1
|
Barchitta M, Maugeri A, La Mastra C, Favara G, La Rosa MC, Magnano San Lio R, Gholizade Atani Y, Gallo G, Agodi A. Pre-pregnancy BMI, gestational weight gain, and telomere length in amniotic fluid: a causal graph analysis. Sci Rep 2024; 14:23396. [PMID: 39379607 PMCID: PMC11461511 DOI: 10.1038/s41598-024-74765-y] [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: 09/25/2023] [Accepted: 09/30/2024] [Indexed: 10/10/2024] Open
Abstract
Previous investigations have suggested a potential association between pre-pregnancy body mass index (BMI) and gestational weight gain (GWG) with telomere length (TL) in various tissues of pregnant women and newborns. Nonetheless, as association does not imply causation, our objective was to investigate the causal connections among pre-pregnancy BMI, GWG, and TL in amniotic fluid. The analysis included 136 mother-child pairs from the Mamma & Bambino cohort, and three causal graph models were developed to depict the interconnections between pre-pregnancy BMI, GWG, and TL. Causal graph analysis was conducted utilizing the do-operator to estimate the causal effect of GWG and the controlled direct effect of pregestational BMI. We revealed that transitioning from non-adequate to adequate GWG had a positive impact on the probability of having "long" TL (i.e., a value greater than the population median) in all three models. When considering the effect of pre-pregnancy BMI, the highest probability of "long" TL was observed in normal weight women with adequate GWG. In contrast, the effect of adequate GWG became minimal among overweight women. These results shed light on the potential causality between pre-pregnancy BMI, GWG, and TL in amniotic fluid, emphasizing the importance of appropriate weight management before and during pregnancy for optimal TL outcomes.
Collapse
Affiliation(s)
- M Barchitta
- Department of Medical and Surgical Sciences and Advanced Technologies 'GF Ingrassia', University of Catania, Catania, Italy
| | - A Maugeri
- Department of Medical and Surgical Sciences and Advanced Technologies 'GF Ingrassia', University of Catania, Catania, Italy
| | - C La Mastra
- Department of Medical and Surgical Sciences and Advanced Technologies 'GF Ingrassia', University of Catania, Catania, Italy
| | - G Favara
- Department of Medical and Surgical Sciences and Advanced Technologies 'GF Ingrassia', University of Catania, Catania, Italy
| | - M C La Rosa
- Department of Medical and Surgical Sciences and Advanced Technologies 'GF Ingrassia', University of Catania, Catania, Italy
| | - R Magnano San Lio
- Department of Medical and Surgical Sciences and Advanced Technologies 'GF Ingrassia', University of Catania, Catania, Italy
| | - Y Gholizade Atani
- Department of Mathematics and Informatics, University of Catania, Catania, Italy
| | - G Gallo
- Department of Mathematics and Informatics, University of Catania, Catania, Italy
| | - A Agodi
- Department of Medical and Surgical Sciences and Advanced Technologies 'GF Ingrassia', University of Catania, Catania, Italy.
| |
Collapse
|
2
|
Gravholt CH, Andersen NH, Christin-Maitre S, Davis SM, Duijnhouwer A, Gawlik A, Maciel-Guerra AT, Gutmark-Little I, Fleischer K, Hong D, Klein KO, Prakash SK, Shankar RK, Sandberg DE, Sas TCJ, Skakkebæk A, Stochholm K, van der Velden JA, Backeljauw PF. Clinical practice guidelines for the care of girls and women with Turner syndrome. Eur J Endocrinol 2024; 190:G53-G151. [PMID: 38748847 DOI: 10.1093/ejendo/lvae050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 04/19/2024] [Indexed: 06/16/2024]
Abstract
Turner syndrome (TS) affects 50 per 100 000 females. TS affects multiple organs through all stages of life, necessitating multidisciplinary care. This guideline extends previous ones and includes important new advances, within diagnostics and genetics, estrogen treatment, fertility, co-morbidities, and neurocognition and neuropsychology. Exploratory meetings were held in 2021 in Europe and United States culminating with a consensus meeting in Aarhus, Denmark in June 2023. Prior to this, eight groups addressed important areas in TS care: (1) diagnosis and genetics, (2) growth, (3) puberty and estrogen treatment, (4) cardiovascular health, (5) transition, (6) fertility assessment, monitoring, and counselling, (7) health surveillance for comorbidities throughout the lifespan, and (8) neurocognition and its implications for mental health and well-being. Each group produced proposals for the present guidelines, which were meticulously discussed by the entire group. Four pertinent questions were submitted for formal GRADE (Grading of Recommendations, Assessment, Development and Evaluation) evaluation with systematic review of the literature. The guidelines project was initiated by the European Society for Endocrinology and the Pediatric Endocrine Society, in collaboration with members from the European Society for Pediatric Endocrinology, the European Society of Human Reproduction and Embryology, the European Reference Network on Rare Endocrine Conditions, the Society for Endocrinology, and the European Society of Cardiology, Japanese Society for Pediatric Endocrinology, Australia and New Zealand Society for Pediatric Endocrinology and Diabetes, Latin American Society for Pediatric Endocrinology, Arab Society for Pediatric Endocrinology and Diabetes, and the Asia Pacific Pediatric Endocrine Society. Advocacy groups appointed representatives for pre-meeting discussions and the consensus meeting.
Collapse
Affiliation(s)
- Claus H Gravholt
- Department of Endocrinology, Aarhus University Hospital, 8200 Aarhus N, Denmark
- Department of Molecular Medicine, Aarhus University Hospital, 8200 Aarhus N, Denmark
- Department of Clinical Medicine, Aarhus University, 8200 Aarhus N, Denmark
| | - Niels H Andersen
- Department of Cardiology, Aalborg University Hospital, 9000 Aalborg, Denmark
| | - Sophie Christin-Maitre
- Endocrine and Reproductive Medicine Unit, Center of Rare Endocrine Diseases of Growth and Development (CMERCD), FIRENDO, Endo ERN Hôpital Saint-Antoine, Sorbonne University, Assistance Publique-Hôpitaux de Paris, 75012 Paris, France
| | - Shanlee M Davis
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO 80045, United States
- eXtraOrdinarY Kids Clinic, Children's Hospital Colorado, Aurora, CO 80045, United States
| | - Anthonie Duijnhouwer
- Department of Cardiology, Radboud University Medical Center, Nijmegen 6500 HB, The Netherlands
| | - Aneta Gawlik
- Departments of Pediatrics and Pediatric Endocrinology, Faculty of Medical Sciences in Katowice, Medical University of Silesia, 40-752 Katowice, Poland
| | - Andrea T Maciel-Guerra
- Area of Medical Genetics, Department of Translational Medicine, School of Medical Sciences, State University of Campinas, 13083-888 São Paulo, Brazil
| | - Iris Gutmark-Little
- Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio 45229, United States
| | - Kathrin Fleischer
- Department of Reproductive Medicine, Nij Geertgen Center for Fertility, Ripseweg 9, 5424 SM Elsendorp, The Netherlands
| | - David Hong
- Division of Interdisciplinary Brain Sciences, Stanford University School of Medicine, Stanford, CA 94304, United States
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA 94304, United States
| | - Karen O Klein
- Rady Children's Hospital, University of California, San Diego, CA 92123, United States
| | - Siddharth K Prakash
- Department of Internal Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030, United States
| | - Roopa Kanakatti Shankar
- Division of Endocrinology, Children's National Hospital, The George Washington University School of Medicine, Washington, DC 20010, United States
| | - David E Sandberg
- Susan B. Meister Child Health Evaluation and Research Center, Department of Pediatrics, University of Michigan, Ann Arbor, MI 48109-2800, United States
- Division of Pediatric Psychology, Department of Pediatrics, University of Michigan, Ann Arbor, MI 48109-2800, United States
| | - Theo C J Sas
- Department the Pediatric Endocrinology, Sophia Children's Hospital, Rotterdam 3015 CN, The Netherlands
- Department of Pediatrics, Centre for Pediatric and Adult Diabetes Care and Research, Rotterdam 3015 CN, The Netherlands
| | - Anne Skakkebæk
- Department of Molecular Medicine, Aarhus University Hospital, 8200 Aarhus N, Denmark
- Department of Clinical Medicine, Aarhus University, 8200 Aarhus N, Denmark
- Department of Clinical Genetics, Aarhus University Hospital, 8200 Aarhus N, Denmark
| | - Kirstine Stochholm
- Department of Endocrinology, Aarhus University Hospital, 8200 Aarhus N, Denmark
- Center for Rare Diseases, Department of Pediatrics, Aarhus University Hospital, 8200 Aarhus N, Denmark
| | - Janielle A van der Velden
- Department of Pediatric Endocrinology, Radboud University Medical Center, Amalia Children's Hospital, Nijmegen 6500 HB, The Netherlands
| | - Philippe F Backeljauw
- Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio 45229, United States
| |
Collapse
|
3
|
Ibarra-Ramírez M, Campos-Acevedo LD, Martínez de Villarreal LE. Chromosomal Abnormalities of Interest in Turner Syndrome: An Update. J Pediatr Genet 2023; 12:263-272. [PMID: 38162151 PMCID: PMC10756729 DOI: 10.1055/s-0043-1770982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/01/2023] [Indexed: 01/03/2024]
Abstract
Turner syndrome (TS) is caused by the total or partial loss of the second sex chromosome; it occurs in 1 every 2,500-3,000 live births. The clinical phenotype is highly variable and includes short stature and gonadal dysgenesis. In 1959, the chromosomal origin of the syndrome was recognized; patients had 45 chromosomes with a single X chromosome. TS presents numerical and structural abnormalities in the sex chromosomes, interestingly only 40% have a 45, X karyotype. The rest of the chromosomal abnormalities include mosaics, deletions of the short and long arms of the X chromosome, rings, and isochromosomes. Despite multiple studies to establish a relationship between the clinical characteristics and the different chromosomal variants in TS, a clear association cannot yet be established. Currently, different mechanisms involved in the phenotype have been explored. This review focuses to analyze the different chromosomal abnormalities and phenotypes in TS and discusses the possible mechanisms that lead to these abnormalities.
Collapse
Affiliation(s)
- Marisol Ibarra-Ramírez
- Department of Genetics, “Dr. José Eleuterio González” University Hospital of the Autonomous University of Nuevo León, Monterrey, México
| | - Luis Daniel Campos-Acevedo
- Department of Genetics, “Dr. José Eleuterio González” University Hospital of the Autonomous University of Nuevo León, Monterrey, México
| | - Laura E. Martínez de Villarreal
- Department of Genetics, “Dr. José Eleuterio González” University Hospital of the Autonomous University of Nuevo León, Monterrey, México
| |
Collapse
|
4
|
Wei C, Wang Y, Hu C. Bioinformatic analysis and experimental validation of the potential gene in the airway inflammation of steroid-resistant asthma. Sci Rep 2023; 13:8098. [PMID: 37208441 DOI: 10.1038/s41598-023-35214-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 05/15/2023] [Indexed: 05/21/2023] Open
Abstract
Steroid-resistant asthma is a troublesome clinical problem in public health. The pathogenesis of steroid-resistant asthma is complex and remains to be explored. In our work, the online Gene Expression Omnibus microarray dataset GSE7368 was used to explore differentially expressed genes (DEGs) between steroid-resistant asthma patients and steroid-sensitive asthma patients. Tissue-specific gene expression of DEGs was analyzed using BioGPS. The enrichment analyses were performed using GO, KEGG, and GSEA analysis. The protein-protein interaction network and key gene cluster were constructed using STRING, Cytoscape, MCODE, and Cytohubba. A steroid-resistant neutrophilic asthma mouse model was established using lipopolysaccharide (LPS) and ovalbumin (OVA). An LPS-stimulated J744A.1 macrophage model was prepared to validate the underlying mechanism of the interesting DEG gene using the quantitative reverse transcription-polymerase chain reaction (qRT-PCR). A total of 66 DEGs were identified, most of which were present in the hematologic/immune system. Enrichment analysis displayed that the enriched pathways were the IL-17 signaling pathway, MAPK signal pathway, Toll-like receptor signaling pathway, and so on. DUSP2, as one of the top upregulated DEGs, has not been clearly demonstrated in steroid-resistant asthma. In our study, we observed that the salubrinal administration (DUSP2 inhibitor) reversed neutrophilic airway inflammation and cytokine responses (IL-17A, TNF-α) in a steroid-resistant asthma mouse model. We also found that salubrinal treatment reduced inflammatory cytokines (CXCL10 and IL-1β) in LPS-stimulated J744A.1 macrophages. DUSP2 may be a candidate target for the therapy of steroid-resistant asthma.
