1
|
Nazzari M, Romitti M, Kip AM, Kamps R, Costagliola S, van de Beucken T, Moroni L, Caiment F. Impact of benzo[a]pyrene, PCB153 and sex hormones on human ESC-Derived thyroid follicles using single cell transcriptomics. ENVIRONMENT INTERNATIONAL 2024; 188:108748. [PMID: 38763096 DOI: 10.1016/j.envint.2024.108748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 04/25/2024] [Accepted: 05/10/2024] [Indexed: 05/21/2024]
Abstract
INTRODUCTION Endocrine disruptors are compounds of manmade origin able to interfere with the endocrine system and constitute an important environmental concern. Indeed, detrimental effects on thyroid physiology and functioning have been described. Differences exist in the susceptibility of human sexes to the incidence of thyroid disorders, like autoimmune diseases or cancer. METHODS To study how different hormonal environments impact the thyroid response to endocrine disruptors, we exposed human embryonic stem cell-derived thyroid organoids to physiological concentrations of sex hormones resembling the serum levels of human females post-ovulation or males of reproductive age for three days. Afterwards, we added 10 µM benzo[a]pyrene or PCB153 for 24 h and analyzed the transcriptome changes via single-cell RNA sequencing with differential gene expression and gene ontology analysis. RESULTS The sex hormones receptors genes AR, ESR1, ESR2 and PGR were expressed at low levels. Among the thyroid markers, only TG resulted downregulated by benzo[a]pyrene or benzo[a]pyrene with the "male" hormones mix. Both hormone mixtures and benzo[a]pyrene alone upregulated ribosomal genes and genes involved in oxidative phosphorylation, while their combination decreased the expression compared to benzo[a]pyrene alone. The "male" mix and benzo[a]pyrene, alone or in combination, upregulated genes involved in lipid transport and metabolism (APOA1, APOC3, APOA4, FABP1, FABP2, FABP6). The combination of "male" hormones and benzo[a]pyrene induced also genes involved in inflammation and NFkB targets. Benzo[a]pyrene upregulated CYP1A1, CYP1B1 and NQO1 irrespective of the hormonal context. The induction was stronger in the "female" mix. Benzo[a]pyrene alone upregulated genes involved in cell cycle regulation, response to reactive oxygen species and apoptosis. PCB153 had a modest effect in presence of "male" hormones, while we did not observe any changes with the "female" mix. CONCLUSION This work shows how single cell transcriptomics can be applied to selectively study the in vitro effects of endocrine disrupters and their interaction with different hormonal contexts.
Collapse
Affiliation(s)
- Marta Nazzari
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, 6229 ER Maastricht, the Netherlands
| | - Mírian Romitti
- Institute of Interdisciplinary Research in Molecular Human Biology (IRIBHM), Université Libre de Bruxelles, 808 Route de Lennik, 1070 Brussels, Belgium
| | - Anna M Kip
- Department of Complex Tissue Regeneration, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University 6229 ER Maastricht, the Netherlands
| | - Rick Kamps
- Department of Toxicogenomics, Maastricht University, 6229 ER Maastricht, the Netherlands
| | - Sabine Costagliola
- Institute of Interdisciplinary Research in Molecular Human Biology (IRIBHM), Université Libre de Bruxelles, 808 Route de Lennik, 1070 Brussels, Belgium
| | - Twan van de Beucken
- Department of Toxicogenomics, Maastricht University, 6229 ER Maastricht, the Netherlands
| | - Lorenzo Moroni
- Department of Complex Tissue Regeneration, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University 6229 ER Maastricht, the Netherlands
| | - Florian Caiment
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, 6229 ER Maastricht, the Netherlands.
