1
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Naciri I, Andrade-Ludena MD, Yang Y, Kong M, Sun S. An emerging link between lncRNAs and cancer sex dimorphism. Hum Genet 2024; 143:831-842. [PMID: 38095719 PMCID: PMC11176266 DOI: 10.1007/s00439-023-02620-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 11/05/2023] [Indexed: 06/15/2024]
Abstract
The prevalence and progression of cancer differ in males and females, and thus, sexual dimorphism in tumor development directly impacts clinical research and medicine. Long non-coding RNAs (lncRNAs) are increasingly recognized as important players in gene expression and various cellular processes, including cancer development and progression. In recent years, lncRNAs have been implicated in the differences observed in cancer incidence, progression, and treatment responses between men and women. Here, we present a brief overview of the current knowledge regarding the role of lncRNAs in cancer sex dimorphism, focusing on how they affect epigenetic processes in male and female mammalian cells. We discuss the potential mechanisms by which lncRNAs may contribute to sex differences in cancer, including transcriptional control of sex chromosomes, hormonal signaling pathways, and immune responses. We also propose strategies for studying lncRNA functions in cancer sex dimorphism. Furthermore, we emphasize the importance of considering sex as a biological variable in cancer research and the need to investigate the role lncRNAs play in mediating these sex differences. In summary, we highlight the emerging link between lncRNAs and cancer sex dimorphism and their potential as therapeutic targets.
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Affiliation(s)
- Ikrame Naciri
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California Irvine, Irvine, CA, 92697, USA
| | - Maria D Andrade-Ludena
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California Irvine, Irvine, CA, 92697, USA
| | - Ying Yang
- Department of Molecular Biology and Biochemistry, School of Biological Sciences, University of California Irvine, Irvine, CA, 92697, USA
| | - Mei Kong
- Department of Molecular Biology and Biochemistry, School of Biological Sciences, University of California Irvine, Irvine, CA, 92697, USA.
| | - Sha Sun
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California Irvine, Irvine, CA, 92697, USA.
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2
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Wang C, Wang J, Wu X, Liu T, Wang F, Zhou H, Chen C, Shi L, Ma L, Liu T, Li C. Comprehensive review on sexual dimorphism to improve scalp acupuncture in nervous system disease. CNS Neurosci Ther 2024; 30:e14447. [PMID: 37665197 PMCID: PMC10805401 DOI: 10.1111/cns.14447] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 07/31/2023] [Accepted: 08/20/2023] [Indexed: 09/05/2023] Open
Abstract
BACKGROUND With the development of modern medicine, the Traditional Chinese Medicine (TCM) combined with western medicine began to be produced and applied. Scalp acupuncture (SA) as a Chinese medicine based on neurological theory, has a great advantage compared with TCM in the treatment of nervous system diseases. METHOD In this paper, we analyze the physiological and pathological manifestations of sexual dimorphism (SD) to illustrate the necessity of SD treatment. In addition, we review the factors that can affect SD and analyze in physiological structure, function, and pathological neurons. Diseases (pathological basis, pathological manifestations, and incidence) and factors leading to gender differences, which to analyze the possibility of gender differences in SA. RESULT Furthermore, we creatively a new insight of SD-SA and provide the complete SD treatment cases on the basis of the existing SA in different kinds of diseases including stroke, migraine, attention deficit hyperactivity disorder (ADHD), and depression. CONCLUSION In summary, we believe that it is feasible to improve the clinical effectiveness of SA, which is able to promote the development of SA, and then provides an actionable evidence for the promotion of precision medicine in the future.
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Affiliation(s)
- Chaojie Wang
- Department of First Clinical Medical CollegeHeilongjiang University of Chinese MedicineHeilongjiangChina
| | - Jiening Wang
- Department of RehabilitationShanghai Seventh People's Hospital Affiliated to Shanghai University of Traditional Chinese MedicineShanghaiChina
| | - Xubo Wu
- Department of RehabilitationShanghai Seventh People's Hospital Affiliated to Shanghai University of Traditional Chinese MedicineShanghaiChina
- School of Rehabilitation ScienceShanghai University of Traditional Chinese MedicineShanghaiChina
| | - Tao Liu
- Department of BioengineeringImperial College LondonLondonUK
| | - Feng Wang
- First Affiliated Hospital of Heilongjiang University of Chinese MedicineHarbinChina
| | - Huanxia Zhou
- Department of RehabilitationShanghai Seventh People's Hospital Affiliated to Shanghai University of Traditional Chinese MedicineShanghaiChina
| | - Chen Chen
- Second Affiliated Hospital of Heilongjiang University of Chinese MedicineHarbinChina
| | - Lijuan Shi
- School of Biological Science and Medical EngineeringBeihang UniversityBeijingChina
| | - Lin Ma
- First Affiliated Hospital of Heilongjiang University of Chinese MedicineHarbinChina
| | - Tiantian Liu
- Department of RehabilitationShanghai Seventh People's Hospital Affiliated to Shanghai University of Traditional Chinese MedicineShanghaiChina
| | - Cancheng Li
- School of Biological Science and Medical EngineeringBeihang UniversityBeijingChina
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3
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Hill MJ, Penning BW, McCann MC, Carpita NC. COMPILE: a GWAS computational pipeline for gene discovery in complex genomes. BMC PLANT BIOLOGY 2022; 22:315. [PMID: 35778686 PMCID: PMC9250234 DOI: 10.1186/s12870-022-03668-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Genome-Wide Association Studies (GWAS) are used to identify genes and alleles that contribute to quantitative traits in large and genetically diverse populations. However, traits with complex genetic architectures create an enormous computational load for discovery of candidate genes with acceptable statistical certainty. We developed a streamlined computational pipeline for GWAS (COMPILE) to accelerate identification and annotation of candidate maize genes associated with a quantitative trait, and then matches maize genes to their closest rice and Arabidopsis homologs by sequence similarity. RESULTS COMPILE executed GWAS using a Mixed Linear Model that incorporated, without compression, recent advancements in population structure control, then linked significant Quantitative Trait Loci (QTL) to candidate genes and RNA regulatory elements contained in any genome. COMPILE was validated using published data to identify QTL associated with the traits of α-tocopherol biosynthesis and flowering time, and identified published candidate genes as well as additional genes and non-coding RNAs. We then applied COMPILE to 274 genotypes of the maize Goodman Association Panel to identify candidate loci contributing to resistance of maize stems to penetration by larvae of the European Corn Borer (Ostrinia nubilalis). Candidate genes included those that encode a gene of unknown function, WRKY and MYB-like transcriptional factors, receptor-kinase signaling, riboflavin synthesis, nucleotide-sugar interconversion, and prolyl hydroxylation. Expression of the gene of unknown function has been associated with pathogen stress in maize and in rice homologs closest in sequence identity. CONCLUSIONS The relative speed of data analysis using COMPILE allowed comparison of population size and compression. Limitations in population size and diversity are major constraints for a trait and are not overcome by increasing marker density. COMPILE is customizable and is readily adaptable for application to species with robust genomic and proteome databases.
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Affiliation(s)
- Matthew J Hill
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, 47907, USA
- Present address: Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA, 02142, USA
- Present address: Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Bryan W Penning
- USDA-ARS Corn, Soybean and Wheat Quality Research Unit, Wooster, OH, 44691, USA
| | - Maureen C McCann
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, 47907, USA
- Present address: Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Nicholas C Carpita
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, 47907, USA.
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, 47907, USA.
- Present address: Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA.
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4
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Lentini A, Cheng H, Noble JC, Papanicolaou N, Coucoravas C, Andrews N, Deng Q, Enge M, Reinius B. Elastic dosage compensation by X-chromosome upregulation. Nat Commun 2022; 13:1854. [PMID: 35388014 PMCID: PMC8987076 DOI: 10.1038/s41467-022-29414-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 03/14/2022] [Indexed: 12/24/2022] Open
Abstract
X-chromosome inactivation and X-upregulation are the fundamental modes of chromosome-wide gene regulation that collectively achieve dosage compensation in mammals, but the regulatory link between the two remains elusive and the X-upregulation dynamics are unknown. Here, we use allele-resolved single-cell RNA-seq combined with chromatin accessibility profiling and finely dissect their separate effects on RNA levels during mouse development. Surprisingly, we uncover that X-upregulation elastically tunes expression dosage in a sex- and lineage-specific manner, and moreover along varying degrees of X-inactivation progression. Male blastomeres achieve X-upregulation upon zygotic genome activation while females experience two distinct waves of upregulation, upon imprinted and random X-inactivation; and ablation of Xist impedes female X-upregulation. Female cells carrying two active X chromosomes lack upregulation, yet their collective RNA output exceeds that of a single hyperactive allele. Importantly, this conflicts the conventional dosage compensation model in which naïve female cells are initially subject to biallelic X-upregulation followed by X-inactivation of one allele to correct the X dosage. Together, our study provides key insights to the chain of events of dosage compensation, explaining how transcript copy numbers can remain remarkably stable across developmental windows wherein severe dose imbalance would otherwise be experienced by the cell.
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Affiliation(s)
- Antonio Lentini
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Huaitao Cheng
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
| | - J C Noble
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Natali Papanicolaou
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Christos Coucoravas
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Nathanael Andrews
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Qiaolin Deng
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Martin Enge
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Björn Reinius
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
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Kawatake-Kuno A, Murai T, Uchida S. The Molecular Basis of Depression: Implications of Sex-Related Differences in Epigenetic Regulation. Front Mol Neurosci 2021; 14:708004. [PMID: 34276306 PMCID: PMC8282210 DOI: 10.3389/fnmol.2021.708004] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 06/14/2021] [Indexed: 12/22/2022] Open
Abstract
Major depressive disorder (MDD) is a leading cause of disability worldwide. Although the etiology and pathophysiology of MDD remain poorly understood, aberrant neuroplasticity mediated by the epigenetic dysregulation of gene expression within the brain, which may occur due to genetic and environmental factors, may increase the risk of this disorder. Evidence has also been reported for sex-related differences in the pathophysiology of MDD, with female patients showing a greater severity of symptoms, higher degree of functional impairment, and more atypical depressive symptoms. Males and females also differ in their responsiveness to antidepressants. These clinical findings suggest that sex-dependent molecular and neural mechanisms may underlie the development of depression and the actions of antidepressant medications. This review discusses recent advances regarding the role of epigenetics in stress and depression. The first section presents a brief introduction of the basic mechanisms of epigenetic regulation, including histone modifications, DNA methylation, and non-coding RNAs. The second section reviews their contributions to neural plasticity, the risk of depression, and resilience against depression, with a particular focus on epigenetic modulators that have causal relationships with stress and depression in both clinical and animal studies. The third section highlights studies exploring sex-dependent epigenetic alterations associated with susceptibility to stress and depression. Finally, we discuss future directions to understand the etiology and pathophysiology of MDD, which would contribute to optimized and personalized therapy.
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Affiliation(s)
- Ayako Kawatake-Kuno
- SK Project, Medical Innovation Center, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Toshiya Murai
- SK Project, Medical Innovation Center, Kyoto University Graduate School of Medicine, Kyoto, Japan.,Department of Psychiatry, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Shusaku Uchida
- SK Project, Medical Innovation Center, Kyoto University Graduate School of Medicine, Kyoto, Japan
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6
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RNA-seq Characterization of Sex-Differences in Adipose Tissue of Obesity Affected Patients: Computational Analysis of Differentially Expressed Coding and Non-Coding RNAs. J Pers Med 2021; 11:jpm11050352. [PMID: 33924951 PMCID: PMC8145808 DOI: 10.3390/jpm11050352] [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: 03/26/2021] [Revised: 04/23/2021] [Accepted: 04/26/2021] [Indexed: 02/07/2023] Open
Abstract
Obesity is a multifactorial disease presenting sex-related differences including adipocyte functions, sex hormone effects, genetics, and metabolic inflammation. These can influence individuals’ risk for metabolic dysfunctions, with an urgent need to perform sex-based analysis to improve prevention, treatment, and rehabilitation programs. This research work is aimed at characterizing the transcriptional differences present in subcutaneous adipose tissue (SAT) of five obesity affected men versus five obesity affected women, with an additional focus on the role of long non-coding RNAs. Through RNA-sequencing, we highlighted the presence of both coding and non-coding differentially expressed RNAs, and with numerous computational analyses we identified the processes in which these genes are implicated, along with their role in co-morbidities development. We report 51 differentially expressed transcripts, 32 of which were coding genes and 19 were non-coding. Using the WGCNA R package (Weighted Correlation Network Analysis, version 1.70-3), we describe the interactions between coding and non-coding RNAs, and the non-coding RNAs association with the insurgence of specific diseases, such as cancer development, neurodegenerative diseases, and schizophrenia. In conclusion, our work highlights a specific gender sex-related transcriptional signature in the SAT of obesity affected patients.
