
| |
Collapse
|
36
|
Widespread DNA hypomethylation and differential gene expression in Turner syndrome. Sci Rep 2016; 6:34220. [PMID: 27687697 PMCID: PMC5043230 DOI: 10.1038/srep34220] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 09/08/2016] [Indexed: 01/15/2023] Open
Abstract
Adults with 45,X monosomy (Turner syndrome) reflect a surviving minority since more than 99% of fetuses with 45,X monosomy die in utero. In adulthood 45,X monosomy is associated with increased morbidity and mortality, although strikingly heterogeneous with some individuals left untouched while others suffer from cardiovascular disease, autoimmune disease and infertility. The present study investigates the leukocyte DNAmethylation profile by using the 450K-Illumina Infinium assay and the leukocyte RNA-expression profile in 45,X monosomy compared with karyotypically normal female and male controls. We present results illustrating that genome wide X-chromosome RNA-expression profile, autosomal DNA-methylation profile, and the X-chromosome methylation profile clearly distinguish Turner syndrome from controls. Our results reveal genome wide hypomethylation with most differentially methylated positions showing a medium level of methylation. Contrary to previous studies, applying a single loci specific analysis at well-defined DNA loci, our results indicate that the hypomethylation extend to repetitive elements. We describe novel candidate genes that could be involved in comorbidity in TS and explain congenital urinary malformations (PRKX), premature ovarian failure (KDM6A), and aortic aneurysm formation (ZFYVE9 and TIMP1).
Collapse
|
37
|
Baik IH, Jo GH, Seo D, Ko MJ, Cho CH, Lee MG, Lee YH. Knockdown of RPL9 expression inhibits colorectal carcinoma growth via the inactivation of Id-1/NF-κB signaling axis. Int J Oncol 2016; 49:1953-1962. [PMID: 27633352 DOI: 10.3892/ijo.2016.3688] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 08/25/2016] [Indexed: 11/06/2022] Open
Abstract
Ribosomal protein L9 (RPL9), a component of the 60S subunit for protein synthesis, is upregulated in human colorectal cancer. In the present study, we investigated whether RPL9 gained extraribosomal function during tumorigenesis and whether targeting of RPL9 with small interfering (si) RNA could alter the course of colorectal cancer progression. Our results showed that siRNA knockdown of RPL9 suppresses colorectal cancer (CRC) cell growth and long-term colony formation through an increase in sub-G1 cell population and a strong induction of apoptotic cell death. To obtain insights into the molecular changes in response to RPL9 knockdown, global changes in gene expression were examined using RNA sequencing. It revealed that RPL9-specific knockdown led to dysregulation of 918 genes in HCT116 and 3178 genes in HT29 cells. Among these, 296 genes showed same directional regulation (128 upregulated and 168 downregulated genes) and were considered as a common RPL9 knockdown signature. Particularly, we found through a network analysis that Id-1, which is functionally associated with activation of NF-κB and cell survival, was commonly downregulated. Subsequent western blot analysis affirmed that RPL9 silencing induced the decrease in the levels of Id-1 and phosphorylated IκBα in both HCT116 and HT29 cells. Also, the same condition decreased the levels of PARP-1 and pro-caspase-3, accelerating apoptosis. Furthermore, inhibition of RPL9 expression significantly suppressed the growth of human CRC xenografts in nude mice. These findings indicate that the function of RPL9 is correlated with Id-1/NF-κB signaling axis and suggest that targeting RPL9 could be an attractive option for molecular therapy of colorectal cancer.