| |
Collapse
|
2
|
He Z, Ouyang Q, Chen Q, Song Y, Hu J, Hu S, He H, Li L, Liu H, Wang J. Molecular mechanisms of hypothalamic-pituitary-ovarian/thyroid axis regulating age at first egg in geese. Poult Sci 2024; 103:103478. [PMID: 38295497 PMCID: PMC10844868 DOI: 10.1016/j.psj.2024.103478] [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: 11/30/2023] [Revised: 01/10/2024] [Accepted: 01/14/2024] [Indexed: 02/02/2024] Open
Abstract
Age at first egg (AFE) has consistently garnered interest as a crucial reproductive indicator within poultry production. Previous studies have elucidated the involvement of the hypothalamic-pituitary-ovarian (HPO) and hypothalamic-pituitary-thyroid (HPT) axes in regulating poultry sexual maturity. Concurrently, there was evidence suggesting a potential co-regulatory relationship between these 2 axes. However, as of now, no comprehensive exploration of the key pathways and genes responsible for the crosstalk between the HPO and HPT axes in the regulation of AFE has been reported. In this study, we conducted a comparative analysis of morphological differences and performed transcriptomic analysis on the hypothalamus, pituitary, thyroid, and ovarian stroma between normal laying group (NG) and abnormal laying group (AG). Morphological results showed that the thyroid index difference (D-) value (thyroid index D-value=right thyroid index-left thyroid index) was significantly (P < 0.05) lower in the NG than in the AG, while the ovarian index was significantly (P < 0.01) higher in the NG than in the AG. Furthermore, between NG and AG, we identified 99, 415, 167, and 1182 differentially expressed genes (DEGs) in the hypothalamus, pituitary, thyroid, and ovarian stroma, respectively. Gene ontology (GO) analysis highlighted that DEGs from 4 tissues were predominantly enriched in the "biological processes" category. Additionally, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that 16, 14, 3, and 26 KEGG pathways were significantly enriched (P < 0.05) in the hypothalamus, pituitary, thyroid, and ovarian stroma. The MAPK signaling pathway emerged as the sole enriched pathway across all 4 tissues. Employing an integrated analysis of the protein-protein interaction (PPI) network and correlation analysis, we found GREB1 emerged as a pivotal component within the HPO axis to regulate estrogen-related signaling in the HPT axis, meanwhile, the HPT axis influenced ovarian development by regulating thyroid hormone-related signaling mainly through OPN5. Then, 10 potential candidate genes were identified, namely IGF1, JUN, ERBB4, KDR, PGF, FGFR1, GREB1, OPN5, DIO3, and THRB. These findings establish a foundation for elucidating the physiological and genetic mechanisms by which the HPO and HPT axes co-regulate goose AFE.
Collapse
Affiliation(s)
- Zhiyu He
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China
| | - Qingyuan Ouyang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China
| | - Qingliang Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China
| | - Yang Song
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China
| | - Jiwei Hu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China
| | - Shenqiang Hu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China
| | - Hua He
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China
| | - Liang Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China
| | - Hehe Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China
| | - Jiwen Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China.
| |
Collapse
|
3
|
Wang J, Lei M, Xu Z. Aberrant expression of PROS1 correlates with human papillary thyroid cancer progression. PeerJ 2021; 9:e11813. [PMID: 34414029 PMCID: PMC8344691 DOI: 10.7717/peerj.11813] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 06/28/2021] [Indexed: 02/05/2023] Open
Abstract
Background Papillary thyroid carcinoma (PTC) is the most common type of thyroid cancer (TC). Considering the important association between cellular immunity and PTC progression, it is worth exploring the biological significance of immune-related signaling in PTC. Methods Several bioinformatics tools, such as R software, WEB-based Gene SeT AnaLysis Toolkit (WebGestalt), Database for Annotation, Visualization and Integrated Discovery (DAVID), Search Tool for the Retrieval of Interacting Genes (STRING) and Cytoscape were used to identify the immune-related hub genes in PTC. Furthermore, in vitro experiments were adopted to identify the proliferation and migration ability of PROS1 knockdown groups and control groups in PTC cells. Results The differentially expressed genes (DEGs) of five datasets from Gene Expression Omnibus (GEO) contained 154 upregulated genes and 193 downregulated genes, with Protein S (PROS1) being the only immune-related hub gene. Quantitative real-time polymerase chain reaction (RT-qPCR) and immunohistochemistry (IHC) have been conducted to prove the high expression of PROS1 in PTC. Moreover, PROS1 expression was significantly correlated with lymph nodes classification. Furthermore, knockdown of PROS1 by shRNAs inhibited the cell proliferation and cell migration in PTC cells. Conclusions The findings unveiled the clinical relevance and significance of PROS1 in PTC and provided potential immune-related biomarkers for PTC development and prognosis.