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7
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Sas-Nowosielska H, Magalska A. Long Noncoding RNAs-Crucial Players Organizing the Landscape of the Neuronal Nucleus. Int J Mol Sci 2021; 22:ijms22073478. [PMID: 33801737 PMCID: PMC8037058 DOI: 10.3390/ijms22073478] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/22/2021] [Accepted: 03/24/2021] [Indexed: 12/25/2022] Open
Abstract
The ability to regulate chromatin organization is particularly important in neurons, which dynamically respond to external stimuli. Accumulating evidence shows that lncRNAs play important architectural roles in organizing different nuclear domains like inactive chromosome X, splicing speckles, paraspeckles, and Gomafu nuclear bodies. LncRNAs are abundantly expressed in the nervous system where they may play important roles in compartmentalization of the cell nucleus. In this review we will describe the architectural role of lncRNAs in the nuclei of neuronal cells.
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8
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Fels JA, Casalena GA, Manfredi G. Sex and oestrogen receptor β have modest effects on gene expression in the mouse brain posterior cortex. Endocrinol Diabetes Metab 2021; 4:e00191. [PMID: 33532622 PMCID: PMC7831211 DOI: 10.1002/edm2.191] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 09/12/2020] [Accepted: 09/21/2020] [Indexed: 12/19/2022] Open
Abstract
Introduction Sex differences in brain cortical function affect cognition, behaviour and susceptibility to neural diseases, but the molecular basis of sexual dimorphism in cortical function is still largely unknown. Oestrogen and oestrogen receptors (ERs), specifically ERβ, the most abundant ER in the cortex, may play a role in determining sex differences in gene expression, which could underlie functional sex differences. However, further investigation is needed to address brain region specificity of the effects of sex and ERβ on gene expression. The goal of this study was to investigate sex differences in gene expression in the mouse posterior cortex, where sex differences in transcription have never been examined, and to determine how genetic ablation of ERβ affects transcription. Methods In this study, we performed unbiased transcriptomics on RNA from the posterior cortex of adult wild-type and ERβ knockout mice (n = 4/sex/genotype). We used unbiased clustering to analyse whole-transcriptome changes between the groups. We also performed differential expression analysis on the data using DESeq2 to identify specific changes in gene expression. Results We found only 27 significantly differentially expressed genes (DEGs) in wild-type (WT) males vs females, of which 17 were autosomal genes. Interestingly, in ERβKO males vs females all the autosomal DEGs were lost. Gene Ontology analysis of the subset of DEGs with sex differences only in the WT cortex revealed a significant enrichment of genes annotated with the function 'cation channel activity'. Moreover, within each sex we found only a few DEGs in ERβKO vs WT mice (8 and 5 in males and females, respectively). Conclusions Overall, our results suggest that in the adult mouse posterior cortex there are surprisingly few sex differences in gene expression, and those that exist are mainly related to cation channel activity. Additionally, they indicate that brain region-specific functional effects of ERβ may be largely post-transcriptional.
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Affiliation(s)
- Jasmine A. Fels
- Feil Family Brain and Mind Research InstituteWeill Cornell MedicineNew YorkNYUSA
| | | | - Giovanni Manfredi
- Feil Family Brain and Mind Research InstituteWeill Cornell MedicineNew YorkNYUSA
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9
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GWAS of Post-Orthodontic Aggressive External Apical Root Resorption Identified Multiple Putative Loci at X-Y Chromosomes. J Pers Med 2020; 10:jpm10040169. [PMID: 33066413 PMCID: PMC7712155 DOI: 10.3390/jpm10040169] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 10/06/2020] [Accepted: 10/12/2020] [Indexed: 12/23/2022] Open
Abstract
Personalized dental medicine requires from precise and customized genomic diagnostic. To conduct an association analysis over multiple putative loci and genes located at chromosomes 2, 4, 8, 12, 18, X, and Y, potentially implicated in an extreme type of external apical root resorption secondary to orthodontic forces (aEARR). A genome-wide association study of aEARR was conducted with 480 patients [ratio~1:3 case/control]. Genomic DNA was extracted and analyzed using the high-throughput Axiom platform with the GeneTitan® MC Instrument. Up to 14,377 single nucleotide polymorphisms (SNPs) were selected at candidate regions and clinical/diagnostic data were recorded. A descriptive analysis of the data along with a backward conditional binary logistic regression was used to calculate odds ratios, with 95% confidence intervals [p < 0.05]. To select the best SNP candidates, a logistic regression model was fitted assuming a log-additive genetic model using R software [p < 0.0001]. In this sample the top lead genetic variants associated with aEARR were two novel putative genes located in the X chromosome, specifically, STAG 2 gene, rs151184635 and RP1-30E17.2 gene, rs55839915. These variants were found to be associated with an increased risk of aEARR, particularly restricted to men [OR: 6.09; 95%CI: 2.6–14.23 and OR: 6.86; 95%CI: 2.65–17.81, respectively]. Marginal associations were found at previously studied variants such as SSP1: rs11730582 [OR: 0.54; 95%CI: 0.34–0.86; p = 0.008], P2RX7: rs1718119 [OR: 0.6; 95%CI: 0.36–1.01; p = 0.047], and TNFRSF11A: rs8086340 [OR: 0.6; 95%CI: 0.38–0.95; p = 0.024]), found solely in females. Multiple putative genetic variants located at chromosomes X and Y are potentially implicated in an extreme phenotype of aEARR. A gender-linked association was noted.
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10
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Liu X, Zhu Y, Wang Y, Li W, Hong X, Zhu X, Xu H. Comparative transcriptome analysis reveals the sexual dimorphic expression profiles of mRNAs and non-coding RNAs in the Asian yellow pond turtle (Meauremys mutica). Gene 2020; 750:144756. [DOI: 10.1016/j.gene.2020.144756] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 04/30/2020] [Accepted: 05/05/2020] [Indexed: 02/07/2023]
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11
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Issler O, van der Zee YY, Ramakrishnan A, Wang J, Tan C, Loh YHE, Purushothaman I, Walker DM, Lorsch ZS, Hamilton PJ, Peña CJ, Flaherty E, Hartley BJ, Torres-Berrío A, Parise EM, Kronman H, Duffy JE, Estill MS, Calipari ES, Labonté B, Neve RL, Tamminga CA, Brennand KJ, Dong Y, Shen L, Nestler EJ. Sex-Specific Role for the Long Non-coding RNA LINC00473 in Depression. Neuron 2020; 106:912-926.e5. [PMID: 32304628 PMCID: PMC7305959 DOI: 10.1016/j.neuron.2020.03.023] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 01/27/2020] [Accepted: 03/23/2020] [Indexed: 12/26/2022]
Abstract
Depression is a common disorder that affects women at twice the rate of men. Here, we report that long non-coding RNAs (lncRNAs), a recently discovered class of regulatory transcripts, represent about one-third of the differentially expressed genes in the brains of depressed humans and display complex region- and sex-specific patterns of regulation. We identified the primate-specific, neuronal-enriched gene LINC00473 as downregulated in prefrontal cortex (PFC) of depressed females but not males. Using viral-mediated gene transfer to express LINC00473 in adult mouse PFC neurons, we mirrored the human sex-specific phenotype by inducing stress resilience solely in female mice. This sex-specific phenotype was accompanied by changes in synaptic function and gene expression selectively in female mice and, along with studies of human neuron-like cells in culture, implicates LINC00473 as a CREB effector. Together, our studies identify LINC00473 as a female-specific driver of stress resilience that is aberrant in female depression.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Animals
- Behavior, Animal
- Depression/genetics
- Depression/metabolism
- Depressive Disorder, Major/genetics
- Depressive Disorder, Major/metabolism
- Down-Regulation
- Female
- Humans
- Male
- Mice
- Mice, Transgenic
- Middle Aged
- Neurons/metabolism
- Prefrontal Cortex/metabolism
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- RNA-Seq
- Resilience, Psychological
- Sex Factors
- Stress, Psychological/genetics
- Stress, Psychological/metabolism
- Young Adult
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Affiliation(s)
- Orna Issler
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yentl Y van der Zee
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; School for Mental Health and Neuroscience, Department of Psychiatry and Neuropsychology, Maastricht University, 6229 ER, Maastricht, the Netherlands
| | - Aarthi Ramakrishnan
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Junshi Wang
- Department of Neuroscience, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Chunfeng Tan
- Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yong-Hwee E Loh
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Immanuel Purushothaman
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Deena M Walker
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Zachary S Lorsch
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Peter J Hamilton
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Catherine J Peña
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Erin Flaherty
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Brigham J Hartley
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Angélica Torres-Berrío
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Eric M Parise
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Hope Kronman
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Julia E Duffy
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Molly S Estill
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Erin S Calipari
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Benoit Labonté
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Rachael L Neve
- Gene Delivery Technology Core, Massachusetts General Hospital, Cambridge, MA 02139, USA
| | - Carol A Tamminga
- Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kristen J Brennand
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yan Dong
- Department of Neuroscience, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Li Shen
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Eric J Nestler
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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12
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Rubin JB, Lagas JS, Broestl L, Sponagel J, Rockwell N, Rhee G, Rosen SF, Chen S, Klein RS, Imoukhuede P, Luo J. Sex differences in cancer mechanisms. Biol Sex Differ 2020; 11:17. [PMID: 32295632 PMCID: PMC7161126 DOI: 10.1186/s13293-020-00291-x] [Citation(s) in RCA: 149] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 03/18/2020] [Indexed: 02/07/2023] Open
Abstract
We now know that cancer is many different diseases, with great variation even within a single histological subtype. With the current emphasis on developing personalized approaches to cancer treatment, it is astonishing that we have not yet systematically incorporated the biology of sex differences into our paradigms for laboratory and clinical cancer research. While some sex differences in cancer arise through the actions of circulating sex hormones, other sex differences are independent of estrogen, testosterone, or progesterone levels. Instead, these differences are the result of sexual differentiation, a process that involves genetic and epigenetic mechanisms, in addition to acute sex hormone actions. Sexual differentiation begins with fertilization and continues beyond menopause. It affects virtually every body system, resulting in marked sex differences in such areas as growth, lifespan, metabolism, and immunity, all of which can impact on cancer progression, treatment response, and survival. These organismal level differences have correlates at the cellular level, and thus, males and females can fundamentally differ in their protections and vulnerabilities to cancer, from cellular transformation through all stages of progression, spread, and response to treatment. Our goal in this review is to cover some of the robust sex differences that exist in core cancer pathways and to make the case for inclusion of sex as a biological variable in all laboratory and clinical cancer research. We finish with a discussion of lab- and clinic-based experimental design that should be used when testing whether sex matters and the appropriate statistical models to apply in data analysis for rigorous evaluations of potential sex effects. It is our goal to facilitate the evaluation of sex differences in cancer in order to improve outcomes for all patients.
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Affiliation(s)
- Joshua B Rubin
- Department of Pediatrics, Washington University School of Medicine, 660 South Euclid Avenue, St Louis, MO, 63110, USA.