Collapse
Affiliation(s)
- Chaochao Wei
- Department of Pulmonary and Critical Care Medicine, Hainan General Hospital, Haikou, People's Republic of China
- Department of Pulmonary and Critical Care Medicine, Affiliated Hainan Hospital of Hainan Medical University, Haikou, People's Republic of China
- Department of Oncology, Xiangya Hospital Central South University, Changsha, People's Republic of China
- Key Laboratory of Emergency and Trauma of Ministry of Education, Hainan Medical University, Haikou, 571199, People's Republic of China
| | - Yang Wang
- Department of Respiratory Medicine (Department of Respiratory and Critical Care Medicine), Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
| | - Chengping Hu
- Department of Respiratory Medicine (Department of Respiratory and Critical Care Medicine), Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China.
| |
Collapse
|
5
|
Zhou H, Zhou Z, Yin Z, Lin J, Ni B, Wang X, Peng Y, Xie W. Genome-wide differential expression analysis of cell-free microRNAs in amniotic fluid of fetus with Down syndrome. GENE REPORTS 2023. [DOI: 10.1016/j.genrep.2022.101726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
6
|
Johannsen EB, Just J, Viuff MH, Okholm TLH, Pedersen SB, Meyer Lauritsen K, Trolle C, Pedersen MGB, Chang S, Fedder J, Skakkebæk A, Gravholt CH. Sex chromosome aneuploidies give rise to changes in the circular RNA profile: A circular transcriptome-wide study of Turner and Klinefelter syndrome across different tissues. Front Genet 2022; 13:928874. [PMID: 35938026 PMCID: PMC9355307 DOI: 10.3389/fgene.2022.928874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/28/2022] [Indexed: 11/13/2022] Open
Abstract
Purpose: The landscape of circular RNAs (circRNAs), an important class of non-coding RNAs that regulate gene expression, has never been described in human disorders of sex chromosome aneuploidies. We profiled circRNAs in Turner syndrome females (45,X; TS) and Klinefelter syndrome males (47,XXY; KS) to investigate how circRNAs respond to a missing or an extra X chromosome. Methods: Samples of blood, muscle and fat were collected from individuals with TS (n = 33) and KS (n = 22) and from male (n = 16) and female (n = 44) controls. CircRNAs were identified using a combination of circRNA identification pipelines (CIRI2, CIRCexplorer2 and circRNA_finder). Results: Differential expression of circRNAs was observed throughout the genome in TS and KS, in all tissues. The host-genes from which several of these circRNAs were derived, were associated with known phenotypic traits. Furthermore, several differentially expressed circRNAs had the potential to capture micro RNAs that targeted protein-coding genes with altered expression in TS and KS. Conclusion: Sex chromosome aneuploidies introduce changes in the circRNA transcriptome, demonstrating that the genomic changes in these syndromes are more complex than hitherto thought. CircRNAs may help explain some of the genomic and phenotypic traits observed in these syndromes.
Collapse
Affiliation(s)
- Emma B. Johannsen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Departments of Clinical Medicine, Aarhus University, Aarhus, Denmark
- *Correspondence: Emma B. Johannsen,
| | - Jesper Just
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Departments of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Mette H. Viuff
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Trine Line Hauge Okholm
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Otolaryngology-Head and Neck Surgery and Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, United States
| | | | - Katrine Meyer Lauritsen
- Steno Diabetes Center, Aarhus University Hospital, Aarhus, Denmark
- Department of Endocrinology, Aarhus University Hospital, Aarhus, Denmark
| | - Christian Trolle
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Endocrinology, Aarhus University Hospital, Aarhus, Denmark
| | | | - Simon Chang
- Department of Endocrinology, Aarhus University Hospital, Aarhus, Denmark
| | - Jens Fedder
- Centre of Andrology and Fertility Clinic, Department D, Odense University Hospital, Odense, Denmark
- Research Unit of Human Reproduction, Institute of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Anne Skakkebæk
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Claus H. Gravholt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Endocrinology, Aarhus University Hospital, Aarhus, Denmark
| |
Collapse
|
7
|
Liu P, Vossaert L. Emerging technologies for prenatal diagnosis: The application of whole genome and RNA sequencing. Prenat Diagn 2022; 42:686-696. [PMID: 35416301 PMCID: PMC10014115 DOI: 10.1002/pd.6146] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 04/06/2022] [Accepted: 04/07/2022] [Indexed: 11/10/2022]
Abstract
DNA sequencing technologies for clinical genetic testing have been rapidly evolving in recent years, and steadily become more important within the field of prenatal diagnostics. This review aims to give an overview of recent developments and to describe how they have the potential to fill the gaps of the currently clinically implemented methods for prenatal diagnosis of various genetic disorders. It has been shown for postnatal testing that whole genome sequencing provides a set of added benefits compared to exome sequencing, and it is to be expected that this will be the case for prenatal testing as well. RNA-sequencing, already used postnatally, can provide valuable complementary data to DNA-based testing, and aid in variant interpretation. While not ready for clinical implementation, emerging technologies such as long-read and Hi-C sequencing analyses might add to the toolbox for interpreting the expanding genetic data sets generated by genome-wide sequencing. Lastly, we also discuss some more practical implications of introducing these emerging technologies, which generate larger and larger genomic data sets, in the prenatal field.
Collapse
Affiliation(s)
- Pengfei Liu
- Baylor College of Medicine and Baylor Genetics, Houston, Texas, USA
| | | |
Collapse
|
8
|
Kim MA, Lee EJ, Yang W, Shin HY, Kim YH, Kim JH. Identification of a novel gene signature in second-trimester amniotic fluid for the prediction of preterm birth. Sci Rep 2022; 12:3085. [PMID: 35361790 PMCID: PMC8971495 DOI: 10.1038/s41598-021-04709-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 11/30/2021] [Indexed: 11/09/2022] Open
Abstract
Preterm birth affects approximately 5% to 7% of live births worldwide and is the leading cause of neonatal morbidity and mortality. Amniotic fluid supernatant (AFS) contains abundant cell-free nucleic acids (cfNAs) that can provide genetic information associated with pregnancy complications. In the current study, cfNAs of AFS in the early second-trimester before the onset of symptoms of preterm birth were analyzed, and we compared gene expression levels between spontaneous preterm birth (n = 5) and term birth (n = 5) groups using sequencing analysis. Differential expression analyses detected 24 genes with increased and 6 genes with decreased expression in the preterm birth group compared to term birth. Upregulated expressions of RDH14, ZNF572, VOPP1, SERPINA12, and TCF15 were validated in an extended AFS sample by quantitative PCR (preterm birth group, n = 21; term birth group, n = 40). Five candidate genes displayed a significant increase in mRNA expression in immortalized trophoblast HTR-8/SVneo cell with H2O2 treatment. Moreover, the expression of five candidate genes was increased to more than twofold by pretreatment with lipopolysaccharide in HTR-8/SVneo cells. Changes in gene expression between preterm birth and term birth is strongly correlated with oxidative stress and infection during pregnancy. Specific expression patterns of genes could be used as potential markers for the early identification of women at risk of having a spontaneous preterm birth.
Collapse
Affiliation(s)
- Min-A Kim
- Department of Obstetrics and Gynecology, Gangnam Severance Hospital, Institute of Women's Life Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Eun-Ju Lee
- Department of Obstetrics and Gynecology, Gangnam Severance Hospital, Institute of Women's Life Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Wookyeom Yang
- Department of Obstetrics and Gynecology, Gangnam Severance Hospital, Institute of Women's Life Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Ha-Yeon Shin
- Department of Obstetrics and Gynecology, Gangnam Severance Hospital, Institute of Women's Life Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Young-Han Kim
- Department of Obstetrics and Gynecology, Severance Hospital, Institute of Women's Life Medical Science, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea.
| | - Jae-Hoon Kim
- Department of Obstetrics and Gynecology, Gangnam Severance Hospital, Institute of Women's Life Medical Science, Yonsei University College of Medicine, Seoul, Korea
| |
Collapse
|
9
|
Xue R, Tang Q, Zhang Y, Xie M, Li C, Wang S, Yang H. Integrative Analyses of Genes Associated With Otologic Disorders in Turner Syndrome. Front Genet 2022; 13:799783. [PMID: 35273637 PMCID: PMC8902304 DOI: 10.3389/fgene.2022.799783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 02/08/2022] [Indexed: 12/02/2022] Open
Abstract
Background: Loss or partial loss of one X chromosome induces Turner syndrome (TS) in females, causing major medical concerns, including otologic disorders. However, the underlying genetic pathophysiology of otologic disorders in TS is mostly unclear. Methods: Ear-related genes of TS (TSEs) were identified by analyzing differentially expressed genes (DEGs) in two Gene Expression Omnibus (GEO)-derived expression profiles and ear-genes in the Comparative Toxicogenomic Database (CTD). Subsequently, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Disease Ontology (DO) analyses; Gene Set Enrichment Analysis (GSEA); and Gene Set Variation Analysis (GSVA) were adopted to study biological functions. Moreover, hub genes within the TSEs were identified by assessing protein-protein interaction (PPI), gene-microRNA, and gene-transcription factor (TF) networks. Drug-Gene Interaction Database (DGIdb) analysis was performed to predict molecular drugs for TS. Furthermore, three machine-learning analysis outcomes were comprehensively compared to explore optimal biomarkers of otologic disorders in TS. Finally, immune cell infiltration was analyzed. Results: The TSEs included 30 significantly upregulated genes and 14 significantly downregulated genes. Enrichment analyses suggested that TSEs play crucial roles in inflammatory responses, phospholipid and glycerolipid metabolism, transcriptional processes, and epigenetic processes, such as histone acetylation, and their importance for inner ear development. Subsequently, we described three hub genes in the PPI network and confirmed their involvement in Wnt/β-catenin signaling pathway and immune cell regulation and roles in maintaining normal auditory function. We also constructed gene-microRNA and gene-TF networks. A novel biomarker (SLC25A6) of the pathogenesis of otologic disorders in TS was identified by comprehensive comparisons of three machine-learning analyses with the best predictive performance. Potential therapeutic agents in TS were predicted using the DGIdb. Immune cell infiltration analysis showed that TSEs are related to immune-infiltrating cells. Conclusion: Overall, our findings have deepened the understanding of the pathophysiology of otologic disorders in TS and made contributions to present a promising biomarker and treatment targets for in-depth research.
Collapse
Affiliation(s)
- Ruoyan Xue
- Department of Otolaryngology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qi Tang
- Department of Otolaryngology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yongli Zhang
- Department of Otolaryngology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Mengyao Xie
- Department of Otolaryngology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chen Li
- Department of Otolaryngology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shu Wang
- Department of Otolaryngology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hua Yang
- Department of Otolaryngology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| |
Collapse
|
10
|
The Relationship between Telomere Length and Gestational Weight Gain: Findings from the Mamma & Bambino Cohort. Biomedicines 2021; 10:biomedicines10010067. [PMID: 35052747 PMCID: PMC8773008 DOI: 10.3390/biomedicines10010067] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 12/22/2021] [Accepted: 12/28/2021] [Indexed: 12/21/2022] Open
Abstract
Inadequate gestational weight gain (GWG) affects a growing number of pregnancies, influencing intrauterine environment and long-term health. Uncovering molecular mechanisms associated with GWG could be helpful to develop public health strategies for tackling this issue. Here, our study aimed to understand the relationship of DNA telomere length with weigh gain during pregnancy, using data and samples from the ongoing prospective “Mamma & Bambino” study (Catania, Italy). GWG was calculated according to the Institute of Medicine (IOM) guidelines. Relative telomere length was assessed by real-time quantitative polymerase chain reaction in 252 samples of maternal leucocyte DNA (mlDNA) and 150 samples of cell-free DNA (cfDNA) from amniotic fluid. We observed that relative telomere length of mlDNA seemed to weakly increase with GWG. In contrast, telomere length of cfDNA exhibited a U-shaped relationship with GWG. Women with adequate GWG showed longer telomere length than those who gained weight inadequately. Accordingly, the logistic regression model confirmed the association between telomere length of cfDNA and adequate GWG, after adjusting for potential confounders. Our findings suggest an early effect of GWG on telomere length of cfDNA, which could represent a molecular mechanism underpinning the effects of maternal behaviours on foetal well-being.