Collapse
Affiliation(s)
- Jing Wang
- Department of Endocrinology, Xiangya Hospital of Central South University, Changsha, Hunan, China.,Department of Pathology, Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Minxiang Lei
- Department of Endocrinology, Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Zhijie Xu
- Department of Pathology, Xiangya Hospital of Central South University, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital of Central South University, Changsha, Hunan, China
| |
Collapse
|
4
|
Dom G, Dmitriev P, Lambot MA, Van Vliet G, Glinoer D, Libert F, Lefort A, Dumont JE, Maenhaut C. Transcriptomic Signature of Human Embryonic Thyroid Reveals Transition From Differentiation to Functional Maturation. Front Cell Dev Biol 2021; 9:669354. [PMID: 34249923 PMCID: PMC8270686 DOI: 10.3389/fcell.2021.669354] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 05/17/2021] [Indexed: 11/16/2022] Open
Abstract
The human thyroid gland acquires a differentiation program as early as weeks 3-4 of embryonic development. The onset of functional differentiation, which manifests by the appearance of colloid in thyroid follicles, takes place during gestation weeks 10-11. By 12-13 weeks functional differentiation is accomplished and the thyroid is capable of producing thyroid hormones although at a low level. During maturation, thyroid hormones yield increases and physiological mechanisms of thyroid hormone synthesis regulation are established. In the present work we traced the process of thyroid functional differentiation and maturation in the course of human development by performing transcriptomic analysis of human thyroids covering the period of gestation weeks 7-11 and comparing it to adult human thyroid. We obtained specific transcriptomic signatures of embryonic and adult human thyroids by comparing them to non-thyroid tissues from human embryos and adults. We defined a non-TSH (thyroid stimulating hormone) dependent transition from differentiation to maturation of thyroid. The study also sought to shed light on possible factors that could replace TSH, which is absent in this window of gestational age, to trigger transition to the emergence of thyroid function. We propose a list of possible genes that may also be involved in abnormalities in thyroid differentiation and/or maturation, hence leading to congenital hypothyroidism. To our knowledge, this study represent the first transcriptomic analysis of human embryonic thyroid and its comparison to adult thyroid.
Collapse
Affiliation(s)
- Geneviève Dom
- School of Medicine, IRIBHM, Université libre de Bruxelles, Brussels, Belgium
- Institute of Interdisciplinary Research in Human and Molecular Biology, Brussels, Belgium
| | - Petr Dmitriev
- School of Medicine, IRIBHM, Université libre de Bruxelles, Brussels, Belgium
- Institute of Interdisciplinary Research in Human and Molecular Biology, Brussels, Belgium
| | | | - Guy Van Vliet
- Département de Pédiatrie, Université de Montréal, Montreal, QC, Canada
- CHU Sainte-Justine, Montreal, QC, Canada
| | - Daniel Glinoer
- Hôpital Saint-Pierre, Université libre de Bruxelles, Brussels, Belgium
| | | | - Anne Lefort
- School of Medicine, IRIBHM, Université libre de Bruxelles, Brussels, Belgium
| | - Jacques E. Dumont
- School of Medicine, IRIBHM, Université libre de Bruxelles, Brussels, Belgium
- Institute of Interdisciplinary Research in Human and Molecular Biology, Brussels, Belgium
| | - Carine Maenhaut
- School of Medicine, IRIBHM, Université libre de Bruxelles, Brussels, Belgium
- Institute of Interdisciplinary Research in Human and Molecular Biology, Brussels, Belgium
| |
Collapse
|
5
|
Antonaros F, Zenatelli R, Guerri G, Bertelli M, Locatelli C, Vione B, Catapano F, Gori A, Vitale L, Pelleri MC, Ramacieri G, Cocchi G, Strippoli P, Caracausi M, Piovesan A. The transcriptome profile of human trisomy 21 blood cells. Hum Genomics 2021; 15:25. [PMID: 33933170 PMCID: PMC8088681 DOI: 10.1186/s40246-021-00325-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 04/14/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Trisomy 21 (T21) is a genetic alteration characterised by the presence of an extra full or partial human chromosome 21 (Hsa21) leading to Down syndrome (DS), the most common form of intellectual disability (ID). It is broadly agreed that the presence of extra genetic material in T21 gives origin to an altered expression of genes located on Hsa21 leading to DS phenotype. The aim of this study was to analyse T21 and normal control blood cell gene expression profiles obtained by total RNA sequencing (RNA-Seq). RESULTS The results were elaborated by the TRAM (Transcriptome Mapper) software which generated a differential transcriptome map between human T21 and normal control blood cells providing