Collapse
Affiliation(s)
- In Hye Baik
- Department of Molecular Medicine, Keimyung University School of Medicine, Daegu, Republic of Korea
| | - Guk-Heui Jo
- Myunggok Eye Research Institute, Kim's Eye Hospital, Konyang University College of Medicine, Seoul, Republic of Korea
| | - Daekwan Seo
- Severance Biomedical Science Institute, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Min Ji Ko
- Department of Molecular Medicine, Keimyung University School of Medicine, Daegu, Republic of Korea
| | - Chi Heum Cho
- Department of Obstetrics and Gynecology, Keimyung University School of Medicine, Daegu, Republic of Korea
| | - Min Goo Lee
- Department of Pharmacology and Brain Korea 21 Project for Medical Sciences, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Yun-Han Lee
- Department of Molecular Medicine, Keimyung University School of Medicine, Daegu, Republic of Korea
| |
Collapse
|
38
|
Taketo T. The role of sex chromosomes in mammalian germ cell differentiation: can the germ cells carrying X and Y chromosomes differentiate into fertile oocytes? Asian J Androl 2016; 17:360-6. [PMID: 25578929 PMCID: PMC4430933 DOI: 10.4103/1008-682x.143306] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The sexual differentiation of germ cells into spermatozoa or oocytes is strictly regulated by their gonadal environment, testis or ovary, which is determined by the presence or absence of the Y chromosome, respectively. Hence, in normal mammalian development, male germ cells differentiate in the presence of X and Y chromosomes, and female germ cells do so in the presence of two X chromosomes. However, gonadal sex reversal occurs in humans as well as in other mammalian species, and the resultant XX males and XY females can lead healthy lives, except for a complete or partial loss of fertility. Germ cells carrying an abnormal set of sex chromosomes are efficiently eliminated by multilayered surveillance mechanisms in the testis, and also, though more variably, in the ovary. Studying the molecular basis for sex-specific responses to a set of sex chromosomes during gametogenesis will promote our understanding of meiotic processes contributing to the evolution of sex determining mechanisms. This review discusses the fate of germ cells carrying various sex chromosomal compositions in mouse models, the limitation of which may be overcome by recent successes in the differentiation of functional germ cells from embryonic stem cells under experimental conditions.
Collapse
Affiliation(s)
- Teruko Taketo
- Department of Surgery, Research Institute of MUHC; Department of Biology; Department of Obstetrics and Gynecology, McGill University, Montreal, Quebec, Canada
| |
Collapse
|
39
|
Clayton JA. Studying both sexes: a guiding principle for biomedicine. FASEB J 2016; 30:519-24. [PMID: 26514164 PMCID: PMC4714546 DOI: 10.1096/fj.15-279554] [Citation(s) in RCA: 216] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 10/19/2015] [Indexed: 11/11/2022]
Abstract
In May 2014, the U.S. National Institutes of Health (NIH) announced that it will ensure that investigators account for sex as a biological variable (SABV) in NIH-funded preclinical research as part of the agency's rigor and transparency initiative. Herein, I describe in more detail the rationale behind the SABV policy component and provide additional detail about policy goals. In short, studying both sexes is a guiding principle in biomedical research that will expand knowledge toward turning discovery into health. NIH expects that considering SABV in preclinical research will help to build a knowledge base that better informs the design of clinical research and trials in humans. Integrating the practice of studying both sexes in preclinical research will, over time, expand our currently incomplete knowledge base that plays a critical role in informing the development of sex- and gender-appropriate medical care for women and men.
Collapse
Affiliation(s)
- Janine Austin Clayton
- Office of Research on Women's Health, National Institutes of Health, Bethesda, Maryland, USA
| |
Collapse
|
40
|
Abstract
Mammals have the oldest sex chromosome system known: the mammalian X and Y chromosomes evolved from ordinary autosomes beginning at least 180 million years ago. Despite their shared ancestry, mammalian Y chromosomes display enormous variation among species in size, gene content, and structural complexity. Several unique features of the Y chromosome--its lack of a homologous partner for crossing over, its functional specialization for spermatogenesis, and its high degree of sequence amplification--contribute to this extreme variation. However, amid this evolutionary turmoil many commonalities have been revealed that have contributed to our understanding of the selective pressures driving the evolution and biology of the Y chromosome. Two biological themes have defined Y-chromosome research over the past six decades: testis determination and spermatogenesis. A third biological theme begins to emerge from recent insights into the Y chromosome's roles beyond the reproductive tract--a theme that promises to broaden the reach of Y-chromosome research by shedding light on fundamental sex differences in human health and disease.