Collapse
|
11
|
Biradar VS, Rajpathak SN, Joshi SR, Deobagkar DD. Functional and regulatory aspects of oxidative stress response in X monosomy. In Vitro Cell Dev Biol Anim 2021; 57:661-675. [PMID: 34505228 DOI: 10.1007/s11626-021-00604-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 06/28/2021] [Indexed: 11/26/2022]
Abstract
The partial/complete loss of one X chromosome in a human female leads to Turner syndrome (TS). TS individuals display a range of phenotypes including short stature, osteoporosis, ovarian malfunction, diabetes, and thyroid dysfunction. Epigenetic factors and regulatory networks are distinctly different in X monosomy (45, X). In a lifetime, an individual is exposed to a variety of stress conditions. To study whether X monosomy cells display a differential response upon exposure to mild stress as compared to normal 46, XX cells and whether this may contribute to various co-morbidities in aneuploid individuals, we have carried out a transcriptomic analysis of human fibroblasts 45, X and 46, XX after exposure to mild oxidative stress. Under these conditions, over 350 transcripts were seen to be differentially expressed in 45, X and 46, XX cells. Pathways associated with oxidative stress were differentially expressed highlighting the differential regulation of genes and associated phenotypes. It could be seen that X monosomy cells are more susceptible to oxidative stress as compared to normal cells and have altered molecular pathways both in normal conditions and also upon exposure to mild oxidative stress. To explore this aspect in detail, we have mapped the expressions of transcription factors (TFs) in 45, X and 46, XX cells. The network of transcription activating factors is differentially regulated in 45, X and 46, XX cells under stress exposure. It is tempting to speculate that the altered ability of 45, X (Turner) cells to respond to stress may play a significant role in the physiological function and altered phenotypes in Turner syndrome.
Collapse
Affiliation(s)
- Vinayak S Biradar
- Molecular Biology Research Laboratory, Department of Zoology, Savitribai Phule Pune University, Pune, India
| | - Shriram N Rajpathak
- Molecular Biology Research Laboratory, Department of Zoology, Savitribai Phule Pune University, Pune, India
- Recombinant Department, Serum Institute of India Pvt. Ltd., Pune, 411 028, India
| | - Suraj R Joshi
- Molecular Biology Research Laboratory, Department of Zoology, Savitribai Phule Pune University, Pune, India
| | - Deepti D Deobagkar
- Molecular Biology Research Laboratory, Department of Zoology, Savitribai Phule Pune University, Pune, India.
- School of Physical Sciences, ISRO Space Technology Cell, Savitribai Phule Pune University, Pune, 411 007, India.
| |
Collapse
|
12
|
Mnif-Feki M, Safi W, Bougacha-Elleuch N, Abid G, Moalla M, Elleuch M, Ben Salah DH, Rekik N, Belguith N, Abdelhedi F, Kammoun T, Hachicha M, Charfi N, Mnif F, Kammoun H, Hadj Kacem H, Hadj-Kacem F, Abid M. Occurrence of Hypopituitarism in Tunisian Turner Syndrome patients: familial versus sporadic cases. Gynecol Endocrinol 2021; 37:848-852. [PMID: 34124982 DOI: 10.1080/09513590.2021.1939298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
OBJECTIVE To explore unusual association between Turner Syndrome (TS) and Hypopituitarism in a Tunisian cohort. METHODS We reported 6 patients with TS associated to Hypopituitarism, including three familial cases except the fourth sister who showed only a TS phenotype. Biochemical analysis, resonance magnetic imaging and cytogenetic analyses were performed. RESULTS The average age of our patients was 17.2 years (11-31 years). They were all referred for short stature and pubertal delay, except for the fourth sister who presented spontaneous puberty with the integrity of the pituitary axis and the presence of an X ring chromosome. Karyotype analysis showed monosomy in 3 cases and a mosaic TS in the 3 remaining cases, including one patient with abnormal X chromosome structure. Somatotropic and corticotropic deficiencies were confirmed in 2 sporadic cases while the gonadotropic and thyrotropic axes were spared. In contrast; familial cases were consistently affected by the integrity of the corticotropic axis. MRI showed pituitary hypoplasia in all familial cases and pituitary stalk interruption syndrome in only one sporadic case. No correlation was found between the chromosome formula and the anterior pituitary involvement. CONCLUSION Co-segregation of congenital Hypopituitarism with pituitary hypoplasia and X chromosome aberrations could imply a molecular anomaly of transcription factors responsible for the differentiation and development of pituitary cells such as PROP1, POUF1, Hesx1, Lhx3, Lhx4. The etiopathogenic link between X chromosome abnormalities and the occurrence of Hypopituitarism remains unclear; however, the progress of molecular biology may clarify the interrelation between transcription factors and sex chromosome segregation abnormalities.
Collapse
Affiliation(s)
- M Mnif-Feki
- Endocrinology-Diabetology Department, CHU Hédi Chaker, Sfax, Tunisia
| | - W Safi
- Endocrinology-Diabetology Department, CHU Hédi Chaker, Sfax, Tunisia
| | - N Bougacha-Elleuch
- Laboratory of Molecular and Functional Genetics, Faculty of Sciences of Sfax, Sfax University, TUNISIA
| | - G Abid
- Department of Medical Imaging, Auxerre Hospital Center, Auxerre, France
| | - M Moalla
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, Sfax, Tunisia
| | - M Elleuch
- Endocrinology-Diabetology Department, CHU Hédi Chaker, Sfax, Tunisia
| | - D H Ben Salah
- Endocrinology-Diabetology Department, CHU Hédi Chaker, Sfax, Tunisia
| | - N Rekik
- Endocrinology-Diabetology Department, CHU Hédi Chaker, Sfax, Tunisia
| | - N Belguith
- Genetic Department, Medicine CHU Hédi Chaker, Sfax, Tunisia
| | - F Abdelhedi
- Genetic Department, Medicine CHU Hédi Chaker, Sfax, Tunisia
| | - T Kammoun
- Pediatric Department, CHU Hédi Chaker, Sfax, Tunisia
| | - M Hachicha
- Pediatric Department, CHU Hédi Chaker, Sfax, Tunisia
| | - N Charfi
- Endocrinology-Diabetology Department, CHU Hédi Chaker, Sfax, Tunisia
| | - F Mnif
- Endocrinology-Diabetology Department, CHU Hédi Chaker, Sfax, Tunisia
| | - H Kammoun
- Genetic Department, Medicine CHU Hédi Chaker, Sfax, Tunisia
| | - H Hadj Kacem
- Department of Applied Biology, College of Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - F Hadj-Kacem
- Endocrinology-Diabetology Department, CHU Hédi Chaker, Sfax, Tunisia
| | - M Abid
- Endocrinology-Diabetology Department, CHU Hédi Chaker, Sfax, Tunisia
| |
Collapse
|
13
|
The amniotic fluid cell-free transcriptome in spontaneous preterm labor. Sci Rep 2021; 11:13481. [PMID: 34188072 PMCID: PMC8242007 DOI: 10.1038/s41598-021-92439-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 06/03/2021] [Indexed: 02/03/2023] Open
Abstract
The amniotic fluid (AF) cell-free RNA was shown to reflect physiological and pathological processes in pregnancy, but its value in the prediction of spontaneous preterm delivery is unknown. Herein we profiled cell-free RNA in AF samples collected from women who underwent transabdominal amniocentesis after an episode of spontaneous preterm labor and subsequently delivered within 24 h (n = 10) or later (n = 28) in gestation. Expression of known placental single-cell RNA-Seq signatures was quantified in AF cell-free RNA and compared between the groups. Random forest models were applied to predict time-to-delivery after amniocentesis. There were 2385 genes differentially expressed in AF samples of women who delivered within 24 h of amniocentesis compared to gestational age-matched samples from women who delivered after 24 h of amniocentesis. Genes with cell-free RNA changes were associated with immune and inflammatory processes related to the onset of labor, and the expression of placental single-cell RNA-Seq signatures of immune cells was increased with imminent delivery. AF transcriptomic prediction models captured these effects and predicted delivery within 24 h of amniocentesis (AUROC = 0.81). These results may inform the development of biomarkers for spontaneous preterm birth.
Collapse
|
14
|
Farooqui A, Alhazmi A, Haque S, Tamkeen N, Mehmankhah M, Tazyeen S, Ali S, Ishrat R. Network-based analysis of key regulatory genes implicated in Type 2 Diabetes Mellitus and Recurrent Miscarriages in Turner Syndrome. Sci Rep 2021; 11:10662. [PMID: 34021221 PMCID: PMC8140125 DOI: 10.1038/s41598-021-90171-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 05/06/2021] [Indexed: 02/04/2023] Open
Abstract
The information on the genotype-phenotype relationship in Turner Syndrome (TS) is inadequate because very few specific candidate genes are linked to its clinical features. We used the microarray data of TS to identify the key regulatory genes implicated with TS through a network approach. The causative factors of two common co-morbidities, Type 2 Diabetes Mellitus (T2DM) and Recurrent Miscarriages (RM), in the Turner population, are expected to be different from that of the general population. Through microarray analysis, we identified nine signature genes of T2DM and three signature genes of RM in TS. The power-law distribution analysis showed that the TS network carries scale-free hierarchical fractal attributes. Through local-community-paradigm (LCP) estimation we find that a strong LCP is also maintained which means that networks are dynamic and heterogeneous. We identified nine key regulators which serve as the backbone of the TS network. Furthermore, we recognized eight interologs functional in seven different organisms from lower to higher levels. Overall, these results offer few key regulators and essential genes that we envisage have potential as therapeutic targets for the TS in the future and the animal models studied here may prove useful in the validation of such targets.
Collapse
Affiliation(s)
- Anam Farooqui
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Alaa Alhazmi
- Medical Laboratory Technology Department, Jazan University, Jazan, Saudi Arabia
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Naaila Tamkeen
- Department of Biosciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Mahboubeh Mehmankhah
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Safia Tazyeen
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Sher Ali
- Department of Life Sciences, Sharda University, Greater Noida, 201310, India
| | - Romana Ishrat
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India.
| |
Collapse
|
15
|
The Amniotic Fluid Cell-Free Transcriptome Provides Novel Information about Fetal Development and Placental Cellular Dynamics. Int J Mol Sci 2021; 22:ijms22052612. [PMID: 33807645 PMCID: PMC7961801 DOI: 10.3390/ijms22052612] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 02/28/2021] [Accepted: 03/02/2021] [Indexed: 12/16/2022] Open
Abstract
The amniotic fluid (AF) is a complex biofluid that reflects fetal well-being during development. AF con be divided into two fractions, the supernatant and amniocytes. The supernatant contains cell-free components, including placenta-derived microparticles, protein, cell-free fetal DNA, and cell-free fetal RNA from the fetus. Cell-free mRNA (cfRNA) analysis holds a special position among high-throughput analyses, such as transcriptomics, proteomics, and metabolomics, owing to its ease of profiling. The AF cell-free transcriptome differs from the amniocyte transcriptome and alters with the progression of pregnancy and is often associated with the development of various organ systems including the fetal lung, skin, brain, pancreas, adrenal gland, gastrointestinal system, etc. The AF cell-free transcriptome is affected not only by normal physiologies, such as fetal sex, gestational age, and fetal maturity, but also by pathologic mechanisms such as maternal obesity, and genetic syndromes (Down, Edward, Turner, etc.), as well as pregnancy complications (preeclampsia, intrauterine growth restriction, preterm birth, etc.). cfRNA in the amniotic fluid originates from the placenta and fetal organs directly contacting the amniotic fluid as well as from the fetal plasma across the placenta. The AF transcriptome may reflect the fetal and placental development and therefore aid in the monitoring of normal and abnormal development.