the gene expression ratios for 17,867 loci. The obtained gene expression profiles were validated through real-time reverse transcription polymerase chain reaction (RT-PCR) assay and compared with previously published data. A post-analysis through transcriptome mapping allowed the identification of the segmental (regional) variation of the expression level across the whole genome (segment-based analysis of expression). Interestingly, the most over-expressed genes encode for interferon-induced proteins, two of them (MX1 and MX2 genes) mapping on Hsa21 (21q22.3). The altered expression of genes involved in mitochondrial translation and energy production also emerged, followed by the altered expression of genes encoding for the folate cycle enzyme, GART, and the folate transporter, SLC19A1. CONCLUSIONS The alteration of these pathways might be linked and involved in the manifestation of ID in DS.
Collapse
Affiliation(s)
- Francesca Antonaros
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy
| | - Rossella Zenatelli
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy.,Current Address: Department of Molecular and Translational Medicine (DMMT), University of Brescia, Viale Europa 11, 24123, Brescia, BS, Italy
| | - Giulia Guerri
- MAGI'S Lab, Via delle Maioliche 57/D, 38068, Rovereto, TN, Italy
| | - Matteo Bertelli
- MAGI'S Lab, Via delle Maioliche 57/D, 38068, Rovereto, TN, Italy
| | - Chiara Locatelli
- Neonatology Unit, St. Orsola-Malpighi Polyclinic, Via Massarenti 9, 40138, Bologna, BO, Italy
| | - Beatrice Vione
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy
| | - Francesca Catapano
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy.,Current Address: Department of Medical Biotechnologies, University of Siena, Strada delle Scotte, 4, 53100, Siena, SI, Italy
| | - Alice Gori
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy
| | - Lorenza Vitale
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy
| | - Maria Chiara Pelleri
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy
| | - Giuseppe Ramacieri
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy
| | - Guido Cocchi
- Neonatology Unit, St. Orsola-Malpighi Polyclinic, Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Via Massarenti 9, 40138, Bologna, BO, Italy
| | - Pierluigi Strippoli
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy
| | - Maria Caracausi
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy.
| | - Allison Piovesan
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy
| |
Collapse
|
6
|
Choukair D, Eberle B, Vick P, Hermanns P, Weiss B, Paramasivam N, Schlesner M, Lornsen K, Roeth R, Klutmann C, Kreis J, Hoffmann GF, Pohlenz J, Rappold GA, Bettendorf M. Identification of Transient Receptor Potential Channel 4-Associated Protein as a Novel Candidate Gene Causing Congenital Primary Hypothyroidism. Horm Res Paediatr 2021; 93:16-29. [PMID: 32428920 DOI: 10.1159/000507114] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 03/10/2020] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Congenital primary hypothyroidism (CH) is the most common endocrine disorder in neonates. METHODS To identify novel genes, we performed whole exome sequencing (WES) in 6 patients with CH due to thyroid dysgenesis (TD). The potential effects of the most relevant variants were analyzed using in silico prediction tools. The most promising candidate gene, transient receptor potential channel 4-associated protein (TRPC4AP), was sequenced in 179 further patients with TD. Expression of TRPC4AP in human thyroid was investigated using RT-PCR. Trpc4ap- functional analysis was performed in Xenopus laevis using Morpholino (MO) antisense oligomers. RESULTS WES identified a likely damaging mutation in TRPC4AP leading to a de novo stop codon p.Q552*. Targeted sequencing of TRPC4AP demonstrated gene variants with predicted damaging potential in 5 patients resulting each in an amino acid exchange (p.P706S, p.F729L, p.S777C, and p.N229S). We demonstrated that TRPC4AP is expressed in human thyroid gland tissue. Using Xenopus laevis, we showed that the volume of the tadpole thyroid anlage was reduced by 20% in Trpc4ap MO knockdowns compared to controls and by 41% in "Clustered Regularly Interspaced Short Palindromic Repeats"/Cas9-mediated gene knockout experiments. DISCUSSION A recognized interaction of TRPC4AP and the NF-kappa-B-essential-modulator encoded by IKBKG gene was identified by IPA analysis. IKBKG plays a role in activation of the NF-κB-signaling pathway and regulates genes involved in proliferation and survival of thyrocytes and expression of key enzymes of thyroid hormone synthesis. CONCLUSION TRPC4AP was identified as a novel candidate gene in TD, but further studies are needed to validate its role in thyroid function.