Collapse
Affiliation(s)
- Jennifer F Hughes
- Whitehead Institute, Howard Hughes Medical Institute, and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142;
| | - David C Page
- Whitehead Institute, Howard Hughes Medical Institute, and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142;
| |
Collapse
|
41
|
Liu H, Liang S, Yang X, Ji Z, Zhao W, Ye X, Rui J. RNAi-mediated RPL34 knockdown suppresses the growth of human gastric cancer cells. Oncol Rep 2015; 34:2267-72. [PMID: 26323242 PMCID: PMC4583519 DOI: 10.3892/or.2015.4219] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 08/07/2015] [Indexed: 01/23/2023] Open
Abstract
An increasing body of evidence suggests that ribosomal proteins may have ribosome-independent functions and may be involved in various physiological and pathological processes. To examine the role of ribosomal protein L34 (RPL34) in cancer transformation, we assessed its expression in gastric cancer cell lines and found it highly expressed. We further used lentivirus-mediated small interfering RNAs (siRNAs) to knockdown RPL34 expression in the human gastric cancer cell line SGC-7901. RNA interference (RNAi)-mediated inhibition of RPL34 expression in SGC-7901 cells significantly suppressed cell proliferation, increased apoptosis and arrested cells in the S phase. The results of the present study suggest that RPL34 plays a critical role in cell proliferation, cell cycle distribution and apoptosis of human malignant gastric cells.
Collapse
Affiliation(s)
- Hui Liu
- Department of Oncology, Wannan Medical College, Wuhu, Anhui 241001, P.R. China
| | - Shaohua Liang
- Department of Oncology, Wannan Medical College, Wuhu, Anhui 241001, P.R. China
| | - Xi Yang
- Department of Oncology, Wannan Medical College, Wuhu, Anhui 241001, P.R. China
| | - Zhaoning Ji
- Department of Medical Oncology, Yijishan Hospital of Wannan Medical College, Wuhu, Anhui 241001, P.R. China
| | - Wenying Zhao
- Department of Medical Oncology, Yijishan Hospital of Wannan Medical College, Wuhu, Anhui 241001, P.R. China
| | - Xiaobing Ye
- Department of Medical Oncology, Yijishan Hospital of Wannan Medical College, Wuhu, Anhui 241001, P.R. China
| | - Jing Rui
- Department of Medical Oncology, Yijishan Hospital of Wannan Medical College, Wuhu, Anhui 241001, P.R. China
| |
Collapse
|
42
|
Loss of RPS41 but not its paralog RPS42 results in altered growth, filamentation and transcriptome changes in Candida albicans. Fungal Genet Biol 2015; 80:31-42. [DOI: 10.1016/j.fgb.2015.03.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 03/23/2015] [Accepted: 03/31/2015] [Indexed: 11/22/2022]
|
43
|
de Las Heras-Rubio A, Perucho L, Paciucci R, Vilardell J, LLeonart ME. Ribosomal proteins as novel players in tumorigenesis. Cancer Metastasis Rev 2015; 33:115-41. [PMID: 24375388 DOI: 10.1007/s10555-013-9460-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Ribosome biogenesis is the most demanding energetic and metabolic expenditure of the cell. The nucleolus, a nuclear compartment, coordinates rRNA transcription, maturation, and assembly into ribosome subunits. The transcription process is highly coordinated with ribosome biogenesis. In this context, ribosomal proteins (RPs) play a crucial role. In the last decade, an increasing number of studies have associated RPs with extraribosomal functions related to proliferation. Importantly, the expression of RPs appears to be deregulated in several human disorders due, at least in part, to genetic mutations. Although the deregulation of RPs in human malignancies is commonly observed, a more complex mechanism is believed to be involved, favoring the tumorigenic process, its progression and metastasis. This review explores the roles of the most frequently mutated oncogenes and tumor suppressor genes in human cancer that modulate ribosome biogenesis, including their interaction with RPs. In this regard, we propose a new focus for novel therapies.