- Department of Neuroscience, Washington University School of Medicine, 660 South Euclid Avenue, St Louis, MO, 63110, USA.
| | - Joseph S Lagas
- Department of Pediatrics, Washington University School of Medicine, 660 South Euclid Avenue, St Louis, MO, 63110, USA
| | - Lauren Broestl
- Department of Pediatrics, Washington University School of Medicine, 660 South Euclid Avenue, St Louis, MO, 63110, USA
| | - Jasmin Sponagel
- Department of Pediatrics, Washington University School of Medicine, 660 South Euclid Avenue, St Louis, MO, 63110, USA
| | - Nathan Rockwell
- Department of Pediatrics, Washington University School of Medicine, 660 South Euclid Avenue, St Louis, MO, 63110, USA
| | - Gina Rhee
- Department of Pediatrics, Washington University School of Medicine, 660 South Euclid Avenue, St Louis, MO, 63110, USA
| | - Sarah F Rosen
- Department of Medicine, Washington University School of Medicine, 660 South Euclid Avenue, St Louis, MO, 63110, USA
| | - Si Chen
- Department of Biomedical Engineering, Washington University School of Medicine, 660 South Euclid Avenue, St Louis, MO, 63110, USA
| | - Robyn S Klein
- Department of Neuroscience, Washington University School of Medicine, 660 South Euclid Avenue, St Louis, MO, 63110, USA
- Department of Medicine, Washington University School of Medicine, 660 South Euclid Avenue, St Louis, MO, 63110, USA
| | - Princess Imoukhuede
- Department of Biomedical Engineering, Washington University School of Medicine, 660 South Euclid Avenue, St Louis, MO, 63110, USA
| | - Jingqin Luo
- Department of Surgery, Washington University School of Medicine, 660 South Euclid Avenue, St Louis, MO, 63110, USA
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13
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The importance of long non-coding RNAs in neuropsychiatric disorders. Mol Aspects Med 2019; 70:127-140. [DOI: 10.1016/j.mam.2019.07.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 06/10/2019] [Accepted: 07/14/2019] [Indexed: 12/20/2022]
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14
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Wan ZY, Lin G, Yue G. Genes for sexual body size dimorphism in hybrid tilapia (Oreochromis sp. x Oreochromis mossambicus). AQUACULTURE AND FISHERIES 2019. [DOI: 10.1016/j.aaf.2019.05.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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15
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Fang H, Disteche CM, Berletch JB. X Inactivation and Escape: Epigenetic and Structural Features. Front Cell Dev Biol 2019; 7:219. [PMID: 31632970 PMCID: PMC6779695 DOI: 10.3389/fcell.2019.00219] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 09/18/2019] [Indexed: 12/27/2022] Open
Abstract
X inactivation represents a complex multi-layer epigenetic mechanism that profoundly modifies chromatin composition and structure of one X chromosome in females. The heterochromatic inactive X chromosome adopts a unique 3D bipartite structure and a location close to the nuclear periphery or the nucleolus. X-linked lncRNA loci and their transcripts play important roles in the recruitment of proteins that catalyze chromatin and DNA modifications for silencing, as well as in the control of chromatin condensation and location of the inactive X chromosome. A subset of genes escapes X inactivation, raising questions about mechanisms that preserve their expression despite being embedded within heterochromatin. Escape gene expression differs between males and females, which can lead to physiological sex differences. We review recent studies that emphasize challenges in understanding the role of lncRNAs in the control of epigenetic modifications, structural features and nuclear positioning of the inactive X chromosome. Second, we highlight new findings about the distribution of genes that escape X inactivation based on single cell studies, and discuss the roles of escape genes in eliciting sex differences in health and disease.
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Affiliation(s)
- He Fang
- Department of Pathology, University of Washington, Seattle, WA, United States
| | - Christine M. Disteche
- Department of Pathology, University of Washington, Seattle, WA, United States
- Department of Medicine, University of Washington, Seattle, WA, United States
| | - Joel B. Berletch
- Department of Pathology, University of Washington, Seattle, WA, United States
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16
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Johansson MM, Pottmeier P, Suciu P, Ahmad T, Zaghlool A, Halvardson J, Darj E, Feuk L, Peuckert C, Jazin E. Novel Y-Chromosome Long Non-Coding RNAs Expressed in Human Male CNS During Early Development. Front Genet 2019; 10:891. [PMID: 31608120 PMCID: PMC6769107 DOI: 10.3389/fgene.2019.00891] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 08/23/2019] [Indexed: 01/01/2023] Open
Abstract
Global microarray gene expression analyses previously demonstrated differences in female and male embryos during neurodevelopment. In particular, before sexual maturation of the gonads, the differences seem to concentrate on the expression of genes encoded on the X- and Y-chromosomes. To investigate genome-wide differences in expression during this early developmental window, we combined high-resolution RNA sequencing with qPCR to analyze brain samples from human embryos during the first trimester of development. Our analysis was tailored for maximum sensitivity to discover Y-chromosome gene expression, but at the same time, it was underpowered to detect X-inactivation escapees. Using this approach, we found that 5 out of 13 expressed gametolog pairs showed unbalanced gene dosage, and as a consequence, a male-biased expression. In addition, we found six novel non-annotated long non-coding RNAs on the Y-chromosome with conserved expression patterns in newborn chimpanzee. The tissue specific and time-restricted expression of these long non-coding RNAs strongly suggests important functions during central nervous system development in human males.
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Affiliation(s)
- Martin M Johansson
- Department of Organismal Biology, EBC, Uppsala University, Uppsala, Sweden
| | - Philipp Pottmeier
- Department of Organismal Biology, EBC, Uppsala University, Uppsala, Sweden
| | - Pascalina Suciu
- Department of Organismal Biology, EBC, Uppsala University, Uppsala, Sweden
| | - Tauseef Ahmad
- Department of Organismal Biology, EBC, Uppsala University, Uppsala, Sweden
| | - Ammar Zaghlool
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jonatan Halvardson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Elisabeth Darj
- Department of Women's and Children's Health, International Maternal and Child Health (IMCH), Uppsala University, Uppsala, Sweden.,Department of Public Health and General Practice, Norwegian University of Science and Technology, Trondheim, Norway
| | - Lars Feuk
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Christiane Peuckert
- Department of Organismal Biology, EBC, Uppsala University, Uppsala, Sweden.,Department of Molecular Biology, Stockholms University, Stockholm, Sweden
| | - Elena Jazin
- Department of Organismal Biology, EBC, Uppsala University, Uppsala, Sweden
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17
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Lalem T, Devaux Y. Circulating microRNAs to predict heart failure after acute myocardial infarction in women. Clin Biochem 2019; 70:1-7. [DOI: 10.1016/j.clinbiochem.2019.05.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 05/22/2019] [Accepted: 05/23/2019] [Indexed: 12/31/2022]
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18
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Ruan Z, Xu Z, Li Z, Lv Y. Integral analyses of survival-related long non-coding RNA MIR210HG and its prognostic role in colon cancer. Oncol Lett 2019; 18:1107-1116. [PMID: 31423171 PMCID: PMC6607050 DOI: 10.3892/ol.2019.10435] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 04/15/2019] [Indexed: 12/27/2022] Open
Abstract
Colon cancer is the third most common cancer worldwide, and lymphatic metastasis is one of the principal factors affecting patient prognosis. Recent studies have revealed that long non-coding RNAs (lncRNAs) serve as important regulators in the pathogenesis of colon cancer, therefore affecting patient survival rates. In the present study, colon cancer-associated lncRNAs were screened based on their influence on patient survival. A number of survival-associated lncRNAs (and their potential mechanisms of action) were identified, with the strongest candidate being MIR210HG. Gene expression correlation and protein-protein interaction (PPI) network analyses were performed to identify MIR210HG-associated genes. Various bioinformatics analyses (including gene ontology and Kyoto Encyclopedia of Genes and Genomes analyses) were conducted to investigate the prognostic role of MIR210HG and its associated genes, in colon cancer. Higher expression levels of MIR210HG were associated with shorter overall survival in patients with colon cancer, which was significant in 373 candidates. Multiple findings indicated that MIR210HG may exert its effects in colon cancer through the modulation of energy metabolism and cell adhesion. Further predictions suggested that MIR210HG may affect colon cancer via transcription and post-transcriptional processing. Collectively, these results provided evidence of a transcriptional regulatory network of MIR210HG in colon cancer, and suggested its potential role as a novel biomarker and therapeutic target for colon cancer.
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Affiliation(s)
- Zhaohui Ruan
- Pharmacy Department, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Zixuan Xu
- Pharmacy Department, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Zhaozhi Li
- Key Laboratory of Bio-resources and Eco-environment, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610000, P.R. China
| | - Yanni Lv
- Pharmacy Department, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
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19
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TAFAZOLI A, BEHJATI F, FARHUD DD, ABBASZADEGAN MR. Combination of Genetics and Nanotechnology for Down Syndrome Modification: A Potential Hypothesis and Review of the Literature. IRANIAN JOURNAL OF PUBLIC HEALTH 2019; 48:371-378. [PMID: 31223563 PMCID: PMC6570805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Down syndrome (DS) is one of the most prevalent genetic disorders in humans. The use of new approaches in genetic engineering and nanotechnology methods in combination with natural cellular phenomenon can modify the disease in affected people. We consider two CRISPR/Cas9 systems to cut a specific region from short arm of the chromosome 21 (Chr21) and replace it with a novel designed DNA construct, containing the essential genes in chromatin remodeling for inactivating of an extra Chr21. This requires mimicking of the natural cellular pattern for inactivation of the extra X chromosome in females. By means of controlled dosage of an appropriate Nano-carrier (a surface engineered Poly D, L-lactide-co-glycolide (PLGA) for integrating the relevant construct in Trisomy21 brain cell culture media and then in DS mouse model, we would be able to evaluate the modification and the reduction of the active extra Chr21 and in turn reduce substantial adverse effects of the disease, like intellectual disabilities. The hypothesis and study seek new insights in Down syndrome modification.
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Affiliation(s)
- Alireza TAFAZOLI
- Department of Analysis and Bioanalysis of Medicine, Faculty of Pharmacy with the Division of Laboratory Medicine, Medical University of Bialystok, Bialystok, Poland, Department of Endocrinology, Diabetology and Internal Medicine, Clinical Research Center, Medical University of Bialystok, Bialystok, Poland
| | - Farkhondeh BEHJATI
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Dariush D. FARHUD
- School of Public Health, Tehran University of Medical Sciences, Tehran, Iran, Department of Basic Sciences, Iranian Academy of Medical Sciences, Tehran, Iran
| | - Mohammad Reza ABBASZADEGAN
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran,Corresponding Author:
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20
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Exploring the involvement of Tac2 in the mouse hippocampal stress response through gene networking. Gene 2019; 696:176-185. [PMID: 30769143 DOI: 10.1016/j.gene.2019.02.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 01/05/2019] [Accepted: 02/01/2019] [Indexed: 01/15/2023]
Abstract
Tachykinin 2 (Tac2) is expressed in a number of areas throughout the brain, including the hippocampus. However, knowledge about its function has been only well explored in the hypothalamus in the context of reproductive health. In this study, we identified and validated increased hippocampal Tac2 mRNA expression in response to chronic mild stress in mice. Expression quantitative trait locus (eQTL) analysis showed Tac2 is cis-regulated in the hippocampus. Using a systems genetics approach, we constructed a Tac2 co-expression network to better understand the relationship between Tac2 and the hippocampal stress response. Our network identified 69 total genes associated with Tac2, several of which encode major neuropeptides involved in hippocampal stress signaling as well as critical genes for producing neural plasticity, indicating that Tac2 is involved in these processes. Pathway analysis for the member of Tac2 gene network revealed a strong connection between Tac2 and neuroactive ligand-receptor interaction, calcium signaling pathway, as well as cardiac muscle contraction. In addition, we also identified 46 stress-related phenotypes, specifically fear conditioning response, that were significantly correlated with Tac2 expression. Our results provide evidence for Tac2 as a strong candidate gene who likely plays a role in hippocampal stress processing and neural plasticity.