Collapse
Affiliation(s)
- Daniela Choukair
- Division of Paediatric Endocrinology, Children's Hospital, University of Heidelberg, Heidelberg, Germany,
| | - Birgit Eberle
- Department of Human Molecular Genetics, University of Heidelberg, Heidelberg, Germany
| | - Philipp Vick
- Department of Zoology, University of Hohenheim, Stuttgart, Germany
| | - Pia Hermanns
- Division of Paediatric Endocrinology, Children's Hospital, University of Mainz, Mainz, Germany
| | - Birgit Weiss
- Department of Human Molecular Genetics, University of Heidelberg, Heidelberg, Germany
| | - Nagarajan Paramasivam
- Theoretical Bioinformatics Division, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Matthias Schlesner
- Bioinformatics and Omics Data Analytics (B240), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Katharina Lornsen
- Genomics and Proteomics Core Facility, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ralph Roeth
- Department of Human Molecular Genetics, University of Heidelberg, Heidelberg, Germany
| | - Carina Klutmann
- Division of Paediatric Endocrinology, Children's Hospital, University of Mainz, Mainz, Germany
| | - Jennifer Kreis
- Department of Zoology, University of Hohenheim, Stuttgart, Germany
| | - Georg F Hoffmann
- Division of Paediatric Endocrinology, Children's Hospital, University of Heidelberg, Heidelberg, Germany
| | - Joachim Pohlenz
- Division of Paediatric Endocrinology, Children's Hospital, University of Mainz, Mainz, Germany
| | - Gudrun A Rappold
- Department of Human Molecular Genetics, University of Heidelberg, Heidelberg, Germany
| | - Markus Bettendorf
- Division of Paediatric Endocrinology, Children's Hospital, University of Heidelberg, Heidelberg, Germany
| |
Collapse
|
7
|
Rahnama R, Mahmoudi AR, Kazemnejad S, Salehi M, Ghahiri A, Soltanghoraee H, Vafaei S, Rezaei A, Zarnani AH. Thyroid peroxidase in human endometrium and placenta: a potential target for anti-TPO antibodies. Clin Exp Med 2020; 21:79-88. [PMID: 32980989 DOI: 10.1007/s10238-020-00663-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 09/12/2020] [Indexed: 11/29/2022]
Abstract
Autoimmune thyroid disease is the most common endocrine disorder during pregnancy. Thyroid autoantibodies (TAs) have been suggested to serve a role in implantation failure and spontaneous abortion. Until now, there are no data on the potential interaction of TAs with human reproductive organs. Here, we set out for the first time to test this hypothesis by studying the expression of thyroid peroxidase (TPO) at gene and protein level in human reproductive organs. Endometrial samples were taken from normal women, and placenta tissues were collected after full-term caesarian section. Expression of TPO messenger RNA (mRNA) was investigated by qRT-PCR. In addition, polyclonal anti-TPO antibodies were produced and the expression of TPO protein in mentioned tissues was evaluated by immunohistochemistry and Western blot analysis. The reactivity of anti-TPO antibody in human embryos was evaluated by immunofluorescent staining. For the first time, our study showed that TPO is expressed at gene and protein levels in endometrium and placenta. TPO expression was mainly localized to glandular and luminal epithelial cells in the endometrium. In placenta, the syncytiotrophoblasts and invasive trophoblast cells were the main cell types that expressed TPO protein. Specific band of approximately 110 kDa was observed in all endometrial and placental tissues by Western blot analysis. However, no expression of TPO protein was observed in human embryo. TPO expression in endometrium and placenta may explain higher frequency of abortion and infertility in patients with thyroid autoimmunity.