Collapse
Affiliation(s)
- A de Las Heras-Rubio
- Oncology and Pathology Group, Institut de Recerca Hospital Vall d'Hebron, Passeig Vall d'Hebron 119-129, 08035, Barcelona, Spain
| | | | | | | | | |
Collapse
|
44
|
Kim TH, Leslie P, Zhang Y. Ribosomal proteins as unrevealed caretakers for cellular stress and genomic instability. Oncotarget 2015; 5:860-71. [PMID: 24658219 PMCID: PMC4011588 DOI: 10.18632/oncotarget.1784] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Ribosomal proteins (RPs) have gained much attention for their extraribosomal functions particularly with respect to p53 regulation. To date, about fourteen RPs have shown to bind to MDM2 and regulate p53. Upon binding to MDM2, the RPs suppress MDM2 E3 ubiquitin ligase activity resulting in the stabilization and activation of p53. Of the RPs that bind to MDM2, RPL5 and RPL11 are the most studied and RPL11 appears to have the most significant role in p53 regulation. Considering that more than 17% of RP species have been shown to interact with MDM2, one of the questions remains unresolved is why so many RPs bind MDM2 and modulate p53. Genes encoding RPs are widely dispersed on different chromosomes in both mice and humans. As components of ribosome, RP expression is tightly regulated to meet the appropriate stoichiometric ratio between RPs and rRNAs. Once genomic instability (e.g. aneuploidy) occurs, transcriptional and translational changes due to change of DNA copy number can result in an imbalance in the expression of RPs including those that bind to MDM2. Such an imbalance in RP expression could lead to failure to assemble functional ribosomes resulting in ribosomal stress. We propose that RPs have evolved ability to regulate MDM2 in response to genomic instability as an additional layer of p53 regulation. Full understanding of the biological roles of RPs could potentially establish RPs as a novel class of therapeutic targets in human diseases such as cancer.
Collapse
Affiliation(s)
- Tae-Hyung Kim
- Department of Radiation Oncology, University of North Carolina, Chapel Hill, NC, USA
| | | | | |
Collapse
|
45
|
Nakhoul H, Ke J, Zhou X, Liao W, Zeng SX, Lu H. Ribosomopathies: mechanisms of disease. PLASMATOLOGY 2014; 7:7-16. [PMID: 25512719 PMCID: PMC4251057 DOI: 10.4137/cmbd.s16952] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 07/03/2014] [Accepted: 07/16/2014] [Indexed: 01/05/2023]
Abstract
Ribosomopathies are diseases caused by alterations in the structure or function of ribosomal components. Progress in our understanding of the role of the ribosome in translational and transcriptional regulation has clarified the mechanisms of the ribosomopathies and the relationship between ribosomal dysfunction and other diseases, especially cancer. This review aims to discuss these topics with updated information.