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21
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Peeters SB, Korecki AJ, Simpson EM, Brown CJ. Human cis-acting elements regulating escape from X-chromosome inactivation function in mouse. Hum Mol Genet 2019; 27:1252-1262. [PMID: 29401310 PMCID: PMC6159535 DOI: 10.1093/hmg/ddy039] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 01/29/2018] [Indexed: 12/18/2022] Open
Abstract
A long-standing question concerning X-chromosome inactivation (XCI) has been how some genes avoid the otherwise stable chromosome-wide heterochromatinization of the inactive X chromosome. As 20% or more of human X-linked genes escape from inactivation, such genes are an important contributor to sex differences in gene expression. Although both human and mouse have genes that escape from XCI, more genes escape in humans than mice, with human escape genes often clustering in larger domains than the single escape genes of mouse. Mouse models offer a well-characterized and readily manipulated system in which to study XCI, but given the differences in genes that escape it is unclear whether the mechanism of escape gene regulation is conserved. To address conservation of the process and the potential to identify elements by modelling human escape gene regulation using mouse, we integrated a human and a mouse BAC each containing an escape gene and flanking subject genes at the mouse X-linked Hprt gene. Escape-level expression and corresponding low promoter DNA methylation of human genes RPS4X and CITED1 demonstrated that the mouse system is capable of recognizing human elements and therefore can be used as a model for further refinement of critical elements necessary for escape from XCI in humans.
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Affiliation(s)
- Samantha B Peeters
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Andrea J Korecki
- Centre for Molecular Medicine and Therapeutics at British Columbia Children's Hospital, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Elizabeth M Simpson
- Centre for Molecular Medicine and Therapeutics at British Columbia Children's Hospital, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Carolyn J Brown
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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22
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Skakkebæk A, Nielsen MM, Trolle C, Vang S, Hornshøj H, Hedegaard J, Wallentin M, Bojesen A, Hertz JM, Fedder J, Østergaard JR, Pedersen JS, Gravholt CH. DNA hypermethylation and differential gene expression associated with Klinefelter syndrome. Sci Rep 2018; 8:13740. [PMID: 30213969 PMCID: PMC6137224 DOI: 10.1038/s41598-018-31780-0] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 08/22/2018] [Indexed: 12/20/2022] Open
Abstract
Klinefelter syndrome (KS) has a prevalence ranging from 85 to 250 per 100.000 newborn boys making it the most frequent sex chromosome aneuploidy in the general population. The molecular basis for the phenotypic traits and morbidity in KS are not clarified. We performed genome-wide DNA methylation profiling of leucocytes from peripheral blood samples from 67 KS patients, 67 male controls and 33 female controls, in addition to genome-wide RNA-sequencing profiling in a subset of 9 KS patients, 9 control males and 13 female controls. Characterization of the methylome as well as the transcriptome of both coding and non-coding genes identified a unique epigenetic and genetic landscape of both autosomal chromosomes as well as the X chromosome in KS. A subset of genes show significant correlation between methylation values and expression values. Gene set enrichment analysis of differentially methylated positions yielded terms associated with well-known comorbidities seen in KS. In addition, differentially expressed genes revealed enrichment for genes involved in the immune system, wnt-signaling pathway and neuron development. Based on our data we point towards new candidate genes, which may be implicated in the phenotype and further point towards non-coding genes, which may be involved in X chromosome inactivation in KS.
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Affiliation(s)
- Anne Skakkebæk
- Department of Endocrinology and Internal Medicine and Medical Research Laboratories, Aarhus University Hospital, 8000, Aarhus, Denmark. .,Department of Clinical Genetics, Aarhus University Hospital, 8200, Aarhus N, Denmark. .,Department of Molecular Medicine, Aarhus University Hospital, 8200, Aarhus N, Denmark.
| | - Morten Muhlig Nielsen
- Department of Molecular Medicine, Aarhus University Hospital, 8200, Aarhus N, Denmark
| | - Christian Trolle
- Department of Endocrinology and Internal Medicine and Medical Research Laboratories, Aarhus University Hospital, 8000, Aarhus, Denmark
| | - Søren Vang
- Department of Molecular Medicine, Aarhus University Hospital, 8200, Aarhus N, Denmark
| | - Henrik Hornshøj
- Department of Molecular Medicine, Aarhus University Hospital, 8200, Aarhus N, Denmark
| | - Jakob Hedegaard
- Department of Molecular Medicine, Aarhus University Hospital, 8200, Aarhus N, Denmark
| | - Mikkel Wallentin
- Center of Functionally Integrative Neuroscience, Aarhus University Hospital, 8000, Aarhus, Denmark.,Center for Semiotics, Aarhus University, 8000, Aarhus, Denmark
| | - Anders Bojesen
- Department of Clinical Genetics, Aarhus University Hospital, 8200, Aarhus N, Denmark
| | - Jens Michael Hertz
- Department of Clinical Genetics, Odense University Hospital, 5000, Odense, Denmark
| | - Jens Fedder
- Centre of Andrology and Fertility Clinic, Odense University Hospital, 5000, Odense, Denmark
| | - John Rosendahl Østergaard
- Centre for Rare Diseases, Department of Pediatrics, Aarhus University Hospital, 8200, Aarhus N, Denmark
| | - Jakob Skou Pedersen
- Department of Molecular Medicine, Aarhus University Hospital, 8200, Aarhus N, Denmark.,Bioinformatics Research Centre, Aarhus University, 8200, Aarhus N, Denmark
| | - Claus Højbjerg Gravholt
- Department of Endocrinology and Internal Medicine and Medical Research Laboratories, Aarhus University Hospital, 8000, Aarhus, Denmark.,Department of Molecular Medicine, Aarhus University Hospital, 8200, Aarhus N, Denmark
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23
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Tsimis ME, Lei J, Rosenzweig JM, Arif H, Shabi Y, Alshehri W, Talbot CC, Baig-Ward KM, Segars J, Graham EM, Burd I. P2X7 receptor blockade prevents preterm birth and perinatal brain injury in a mouse model of intrauterine inflammation. Biol Reprod 2018; 97:230-239. [PMID: 29044426 DOI: 10.1093/biolre/iox081] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 07/25/2017] [Indexed: 01/02/2023] Open
Abstract
The P2X7 is an adenosine triphosphate (ATP)-gated ion channel involved in several facets of immune activation and neuronal function through its importance in interleukin (IL)-1β secretion. We hypothesized that blockade of P2X7 would prevent perinatal brain injury associated with exposure to intrauterine (IU) inflammation. Dams received 45 mg/kg of Brilliant Blue G (BBG), a specific P2X7 receptor (P2X7R) antagonist, on gestation day 17 (E17) prior to administration of lipopolysaccharide (LPS) or phosphate-buffered saline (PBS). Furthermore, we utilized embryo transfer experiments to delineate whether the P2X7 was the key mediator of IU inflammation-associated brain injury on maternal or fetal sides. In these experiments, P2X7-/- dams were embryo-transferred wild type embryos and wild type dams were embryo-transferred P2X7-/- embryos. In the mouse model of intrauterine inflammation, pharmacologic blockade of P2X7R reduced preterm birth rate, improved offspring performance on neuromotor tests as well as the dendritic arborization and density of cortical neurons. Embryo transfer experiments demonstrated the importance of maternal P2X7R in IU inflammation-mediated effects on offspring. Both genetic and pharmacologic blockade of IL-1β signaling, by targeting maternal P2X7R, ameliorated perinatal brain injury following exposure to IU inflammation. Specific targeting of maternal P2X7R may provide a clinically useful tool to prevent both preterm birth and prematurity-associated perinatal brain injury, and further studies are urgently needed.
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Affiliation(s)
- Michael E Tsimis
- Department of Gynecology and Obstetrics, Division of Maternal-Fetal Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Integrated Research Center for Fetal Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jun Lei
- Department of Gynecology and Obstetrics, Division of Maternal-Fetal Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Integrated Research Center for Fetal Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jason M Rosenzweig
- Department of Gynecology and Obstetrics, Division of Maternal-Fetal Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Integrated Research Center for Fetal Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hattan Arif
- Department of Gynecology and Obstetrics, Division of Maternal-Fetal Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Integrated Research Center for Fetal Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Yahya Shabi
- Department of Gynecology and Obstetrics, Division of Maternal-Fetal Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Integrated Research Center for Fetal Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Wael Alshehri
- Department of Gynecology and Obstetrics, Division of Maternal-Fetal Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Integrated Research Center for Fetal Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Connie C Talbot
- Integrated Research Center for Fetal Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - K Maravet Baig-Ward
- Department of Gynecology and Obstetrics, Division of Reproductive Science and Women's Health Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - James Segars
- Department of Gynecology and Obstetrics, Division of Reproductive Science and Women's Health Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ernest M Graham
- Department of Gynecology and Obstetrics, Division of Maternal-Fetal Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Neuroscience Intensive Care Nursery Program, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Irina Burd
- Department of Gynecology and Obstetrics, Division of Maternal-Fetal Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Integrated Research Center for Fetal Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Neuroscience Intensive Care Nursery Program, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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24
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Printzlau F, Wolstencroft J, Skuse DH. Cognitive, behavioral, and neural consequences of sex chromosome aneuploidy. J Neurosci Res 2017; 95:311-319. [PMID: 27870409 DOI: 10.1002/jnr.23951] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 08/25/2016] [Accepted: 09/06/2016] [Indexed: 02/04/2023]
Abstract
The X chromosome has played a critical role in the development of sexually selected characteristics for over 300 million years, and during that time it has accumulated a disproportionate number of genes concerned with mental functions. There are relatively specific effects of X-linked genes on social cognition, language, emotional regulation, visuospatial, and numerical skills. Many human X-linked genes outside the X-Y pairing pseudoautosomal regions escape X-inactivation. Dosage differences in the expression of such genes (which constitute at least 15% of the total) are likely to play an important role in male-female neural differentiation, and in cognitive deficits and behavioral characteristics, particularly in the realm of social communication, that are associated with sex chromosome aneuploidies. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Frida Printzlau
- Great Ormond Street Hospital Institute of Child Health, University College London, United Kingdom
| | - Jeanne Wolstencroft
- Great Ormond Street Hospital Institute of Child Health, University College London, United Kingdom
| | - David H Skuse
- Great Ormond Street Hospital Institute of Child Health, University College London, United Kingdom
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25
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Arnold AP. A general theory of sexual differentiation. J Neurosci Res 2017; 95:291-300. [PMID: 27870435 DOI: 10.1002/jnr.23884] [Citation(s) in RCA: 155] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 07/13/2016] [Accepted: 07/25/2016] [Indexed: 12/16/2022]
Abstract
A general theory of mammalian sexual differentiation is proposed. All biological sex differences are the result of the inequality in effects of the sex chromosomes, which are the only factors that differ in XX vs. XY zygotes. This inequality leads to male-specific effects of the Y chromosome, including expression of the testis-determining gene Sry that causes differentiation of testes. Thus, Sry sets up lifelong sex differences in effects of gonadal hormones. Y genes also act outside of the gonads to cause male-specific effects. Differences in the number of X chromosomes between XX and XY cells cause sex differences in expression (1) of Xist, (2) of X genes that escape inactivation, and (3) of parentally imprinted X genes. Sex differences in phenotype are ultimately the result of multiple, independent sex-biasing factors, hormonal and sex chromosomal. These factors act in parallel and in combination to induce sex differences. They also can offset each other to reduce sex differences. Other mechanisms, operating at the level of populations, cause groups of males to differ on average from groups of females. The theory frames questions for further study, and directs attention to inherent sex-biasing factors that operate in many tissues to cause sex differences, and to cause sex-biased protection from disease. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Arthur P Arnold
- Department of Integrative Biology & Physiology, and Laboratory of Neuroendocrinology of the Brain Research Institute, University of California, Los Angeles, Los Angeles, California
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26
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Carrel L, Brown CJ. When the Lyon(ized chromosome) roars: ongoing expression from an inactive X chromosome. Philos Trans R Soc Lond B Biol Sci 2017; 372:20160355. [PMID: 28947654 PMCID: PMC5627157 DOI: 10.1098/rstb.2016.0355] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/24/2017] [Indexed: 12/21/2022] Open
Abstract
A tribute to Mary Lyon was held in October 2016. Many remarked about Lyon's foresight regarding many intricacies of the X-chromosome inactivation process. One such example is that a year after her original 1961 hypothesis she proposed that genes with Y homologues should escape from X inactivation to achieve dosage compensation between males and females. Fifty-five years later we have learned many details about these escapees that we attempt to summarize in this review, with a particular focus on recent findings. We now know that escapees are not rare, particularly on the human X, and that most lack functionally equivalent Y homologues, leading to their increasingly recognized role in sexually dimorphic traits. Newer sequencing technologies have expanded profiling of primary tissues that will better enable connections to sex-biased disorders as well as provide additional insights into the X-inactivation process. Chromosome organization, nuclear location and chromatin environments distinguish escapees from other X-inactivated genes. Nevertheless, several big questions remain, including what dictates their distinct epigenetic environment, the underlying basis of species differences in escapee regulation, how different classes of escapees are distinguished, and the roles that local sequences and chromosome ultrastructure play in escapee regulation.This article is part of the themed issue 'X-chromosome inactivation: a tribute to Mary Lyon'.