Collapse
Affiliation(s)
- Reyhane Rahnama
- Department of Immunology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Ahmad-Reza Mahmoudi
- Immunology Research Center, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran
| | - Somayeh Kazemnejad
- Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Mansour Salehi
- Department of Genetic, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Ataollah Ghahiri
- Department of Gynecology and Obstetrics, Al-Zahra University Hospital, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Haleh Soltanghoraee
- Avicenna Infertility Clinic, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Sedigheh Vafaei
- Reproductive Immunology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Abbas Rezaei
- Department of Immunology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran.
| | - Amir Hassan Zarnani
- Reproductive Immunology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran. .,Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran. .,Immunology Research Center (IRC), Iran University of Medical Sciences, Tehran, Iran.
| |
Collapse
|
8
|
Portrait of Tissue-Specific Coexpression Networks of Noncoding RNAs (miRNA and lncRNA) and mRNAs in Normal Tissues. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2019; 2019:9029351. [PMID: 31565069 PMCID: PMC6745163 DOI: 10.1155/2019/9029351] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 08/01/2019] [Accepted: 08/10/2019] [Indexed: 02/01/2023]
Abstract
Genes that encode proteins playing a role in more than one biological process are frequently dependent on their tissue context, and human diseases result from the altered interplay of tissue- and cell-specific processes. In this work, we performed a computational approach that identifies tissue-specific co-expression networks by integrating miRNAs, long-non-coding RNAs, and mRNAs in more than eight thousands of human samples from thirty normal tissue types. Our analysis (1) shows that long-non coding RNAs and miRNAs have a high specificity, (2) confirms several known tissue-specific RNAs, and (3) identifies new tissue-specific co-expressed RNAs that are currently still not described in the literature. Some of these RNAs interact with known tissue-specific RNAs or are crucial in key cancer functions, suggesting that they are implicated in tissue specification or cell differentiation.
Collapse
|
9
|
Reference quantitative transcriptome dataset for adult Caenorhabditis elegans. Data Brief 2019; 25:104152. [PMID: 31440537 PMCID: PMC6700341 DOI: 10.1016/j.dib.2019.104152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 06/05/2019] [Accepted: 06/06/2019] [Indexed: 02/06/2023] Open
Abstract
Caenorhabditis elegans is a nematode widely used in biology and genomics as a model organism. We provide an integrated, quantitative reference map for the transcriptome of whole, wild type Bristol N2 strain C. elegans worms. The map has been obtained by meta-analysis of 110 gene expression profiles available in Gene Expression Omnibus (GEO) repository and integrated using the computational biology tool Transcriptome Mapper (TRAM). Following probe assignment to the relative locus and intra- and inter-sample normalization (in particular using the scaled quantile method), a mean, consensus reference value is provided for 45,932 transcripts, along with standard deviation. Expression values are all mapped in the context of genomic coordinates. The map provides easy access to relationships among expression values of different genes in this standard condition, highlights genomic segments with relatively high over-/under-expression and may serve as a reference to test for gene expression variation for both individual genes and the whole transcriptome in specific biological conditions (e.g. mutated strains or differently grown worms).