Collapse
Affiliation(s)
- Hani Nakhoul
- Department of Biochemistry and Molecular Biology and Cancer Center, Tulane University, School of Medicine, New Orleans, Louisiana, LA, USA
| | - Jiangwei Ke
- Department of Biochemistry and Molecular Biology and Cancer Center, Tulane University, School of Medicine, New Orleans, Louisiana, LA, USA. ; Department of Laboratory Medicine, Jiangxi Children's Hospital, Nanchang, Jiangxi, China
| | - Xiang Zhou
- Department of Biochemistry and Molecular Biology and Cancer Center, Tulane University, School of Medicine, New Orleans, Louisiana, LA, USA
| | - Wenjuan Liao
- Department of Biochemistry and Molecular Biology and Cancer Center, Tulane University, School of Medicine, New Orleans, Louisiana, LA, USA
| | - Shelya X Zeng
- Department of Biochemistry and Molecular Biology and Cancer Center, Tulane University, School of Medicine, New Orleans, Louisiana, LA, USA
| | - Hua Lu
- Department of Biochemistry and Molecular Biology and Cancer Center, Tulane University, School of Medicine, New Orleans, Louisiana, LA, USA
| |
Collapse
|
46
|
Chida J, Araki H, Maeda Y. Specific growth suppression of human cancer cells by targeted delivery of Dictyostelium mitochondrial ribosomal protein S4. Cancer Cell Int 2014; 14:56. [PMID: 24976792 PMCID: PMC4074393 DOI: 10.1186/1475-2867-14-56] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2014] [Accepted: 06/09/2014] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND In general, growth and differentiation are mutually exclusive but are cooperatively regulated throughout development. Thus, the process of a cell's switching from growth to differentiation is of great importance not only for the development of organisms but also for malignant transformation, in which this process is reversed. We have previously demonstrated using a Dictyostelium model system that the Dictyostelium mitochondrial ribosomal protein S4 (Dd-mrp4) gene expression is essential for the initiation of cell differentiation: Dd-mrp4-null cells fail to initiate differentiation, while the initial step of cell differentiation and the subsequent morphogenesis are markedly enhanced in mrp4 (OE) cells overexpressing the Dd-mrp4 in the extramitochondrial cytoplasm. This raised a possibility that the ectopically enforced expression of the Dd-mrp4 in human cells might inhibit their growth, particularly of malignant tumor cells, by inducing cell differentiation. METHODS FOUR KINDS OF HUMAN TUMOR CELL LINES WERE TRANSFECTED BY THREE KIND OF VECTOR CONSTRUCTS (THE EMPTY VECTOR: pcDNA3.1 (Mock); pcDNA3.1-rps4 bearing Dictyostelium cytoplasmic ribosomal protein S4; pcDNA3.1-mrp4 bearing Dictyostelium mitochondrial ribosomal protein S4). As controls, four kinds of human primary cultured cells were similarly transfected by the above vector constructs. After transfection, growth kinetics of cells was analyzed using cell viability assay, and also the TUNEL method was used for evaluation of apoptotic cells. RESULTS Ectopically expressed Dd-mrp4 suppressed cell proliferation through inducing apoptotic cell death specifically in the human lung adenocarcinoma (A549), epithelial cervical cancer (HeLa), hepatocellular carcinoma (HepG2) and colonic carcinoma (Caco-2), but not in primary cultured normal cells, such as human brain microvascular endothelial cells (HBMECs); human umbilical vein endothelial cells (HUVECs) and human normal hepatocytes (hHeps™), with one exception (human cardiac fibloblasts (HCF)). CONCLUSION The present finding that the ectopically enforced expression of Dd-mrp4 in human several tumor cell lines specifically suppresses their proliferation suggests strongly that the Dd-mrp4 gene derived from Dictyostelium mitochondria may provide a new promising therapeutic strategy for disrupting cell viability pathways in human cancers.