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Affiliation(s)
- Laura Carrel
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, 500 University Drive, Mail code H171, Hershey, PA 17033, USA
| | - Carolyn J Brown
- Department of Medical Genetics, Molecular Epigenetics Group, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, Canada BC V6T 1Z3
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Zettergren A, Karlsson S, Studer E, Sarvimäki A, Kettunen P, Thorsell A, Sihlbom C, Westberg L. Proteomic analyses of limbic regions in neonatal male, female and androgen receptor knockout mice. BMC Neurosci 2017; 18:9. [PMID: 28056817 PMCID: PMC5217640 DOI: 10.1186/s12868-016-0332-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 12/28/2016] [Indexed: 11/10/2022] Open
Abstract
Background It is well-established that organizational effects of sex steroids during early development are fundamental for sex-typical displays of, for example, mating and aggressive behaviors in rodents and other species. Male and female brains are known to differ with respect to neuronal morphology in particular regions of the brain, including the number and size of neurons, and the density and length of dendrites in nuclei of hypothalamus and amygdala. The aim of the present study was to use global proteomics to identify proteins differentially expressed in hypothalamus/amygdala during early development (postnatal day 8) of male, female and conditional androgen receptor knockout (ARNesDel) male mice, lacking androgen receptors specifically in the brain. Furthermore, verification of selected sexually dimorphic proteins was performed using targeted proteomics. Results Our proteomic approach, iTRAQ, allowed us to investigate expression differences in the 2998 most abundantly expressed proteins in our dissected tissues. Approximately 170 proteins differed between the sexes, and 38 proteins between ARNesDel and control males (p < 0.05). In line with previous explorative studies of sexually dimorphic gene expression we mainly detected subtle protein expression differences (fold changes <1.3). The protein MARCKS (myristoylated alanine rich C kinase substrate), having the largest fold change of the proteins selected from the iTRAQ analyses and of known importance for synaptic transmission and dendritic branching, was confirmed by targeted proteomics as differentially expressed between the sexes. Conclusions Overall, our results provide solid evidence that a large number of proteins show sex differences in their brain expression and could potentially be involved in brain sexual differentiation. Furthermore, our finding of a sexually dimorphic expression of MARCKS in the brain during development warrants further investigation on the involvement in sexual differentiation of this protein. Electronic supplementary material The online version of this article (doi:10.1186/s12868-016-0332-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anna Zettergren
- Department of Pharmacology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, POB 431, 405 30, Göteborg, Sweden.,Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Göteborg, Sweden
| | - Sara Karlsson
- Department of Pharmacology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, POB 431, 405 30, Göteborg, Sweden
| | - Erik Studer
- Department of Pharmacology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, POB 431, 405 30, Göteborg, Sweden
| | - Anna Sarvimäki
- Department of Pharmacology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, POB 431, 405 30, Göteborg, Sweden
| | - Petronella Kettunen
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Göteborg, Sweden.,Department of Neuropathology, Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Annika Thorsell
- The Proteomics Core Facility, Sahlgrenska Academy, University of Gothenburg, Göteborg, Sweden
| | - Carina Sihlbom
- The Proteomics Core Facility, Sahlgrenska Academy, University of Gothenburg, Göteborg, Sweden
| | - Lars Westberg
- Department of Pharmacology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, POB 431, 405 30, Göteborg, Sweden.
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Bearoff F, Del Rio R, Case LK, Dragon JA, Nguyen-Vu T, Lin CY, Blankenhorn EP, Teuscher C, Krementsov DN. Natural genetic variation profoundly regulates gene expression in immune cells and dictates susceptibility to CNS autoimmunity. Genes Immun 2016; 17:386-395. [PMID: 27653816 PMCID: PMC5133152 DOI: 10.1038/gene.2016.37] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 08/15/2016] [Accepted: 08/18/2016] [Indexed: 02/08/2023]
Abstract
Regulation of gene expression in immune cells is known to be under genetic control, and likely contributes to susceptibility to autoimmune diseases such as multiple sclerosis (MS). How this occurs in concert across multiple immune cell types is poorly understood. Using a mouse model that harnesses the genetic diversity of wild-derived mice, more accurately reflecting genetically diverse human populations, we provide an extensive characterization of the genetic regulation of gene expression in five different naive immune cell types relevant to MS. The immune cell transcriptome is shown to be under profound genetic control, exhibiting diverse patterns: global, cell-specific and sex-specific. Bioinformatic analysis of the genetically controlled transcript networks reveals reduced cell type specificity and inflammatory activity in wild-derived PWD/PhJ mice, compared with the conventional laboratory strain C57BL/6J. Additionally, candidate MS-GWAS (genome-wide association study candidate genes for MS susceptibility) genes were significantly enriched among transcripts overrepresented in C57BL/6J cells compared with PWD. These expression level differences correlate with robust differences in susceptibility to experimental autoimmune encephalomyelitis, the principal model of MS, and skewing of the encephalitogenic T-cell responses. Taken together, our results provide functional insights into the genetic regulation of the immune transcriptome, and shed light on how this in turn contributes to susceptibility to autoimmune disease.
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Affiliation(s)
- F Bearoff
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
| | - R Del Rio
- Department of Medicine, University of Vermont, Burlington, VT, USA
| | - L K Case
- The Jackson Laboratory, Bar Harbor, ME, USA
| | - J A Dragon
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT, USA
| | - T Nguyen-Vu
- Center for Nuclear Receptors and Cell Signaling, Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - C-Y Lin
- Center for Nuclear Receptors and Cell Signaling, Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - E P Blankenhorn
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
| | - C Teuscher
- Department of Medicine, University of Vermont, Burlington, VT, USA
- Department of Pathology, University of Vermont, Burlington, VT, USA
| | - D N Krementsov
- Department of Medicine, University of Vermont, Burlington, VT, USA
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Gao Q, Ren H, Chen M, Niu Z, Tao H, Jia Y, Zhang J, Li W. Long non-coding RNAs regulate effects of β-crystallin B2 on mouse ovary development. Mol Med Rep 2016; 14:4223-4231. [PMID: 27666820 PMCID: PMC5101957 DOI: 10.3892/mmr.2016.5761] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 09/06/2016] [Indexed: 11/11/2022] Open
Abstract
β-crystallin B2 (CRYBB2) knockout mice exhibit morphological and functional abnormalities in the ovary. Long non‑coding RNAs (lncRNAs) regulate gene transcription and translation, and epigenetic modification of genomic DNA. The present study investigated the role of lncRNAs in mediating the effects of CRYBB2 in the regulation of ovary development in mice. In the current study, ovary tissues from wild‑type (WT) and CRYBB2 knockout mice were subjected to lncRNA and mRNA microarray profiling. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to group the differentially expressed lncRNAs into regulated gene pathways and functions. The correlation matrix method was used to establish a network of lncRNA and mRNA co‑expression. Quantitative reverse transcription-polymerase chain reaction (RT‑qPCR) was used to verify expression of a number of these differentially expressed lncRNAs and mRNAs. There were 157 differentially expressed lncRNAs and 1,085 differentially expressed mRNAs between ovary tissues from WT and CRYBB2 knockout mice. The GO and KEGG analyses indicated that these differentially expressed lncRNAs and mRNAs were important in Ca2+ signaling and ligand and receptor interactions. The correlation matrix method established an lncRNA and mRNA co‑expression network, consisting of 53 lncRNAs and 45 mRNAs with 98 nodes and 75 connections. RT‑qPCR confirmed downregulation of lncRNA A‑30‑P01019163 expression, which further downregulated its downstream gene purinergic receptor P2X, ligand‑gated ion channel, 7 (P2rx7) expression in ovary tissues from CRYBB2 knockout mice. In conclusion, CRYBB2 regulates expression of different lncRNAs to influence ovary development. lncRNA A‑30‑P01019163 may affect ovarian cell cycle and proliferation by regulating P2rx7 expression in the ovary.
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Affiliation(s)
- Qian Gao
- Department of Laboratory Diagnosis, Changhai Hospital, The Second Military Medical University, Shanghai 200433, P.R. China
| | - Hanxiao Ren
- Department of Laboratory Diagnosis, Changhai Hospital, The Second Military Medical University, Shanghai 200433, P.R. China
| | - Mingkun Chen
- Department of Laboratory Diagnosis, Changhai Hospital, The Second Military Medical University, Shanghai 200433, P.R. China
| | - Ziguang Niu
- Department of Laboratory Diagnosis, Changhai Hospital, The Second Military Medical University, Shanghai 200433, P.R. China
| | - Haibo Tao
- Department of Laboratory Diagnosis, Changhai Hospital, The Second Military Medical University, Shanghai 200433, P.R. China
| | - Yin Jia
- Department of Laboratory Diagnosis, Changhai Hospital, The Second Military Medical University, Shanghai 200433, P.R. China
| | - Jianrong Zhang
- Department of Laboratory Diagnosis, Changhai Hospital, The Second Military Medical University, Shanghai 200433, P.R. China
| | - Wenjie Li
- Department of Laboratory Diagnosis, Changhai Hospital, The Second Military Medical University, Shanghai 200433, P.R. China
- Correspondence to: Dr Wenjie Li, Department of Laboratory Diagnosis, Changhai Hospital, The Second Military Medical University, 168 Changhai Road, Shanghai 200433, P.R. China, E-mail:
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30
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Sanchis-Segura C, Becker JB. Why we should consider sex (and study sex differences) in addiction research. Addict Biol 2016; 21:995-1006. [PMID: 27029841 DOI: 10.1111/adb.12382] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 02/02/2016] [Indexed: 12/31/2022]
Abstract
Among mammals, every cell has a biological sex, and the sex of an individual pervades its body and brain. In this review, we describe the processes through which mammals become phenotypically male or female by organizational and activational influences of genes and hormones throughout development. We emphasized that the molecular and cellular changes triggered by sex chromosomes and steroid hormones may generate sex differences in overt physiological functions and behavior, but they may alternatively promote end-point convergences between males and females. Clinical and pre-clinical evidences suggest that sex and gender differences modulate drug consumption as well as of the transition towards drug-promoted pathological states such as dependence and addiction. Additionally, sex differences in drug pharmacokinetics and pharmacodynamics will also influence dependence and addiction as well as side effects of drugs. These effects will further interact with socially gendered factors to result in sex differences in the access to, engagement in and efficacy of any therapeutic attempt. Finally, we maintain that 'sex sameness' is as important as 'sex differences' when building a complete understanding of biology for both males and females and provide a framework with which to classify and guide investigation into the mechanisms mediating sex differences and sex sameness.