Collapse
|
16
|
Zhang X, Hong D, Ma S, Ward T, Ho M, Pattni R, Duren Z, Stankov A, Bade Shrestha S, Hallmayer J, Wong WH, Reiss AL, Urban AE. Integrated functional genomic analyses of Klinefelter and Turner syndromes reveal global network effects of altered X chromosome dosage. Proc Natl Acad Sci U S A 2020; 117:4864-4873. [PMID: 32071206 PMCID: PMC7060706 DOI: 10.1073/pnas.1910003117] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
In both Turner syndrome (TS) and Klinefelter syndrome (KS) copy number aberrations of the X chromosome lead to various developmental symptoms. We report a comparative analysis of TS vs. KS regarding differences at the genomic network level measured in primary samples by analyzing gene expression, DNA methylation, and chromatin conformation. X-chromosome inactivation (XCI) silences transcription from one X chromosome in female mammals, on which most genes are inactive, and some genes escape from XCI. In TS, almost all differentially expressed escape genes are down-regulated but most differentially expressed inactive genes are up-regulated. In KS, differentially expressed escape genes are up-regulated while the majority of inactive genes appear unchanged. Interestingly, 94 differentially expressed genes (DEGs) overlapped between TS and female and KS and male comparisons; and these almost uniformly display expression changes into opposite directions. DEGs on the X chromosome and the autosomes are coexpressed in both syndromes, indicating that there are molecular ripple effects of the changes in X chromosome dosage. Six potential candidate genes (RPS4X, SEPT6, NKRF, CX0rf57, NAA10, and FLNA) for KS are identified on Xq, as well as candidate central genes on Xp for TS. Only promoters of inactive genes are differentially methylated in both syndromes while escape gene promoters remain unchanged. The intrachromosomal contact map of the X chromosome in TS exhibits the structure of an active X chromosome. The discovery of shared DEGs indicates the existence of common molecular mechanisms for gene regulation in TS and KS that transmit the gene dosage changes to the transcriptome.
Collapse
Affiliation(s)
- Xianglong Zhang
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA 94305
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
| | - David Hong
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA 94305;
| | - Shining Ma
- Department of Statistics, Stanford University, Stanford, CA 94305
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305
| | - Thomas Ward
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA 94305
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
| | - Marcus Ho
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA 94305
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
| | - Reenal Pattni
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA 94305
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
| | - Zhana Duren
- Department of Statistics, Stanford University, Stanford, CA 94305
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305
| | - Atanas Stankov
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA 94305
| | - Sharon Bade Shrestha
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA 94305
| | - Joachim Hallmayer
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA 94305
| | - Wing Hung Wong
- Department of Statistics, Stanford University, Stanford, CA 94305;
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305
| | - Allan L Reiss
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA 94305;
| | - Alexander E Urban
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA 94305;
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
| |
Collapse
|
17
|
Tarca AL, Romero R, Pique-Regi R, Pacora P, Done B, Kacerovsky M, Bhatti G, Jaiman S, Hassan SS, Hsu CD, Gomez-Lopez N. Amniotic fluid cell-free transcriptome: a glimpse into fetal development and placental cellular dynamics during normal pregnancy. BMC Med Genomics 2020; 13:25. [PMID: 32050959 PMCID: PMC7017452 DOI: 10.1186/s12920-020-0690-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 01/29/2020] [Indexed: 02/07/2023] Open
Abstract
Background The amniotic fluid (AF) cell-free transcriptome is modulated by physiologic and pathologic processes during pregnancy. AF gene expression changes with advancing gestation reflect fetal development and organ maturation; yet, defining normal expression and splicing patterns for biomarker discovery in obstetrics requires larger heterogeneous cohorts, evaluation of potential confounding factors, and novel analytical approaches. Methods Women with a normal pregnancy who had an AF sample collected during midtrimester (n = 30) or at term gestation (n = 68) were included. Expression profiling at exon level resolution was performed using Human Transcriptome Arrays. Differential expression was based on moderated t-test adjusted p < 0.05 and fold change > 1.25; for differential splicing, a splicing index > 2 and adjusted p < 0.05 were required. Functional profiling was used to interpret differentially expressed or spliced genes. The expression of tissue-specific and cell-type specific signatures defined by single-cell genomics was quantified and correlated with covariates. In-silico validation studies were performed using publicly available datasets. Results 1) 64,071 genes were detected in AF, with 11% of the coding and 6% of the non-coding genes being differentially expressed between midtrimester and term gestation. Expression changes were highly correlated with those previously reported (R > 0.79, p < 0.001) and featured increased expression of genes specific to the trachea, salivary glands, and lung and decreased expression of genes specific to the cardiac myocytes, uterus, and fetal liver, among others. 2) Single-cell RNA-seq signatures of the cytotrophoblast, Hofbauer cells, erythrocytes, monocytes, T and B cells, among others, showed complex patterns of modulation with gestation (adjusted p < 0.05). 3) In 17% of the genes detected, we found differential splicing with advancing gestation in genes related to brain development processes and immunity pathways, including some that were missed based on differential expression analysis alone. Conclusions This represents the largest AF transcriptomics study in normal pregnancy, reporting for the first time that single-cell genomic signatures can be tracked in the AF and display complex patterns of expression during gestation. We also demonstrate a role for alternative splicing in tissue-identity acquisition, organ development, and immune processes. The results herein may have implications for the development of fetal testing to assess placental function and fetal organ maturity.
Collapse
Affiliation(s)
- Adi L Tarca
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, 𝐸𝑢𝑛𝑖𝑐𝑒 𝐾𝑒𝑛𝑛𝑒𝑑𝑦 𝑆ℎ𝑟𝑖𝑣𝑒𝑟 National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services (NICHD/NIH/DHHS), Detroit, MI, USA. .,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA. .,Department of Computer Science, Wayne State University College of Engineering, Detroit, MI, USA.
| | - Roberto Romero
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, 𝐸𝑢𝑛𝑖𝑐𝑒 𝐾𝑒𝑛𝑛𝑒𝑑𝑦 𝑆ℎ𝑟𝑖𝑣𝑒𝑟 National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services (NICHD/NIH/DHHS), Detroit, MI, USA. .,Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI, USA. .,Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, USA. .,Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA. .,Detroit Medical Center, Detroit, MI, USA. .,Department of Pathology, Hutzel Women's Hospital, Wayne State University School of Medicine, Detroit, MI, USA.
| | - Roger Pique-Regi
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, 𝐸𝑢𝑛𝑖𝑐𝑒 𝐾𝑒𝑛𝑛𝑒𝑑𝑦 𝑆ℎ𝑟𝑖𝑣𝑒𝑟 National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services (NICHD/NIH/DHHS), Detroit, MI, USA.,Department of Computer Science, Wayne State University College of Engineering, Detroit, MI, USA
| | - Percy Pacora
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, 𝐸𝑢𝑛𝑖𝑐𝑒 𝐾𝑒𝑛𝑛𝑒𝑑𝑦 𝑆ℎ𝑟𝑖𝑣𝑒𝑟 National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services (NICHD/NIH/DHHS), Detroit, MI, USA.,Department of Computer Science, Wayne State University College of Engineering, Detroit, MI, USA
| | - Bogdan Done
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, 𝐸𝑢𝑛𝑖𝑐𝑒 𝐾𝑒𝑛𝑛𝑒𝑑𝑦 𝑆ℎ𝑟𝑖𝑣𝑒𝑟 National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services (NICHD/NIH/DHHS), Detroit, MI, USA
| | - Marian Kacerovsky
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, 𝐸𝑢𝑛𝑖𝑐𝑒 𝐾𝑒𝑛𝑛𝑒𝑑𝑦 𝑆ℎ𝑟𝑖𝑣𝑒𝑟 National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services (NICHD/NIH/DHHS), Detroit, MI, USA.,Department of Computer Science, Wayne State University College of Engineering, Detroit, MI, USA
| | - Gaurav Bhatti
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, 𝐸𝑢𝑛𝑖𝑐𝑒 𝐾𝑒𝑛𝑛𝑒𝑑𝑦 𝑆ℎ𝑟𝑖𝑣𝑒𝑟 National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services (NICHD/NIH/DHHS), Detroit, MI, USA.,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Sunil Jaiman
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, 𝐸𝑢𝑛𝑖𝑐𝑒 𝐾𝑒𝑛𝑛𝑒𝑑𝑦 𝑆ℎ𝑟𝑖𝑣𝑒𝑟 National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services (NICHD/NIH/DHHS), Detroit, MI, USA.,Department of Pathology, Hutzel Women's Hospital, Wayne State University School of Medicine, Detroit, MI, USA
| | - Sonia S Hassan
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, 𝐸𝑢𝑛𝑖𝑐𝑒 𝐾𝑒𝑛𝑛𝑒𝑑𝑦 𝑆ℎ𝑟𝑖𝑣𝑒𝑟 National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services (NICHD/NIH/DHHS), Detroit, MI, USA.,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA.,Department of Physiology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Chaur-Dong Hsu
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, 𝐸𝑢𝑛𝑖𝑐𝑒 𝐾𝑒𝑛𝑛𝑒𝑑𝑦 𝑆ℎ𝑟𝑖𝑣𝑒𝑟 National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services (NICHD/NIH/DHHS), Detroit, MI, USA.,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA.,Department of Physiology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Nardhy Gomez-Lopez
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, 𝐸𝑢𝑛𝑖𝑐𝑒 𝐾𝑒𝑛𝑛𝑒𝑑𝑦 𝑆ℎ𝑟𝑖𝑣𝑒𝑟 National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services (NICHD/NIH/DHHS), Detroit, MI, USA. .,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA. .,Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicin, Detroit, MI, USA.
| |
Collapse
|
18
|
Wang H, Zhu H, Zhu W, Xu Y, Wang N, Han B, Song H, Qiao J. Bioinformatic Analysis Identifies Potential Key Genes in the Pathogenesis of Turner Syndrome. Front Endocrinol (Lausanne) 2020; 11:104. [PMID: 32210915 PMCID: PMC7069359 DOI: 10.3389/fendo.2020.00104] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 02/18/2020] [Indexed: 12/29/2022] Open
Abstract
Background: Turner syndrome (TS) is a sex chromosome aneuploidy with a variable spectrum of symptoms including short stature, ovarian failure and skeletal abnormalities. The etiology of TS is complex, and the mechanisms driving its pathogenesis remain unclear. Methods: In our study, we used the online Gene Expression Omnibus (GEO) microarray expression profiling dataset GSE46687 to identify differentially expressed genes (DEGs) between monosomy X TS patients and normal female individuals. The relevant data on 26 subjects with TS (45,XO) and 10 subjects with the normal karyotype (46,XX) was investigated. Then, tissue-specific gene expression, functional enrichment, and protein-protein interaction (PPI) network analyses were performed, and the key modules were identified. Results: In total, 25 upregulated and 60 downregulated genes were identified in the differential expression analysis. The tissue-specific gene expression analysis of the DEGs revealed that the system with the most highly enriched tissue-specific gene expression was the hematologic/immune system, followed by the skin/skeletal muscle and neurologic systems. The PPI network analysis, construction of key modules and manual screening of tissue-specific gene expression resulted in the identification of the following five genes of interest: CD99, CSF2RA, MYL9, MYLPF, and IGFBP2. CD99 and CSF2RA are involved in the hematologic/immune system, MYL9 and MYLPF are related to the circulatory system, and IGFBP2 is related to skeletal abnormalities. In addition, several genes of interest with possible roles in the pathogenesis of TS were identified as being associated with the hematologic/immune system or metabolism. Conclusion: This discovery-driven analysis may be a useful method for elucidating novel mechanisms underlying TS. However, more experiments are needed to further explore the relationships between these genes and TS in the future.