Collapse
Affiliation(s)
- Junji Chida
- Division of Molecular Neurobiology, Institute for Enzyme Research, The University of Tokushima, Kuramoto-cho, Tokushima 770-8503, Japan
| | - Hikaru Araki
- Division of Enzyme Chemistry, Institute for Enzyme Research, The University of Tokushima, Kuramoto-cho, Tokushima 770-8503, Japan
| | - Yasuo Maeda
- Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Aoba, Sendai 980-8578, Japan
| |
Collapse
|
47
|
Rajpathak SN, Vellarikkal SK, Patowary A, Scaria V, Sivasubbu S, Deobagkar DD. Human 45,X fibroblast transcriptome reveals distinct differentially expressed genes including long noncoding RNAs potentially associated with the pathophysiology of Turner syndrome. PLoS One 2014; 9:e100076. [PMID: 24932682 PMCID: PMC4059722 DOI: 10.1371/journal.pone.0100076] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 05/21/2014] [Indexed: 01/09/2023] Open
Abstract
Turner syndrome is a chromosomal abnormality characterized by the absence of whole or part of the X chromosome in females. This X aneuploidy condition is associated with a diverse set of clinical phenotypes such as gonadal dysfunction, short stature, osteoporosis and Type II diabetes mellitus, among others. These phenotypes differ in their severity and penetrance among the affected individuals. Haploinsufficiency for a few X linked genes has been associated with some of these disease phenotypes. RNA sequencing can provide valuable insights to understand molecular mechanism of disease process. In the current study, we have analysed the transcriptome profiles of human untransformed 45,X and 46,XX fibroblast cells and identified differential expression of genes in these two karyotypes. Functional analysis revealed that these differentially expressing genes are associated with bone differentiation, glucose metabolism and gonadal development pathways. We also report differential expression of lincRNAs in X monosomic cells. Our observations provide a basis for evaluation of cellular and molecular mechanism(s) in the establishment of Turner syndrome phenotypes.
Collapse
Affiliation(s)
- Shriram N Rajpathak
- Centre of Advanced Studies, Department of Zoology, University of Pune, Pune, India
| | - Shamsudheen Karuthedath Vellarikkal
- Genomics and Molecular medicine, CSIR Institute of Genomics and Integrative Biology, Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi, India
| | - Ashok Patowary
- GN Ramachandran Knowledge Centre for Genome Informatics, CSIR Institute of Genomics and Integrative Biology, Delhi, India
| | - Vinod Scaria
- GN Ramachandran Knowledge Centre for Genome Informatics, CSIR Institute of Genomics and Integrative Biology, Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi, India
| | - Sridhar Sivasubbu
- Genomics and Molecular medicine, CSIR Institute of Genomics and Integrative Biology, Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi, India
| | - Deepti D Deobagkar
- Centre of Advanced Studies, Department of Zoology, University of Pune, Pune, India
| |
Collapse
|
48
|
Shah K, McCormack CE, Bradbury NA. Do you know the sex of your cells? Am J Physiol Cell Physiol 2014; 306:C3-18. [PMID: 24196532 PMCID: PMC3919971 DOI: 10.1152/ajpcell.00281.2013] [Citation(s) in RCA: 143] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 10/31/2013] [Indexed: 11/22/2022]
Abstract
Do you know the sex of your cells? Not a question that is frequently heard around the lab bench, yet thanks to recent research is probably one that should be asked. It is self-evident that cervical epithelial cells would be derived from female tissue and prostate cells from a male subject (exemplified by HeLa and LnCaP, respectively), yet beyond these obvious examples, it would be true to say that the sex of cell lines derived from non-reproductive tissue, such as lung, intestine, kidney, for example, is given minimal if any thought. After all, what possible impact could the presence of a Y chromosome have on the biochemistry and cell biology of tissues such as the exocrine pancreatic acini? Intriguingly, recent evidence has suggested that far from being irrelevant, genes expressed on the sex chromosomes can have a marked impact on the biology of such diverse tissues as neurons and renal cells. It is also policy of AJP-Cell Physiology that the source of all cells utilized (species, sex, etc.) should be clearly indicated when submitting an article for publication, an instruction that is rarely followed (http://www.the-aps.org/mm/Publications/Info-For-Authors/Composition). In this review we discuss recent data arguing that the sex of cells being used in experiments can impact the cell's biology, and we provide a table outlining the sex of cell lines that have appeared in AJP-Cell Physiology over the past decade.