Collapse
|
10
|
Godlewska M, Banga PJ. Thyroid peroxidase as a dual active site enzyme: Focus on biosynthesis, hormonogenesis and thyroid disorders of autoimmunity and cancer. Biochimie 2019; 160:34-45. [DOI: 10.1016/j.biochi.2019.02.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 02/05/2019] [Indexed: 01/02/2023]
|
11
|
Vitale L, Piovesan A, Antonaros F, Strippoli P, Pelleri MC, Caracausi M. Dataset of differential gene expression between total normal human thyroid and histologically normal thyroid adjacent to papillary thyroid carcinoma. Data Brief 2019; 24:103835. [PMID: 31049370 PMCID: PMC6479735 DOI: 10.1016/j.dib.2019.103835] [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: 12/20/2018] [Revised: 02/28/2019] [Accepted: 03/07/2019] [Indexed: 12/16/2022] Open
Abstract
This article contains further data and information from our published manuscript [1]. We aim to identify significant transcriptome alterations of total normal human thyroid vs. histologically normal thyroid adjacent to papillary thyroid carcinoma. We performed a systematic meta-analysis of all the available gene expression profiles for the whole organ also collecting gene expression data for the normal thyroid adjacent to papillary thyroid carcinoma. A differential quantitative transcriptome reference map was generated by using TRAM (Transcriptome Mapper) software able to combine, normalize and integrate a total of 35 datasets from total normal thyroid and 40 datasets from histologically normal thyroid adjacent to papillary thyroid carcinoma from different sources. This analysis identified genes and genome segments that significantly discriminated the two groups of samples. Differentially expressed genes were grouped and enrichment function analyses were performed identifying the main features of the differentially expressed genes between total normal thyroid and histologically normal thyroid adjacent to papillary thyroid carcinoma. The search for housekeeping genes retrieved 414 loci.
Collapse
|
12
|
Zou M, Alzahrani AS, Al-Odaib A, Alqahtani MA, Babiker O, Al-Rijjal RA, BinEssa HA, Kattan WE, Al-Enezi AF, Al Qarni A, Al-Faham MSA, Baitei EY, Alsagheir A, Meyer BF, Shi Y. Molecular Analysis of Congenital Hypothyroidism in Saudi Arabia: SLC26A7 Mutation Is a Novel Defect in Thyroid Dyshormonogenesis. J Clin Endocrinol Metab 2018; 103:1889-1898. [PMID: 29546359 DOI: 10.1210/jc.2017-02202] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 03/07/2018] [Indexed: 12/21/2022]
Abstract
CONTEXT Congenital hypothyroidism (CH) is the most common neonatal endocrine disorder, affecting one in 3000 to 4000 newborns. Since the introduction of a newborn screening program in 1988, more than 300 cases have been identified. The underlying genetic defects have not been systematically studied. OBJECTIVE To identify the mutation spectrum of CH-causing genes. METHODS Fifty-five patients from 47 families were studied by next-generation exome sequencing. RESULTS Mutations were identified in 52.7% of patients (29 of 55) in the following 11 genes: TG, TPO, DUOX2, SLC26A4, SLC26A7, TSHB, TSHR, NKX2-1, PAX8, CDCA8, and HOXB3. Among 30 patients with thyroid dyshormonogenesis, biallelic TG mutations were found in 12 patients (40%), followed by biallelic mutations in TPO (6.7%), SLC26A7 (6.7%), and DUOX2 (3.3%). Monoallelic SLC26A4 mutations were found in two patients, one of them coexisting with two tandem biallelic deletions in SLC26A7. In 25 patients with thyroid dysgenesis, biallelic mutations in TSHR were found in six patients (24%). Biallelic mutations in TSHB, PAX 8, NKX2-1, or HOXB3 were found once in four different patients. A monoallelic CDCA8 mutation was found in one patient. Most mutations were novel, including three TG, two TSHR, and one each in DUOX2, TPO, SLC26A7, TSHB, NKX2-1, PAX8, CDCA8, and HOXB3. SLC26A7 and HOXB3 were novel genes associated with thyroid dyshormonogenesis and dysgenesis, respectively. CONCLUSIONS TG and TSHR mutations are the most common genetic defects in Saudi patients with CH. The prevalence of other disease-causing mutations is low, reflecting the consanguineous nature of the population. SLC26A7 mutations appear to be associated with thyroid dyshormonogenesis.