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Affiliation(s)
- Carla Sanchis-Segura
- Departament de Psicologia básica, clínica i psicobiologia. Área de Psicobiología; Universitat Jaume I; Castellón de la Plana Spain
| | - Jill B. Becker
- Department of Psychology and Molecular and Behavioral Neuroscience Institute; University of Michigan; Ann Arbor MI USA
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31
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Viggiano E, Ergoli M, Picillo E, Politano L. Determining the role of skewed X-chromosome inactivation in developing muscle symptoms in carriers of Duchenne muscular dystrophy. Hum Genet 2016; 135:685-98. [PMID: 27098336 DOI: 10.1007/s00439-016-1666-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 03/29/2016] [Indexed: 11/24/2022]
Abstract
Duchenne and Becker dystrophinopathies (DMD and BMD) are X-linked recessive disorders caused by mutations in the dystrophin gene that lead to absent or reduced expression of dystrophin in both skeletal and heart muscles. DMD/BMD female carriers are usually asymptomatic, although about 8 % may exhibit muscle or cardiac symptoms. Several mechanisms leading to a reduced dystrophin have been hypothesized to explain the clinical manifestations and, in particular, the role of the skewed XCI is questioned. In this review, the mechanism of XCI and its involvement in the phenotype of BMD/DMD carriers with both a normal karyotype or with X;autosome translocations with breakpoints at Xp21 (locus of the DMD gene) will be analyzed. We have previously observed that DMD carriers with moderate/severe muscle involvement, exhibit a moderate or extremely skewed XCI, in particular if presenting with an early onset of symptoms, while DMD carriers with mild muscle involvement present a random XCI. Moreover, we found that among 87.1 % of the carriers with X;autosome translocations involving the locus Xp21 who developed signs and symptoms of dystrophinopathy such as proximal muscle weakness, difficulty to run, jump and climb stairs, 95.2 % had a skewed XCI pattern in lymphocytes. These data support the hypothesis that skewed XCI is involved in the onset of phenotype in DMD carriers, the X chromosome carrying the normal DMD gene being preferentially inactivated and leading to a moderate-severe muscle involvement.
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Affiliation(s)
- Emanuela Viggiano
- Cardiomyology and Medical Genetics, Department of Experimental Medicine, I Policlinico, Second University of Naples, Piazza Miraglia, 80138, Naples, Italy
| | - Manuela Ergoli
- Cardiomyology and Medical Genetics, Department of Experimental Medicine, I Policlinico, Second University of Naples, Piazza Miraglia, 80138, Naples, Italy
| | - Esther Picillo
- Cardiomyology and Medical Genetics, Department of Experimental Medicine, I Policlinico, Second University of Naples, Piazza Miraglia, 80138, Naples, Italy
| | - Luisa Politano
- Cardiomyology and Medical Genetics, Department of Experimental Medicine, I Policlinico, Second University of Naples, Piazza Miraglia, 80138, Naples, Italy.
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32
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Vied C, Ray S, Badger CD, Bundy JL, Arbeitman MN, Nowakowski RS. Transcriptomic analysis of the hippocampus from six inbred strains of mice suggests a basis for sex-specific susceptibility and severity of neurological disorders. J Comp Neurol 2016; 524:2696-710. [DOI: 10.1002/cne.23989] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 02/12/2016] [Accepted: 02/18/2016] [Indexed: 12/13/2022]
Affiliation(s)
- Cynthia Vied
- Department of Biomedical Sciences, College of Medicine; Florida State University; Tallahassee Florida 32306
| | - Surjyendu Ray
- Department of Biomedical Sciences, College of Medicine; Florida State University; Tallahassee Florida 32306
- Department of Computer Science; Florida State University; Tallahassee Florida 32306
| | - Crystal-Dawn Badger
- Department of Biomedical Sciences, College of Medicine; Florida State University; Tallahassee Florida 32306
| | - Joseph L. Bundy
- Department of Biomedical Sciences, College of Medicine; Florida State University; Tallahassee Florida 32306
| | - Michelle N. Arbeitman
- Department of Biomedical Sciences, College of Medicine; Florida State University; Tallahassee Florida 32306
- Center for Genomics and Personalized Medicine; Florida State University; Tallahassee Florida 32306
| | - Richard S. Nowakowski
- Department of Biomedical Sciences, College of Medicine; Florida State University; Tallahassee Florida 32306
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Abstract
Differentiated sex chromosomes in mammals and other vertebrates evolved independently but in strikingly similar ways. Vertebrates with differentiated sex chromosomes share the problems of the unequal expression of the genes borne on sex chromosomes, both between the sexes and with respect to autosomes. Dosage compensation of genes on sex chromosomes is surprisingly variable - and can even be absent - in different vertebrate groups. Systems that compensate for different gene dosages include a wide range of global, regional and gene-by-gene processes that differ in their extent and their molecular mechanisms. However, many elements of these control systems are similar across distant phylogenetic divisions and show parallels to other gene silencing systems. These dosage systems cannot be identical by descent but were probably constructed from elements of ancient silencing mechanisms that are ubiquitous among vertebrates and shared throughout eukaryotes.
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34
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Mueller JC, Kuhl H, Timmermann B, Kempenaers B. Characterization of the genome and transcriptome of the blue tit Cyanistes caeruleus: polymorphisms, sex-biased expression and selection signals. Mol Ecol Resour 2015. [PMID: 26220359 DOI: 10.1111/1755-0998.12450] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Decoding genomic sequences and determining their variation within populations has potential to reveal adaptive processes and unravel the genetic basis of ecologically relevant trait variation within a species. The blue tit Cyanistes caeruleus--a long-time ecological model species--has been used to investigate fitness consequences of variation in mating and reproductive behaviour. However, very little is known about the underlying genetic changes due to natural and sexual selection in the genome of this songbird. As a step to bridge this gap, we assembled the first draft genome of a single blue tit, mapped the transcriptome of five females and five males to this reference, identified genomewide variants and performed sex-differential expression analysis in the gonads, brain and other tissues. In the gonads, we found a high number of sex-biased genes, and of those, a similar proportion were sex-limited (genes only expressed in one sex) in males and females. However, in the brain, the proportion of female-limited genes within the female-biased gene category (82%) was substantially higher than the proportion of male-limited genes within the male-biased category (6%). This suggests a predominant on-off switching mechanism for the female-limited genes. In addition, most male-biased genes were located on the Z-chromosome, indicating incomplete dosage compensation for the male-biased genes. We called more than 500,000 SNPs from the RNA-seq data. Heterozygote detection in the single reference individual was highly congruent between DNA-seq and RNA-seq calling. Using information from these polymorphisms, we identified potential selection signals in the genome. We list candidate genes which can be used for further sequencing and detailed selection studies, including genes potentially related to meiotic drive evolution. A public genome browser of the blue tit with the described information is available at http://public-genomes-ngs.molgen.mpg.de.
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Affiliation(s)
- Jakob C Mueller
- Department of Behavioural Ecology & Evolutionary Genetics, Max Planck Institute for Ornithology, 82319 Seewiesen, Germany
| | - Heiner Kuhl
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
| | - Bernd Timmermann
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
| | - Bart Kempenaers
- Department of Behavioural Ecology & Evolutionary Genetics, Max Planck Institute for Ornithology, 82319 Seewiesen, Germany
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D'Amico F, Skarmoutsou E, Mazzarino MC. The sex bias in systemic sclerosis: on the possible mechanisms underlying the female disease preponderance. Clin Rev Allergy Immunol 2015; 47:334-43. [PMID: 24126759 DOI: 10.1007/s12016-013-8392-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Systemic sclerosis is a multifactorial and heterogeneous disease. Genetic and environmental factors are known to interplay in the onset and progression of systemic sclerosis. Sex plays an important and determinant role in the development of such a disorder. Systemic sclerosis shows a significant female preponderance. However, the reason for this female preponderance is incompletely understood. Hormonal status, genetic and epigenetic differences, and lifestyle have been considered in order to explain female preponderance in systemic sclerosis. Sex chromosomes play a determinant role in contributing to systemic sclerosis onset and progression, as well as in its sex-biased prevalence. It is known, in fact, that X chromosome contains many sex- and immuno-related genes, thus contributing to immuno tolerance and sex hormone status. This review focuses mainly on the recent progress on epigenetic mechanisms--exclusively linked to the X chromosome--which would contribute to the development of systemic sclerosis. Furthermore, we report also some hypotheses (dealing with skewed X chromosome inactivation, X gene reactivation, acquired monosomy) that have been proposed in order to justify the female preponderance in autoimmune diseases. However, despite the intensive efforts in elucidating the mechanisms involved in the pathogenesis of systemic sclerosis, many questions remain still unanswered.
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Affiliation(s)
- Fabio D'Amico
- Department of Bio-medical Sciences, University of Catania, via Androne 83, 95124, Catania, Italy,
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Mobasheri MB, Shirkoohi R, Modarressi MH. Cancer/Testis OIP5 and TAF7L Genes are Up-Regulated in Breast Cancer. Asian Pac J Cancer Prev 2015; 16:4623-8. [DOI: 10.7314/apjcp.2015.16.11.4623] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Stocks M, Dean R, Rogell B, Friberg U. Sex-specific trans-regulatory variation on the Drosophila melanogaster X chromosome. PLoS Genet 2015; 11:e1005015. [PMID: 25679222 PMCID: PMC4334168 DOI: 10.1371/journal.pgen.1005015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Accepted: 01/22/2015] [Indexed: 11/19/2022] Open
Abstract
The X chromosome constitutes a unique genomic environment because it is present in one copy in males, but two copies in females. This simple fact has motivated several theoretical predictions with respect to how standing genetic variation on the X chromosome should differ from the autosomes. Unmasked expression of deleterious mutations in males and a lower census size are expected to reduce variation, while allelic variants with sexually antagonistic effects, and potentially those with a sex-specific effect, could accumulate on the X chromosome and contribute to increased genetic variation. In addition, incomplete dosage compensation of the X chromosome could potentially dampen the male-specific effects of random mutations, and promote the accumulation of X-linked alleles with sexually dimorphic phenotypic effects. Here we test both the amount and the type of genetic variation on the X chromosome within a population of Drosophila melanogaster, by comparing the proportion of X linked and autosomal trans-regulatory SNPs with a sexually concordant and discordant effect on gene expression. We find that the X chromosome is depleted for SNPs with a sexually concordant effect, but hosts comparatively more SNPs with a sexually discordant effect. Interestingly, the contrasting results for SNPs with sexually concordant and discordant effects are driven by SNPs with a larger influence on expression in females than expression in males. Furthermore, the distribution of these SNPs is shifted towards regions where dosage compensation is predicted to be less complete. These results suggest that intrinsic properties of dosage compensation influence either the accumulation of different types of trans-factors and/or their propensity to accumulate mutations. Our findings document a potential mechanistic basis for sex-specific genetic variation, and identify the X as a reservoir for sexually dimorphic phenotypic variation. These results have general implications for X chromosome evolution, as well as the genetic basis of sex-specific evolutionary change.
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Affiliation(s)
- Michael Stocks
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
- Department of Plant Ecology and Evolution, Uppsala University, Uppsala, Sweden
| | - Rebecca Dean
- Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
- * E-mail: (RD); (UF)
| | - Björn Rogell
- Department of Animal Ecology, Uppsala University, Uppsala, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Urban Friberg
- Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden
- IFM Biology, AVIAN Behaviour and Genomics group, Linköping University, Linköping, Sweden
- * E-mail: (RD); (UF)
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Scerbo MJ, Freire-Regatillo A, Cisternas CD, Brunotto M, Arevalo MA, Garcia-Segura LM, Cambiasso MJ. Neurogenin 3 mediates sex chromosome effects on the generation of sex differences in hypothalamic neuronal development. Front Cell Neurosci 2014; 8:188. [PMID: 25071448 PMCID: PMC4086225 DOI: 10.3389/fncel.2014.00188] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 06/19/2014] [Indexed: 01/01/2023] Open
Abstract
The organizational action of testosterone during critical periods of development is the cause of numerous sex differences in the brain. However, sex differences in neuritogenesis have been detected in primary neuronal hypothalamic cultures prepared before the peak of testosterone production by fetal testis. In the present study we assessed the hypothesis of that cell-autonomous action of sex chromosomes can differentially regulate the expression of the neuritogenic gene neurogenin 3 (Ngn3) in male and female hypothalamic neurons, generating sex differences in neuronal development. Neuronal cultures were prepared from male and female E14 mouse hypothalami, before the fetal peak of testosterone. Female neurons showed enhanced neuritogenesis and higher expression of Ngn3 than male neurons. The silencing of Ngn3 abolished sex differences in neuritogenesis, decreasing the differentiation of female neurons. The sex difference in Ngn3 expression was determined by sex chromosomes, as demonstrated using the four core genotypes mouse model, in which a spontaneous deletion of the testis-determining gene Sry from the Y chromosome was combined with the insertion of the Sry gene onto an autosome. In addition, the expression of Ngn3, which is also known to mediate the neuritogenic actions of estradiol, was increased in the cultures treated with the hormone, but only in those from male embryos. Furthermore, the hormone reversed the sex differences in neuritogenesis promoting the differentiation of male neurons. These findings indicate that Ngn3 mediates both cell-autonomous actions of sex chromosomes and hormonal effects on neuritogenesis.