Collapse
Affiliation(s)
- Kalpit Shah
- Department of Physiology and Biophysics, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, Illinois
| | | | | |
Collapse
|
49
|
Staedtler F, Hartmann N, Letzkus M, Bongiovanni S, Scherer A, Marc P, Johnson KJ, Schumacher MM. Robust and tissue-independent gender-specific transcript biomarkers. Biomarkers 2013; 18:436-45. [PMID: 23829492 DOI: 10.3109/1354750x.2013.811538] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
CONTEXT Correct gender assignment in humans at the molecular level is crucial in many scientific disciplines and applied areas. MATERIALS AND METHODS Candidate gender markers were identified through supervised statistical analysis of genome wide microarray expression data from human blood samples (N = 123, 58 female, 65 male) as a training set. The potential of the markers to predict undisclosed tissue donor gender was tested on microarray data from 13 healthy and 11 cancerous human tissue collections (internal) and external datasets from samples of varying tissue origin. The abundance of some genes in the marker panel was quantified by RT-PCR as alternative analytical technology. RESULTS We identified and qualified predictive, gender-specific transcript markers based on a set of five genes (RPS4Y1, EIF1AY, DDX3Y, KDM5D and XIST). CONCLUSION Gene expression marker panels can be used as a robust tissue- and platform-independent predictive approach for gender determination.
Collapse
Affiliation(s)
- Frank Staedtler
- Novartis Institutes for BioMedical Research (NIBR), Biomarker Development, Basel, Switzerland.
| | | | | | | | | | | | | | | |
Collapse
|
50
|
Sudhamalla B, Kumar M, Kumar RS, Sashi P, Yasin UM, Ramakrishna D, Rao PN, Bhuyan AK. Enzyme dimension of the ribosomal protein S4 across plant and animal kingdoms. Biochim Biophys Acta Gen Subj 2013; 1830:5335-41. [PMID: 23791937 DOI: 10.1016/j.bbagen.2013.06.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 05/10/2013] [Accepted: 06/09/2013] [Indexed: 01/28/2023]
Abstract
BACKGROUND The protein S4 of the smaller ribosomal subunit is centrally important for its anchorage role in ribosome assembly and rRNA binding. Eubacterial S4 also facilitates synthesis of rRNA, and restrains translation of ribosomal proteins of the same polycistronic mRNA. Eukaryotic S4 has no homolog in eubacterial kingdom, nor are such extraribosomal functions of S4 known in plants and animals even as genetic evidence suggests that deficiency of S4X isoform in 46,XX human females may produce Turner syndrome (45,XO). METHODS Recombinant human S4X and rice S4 were used to determine their enzymatic action in the cleavage of synthetic peptide substrates and natural proteins. We also studied autoproteolysis of the recombinant S4 proteins, and examined the growth and proliferation of S4-transfected human embryonic kidney cells. RESULTS Extraribosomal enzyme nature of eukaryotic S4 is described. Both human S4X and rice S4 are cysteine proteases capable of hydrolyzing a wide spectrum of peptides and natural proteins of diverse origin. Whereas rice S4 also cleaves the -XXXD↓- consensus sequence assumed to be specific for caspase-9 and granzyme B, human S4 does not. Curiously, both human and rice S4 show multiple-site autoproteolysis leading to self-annihilation. Overexpression of human S4 blocks the growth and proliferation of transfected embryonic kidney cells, presumably due to the extraribosomal enzyme trait reported. CONCLUSIONS The S4 proteins of humans and rice, prototypes of eukaryota, are non-specific cysteine proteases in the extraribosomal milieu. GENERAL SIGNIFICANCE The enzyme nature of S4 is relevant toward understanding not only the origin of ribosomal proteins, but also processes in cell biology and diseases.
Collapse
Affiliation(s)
- Babu Sudhamalla
- School of Chemistry, University of Hyderabad, Hyderabad 500 046, India
| | | | | | | | | | | | | | | |
Collapse
|