Collapse
Affiliation(s)
- Hao Wang
- Department of Endocrinology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hui Zhu
- Department of Endocrinology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wenjiao Zhu
- Department of Endocrinology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yue Xu
- Department of Endocrinology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Nan Wang
- Department of Endocrinology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bing Han
- Department of Endocrinology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Huaidong Song
- Research Centre for Clinical Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jie Qiao
- Department of Endocrinology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| |
Collapse
|
19
|
Cheung CY, Anderson DF, Brace RA. Multiomics analyses of vesicular transport pathway-specific transcripts and proteins in ovine amnion: responses to altered intramembranous transport. Physiol Genomics 2019; 51:267-278. [PMID: 31150314 DOI: 10.1152/physiolgenomics.00003.2019] [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] [Indexed: 11/22/2022] Open
Abstract
Amniotic fluid volume (AFV) is determined by the rate of intramembranous (IM) transport of amniotic fluid (AF) across the amnion. This transport is regulated by fetal urine-derived stimulators and AF inhibitors. Our objective was to utilize a multiomics approach to determine the IM transport pathways and identify the regulators. Four groups of fetal sheep with experimentally induced alterations in IM transport rate were studied: control, urine drainage (UD), urine drainage with fluid replacement (UDR), and intra-amniotic fluid infusion (IA). Amnion, AF, and fetal urine were subjected to transcriptomics (RNA-Seq) and proteomics studies followed by Ingenuity Pathway Analysis. The analysis uncovered nine transport-associated pathways and four groups of differentially expressed transcripts and proteins. These can be categorized into mediators of vesicular uptake and endocytosis, intracellular trafficking, pathway activation and signaling, and energy metabolism. UD decreased IM transport rate and AFV in conjunction with enhanced expression of vesicular endocytosis regulators but reduced expression of intracellular trafficking mediators. With UDR, IM transport rate decreased and AFV increased. Energy metabolism activators increased while trafficking mediators decreased in expression. IA increased IM transport rate and AFV together with enhanced expressions of vesicular endocytosis and trafficking mediators. We conclude that IM transport across the amnion is regulated by multiple vesicular transcytotic and signaling pathways and that the mediators of intracellular trafficking most likely play an important role in determining the rate of IM transport. Furthermore, the motor protein cytoplasmic dynein light chain-1, which coexpressed in AF and fetal urine, may function as a urine-derived IM transport stimulator.
Collapse
Affiliation(s)
- Cecilia Y Cheung
- Department of Obstetrics and Gynecology, Oregon Health and Science University , Portland, Oregon.,Center for Developmental Health, Oregon Health and Science University , Portland, Oregon
| | - Debra F Anderson
- Center for Developmental Health, Oregon Health and Science University , Portland, Oregon
| | - Robert A Brace
- Department of Obstetrics and Gynecology, Oregon Health and Science University , Portland, Oregon.,Center for Developmental Health, Oregon Health and Science University , Portland, Oregon
| |
Collapse
|
20
|
Cui X, Cui Y, Shi L, Luan J, Zhou X, Han J. A preliminary study on the mechanism of skeletal abnormalities in Turner syndrome using inducing pluripotent stem cells (iPS)- based disease models. Intractable Rare Dis Res 2019; 8:113-119. [PMID: 31218161 PMCID: PMC6557239 DOI: 10.5582/irdr.2019.01025] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Osteoporosis represent one of main characteristics of Turner syndrome (TS), a rare diseases caused by aberrant deletion of X chromosomes, however, the underlying pathological mechanism remains unknown yet. In this study, we used pluripotent stem cells (iPSCs) derived from a Turner syndrome patient and a health control to induce functional osteoblasts and osteoclasts, in order to compare their difference in these two differentiation. We successfully produced functional osteoblasts and osteoclasts from iPSCs through embryoid bodies (EBs) and mesoderm stages, as demonstrated obvious mineralized nodules and multi-nuclear giant cells with positive tartrate-resistant acid phosphatase (TRAP) staining, and significant up-regulated differentiation marker genes. Interestingly, we found that there was no significant difference in phenotype and marker genes expression between osteoblasts from Turner syndrome and healthy control iPSCs. In contrast, Turner syndrome showed increased osteoclastogenesis compared to the healthy control indicating higher frequency of multi-nuclear TRAP staining cells and elevated osteoclast marker genes TRAP, MMP9, CA2, OSCAR. Therefore, our results suggest that the low bone density of Turner syndrome patients may be caused by aberrant osteoclast differentiation, and further investigation towards osteoclast function under Turner syndrome is deserved.
Collapse
Affiliation(s)
- Xiaoxiao Cui
- School of Medicine and Life Sciences, University of Jinan-Shandong Academy of Medical Sciences, Ji'nan, Chinan
- Key Laboratory for Rare Disease Research of Shandong Province, Key Laboratory for Biotech Drugs of the Ministry of Health, Shandong Medical Biotechnological Center, Shandong Academy of Medical Sciences, Ji'nan, China
| | - Yazhou Cui
- Key Laboratory for Rare Disease Research of Shandong Province, Key Laboratory for Biotech Drugs of the Ministry of Health, Shandong Medical Biotechnological Center, Shandong Academy of Medical Sciences, Ji'nan, China
| | - Liang Shi
- Key Laboratory for Rare Disease Research of Shandong Province, Key Laboratory for Biotech Drugs of the Ministry of Health, Shandong Medical Biotechnological Center, Shandong Academy of Medical Sciences, Ji'nan, China
| | - Jing Luan
- Key Laboratory for Rare Disease Research of Shandong Province, Key Laboratory for Biotech Drugs of the Ministry of Health, Shandong Medical Biotechnological Center, Shandong Academy of Medical Sciences, Ji'nan, China
| | - Xiaoyan Zhou
- Key Laboratory for Rare Disease Research of Shandong Province, Key Laboratory for Biotech Drugs of the Ministry of Health, Shandong Medical Biotechnological Center, Shandong Academy of Medical Sciences, Ji'nan, China
| | - Jinxiang Han
- Key Laboratory for Rare Disease Research of Shandong Province, Key Laboratory for Biotech Drugs of the Ministry of Health, Shandong Medical Biotechnological Center, Shandong Academy of Medical Sciences, Ji'nan, China
- Address correspondence to:Dr. Jinxiang Han, Key Laboratory for Rare Disease Research of Shandong Province, Key Laboratory for Biotech Drugs of the Ministry of Health, Shandong Medical Biotechnological Center, Shandong Academy of Medical Sciences, Ji'nan, Shandong 250062, China. E-mail:
| |
Collapse
|
21
|
Viuff M, Skakkebaek A, Nielsen MM, Chang S, Gravholt CH. Epigenetics and genomics in Turner syndrome. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2019; 181:68-75. [PMID: 30811826 DOI: 10.1002/ajmg.c.31683] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Accepted: 01/10/2019] [Indexed: 12/20/2022]
Abstract
The pathogenesis of Turner syndrome (TS) and the genotype-phenotype relationship has been thoroughly investigated during the last decade. It has become evident that the phenotype seen in TS does not only depend on simple gene dosage as a result of X chromosome monosomy. The origin of TS specific comorbidities such as infertility, cardiac malformations, bone dysgenesis, and autoimmune diseases may depend on a complex relationship between genes as well as transcriptional and epigenetic factors affecting gene expression across the genome. Furthermore, two individuals with TS with the exact same karyotype may exhibit completely different traits, suggesting that no conventional genotype-phenotype relationship exists. Here, we review the different genetic mechanisms behind differential gene expression, and highlight potential key-genes essential to the comorbidities seen in TS and other X chromosome aneuploidy syndromes. KDM6A, important for germ cell development, has shown to be differentially expressed and methylated in Turner and Klinefelter syndrome across studies. Furthermore, TIMP1/TIMP3 genes seem to affect the prevalence of bicuspid aortic valve. KDM5C could play a role in the neurocognitive development of Turner and Klinefelter syndrome. However, further research is needed to elucidate the genetic mechanism behind the phenotypic variability and the different phenotypic traits seen in TS.
Collapse
Affiliation(s)
- Mette Viuff
- Department of Endocrinology and Internal Medicine (MEA), Aarhus University Hospital, Aarhus, Denmark.,Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Anne Skakkebaek
- Department of Endocrinology and Internal Medicine (MEA), Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Morten M Nielsen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Simon Chang
- Department of Endocrinology and Internal Medicine (MEA), Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Biochemistry, Esbjerg Sygehus, Denmark
| | - Claus H Gravholt
- Department of Endocrinology and Internal Medicine (MEA), Aarhus University Hospital, Aarhus, Denmark.,Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| |
Collapse
|
22
|
Bianchi DW. Turner syndrome: New insights from prenatal genomics and transcriptomics. AMERICAN JOURNAL OF MEDICAL GENETICS. PART C, SEMINARS IN MEDICAL GENETICS 2019; 181:10.1002/ajmg.c.31675. [PMID: 30706680 PMCID: PMC10110351 DOI: 10.1002/ajmg.c.31675] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 12/30/2018] [Indexed: 01/08/2023]
Abstract
In some parts of the world, prenatal screening using analysis of circulating cell-free (cf) DNA in the plasma of pregnant women has become part of routine prenatal care with limited professional guidelines and without significant input from the Turner syndrome community. In contrast to the very high positive predictive values (PPVs) achieved with cfDNA analysis for trisomy 21 (91% for high-risk and 82% for low-risk cases), the PPVs for monosomy X are much lower (~26%). This is because the maternal plasma sample contains both maternal cfDNA and placental DNA, which is a proxy for the fetal genome. Underlying biological mechanisms for false positive monosomy X screening results include confined placental mosaicism, co-twin demise, and maternal mosaicism. Somatic loss of a single X chromosome in the mother is a natural phenomenon that occurs with aging; this could explain many of the false positive cfDNA results. There is also increased awareness of women who have constitutional mosaicism for 45, X who are fertile. It is important to recognize that a positive cfDNA screen for 45, X does not mean that the fetus has Turner syndrome. A follow-up diagnostic test, either amniocentesis or neonatal karyotype/chromosome microarray, is recommended. Research studies on cell-free mRNA in second trimester amniotic fluid, which is almost exclusively fetal, demonstrate consistent dysregulation of genes involved in the hematologic, immune, and neurologic systems. This suggests that some of the pathophysiology of Turner syndrome occurs early in fetal life and presents novel opportunities for consideration of antenatal treatments.
Collapse
Affiliation(s)
- Diana W Bianchi
- Section on Prenatal Genomics and Fetal Therapy, Medical Genetics Branch, National Human Genome Research Institute, and Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| |
Collapse
|
23
|
Zhang R, Geng S, Qin Z, Tang Z, Liu C, Liu D, Song G, Li Y, Zhang S, Li W, Gao J, Han X, Li G. The genome-wide transcriptional consequences of the nullisomic-tetrasomic stocks for homoeologous group 7 in bread wheat. BMC Genomics 2019; 20:29. [PMID: 30630423 PMCID: PMC6327598 DOI: 10.1186/s12864-018-5421-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 12/27/2018] [Indexed: 11/16/2022] Open
Abstract
Background Hexaploid bread wheat (Triticum aestivum L) arose by two polyploidisation events from three diploid species with homoeologous genomes. Nullisomic-tetrasomic (nulli-tetra or NT) lines are aneuploid wheat plants lacking two and adding two of six homoeologous chromosomes. These plants can grow normally, but with significantly morphological variations because the adding two chromosomes or the remaining four chromosomes compensate for those absent. Despite these interesting phenomena, detailed molecular mechanisms underlying dosage deletion and compensation in these useful genetic materials have not been determined. Results By sequencing the transcriptomes of leaves in two-week-old seedlings, we showed that the profiles of differentially expressed genes between NT stocks for homoeologous group 7 and the parent hexaploid Chinese Spring (CS) occurred throughout the whole genome with a subgenome and chromosome preference. The deletion effect of nulli-chromosomes was compensated partly by the tetra-chromosomes via the dose level of expressed genes, according to the types of homoeologous genes. The functions of differentially regulated genes primarily focused on carbon metabolic process, photosynthesis process, hormone metabolism, and responding to stimulus, and etc., which might be related to the defective phenotypes that included reductions in plant height, flag leaf length, spikelet number, and kernels per spike. Conclusions The perturbation of the expression levels of transcriptional genes among the NT stocks for homoeologous group 7 demonstrated the gene dosage effect of the subgenome at the genome-wide level. The gene dosage deletion and compensation can be used as a model to elucidate the functions of the subgenomes in modern polyploid plants. Electronic supplementary material The online version of this article (10.1186/s12864-018-5421-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Rongzhi Zhang
- Key Laboratory of Wheat Biology & Genetic Improvement on North Yellow & Huai River Valley, Ministry of Agriculture, National Engineering Laboratory for Wheat & Maize, Institute of Crop Science, Shandong Academy of Agricultural Sciences (SAAS), #202, Road of Gongyebei, Jinan, 250100, China.