Collapse
Affiliation(s)
- Minjing Zou
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Ali S Alzahrani
- Department of Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Ali Al-Odaib
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | | | - Omer Babiker
- Department of Medicine, King Abdulaziz Hospital, National Guard Health Affairs, Al Ahsa, Saudi Arabia
| | - Roua A Al-Rijjal
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Huda A BinEssa
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Walaa E Kattan
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Anwar F Al-Enezi
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Ali Al Qarni
- Department of Pediatrics, King Abdulaziz Hospital, National Guard Health Affairs, Al Ahsa, Saudi Arabia
| | - Manar S A Al-Faham
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Essa Y Baitei
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Afaf Alsagheir
- Department of Pediatrics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Brian F Meyer
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Yufei Shi
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| |
Collapse
|
13
|
Pelleri MC, Cattani C, Vitale L, Antonaros F, Strippoli P, Locatelli C, Cocchi G, Piovesan A, Caracausi M. Integrated Quantitative Transcriptome Maps of Human Trisomy 21 Tissues and Cells. Front Genet 2018; 9:125. [PMID: 29740474 PMCID: PMC5928158 DOI: 10.3389/fgene.2018.00125] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 03/27/2018] [Indexed: 12/17/2022] Open
Abstract
Down syndrome (DS) is due to the presence of an extra full or partial chromosome 21 (Hsa21). The identification of genes contributing to DS pathogenesis could be the key to any rational therapy of the associated intellectual disability. We aim at generating quantitative transcriptome maps in DS integrating all gene expression profile datasets available for any cell type or tissue, to obtain a complete model of the transcriptome in terms of both expression values for each gene and segmental trend of gene expression along each chromosome. We used the TRAM (Transcriptome Mapper) software for this meta-analysis, comparing transcript expression levels and profiles between DS and normal brain, lymphoblastoid cell lines, blood cells, fibroblasts, thymus and induced pluripotent stem cells, respectively. TRAM combined, normalized, and integrated datasets from different sources and across diverse experimental platforms. The main output was a linear expression value that may be used as a reference for each of up to 37,181 mapped transcripts analyzed, related to both known genes and expression sequence tag (EST) clusters. An independent example in vitro validation of fibroblast transcriptome map data was performed through “Real-Time” reverse transcription polymerase chain reaction showing an excellent correlation coefficient (r = 0.93, p < 0.0001) with data obtained in silico. The availability of linear expression values for each gene allowed the testing of the gene dosage hypothesis of the expected 3:2 DS/normal ratio for Hsa21 as well as other human genes in DS, in addition to listing genes differentially expressed with statistical significance. Although a fraction of Hsa21 genes escapes dosage effects, Hsa21 genes are selectively over-expressed in DS samples compared to genes from other chromosomes, reflecting a decisive role in the pathogenesis of the syndrome. Finally, the analysis of chromosomal segments reveals a high prevalence of Hsa21 over-expressed segments over the other genomic regions, suggesting, in particular, a specific region on Hsa21 that appears to be frequently over-expressed (21q22). Our complete datasets are released as a new framework to investigate transcription in DS for individual genes as well as chromosomal segments in different cell types and tissues.
Collapse
Affiliation(s)
- Maria Chiara Pelleri
- Department of Experimental, Diagnostic and Specialty Medicine, Unit of Histology, Embryology and Applied Biology, University of Bologna, Bologna, Italy
| | - Chiara Cattani
- Department of Experimental, Diagnostic and Specialty Medicine, Unit of Histology, Embryology and Applied Biology, University of Bologna, Bologna, Italy
| | - Lorenza Vitale
- Department of Experimental, Diagnostic and Specialty Medicine, Unit of Histology, Embryology and Applied Biology, University of Bologna, Bologna, Italy
| | - Francesca Antonaros
- Department of Experimental, Diagnostic and Specialty Medicine, Unit of Histology, Embryology and Applied Biology, University of Bologna, Bologna, Italy
| | - Pierluigi Strippoli
- Department of Experimental, Diagnostic and Specialty Medicine, Unit of Histology, Embryology and Applied Biology, University of Bologna, Bologna, Italy
| | - Chiara Locatelli
- Neonatology Unit, Sant'Orsola-Malpighi Polyclinic, Bologna, Italy
| | - Guido Cocchi
- Neonatology Unit, Sant'Orsola-Malpighi Polyclinic, Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Allison Piovesan
- Department of Experimental, Diagnostic and Specialty Medicine, Unit of Histology, Embryology and Applied Biology, University of Bologna, Bologna, Italy
| | - Maria Caracausi
- Department of Experimental, Diagnostic and Specialty Medicine, Unit of Histology, Embryology and Applied Biology, University of Bologna, Bologna, Italy
| |
Collapse
|