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Affiliation(s)
- María J Scerbo
- Laboratory of Neurophysiology, Instituto de Investigación Médica Mercedes y Martín Ferreyra, INIMEC-CONICET - Universidad Nacional de Córdoba Córdoba, Argentina
| | | | - Carla D Cisternas
- Laboratory of Neurophysiology, Instituto de Investigación Médica Mercedes y Martín Ferreyra, INIMEC-CONICET - Universidad Nacional de Córdoba Córdoba, Argentina ; Departamento de Biología Bucal, Facultad de Odontología - Universidad Nacional de Córdoba Córdoba, Argentina
| | - Mabel Brunotto
- Departamento de Biología Bucal, Facultad de Odontología - Universidad Nacional de Córdoba Córdoba, Argentina
| | - Maria A Arevalo
- Instituto Cajal, Consejo Superior de Investigaciones Científicas Madrid, Spain
| | | | - María J Cambiasso
- Laboratory of Neurophysiology, Instituto de Investigación Médica Mercedes y Martín Ferreyra, INIMEC-CONICET - Universidad Nacional de Córdoba Córdoba, Argentina ; Departamento de Biología Bucal, Facultad de Odontología - Universidad Nacional de Córdoba Córdoba, Argentina
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Merzouk S, Deuve JL, Dubois A, Navarro P, Avner P, Morey C. Lineage-specific regulation of imprinted X inactivation in extraembryonic endoderm stem cells. Epigenetics Chromatin 2014; 7:11. [PMID: 25053977 PMCID: PMC4105886 DOI: 10.1186/1756-8935-7-11] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 06/02/2014] [Indexed: 01/09/2023] Open
Abstract
Background Silencing of the paternal X chromosome (Xp), a phenomenon known as imprinted X-chromosome inactivation (I-XCI), characterises, amongst mouse extraembryonic lineages, the primitive endoderm and the extraembryonic endoderm (XEN) stem cells derived from it. Results Using a combination of chromatin immunoprecipitation characterisation of histone modifications and single-cell expression studies, we show that whilst the Xp in XEN cells, like the inactive X chromosome in other cell types, globally accumulates the repressive histone mark H3K27me3, a large number of Xp genes locally lack H3K27me3 and escape from I-XCI. In most cases this escape is specific to the XEN cell lineage. Importantly, the degree of escape and the genes concerned remain unchanged upon XEN conversion into visceral endoderm, suggesting stringent control of I-XCI in XEN derivatives. Surprisingly, chemical inhibition of EZH2, a member of the Polycomb repressive complex 2 (PRC2), and subsequent loss of H3K27me3 on the Xp, do not drastically perturb the pattern of silencing of Xp genes in XEN cells. Conclusions The observations that we report here suggest that the maintenance of gene expression profiles of the inactive Xp in XEN cells involves a tissue-specific mechanism that acts partly independently of PRC2 catalytic activity.
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Affiliation(s)
- Sarra Merzouk
- Mouse Molecular Genetics Laboratory, Pasteur Institute, 25 rue du Dr Roux, 75015 Paris, France ; Pasteur Cell, Pierre and Marie Curie University (UPMC), 25 rue du Dr Roux, 75015 Paris, France
| | - Jane Lynda Deuve
- Mouse Molecular Genetics Laboratory, Pasteur Institute, 25 rue du Dr Roux, 75015 Paris, France ; Present address: Pierre and Marie Curie University (UPMC), UMR7622, Institute of Biology of Paris-Seine (IBPS), 75005 Paris, France
| | - Agnès Dubois
- Mouse Molecular Genetics Laboratory, Pasteur Institute, 25 rue du Dr Roux, 75015 Paris, France ; Present address: Epigenetics of Stem Cells Laboratory', Pasteur Institute, 25 rue du Dr Roux, 75015 Paris, France
| | - Pablo Navarro
- Present address: Epigenetics of Stem Cells Laboratory', Pasteur Institute, 25 rue du Dr Roux, 75015 Paris, France
| | - Philip Avner
- Mouse Molecular Genetics Laboratory, Pasteur Institute, 25 rue du Dr Roux, 75015 Paris, France ; Present address: Dynamics of Epigenetic Regulation, EMBL Monterotondo, Adriano Buzzati-Traverso Campus, Via Ramarini 32, 00015 Monterotondo, Italy
| | - Céline Morey
- Mouse Molecular Genetics Laboratory, Pasteur Institute, 25 rue du Dr Roux, 75015 Paris, France
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40
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Deng X, Berletch JB, Nguyen DK, Disteche CM. X chromosome regulation: diverse patterns in development, tissues and disease. Nat Rev Genet 2014; 15:367-78. [PMID: 24733023 PMCID: PMC4117651 DOI: 10.1038/nrg3687] [Citation(s) in RCA: 216] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Genes on the mammalian X chromosome are present in one copy in males and two copies in females. The complex mechanisms that regulate the X chromosome lead to evolutionary and physiological variability in gene expression between species, the sexes, individuals, developmental stages, tissues and cell types. In early development, delayed and incomplete X chromosome inactivation (XCI) in some species causes variability in gene expression. Additional diversity stems from escape from XCI and from mosaicism or XCI skewing in females. This causes sex-specific differences that manifest as differential gene expression and associated phenotypes. Furthermore, the complexity and diversity of X dosage regulation affect the severity of diseases caused by X-linked mutations.
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Affiliation(s)
- Xinxian Deng
- Department of Pathology, School of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, Washington 98115, USA
| | - Joel B Berletch
- Department of Pathology, School of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, Washington 98115, USA
| | - Di K Nguyen
- Department of Pathology, School of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, Washington 98115, USA
| | - Christine M Disteche
- 1] Department of Pathology, School of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, Washington 98115, USA. [2] Department of Medicine, School of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, Washington 98115, USA
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Abstract
Genes on the mammalian X chromosome are present in one copy in males and two copies in females. The complex mechanisms that regulate the X chromosome lead to evolutionary and physiological variability in gene expression between species, the sexes, individuals, developmental stages, tissues and cell types. In early development, delayed and incomplete X chromosome inactivation (XCI) in some species causes variability in gene expression. Additional diversity stems from escape from XCI and from mosaicism or XCI skewing in females. This causes sex-specific differences that manifest as differential gene expression and associated phenotypes. Furthermore, the complexity and diversity of X dosage regulation affect the severity of diseases caused by X-linked mutations.
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42
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Deng X, Berletch JB, Nguyen DK, Disteche CM. X chromosome regulation: diverse patterns in development, tissues and disease. Nat Rev Genet 2014. [PMID: 24733023 DOI: 10.1038/nrg3687,+10.1038/nrn3745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Genes on the mammalian X chromosome are present in one copy in males and two copies in females. The complex mechanisms that regulate the X chromosome lead to evolutionary and physiological variability in gene expression between species, the sexes, individuals, developmental stages, tissues and cell types. In early development, delayed and incomplete X chromosome inactivation (XCI) in some species causes variability in gene expression. Additional diversity stems from escape from XCI and from mosaicism or XCI skewing in females. This causes sex-specific differences that manifest as differential gene expression and associated phenotypes. Furthermore, the complexity and diversity of X dosage regulation affect the severity of diseases caused by X-linked mutations.
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Affiliation(s)
- Xinxian Deng
- Department of Pathology, School of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, Washington 98115, USA
| | - Joel B Berletch
- Department of Pathology, School of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, Washington 98115, USA
| | - Di K Nguyen
- Department of Pathology, School of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, Washington 98115, USA
| | - Christine M Disteche
- 1] Department of Pathology, School of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, Washington 98115, USA. [2] Department of Medicine, School of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, Washington 98115, USA
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Alvarez-Dominguez JR, Hu W, Gromatzky AA, Lodish HF. Long noncoding RNAs during normal and malignant hematopoiesis. Int J Hematol 2014; 99:531-41. [PMID: 24609766 DOI: 10.1007/s12185-014-1552-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 01/25/2014] [Accepted: 02/18/2014] [Indexed: 11/28/2022]
Abstract
Long noncoding RNAs (lncRNAs) are increasingly recognized to contribute to cellular development via diverse mechanisms during both health and disease. Here, we highlight recent progress on the study of lncRNAs that function in the development of blood cells. We emphasize lncRNAs that regulate blood cell fates through epigenetic control of gene expression, an emerging theme among functional lncRNAs. Many of these noncoding genes and their targets become dysregulated during malignant hematopoiesis, directly implicating lncRNAs in blood cancers such as leukemia. In a few cases, dysregulation of an lncRNA alone leads to malignant hematopoiesis in a mouse model. Thus, lncRNAs may be not only useful as markers for the diagnosis and prognosis of cancers of the blood, but also as potential targets for novel therapies.
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Diggs-Andrews KA, Brown JA, Gianino SM, Rubin JB, Wozniak DF, Gutmann DH. Sex Is a major determinant of neuronal dysfunction in neurofibromatosis type 1. Ann Neurol 2014; 75:309-16. [PMID: 24375753 DOI: 10.1002/ana.24093] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Revised: 11/06/2013] [Accepted: 12/06/2013] [Indexed: 01/04/2023]
Abstract
OBJECTIVE Children with neurofibromatosis-1 (NF1) are at risk for developing numerous nervous system abnormalities, including cognitive problems and brain tumors (optic pathway glioma). Currently, there are few prognostic factors that predict clinical manifestations or outcomes in patients, even in families with an identical NF1 gene mutation. In this study, we leveraged Nf1 genetically engineered mice (GEM) to define the potential role of sex as a clinically relevant modifier of NF1-associated neuronal dysfunction. METHODS Deidentified clinical data were analyzed to determine the impact of sex on optic glioma-associated visual decline in children with NF1. In addition, Nf1 GEM were employed as experimental platforms to investigate sexually dimorphic differences in learning/memory, visual acuity, retinal ganglion cell (RGC) death, and Nf1 protein (neurofibromin)-regulated signaling pathway function (Ras activity, cyclic adenosine monophosphate [cAMP], and dopamine levels). RESULTS Female patients with NF1-associated optic glioma were twice as likely to undergo brain magnetic resonance imaging for visual symptoms and 3× more likely to require treatment for visual decline than their male counterparts. As such, only female Nf1 GEM exhibited a decrement in optic glioma-associated visual acuity, shorter RGC axons, and attenuated cAMP levels. In contrast, only male Nf1 GEM showed spatial learning/memory deficits, increased Ras activity, and reduced dopamine levels. INTERPRETATION Collectively, these observations establish sex as a major prognostic factor underlying neuronal dysfunction in NF1, and suggest that sex should be considered when interpreting future preclinical and clinical study results.