| | - Shuaifeng Geng
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhengrui Qin
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zongxiang Tang
- Agronomy College, Sichuan Agricultural University, Wenjiang, Chengdu, 610054, China
| | - Cheng Liu
- Key Laboratory of Wheat Biology & Genetic Improvement on North Yellow & Huai River Valley, Ministry of Agriculture, National Engineering Laboratory for Wheat & Maize, Institute of Crop Science, Shandong Academy of Agricultural Sciences (SAAS), #202, Road of Gongyebei, Jinan, 250100, China
| | - Dongfeng Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Guoqi Song
- Key Laboratory of Wheat Biology & Genetic Improvement on North Yellow & Huai River Valley, Ministry of Agriculture, National Engineering Laboratory for Wheat & Maize, Institute of Crop Science, Shandong Academy of Agricultural Sciences (SAAS), #202, Road of Gongyebei, Jinan, 250100, China
| | - Yulian Li
- Key Laboratory of Wheat Biology & Genetic Improvement on North Yellow & Huai River Valley, Ministry of Agriculture, National Engineering Laboratory for Wheat & Maize, Institute of Crop Science, Shandong Academy of Agricultural Sciences (SAAS), #202, Road of Gongyebei, Jinan, 250100, China
| | - Shujuan Zhang
- Key Laboratory of Wheat Biology & Genetic Improvement on North Yellow & Huai River Valley, Ministry of Agriculture, National Engineering Laboratory for Wheat & Maize, Institute of Crop Science, Shandong Academy of Agricultural Sciences (SAAS), #202, Road of Gongyebei, Jinan, 250100, China
| | - Wei Li
- Key Laboratory of Wheat Biology & Genetic Improvement on North Yellow & Huai River Valley, Ministry of Agriculture, National Engineering Laboratory for Wheat & Maize, Institute of Crop Science, Shandong Academy of Agricultural Sciences (SAAS), #202, Road of Gongyebei, Jinan, 250100, China
| | - Jie Gao
- Key Laboratory of Wheat Biology & Genetic Improvement on North Yellow & Huai River Valley, Ministry of Agriculture, National Engineering Laboratory for Wheat & Maize, Institute of Crop Science, Shandong Academy of Agricultural Sciences (SAAS), #202, Road of Gongyebei, Jinan, 250100, China
| | - Xiaodong Han
- Key Laboratory of Wheat Biology & Genetic Improvement on North Yellow & Huai River Valley, Ministry of Agriculture, National Engineering Laboratory for Wheat & Maize, Institute of Crop Science, Shandong Academy of Agricultural Sciences (SAAS), #202, Road of Gongyebei, Jinan, 250100, China
| | - Genying Li
- Key Laboratory of Wheat Biology & Genetic Improvement on North Yellow & Huai River Valley, Ministry of Agriculture, National Engineering Laboratory for Wheat & Maize, Institute of Crop Science, Shandong Academy of Agricultural Sciences (SAAS), #202, Road of Gongyebei, Jinan, 250100, China.
| |
Collapse
|
24
|
Jung YW, Shim JI, Shim SH, Shin YJ, Shim SH, Chang SW, Cha DH. Global gene expression analysis of cell-free RNA in amniotic fluid from women destined to develop preeclampsia. Medicine (Baltimore) 2019; 98:e13971. [PMID: 30653101 PMCID: PMC6370049 DOI: 10.1097/md.0000000000013971] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Preeclampsia (PE) is a disorder specific to pregnancy characterized by new-onset hypertension and proteinuria after 20 weeks of gestation. There is no definite treatment for PE except delivery of the placenta. The purpose of this study was to elucidate the biological pathways involved in the development of PE and to discover a novel biomarker for PE by performing global gene expression analysis of amniotic fluid cell-free RNA.The participants were recruited from the Department of Obstetrics and Gynecology of CHA Gangnam Medical Center (Seoul, Korea) between March 2014 and February 2015. Eight samples were collected from 8 subjects at second trimester who were later diagnosed with PE. From the amniotic fluid samples, cell-free RNA extraction was performed and gene expression was analyzed using the GeneChip PrimeView Array. Transcriptome data previously analyzed by our group from 9 euploid mid-trimester amniotic fluid samples were used as the control for comparative analysis. Functional analysis of the probe sets was performed using the online Database for Annotation, Visualization, and Integrated Discovery (DAVID) toolkit 6.7.We identified 1841 differentially expressed genes (DEGs) between the PE group and the control. Of these, 1557 genes were upregulated in the PE group, while 284 genes were upregulated in the control. The functional annotation of DEGs identified specific enriched functions such as "transport," "signal transduction," and "stress response." Functional annotation clustering with enriched genes in the PE group revealed that translation-related genes, cell-cell adhesion genes, and immune-related genes were enriched. KEGG pathway analysis showed that several biological pathways, including the ribosome pathway and various immune pathways, were dysregulated. Several genes, including RPS29, IGF-2, and UBC, were significantly upregulated in PE, up to tenfold.This study provides the first genome-wide expression analysis of amniotic fluid cell-free RNA in PE. The results showed that gene expression involving the ribosome pathway and immunologic pathways are dysregulated in PE. Our results will aid in understanding the underlying pathogenesis of PE.
Collapse
Affiliation(s)
- Yong Wook Jung
- Department of Obstetrics and Gynecology, CHA Gangnam Medical Center
| | - Jung In Shim
- Department of Obstetrics and Gynecology, CHA Gangnam Medical Center
| | - So Hyun Shim
- Department of Obstetrics and Gynecology, CHA Gangnam Medical Center
| | - Yun-jeong Shin
- Genetics Laboratory, Fertility Center of CHA Gangnam Medical Center, CHA University, Seoul
| | - Sung Han Shim
- Genetics Laboratory, Fertility Center of CHA Gangnam Medical Center, CHA University, Seoul
| | - Sung Woon Chang
- Department of Obstetrics and Gynecology, CHA Bundang Medical Center, CHA University, Seongnam-si, Republic of Korea
| | - Dong Hyun Cha
- Department of Obstetrics and Gynecology, CHA Gangnam Medical Center
- Genetics Laboratory, Fertility Center of CHA Gangnam Medical Center, CHA University, Seoul
| |
Collapse
|
25
|
The Impact of Epigenetic Signatures on Amniotic Fluid Stem Cell Fate. Stem Cells Int 2018; 2018:4274518. [PMID: 30627172 PMCID: PMC6304862 DOI: 10.1155/2018/4274518] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 10/04/2018] [Indexed: 02/07/2023] Open
Abstract
Epigenetic modifications play a significant role in determining the fate of stem cells and in directing the differentiation into multiple lineages. Current evidence indicates that mechanisms involved in chromatin regulation are essential for maintaining stable cell identities. There is a tight correlation among DNA methylation, histone modifications, and small noncoding RNAs during the epigenetic control of stem cells' differentiation; however, to date, the precise mechanism is still not clear. In this context, amniotic fluid stem cells (AFSCs) represent an interesting model due to their unique features and the possible advantages of their use in regenerative medicine. Recent studies have elucidated epigenetic profiles involved in AFSCs' lineage commitment and differentiation. In order to use these cells effectively for therapeutic purposes, it is necessary to understand the basis of multiple-lineage potential and elaborate in detail how cell fate decisions are made and memorized. The present review summarizes the most recent findings on epigenetic mechanisms of AFSCs with a focus on DNA methylation, histone modifications, and microRNAs (miRNAs) and addresses how their unique signatures contribute to lineage-specific differentiation.
Collapse
|
26
|
Abstract
Background Monosomy of the X chromosome is the most frequent genetic abnormality in human as it is present in approximately 2% of all conceptions, although 99% of these embryos are spontaneously miscarried. In postnatal life, clinical features of Turner syndrome may include typical dysmorphic stigmata, short stature, sexual infantilism, and renal, cardiac, skeletal, endocrine and metabolic abnormalities. Main text Turner syndrome is due to a partial or total loss of the second sexual chromosome, resulting in the development of highly variable clinical features. This phenotype may not merely be due to genomic imbalance from deleted genes but may also result from additive influences on associated genes within a given gene network, with an altered regulation of gene expression triggered by the absence of the second sex chromosome. Current studies in human and mouse models have demonstrated that this chromosomal abnormality leads to epigenetic changes, including differential DNA methylation in specific groups of downstream target genes in pathways associated with several clinical and metabolic features, mostly on autosomal chromosomes. In this article, we begin exploring the potential involvement of both genetic and epigenetic factors in the origin of X chromosome monosomy. We review the dispute between the meiotic and post-zygotic origins of 45,X monosomy, by mainly analyzing the findings from several studies that compare gene expression of the 45,X monosomy to their euploid and/or 47,XXX trisomic cell counterparts on peripheral blood mononuclear cells, amniotic fluid, human fibroblast cells, and induced pluripotent human cell lines. From these studies, a profile of epigenetic changes seems to emerge in response to chromosomal imbalance. An interesting finding of all these studies is that methylation-based and expression-based pathway analyses are complementary, rather than overlapping, and are correlated with the clinical picture displayed by TS subjects. Conclusions The clarification of these possible causal pathways may have future implications in increasing the life expectancy of these patients and may provide informative targets for early pharmaceutical intervention.
Collapse
Affiliation(s)
- Francisco Álvarez-Nava
- Biological Sciences School, Faculty of Biological Sciences, Central University of Ecuador, Quito, Ecuador
| | - Roberto Lanes
- Pediatric Endocrine Unit, Hospital de Clínicas Caracas, Caracas, Venezuela
| |
Collapse
|
27
|
Cho HY, Cho Y, Shin YJ, Park J, Shim S, Jung Y, Shim S, Cha D. Functional analysis of cell-free RNA using mid-trimester amniotic fluid supernatant in pregnancy with the fetal growth restriction. Medicine (Baltimore) 2018; 97:e9572. [PMID: 29480850 PMCID: PMC5943846 DOI: 10.1097/md.0000000000009572] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The prediction and monitoring of fetal growth restriction (FGR) fetuses has become with the use of ultrasound. However, these tools lack the fundamental evidence for the growth of fetus with FGR excluding pathogenic factors.Amniotic fluid samples were obtained from pregnant women for fetal karyotyping and genetic diagnosis at 16 to 19 weeks of gestation. For this study, 15 FGR and 9 control samples were selected, and cell-free fetal RNA was isolated from each supernatant of the amniotic fluid for microarray analysis.In this study, 411 genes were differentially expressed between the FGR and control group. Of these genes, 316 genes were up-regulated, while 95 genes were down-regulated. In terms of gene ontology, the up-regulated genes were highly related to metabolic process as well as protein synthesis, while the down-regulated genes were related to receptor activity and biological adhesion. In terms of tissue-specific expression, the up-regulated genes were involved in various organs while down-regulated genes were involved only in the brain. In terms of organ-specific expression, many genes were enriched for B-cell lymphoma, pancreas, eye, placenta, epithelium, skin, and muscle. In the functional significance of gene, low-density lipoprotein receptor-related protein 10 (LRP10) was significantly increased (6-fold) and insulin-like growth factor (IGF-2) was dramatically increased (17-fold) in the FGR cases.The results show that the important brain-related genes are predominantly down-regulated in the intrauterine growth restriction fetuses during the second trimester of pregnancy. This study also suggested possible genes related to fetal development such as B-cell lymphoma, LRP10, and IGF-2. To monitor the fetal development, further study may be needed to elucidate the role of the genes identified.