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Affiliation(s)
- Kelly A Diggs-Andrews
- Departments of Neurology, Washington University School of Medicine, Box 8111, 660 South Euclid Avenue, St Louis, MO
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45
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Unterwald EM, Page ME, Brown TB, Miller JS, Ruiz M, Pescatore KA, Xu B, Reichardt LF, Beverley J, Tang B, Steiner H, Thomas EA, Ehrlich ME. Behavioral and transcriptome alterations in male and female mice with postnatal deletion of TrkB in dorsal striatal medium spiny neurons. Mol Neurodegener 2013; 8:47. [PMID: 24369067 PMCID: PMC3880973 DOI: 10.1186/1750-1326-8-47] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 12/19/2013] [Indexed: 01/05/2023] Open
Abstract
Background The high affinity tyrosine kinase receptor, TrkB, is the primary receptor for brain derived neurotrophic factor (BDNF) and plays an important role in development, maintenance and plasticity of the striatal output medium size spiny neuron. The striatal BDNF/TrkB system is thereby implicated in many physiologic and pathophysiologic processes, the latter including mood disorders, addiction, and Huntington’s disease. We crossed a mouse harboring a transgene directing cre-recombinase expression primarily to postnatal, dorsal striatal medium spiny neurons, to a mouse containing a floxed TrkB allele (fB) mouse designed for deletion of TrkB to determine its role in the adult striatum. Results We found that there were sexually dimorphic alterations in behaviors in response to stressful situations and drugs of abuse. Significant sex and/or genotype differences were found in the forced swim test of depression-like behaviors, anxiety-like behaviors on the elevated plus maze, and cocaine conditioned reward. Microarray analysis of dorsal striatum revealed significant dysregulation in individual and groups of genes that may contribute to the observed behavioral responses and in some cases, represent previously unidentified downstream targets of TrkB. Conclusions The data point to a set of behaviors and changes in gene expression following postnatal deletion of TrkB in the dorsal striatum distinct from those in other brain regions.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Michelle E Ehrlich
- Farber Institute for Neurosciences, Thomas Jefferson University, Philadelphia, PA 19107, USA.
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Horvath LM, Li N, Carrel L. Deletion of an X-inactivation boundary disrupts adjacent gene silencing. PLoS Genet 2013; 9:e1003952. [PMID: 24278033 PMCID: PMC3836711 DOI: 10.1371/journal.pgen.1003952] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 09/27/2013] [Indexed: 12/03/2022] Open
Abstract
In mammalian females, genes on one X are largely silenced by X-chromosome inactivation (XCI), although some “escape” XCI and are expressed from both Xs. Escapees can closely juxtapose X-inactivated genes and provide a tractable model for assessing boundary function at epigenetically regulated loci. To delimit sequences at an XCI boundary, we examined female mouse embryonic stem cells carrying X-linked BAC transgenes derived from an endogenous escape locus. Previously we determined that large BACs carrying escapee Kdm5c and flanking X-inactivated transcripts are properly regulated. Here we identify two lines with truncated BACs that partially and completely delete the distal Kdm5c XCI boundary. This boundary is not required for escape, since despite integrating into regions that are normally X inactivated, transgenic Kdm5c escapes XCI, as determined by RNA FISH and by structurally adopting an active conformation that facilitates long-range preferential association with other escapees. Yet, XCI regulation is disrupted in the transgene fully lacking the distal boundary; integration site genes up to 350 kb downstream of the transgene now inappropriately escape XCI. Altogether, these results reveal two genetically separable XCI regulatory activities at Kdm5c. XCI escape is driven by a dominant element(s) retained in the shortest transgene that therefore lies within or upstream of the Kdm5c locus. Additionally, the distal XCI boundary normally plays an essential role in preventing nearby genes from escaping XCI. Early in mammalian female development, one X chromosome is largely silenced to equalize X-linked gene expression between the sexes. Nevertheless, some genes “escape” this silencing and therefore are expressed from both X chromosomes. Understanding how these escape genes are regulated, particularly when they closely juxtapose silenced genes, may give important insight into regulatory transitions throughout the genome. To evaluate sequences that are essential for appropriate inactive X expression we analyzed large transgenes that integrated on the X chromosome in mouse embryonic stem cells. Transgenes that include an escape gene, Kdm5c, but lack all or part of the downstream sequences, including the X-inactivation boundary, still escape X inactivation. Nevertheless, downstream genes at the transgene insertion site are misregulated and now inappropriately escape X inactivation as well. These data identify two important regulatory activities at this locus. First, sequences retained within the truncated transgene are sufficient to direct the Kdm5c gene to escape X inactivation. Further, we have uncovered a function for an X-inactivation boundary in protecting adjacent genes from escape.
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Affiliation(s)
- Lindsay M. Horvath
- Department of Biochemistry and Molecular Biology, Pennsylvania State College of Medicine, Hershey, Pennsylvania, United States of America
| | - Nan Li
- Department of Biochemistry and Molecular Biology, Pennsylvania State College of Medicine, Hershey, Pennsylvania, United States of America
| | - Laura Carrel
- Department of Biochemistry and Molecular Biology, Pennsylvania State College of Medicine, Hershey, Pennsylvania, United States of America
- * E-mail:
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Krishnan J, Mishra RK. Emerging trends of long non-coding RNAs in gene activation. FEBS J 2013; 281:34-45. [PMID: 24165279 DOI: 10.1111/febs.12578] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Revised: 09/05/2013] [Accepted: 10/15/2013] [Indexed: 01/09/2023]
Abstract
The RNA world has gained increasing importance in the recent past as its role beyond coding for proteins and components of translational machinery is becoming more and more prominent. Recent studies have shown pervasive transcription throughout the genome generating a large number of non-coding RNAs (ncRNAs) but few of these RNAs have been shown to perform regulatory functions. Among the regulatory RNAs, the long non-coding RNAs (lncRNAs) form an interesting class which, with their ability to bind to a variety of targets, can play pivotal roles in cellular processes including regulation of gene expression. While lncRNAs are well known for their role in repressing gene expression, their role in gene activation is only emerging from recent studies. Here we review how the lncRNAs can mediate gene activation by a variety of mechanisms and explore their importance in biological processes.
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Affiliation(s)
- Jaya Krishnan
- Centre for Cellular and Molecular Biology, CSIR, Hyderabad, India
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48
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Qureshi IA, Mehler MF. Long non-coding RNAs: novel targets for nervous system disease diagnosis and therapy. Neurotherapeutics 2013; 10:632-46. [PMID: 23817781 PMCID: PMC3805860 DOI: 10.1007/s13311-013-0199-0] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The human genome encodes tens of thousands of long non-coding RNAs (lncRNAs), a novel and important class of genes. Our knowledge of lncRNAs has grown exponentially since their discovery within the last decade. lncRNAs are expressed in a highly cell- and tissue-specific manner, and are particularly abundant within the nervous system. lncRNAs are subject to post-transcriptional processing and inter- and intra-cellular transport. lncRNAs act via a spectrum of molecular mechanisms leveraging their ability to engage in both sequence-specific and conformational interactions with diverse partners (DNA, RNA, and proteins). Because of their size, lncRNAs act in a modular fashion, bringing different macromolecules together within the three-dimensional context of the cell. lncRNAs thus coordinate the execution of transcriptional, post-transcriptional, and epigenetic processes and critical biological programs (growth and development, establishment of cell identity, and deployment of stress responses). Emerging data reveal that lncRNAs play vital roles in mediating the developmental complexity, cellular diversity, and activity-dependent plasticity that are hallmarks of brain. Corresponding studies implicate these factors in brain aging and the pathophysiology of brain disorders, through evolving paradigms including the following: (i) genetic variation in lncRNA genes causes disease and influences susceptibility; (ii) epigenetic deregulation of lncRNAs genes is associated with disease; (iii) genomic context links lncRNA genes to disease genes and pathways; and (iv) lncRNAs are otherwise interconnected with known pathogenic mechanisms. Hence, lncRNAs represent prime targets that can be exploited for diagnosing and treating nervous system diseases. Such clinical applications are in the early stages of development but are rapidly advancing because of existing expertise and technology platforms that are readily adaptable for these purposes.
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Affiliation(s)
- Irfan A. Qureshi
- />Roslyn and Leslie Goldstein Laboratory for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, New York USA
- />Institute for Brain Disorders and Neural Regeneration, Albert Einstein College of Medicine, Bronx, New York USA
- />Department of Neurology, Albert Einstein College of Medicine, Bronx, New York USA
- />Rose F. Kennedy Center for Research on Intellectual and Developmental Disabilities, Albert Einstein College of Medicine, 1410 Pelham Parkway South, Room 401, Bronx, New York 10461 USA
| | - Mark F. Mehler
- />Roslyn and Leslie Goldstein Laboratory for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, New York USA
- />Institute for Brain Disorders and Neural Regeneration, Albert Einstein College of Medicine, Bronx, New York USA
- />Department of Neurology, Albert Einstein College of Medicine, Bronx, New York USA
- />Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York USA
- />Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, New York USA
- />Rose F. Kennedy Center for Research on Intellectual and Developmental Disabilities, Albert Einstein College of Medicine, 1410 Pelham Parkway South, Room 401, Bronx, New York 10461 USA
- />Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, New York USA
- />Ruth L. and David S. Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, New York USA
- />Center for Epigenomics, Albert Einstein College of Medicine, Bronx, New York USA
- />Institute for Aging Research, Albert Einstein College of Medicine, Bronx, New York USA
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Link JC, Chen X, Arnold AP, Reue K. Metabolic impact of sex chromosomes. Adipocyte 2013; 2:74-9. [PMID: 23805402 PMCID: PMC3661109 DOI: 10.4161/adip.23320] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Revised: 12/13/2012] [Accepted: 12/17/2012] [Indexed: 02/08/2023] Open
Abstract
Obesity and associated metabolic diseases are sexually dimorphic. To provide better diagnosis and treatment for both sexes, it is of interest to identify the factors that underlie male/female differences in obesity. Traditionally, sexual dimorphism has been attributed to effects of gonadal hormones, which influence numerous metabolic processes. However, the XX/XY sex chromosome complement is an additional factor that may play a role. Recent data using the four core genotypes mouse model have revealed that sex chromosome complement—independently from gonadal sex—plays a role in adiposity, feeding behavior, fatty liver and glucose homeostasis. Potential mechanisms for the effects of sex chromosome complement include differential gene dosage from X chromosome genes that escape inactivation, and distinct genomic imprints on X chromosomes inherited from maternal or paternal parents. Here we review recent data in mice and humans concerning the potential impact of sex chromosome complement on obesity and metabolic disease.
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50
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Gabory A, Roseboom TJ, Moore T, Moore LG, Junien C. Placental contribution to the origins of sexual dimorphism in health and diseases: sex chromosomes and epigenetics. Biol Sex Differ 2013; 4:5. [PMID: 23514128 PMCID: PMC3618244 DOI: 10.1186/2042-6410-4-5] [Citation(s) in RCA: 240] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Accepted: 03/04/2013] [Indexed: 12/17/2022] Open
Abstract
Sex differences occur in most non-communicable diseases, including metabolic diseases, hypertension, cardiovascular disease, psychiatric and neurological disorders and cancer. In many cases, the susceptibility to these diseases begins early in development. The observed differences between the sexes may result from genetic and hormonal differences and from differences in responses to and interactions with environmental factors, including infection, diet, drugs and stress. The placenta plays a key role in fetal growth and development and, as such, affects the fetal programming underlying subsequent adult health and accounts, in part for the developmental origin of health and disease (DOHaD). There is accumulating evidence to demonstrate the sex-specific relationships between diverse environmental influences on placental functions and the risk of disease later in life. As one of the few tissues easily collectable in humans, this organ may therefore be seen as an ideal system for studying how male and female placenta sense nutritional and other stresses, such as endocrine disruptors. Sex-specific regulatory pathways controlling sexually dimorphic characteristics in the various organs and the consequences of lifelong differences in sex hormone expression largely account for such responses. However, sex-specific changes in epigenetic marks are generated early after fertilization, thus before adrenal and gonad differentiation in the absence of sex hormones and in response to environmental conditions. Given the abundance of X-linked genes involved in placentogenesis, and the early unequal gene expression by the sex chromosomes between males and females, the role of X- and Y-chromosome-linked genes, and especially those involved in the peculiar placenta-specific epigenetics processes, giving rise to the unusual placenta epigenetic landscapes deserve particular attention. However, even with recent developments in this field, we still know little about the mechanisms underlying the early sex-specific epigenetic marks resulting in sex-biased gene expression of pathways and networks. As a critical messenger between the maternal environment and the fetus, the placenta may play a key role not only in buffering environmental effects transmitted by the mother but also in expressing and modulating effects due to preconceptional exposure of both the mother and the father to stressful conditions.
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Affiliation(s)
- Anne Gabory
- INRA, UMR1198 Biologie du Développement et Reproduction, Jouy-en-Josas, F-78352, France.
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