Collapse
Affiliation(s)
- Hee Young Cho
- Department of Obstetrics and Gynecology, CHA Bundang Medical Center, CHA University, Seongnam
| | - Yeonkyung Cho
- Department of Obstetrics and Gynecology, CHA Gangnam Medical Center, CHA University
| | - Yun-Jeong Shin
- Genetic Laboratory, CHA Gangnam Medical Center, CHA University, Seoul, Korea
| | - Jieun Park
- Genetic Laboratory, CHA Gangnam Medical Center, CHA University, Seoul, Korea
| | - Sunghan Shim
- Genetic Laboratory, CHA Gangnam Medical Center, CHA University, Seoul, Korea
| | - Yongwook Jung
- Department of Obstetrics and Gynecology, CHA Gangnam Medical Center, CHA University
| | - Sungshin Shim
- Department of Obstetrics and Gynecology, CHA Gangnam Medical Center, CHA University
| | - Donghyun Cha
- Department of Obstetrics and Gynecology, CHA Gangnam Medical Center, CHA University
- Genetic Laboratory, CHA Gangnam Medical Center, CHA University, Seoul, Korea
| |
Collapse
|
28
|
Jang JH, Jung YW, Shim SH, Sin YJ, Lee KJ, Shim SS, Ahn EH, Cha DH. Global gene expression changes of amniotic fluid cell free RNA according to fetal development. Eur J Obstet Gynecol Reprod Biol 2017; 216:104-110. [DOI: 10.1016/j.ejogrb.2017.07.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 07/04/2017] [Accepted: 07/10/2017] [Indexed: 11/27/2022]
|
29
|
Green T, Naylor PE, Davies W. Attention deficit hyperactivity disorder (ADHD) in phenotypically similar neurogenetic conditions: Turner syndrome and the RASopathies. J Neurodev Disord 2017; 9:25. [PMID: 28694877 PMCID: PMC5502326 DOI: 10.1186/s11689-017-9205-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 05/18/2017] [Indexed: 11/17/2022] Open
Abstract
Background ADHD (attention deficit hyperactivity disorder) is a common neurodevelopmental disorder. There has been extensive clinical and basic research in the field of ADHD over the past 20 years, but the mechanisms underlying ADHD risk are multifactorial, complex and heterogeneous and, as yet, are poorly defined. In this review, we argue that one approach to address this challenge is to study well-defined disorders to provide insights into potential biological pathways that may be involved in idiopathic ADHD. Main body To address this premise, we selected two neurogenetic conditions that are associated with significantly increased ADHD risk: Turner syndrome and the RASopathies (of which Noonan syndrome and neurofibromatosis type 1 are the best-defined with regard to ADHD-related phenotypes). These syndromes were chosen for two main reasons: first, because intellectual functioning is relatively preserved, and second, because they are strikingly phenotypically similar but are etiologically distinct. We review the cognitive, behavioural, neural and cellular phenotypes associated with these conditions and examine their relevance as a model for idiopathic ADHD. Conclusion We conclude by discussing current and future opportunities in the clinical and basic research of these conditions, which, in turn, may shed light upon the biological pathways underlying idiopathic ADHD.
Collapse
Affiliation(s)
- Tamar Green
- Center for Interdisciplinary Brain Sciences Research, Stanford University School of Medicine, Stanford, USA
| | - Paige E Naylor
- Department of Clinical Psychology, Palo Alto University, Palo Alto, CA USA
| | - William Davies
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics and Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK.,School of Psychology, Cardiff University, Tower Building, 70, Park Place, Cardiff, CF10 3AT UK.,Neuroscience and Mental Health Research Institute, Cardiff University, Cardiff, UK
| |
Collapse
|
30
|
Zwemer LM, Nolin SL, Okamoto PM, Eisenberg M, Wick HC, Bianchi DW. Global transcriptome dysregulation in second trimester fetuses with FMR1 expansions. Prenat Diagn 2016; 37:43-52. [PMID: 27646161 DOI: 10.1002/pd.4928] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 08/30/2016] [Accepted: 09/14/2016] [Indexed: 02/06/2023]
Abstract
OBJECTIVE We tested the hypothesis that FMR1 expansions would result in global gene dysregulation as early as the second trimester of human fetal development. METHOD Using cell-free fetal RNA obtained from amniotic fluid supernatant and expression microarrays, we compared RNA levels in samples from fetuses with premutation or full mutation allele expansions with control samples. RESULTS We found clear signals of differential gene expression relating to a variety of cellular functions, including ubiquitination, mitochondrial function, and neuronal/synaptic architecture. Additionally, among the genes showing differential gene expression, we saw links to related diseases of intellectual disability and motor function. Finally, within the unique molecular phenotypes established for each mutation set, we saw clear signatures of mitochondrial dysfunction and disrupted neurological function. Patterns of differential gene expression were very different in male and female fetuses with premutation alleles. CONCLUSION These results support a model for which genetic misregulation during fetal development may set the stage for late clinical manifestations of FMR1-related disorders. © 2016 John Wiley & Sons, Ltd.
Collapse
Affiliation(s)
- Lillian M Zwemer
- Mother Infant Research Institute, Tufts Medical Center, Boston, MA, USA
| | - Sarah L Nolin
- New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY, USA
| | - Patricia M Okamoto
- Integrated Genetics/Laboratory Corporation of America® Holdings, Westborough, MA, USA
| | - Marcia Eisenberg
- Laboratory Corporation of America® Holdings, Research Triangle Park, NC, USA
| | - Heather C Wick
- Department of Computer Science, Tufts University, Medford, MA, USA
| | - Diana W Bianchi
- Mother Infant Research Institute, Tufts Medical Center, Boston, MA, USA
| |
Collapse
|
31
|
Widespread DNA hypomethylation and differential gene expression in Turner syndrome. Sci Rep 2016; 6:34220. [PMID: 27687697 PMCID: PMC5043230 DOI: 10.1038/srep34220] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 09/08/2016] [Indexed: 01/15/2023] Open
Abstract
Adults with 45,X monosomy (Turner syndrome) reflect a surviving minority since more than 99% of fetuses with 45,X monosomy die in utero. In adulthood 45,X monosomy is associated with increased morbidity and mortality, although strikingly heterogeneous with some individuals left untouched while others suffer from cardiovascular disease, autoimmune disease and infertility. The present study investigates the leukocyte DNAmethylation profile by using the 450K-Illumina Infinium assay and the leukocyte RNA-expression profile in 45,X monosomy compared with karyotypically normal female and male controls. We present results illustrating that genome wide X-chromosome RNA-expression profile, autosomal DNA-methylation profile, and the X-chromosome methylation profile clearly distinguish Turner syndrome from controls. Our results reveal genome wide hypomethylation with most differentially methylated positions showing a medium level of methylation. Contrary to previous studies, applying a single loci specific analysis at well-defined DNA loci, our results indicate that the hypomethylation extend to repetitive elements. We describe novel candidate genes that could be involved in comorbidity in TS and explain congenital urinary malformations (PRKX), premature ovarian failure (KDM6A), and aortic aneurysm formation (ZFYVE9 and TIMP1).
Collapse
|
32
|
Jung YW, Shim SS, Park JE, Sung SR, Shim SH, Park HR, Cha DH. Analysis of the cell-free amniotic fluid transcriptome expressed during the euploid mid-trimester of pregnancy. Eur J Obstet Gynecol Reprod Biol 2016; 203:94-8. [DOI: 10.1016/j.ejogrb.2016.05.040] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 04/26/2016] [Accepted: 05/21/2016] [Indexed: 12/27/2022]
|
33
|
Sun T, Li W, Li T, Ling S. microRNA Profiling of Amniotic Fluid: Evidence of Synergy of microRNAs in Fetal Development. PLoS One 2016; 11:e0153950. [PMID: 27166676 PMCID: PMC4864075 DOI: 10.1371/journal.pone.0153950] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 04/06/2016] [Indexed: 11/18/2022] Open
Abstract
Amniotic fluid (AF) continuously exchanges molecules with the fetus, playing critical roles in fetal development especially via its complex components. Among these components, microRNAs are thought to be transferred between cells loaded in microvesicles. However, the functions of AF microRNAs remain unknown. To date, few studies have examined microRNAs in amniotic fluid. In this study, we employed miRCURY Locked Nucleotide Acid arrays to profile the dynamic expression of microRNAs in AF from mice on embryonic days E13, E15, and E17. At these times, 233 microRNAs were differentially expressed (p< 0.01), accounting for 23% of the total Mus musculus microRNAs. These differentially-expressed microRNAs were divided into two distinct groups based on their expression patterns. Gene ontology analysis showed that the intersectional target genes of these differentially-expressed microRNAs were mainly distributed in synapse, synaptosome, cell projection, and cytoskeleton. Pathway analysis revealed that the target genes of the two groups of microRNAs were synergistically enriched in axon guidance, focal adhesion, and MAPK signaling pathways. MicroRNA-mRNA network analysis and gene- mapping showed that these microRNAs synergistically regulated cell motility, cell proliferation and differentiation, and especially the axon guidance process. Cancer pathways associated with growth and proliferation were also enriched in AF. Taken together, the results of this study are the first to show the functions of microRNAs in AF during fetal development, providing novel insights into interpreting the roles of AF microRNAs in fetal development.
Collapse
Affiliation(s)
- Tingting Sun
- Institute of Neuroscience and Anatomy, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Weiyun Li
- Institute of Neuroscience and Anatomy, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Tianpeng Li
- College of Environmental Science and Engineering, Donghua University, Shanghai, 201620, China
| | - Shucai Ling
- Institute of Neuroscience and Anatomy, Zhejiang University School of Medicine, Hangzhou, 310058, China
- * E-mail:
| |
Collapse
|
34
|
Bougacha-Elleuch N, Elleuch M, Charfi N, Mnif F, Belghith N, Abdelhedi F, Kammoun H, Hachicha M, Mnif M, Abid M. Unusual association of turner syndrome and hypopituitarism in a Tunisian family. Curr Res Transl Med 2016; 64:9-13. [DOI: 10.1016/j.retram.2016.01.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Accepted: 01/08/2016] [Indexed: 11/30/2022]
|
35
|
Sharma A, Jamil MA, Nuesgen N, Schreiner F, Priebe L, Hoffmann P, Herns S, Nöthen MM, Fröhlich H, Oldenburg J, Woelfle J, El-Maarri O. DNA methylation signature in peripheral blood reveals distinct characteristics of human X chromosome numerical aberrations. Clin Epigenetics 2015. [PMID: 26221191 PMCID: PMC4517491 DOI: 10.1186/s13148-015-0112-2] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Abnormal sex chromosome numbers in humans are observed in Turner (45,X) and Klinefelter (47,XXY) syndromes. Both syndromes are associated with several clinical phenotypes, whose molecular mechanisms are obscure, and show a range of inter-individual penetrance. In order to understand the effect of abnormal numbers of X chromosome on the methylome and its correlation to the variable clinical phenotype, we performed a genome-wide methylation analysis using MeDIP and Illumina's Infinium assay on individuals with four karyotypes: 45,X, 46,XY, 46,XX, and 47,XXY. RESULTS DNA methylation changes were widespread on all autosomal chromosomes in 45,X and in 47,XXY individuals, with Turner individuals presenting five times more affected loci. Differentially methylated CpGs, in most cases, have intermediate methylation levels and tend to occur outside CpG islands, especially in individuals with Turner syndrome. The X inactivation process appears to be less effective in Klinefelter syndrome as methylation on the X was decreased compared to normal female samples. In a large number of individuals, we verified several loci by pyrosequencing and observed only weak inter-loci correlations between the verified regions. This suggests a certain stochastic/random contribution to the methylation changes at each locus. Interestingly, methylation patterns on some PAR2 loci differ between male and Turner syndrome individuals and between female and Klinefelter syndrome individuals, which possibly contributed to this distinguished and unique autosomal methylation patterns in Turner and Klinefelter syndrome individuals. CONCLUSIONS The presented data clearly show that gain or loss of an X chromosome results in different epigenetic effects, which are not necessary opposite.
Collapse
Affiliation(s)
- Amit Sharma
- Institute of Experimental Hematology and Transfusion Medicine, University of Bonn, Sigmund-Freud Str. 25, 53127 Bonn, Germany
| | - Muhammad Ahmer Jamil
- Institute of Experimental Hematology and Transfusion Medicine, University of Bonn, Sigmund-Freud Str. 25, 53127 Bonn, Germany
| | - Nicole Nuesgen
- Institute of Experimental Hematology and Transfusion Medicine, University of Bonn, Sigmund-Freud Str. 25, 53127 Bonn, Germany
| | - Felix Schreiner
- Pediatric Endocrinology Division, Children's Hospital, University of Bonn, Bonn, Germany
| | - Lutz Priebe
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Stefan Herns
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Holger Fröhlich
- Institute for Computer Science, c/o Bonn-Aachen International Center for IT, Algorithmic Bioinformatics, University of Bonn, Dahlmannstr. 2, 53113 Bonn, Germany
| | - Johannes Oldenburg
- Institute of Experimental Hematology and Transfusion Medicine, University of Bonn, Sigmund-Freud Str. 25, 53127 Bonn, Germany
| | - Joachim Woelfle
- Pediatric Endocrinology Division, Children's Hospital, University of Bonn, Bonn, Germany
| | - Osman El-Maarri
- Institute of Experimental Hematology and Transfusion Medicine, University of Bonn, Sigmund-Freud Str. 25, 53127 Bonn, Germany
| |
Collapse
|
36
|
Kang JH, Park HJ, Jung YW, Shim SH, Sung SR, Park JE, Cha DH, Ahn EH. Comparative Transcriptome Analysis of Cell-Free Fetal RNA from Amniotic Fluid and RNA from Amniocytes in Uncomplicated Pregnancies. PLoS One 2015; 10:e0132955. [PMID: 26181329 PMCID: PMC4504687 DOI: 10.1371/journal.pone.0132955] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 06/21/2015] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVES We aimed to compare tissue-specific expression profiles and biological pathways of RNA from amniocytes and amniotic fluid supernatant (AFS) from second-trimester pregnancies by using transcriptome analysis. Additionally, we wanted to explore whether cell-free RNA from AFS exhibits a unique gene expression signature that more adequately reflects the fetal developmental process than amniocyte RNA. METHODS Amniotic fluid samples were prospectively collected in the second trimester of pregnancy from euploid fetuses. Total RNA was extracted from amniocytes and AFS and hybridized to Affymetrix GeneChip Human Arrays. Significantly differentially expressed transcripts between amniocytes and AFS were obtained by using Welch's t-test. Unsupervised hierarchical clustering was used to visualize overall expression characteristics and differences in transcripts between AFS and amniocytes. The biological functions of selected genes were analyzed using various online Gene Ontology databases. RESULTS A total of 3,072 and 15,633 transcripts were detected in the second-trimester AFS and amniocytes, respectively. Hierarchical clustering revealed differential transcript expression between AFS and amniocytes. We found 353 genes that were specifically enriched in the AFS only, and tissue expression analysis showed enrichment of brain-specific genes in the AFS. Biological pathway analysis revealed that AFS-specific transcripts were mainly involved in embryonic development, cardiovascular development, and cellular morphology pathways. CONCLUSION This study demonstrated differential tissue-specific gene expression profiles and biological pathways between AFS and amniocytes. The results suggested that AFS is the preferred RNA source to investigate potential biomarkers of fetal neurodevelopment.
Collapse
Affiliation(s)
- J. H. Kang
- Department of Obstetrics and Gynecology, CHA Graduate School of Medicine, CHA University, Seoul, Republic of Korea
- Department of Obstetrics and Gynecology, Zion Women’s hospital, Suwon, Republic of Korea
| | - H. J. Park
- Department of Obstetrics and Gynecology, CHA Gangnam Medical Center, CHA University, Seoul, Republic of Korea
| | - Y. W. Jung
- Department of Obstetrics and Gynecology, CHA Gangnam Medical Center, CHA University, Seoul, Republic of Korea
| | - S. H. Shim
- Genetic Laboratory, Fertility Center of CHA Gangnam Medical Center, CHA University, Seoul, Republic of Korea
| | - S. R. Sung
- Genetic Laboratory, Fertility Center of CHA Gangnam Medical Center, CHA University, Seoul, Republic of Korea
| | - J. E. Park
- Genetic Laboratory, Fertility Center of CHA Gangnam Medical Center, CHA University, Seoul, Republic of Korea
| | - D. H. Cha
- Department of Obstetrics and Gynecology, CHA Gangnam Medical Center, CHA University, Seoul, Republic of Korea
- * E-mail: (DHC); (EHA)
| | - E. H Ahn
- Department of Obstetrics and Gynecology, CHA Bundang Medical Center, CHA University, Seongnam, Republic of Korea
- * E-mail: (DHC); (EHA)
| |
Collapse
|
37
|
Edlow AG, Slonim DK, Wick HC, Hui L, Bianchi DW. The pathway not taken: understanding 'omics data in the perinatal context. Am J Obstet Gynecol 2015; 213:59.e1-59.e172. [PMID: 25772209 DOI: 10.1016/j.ajog.2015.03.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 01/20/2015] [Accepted: 03/10/2015] [Indexed: 01/19/2023]
Abstract
OBJECTIVE 'Omics analysis of large datasets has an increasingly important role in perinatal research, but understanding gene expression analyses in the fetal context remains a challenge. We compared the interpretation provided by a widely used systems biology resource (ingenuity pathway analysis [IPA]) with that from gene set enrichment analysis (GSEA) with functional annotation curated specifically for the fetus (Developmental FunctionaL Annotation at Tufts [DFLAT]). STUDY DESIGN Using amniotic fluid supernatant transcriptome datasets previously produced by our group, we analyzed 3 different developmental perturbations: aneuploidy (Trisomy 21 [T21]), hemodynamic (twin-twin transfusion syndrome [TTTS]), and metabolic (maternal obesity) vs sex- and gestational age-matched control subjects. Differentially expressed probe sets were identified with the use of paired t-tests with the Benjamini-Hochberg correction for multiple testing (P < .05). Functional analyses were performed with IPA and GSEA/DFLAT. Outputs were compared for biologic relevance to the fetus. RESULTS Compared with control subjects, there were 414 significantly dysregulated probe sets in T21 fetuses, 2226 in TTTS recipient twins, and 470 in fetuses of obese women. Each analytic output was unique but complementary. For T21, both IPA and GSEA/DFLAT identified dysregulation of brain, cardiovascular, and integumentary system development. For TTTS, both analytic tools identified dysregulation of cell growth/proliferation, immune and inflammatory signaling, brain, and cardiovascular development. For maternal obesity, both tools identified dysregulation of immune and inflammatory signaling, brain and musculoskeletal development, and cell death. GSEA/DFLAT identified substantially more dysregulated biologic functions in fetuses of obese women (1203 vs 151). For all 3 datasets, GSEA/DFLAT provided more comprehensive information about brain development. IPA consistently provided more detailed annotation about cell death. IPA produced many dysregulated terms that pertained to cancer (14 in T21, 109 in TTTS, 26 in maternal obesity); GSEA/DFLAT did not. CONCLUSION Interpretation of the fetal amniotic fluid supernatant transcriptome depends on the analytic program, which suggests that >1 resource should be used. Within IPA, physiologic cellular proliferation in the fetus produced many "false positive" annotations that pertained to cancer, which reflects its bias toward adult diseases. This study supports the use of gene annotation resources with a developmental focus, such as DFLAT, for 'omics studies in perinatal medicine.
Collapse
|
38
|
Noto K, Majidi S, Edlow AG, Wick HC, Bianchi DW, Slonim DK. CSAX: Characterizing Systematic Anomalies in eXpression Data. J Comput Biol 2015; 22:402-13. [PMID: 25651392 PMCID: PMC4424968 DOI: 10.1089/cmb.2014.0155] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Methods for translating gene expression signatures into clinically relevant information have typically relied upon having many samples from patients with similar molecular phenotypes. Here, we address the question of what can be done when it is relatively easy to obtain healthy patient samples, but when abnormalities corresponding to disease states may be rare and one-of-a-kind. The associated computational challenge, anomaly detection, is a well-studied machine-learning problem. However, due to the dimensionality and variability of expression data, existing methods based on feature space analysis or individual anomalously expressed genes are insufficient. We present a novel approach, CSAX, that identifies pathways in an individual sample in which the normal expression relationships are disrupted. To evaluate our approach, we have compiled and released a compendium of public expression data sets, reformulated to create a test bed for anomaly detection. We demonstrate the accuracy of CSAX on the data sets in our compendium, compare it to other leading methods, and show that CSAX aids in both identifying anomalies and explaining their underlying biology. We describe an approach to characterizing the difficulty of specific expression anomaly detection tasks. We then illustrate CSAX's value in two developmental case studies. Confirming prior hypotheses, CSAX highlights disruption of platelet activation pathways in a neonate with retinopathy of prematurity and identifies, for the first time, dysregulated oxidative stress response in second trimester amniotic fluid of fetuses with obese mothers. Our approach provides an important step toward identification of individual disease patterns in the era of precision medicine.
Collapse
Affiliation(s)
- Keith Noto
- 1 AncestryDNA , San Francisco, California
| | | | | | | | | | | |
Collapse
|
39
|
Zwemer LM, Bianchi DW. The amniotic fluid transcriptome as a guide to understanding fetal disease. Cold Spring Harb Perspect Med 2015; 5:cshperspect.a023101. [PMID: 25680981 DOI: 10.1101/cshperspect.a023101] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Numerous recent studies have shown the power of cell-free fetal RNA, obtained from amniotic fluid supernatant, to report on the development of the living fetus in real time. Examination of these transcripts on a genome-wide basis has led to new insights into the prenatal pathophysiology of multiple genetic, developmental, and environmental diseases. Each studied condition presents a unique, characteristic fetal transcriptome, which points to specific disrupted molecular pathways. These studies have also improved our knowledge of the normal development of the human fetus, revealing gestational age-related dynamic gene expression from a variety of organs. Analysis of the fetal transcriptome in normal and abnormal development has led to novel approaches for in utero prenatal treatment.
Collapse
Affiliation(s)
- Lillian M Zwemer
- Mother Infant Research Institute, Tufts Medical Center, Boston, Massachusetts 02111
| | - Diana W Bianchi
- Mother Infant Research Institute, Tufts Medical Center, Boston, Massachusetts 02111
| |
Collapse
|
40
|
Levitsky LL, Luria AHO, Hayes FJ, Lin AE. Turner syndrome: update on biology and management across the life span. Curr Opin Endocrinol Diabetes Obes 2015; 22:65-72. [PMID: 25517026 DOI: 10.1097/med.0000000000000128] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
PURPOSE OF REVIEW We review recent understanding of the pathophysiology, molecular biology, and management of Turner syndrome. RECENT FINDINGS Sophisticated genetic techniques are able to detect mosaicism in one-third of individuals previously thought to have monosomy X. Prenatal detection using maternal blood should permit noninvasive detection of most fetuses with an X chromosome abnormality. Disproportionate growth with short limbs has been documented in this condition, and a target gene of short stature homeobox, connective tissue growth factor (Ctgf), has been described. Liver disease is more common in Turner syndrome than previously recognized. Most girls have gonadal failure. Spontaneous puberty and menarche is more commonly seen in girls with XX mosaicism. Low-dose estrogen replacement therapy may be given early to induce a more normal onset and tempo of puberty. Oocyte donation for assisted reproduction carries a substantial risk, particularly if the woman has known cardiac or aortic disease. Neurodevelopmental differences in Turner syndrome are beginning to be correlated with differences in brain anatomy. SUMMARY An increased understanding of the molecular basis for aspects of this disorder is now developing. In addition, a renewed focus on health maintenance through the life span should provide better general and targeted healthcare for these girls and women.
Collapse
Affiliation(s)
- Lynne L Levitsky
- aPediatric Endocrine Unit, Department of Pediatrics, Massachusetts General Hospital bGenetics Residency Program, Harvard Medical School cBoston Children's Hospital dReproductive Endocrine Unit, Department of Medicine, Massachusetts General Hospital eGenetics Unit, Mass General Hospital for Children, Massachusetts, Boston, USA
| | | | | | | |
Collapse
|