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Al-Kurbi AA, Da'as SI, Aamer W, Krishnamoorthy N, Poggiolini I, Abdelrahman D, Elbashir N, Al-Shabeeb Akil A, Glass GE, Fakhro KA. A recessive variant in SIM2 in a child with complex craniofacial anomalies and global developmental delay. Eur J Med Genet 2022; 65:104455. [PMID: 35182808 DOI: 10.1016/j.ejmg.2022.104455] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 02/02/2022] [Accepted: 02/14/2022] [Indexed: 11/26/2022]
Abstract
Rare deletions and duplications on the long arm of Chromosome 21 have previously been reported in many patients with craniofacial and developmental phenotypes. However, this Down Syndrome Critical Region (DSCR) contains multiple genes, making identifying a single causative gene difficult. Here, we report a case of a boy with bicoronal craniosynostosis, facial dysmorphism, developmental delay, and intellectual impairment who was found by whole genome sequencing to have a homozygous missense mutation in the Single-Minded Homolog 2 (SIM2) gene (c.461 A > G, p.Tyr154Cys) within the DSCR. SIM2 encodes an essential bHLH and PAS domain transcription factor expressed during fetal brain development and acts as a master regulator of neurogenesis. This variant is globally very rare, segregates in the family, and is predicted to be highly deleterious by in silico analysis, 3D molecular modeling of protein structure, and functional analysis of zebrafish models. Zebrafish expressing the human SIM2p.Y154C variant displayed a progressed microcephaly-like phenotype and head shape abnormalities. When combined with careful phenotyping of the patient vis-à-vis previously reported cases harboring structural variants in this critical 21q22 region, the data support a pathogenic role of SIM2 in this complex syndrome and demonstrates the utility of next-generation sequencing in prioritizing genes in contiguous deletions/duplications syndromes and diagnosing microarray-negative patients in the craniofacial clinic.
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Affiliation(s)
- Alya A Al-Kurbi
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, 34110, Qatar; Department of Human Genetics, Sidra Medicine, 26999, Doha, Qatar
| | - Sahar Isa Da'as
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, 34110, Qatar; Department of Human Genetics, Sidra Medicine, 26999, Doha, Qatar
| | - Waleed Aamer
- Department of Human Genetics, Sidra Medicine, 26999, Doha, Qatar
| | | | | | - Doua Abdelrahman
- Department of Human Genetics, Sidra Medicine, 26999, Doha, Qatar
| | - Najwa Elbashir
- Department of Human Genetics, Sidra Medicine, 26999, Doha, Qatar
| | | | - Graeme E Glass
- Division of Plastic and Craniofacial Surgery, Sidra Medicine, 26999, Doha, Qatar
| | - Khalid A Fakhro
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, 34110, Qatar; Department of Human Genetics, Sidra Medicine, 26999, Doha, Qatar; Department of Genetic Medicine, Weill Cornell Medical College, Doha, 24144, Qatar.
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Osuna-Marco MP, López-Barahona M, López-Ibor B, Tejera ÁM. Ten Reasons Why People With Down Syndrome are Protected From the Development of Most Solid Tumors -A Review. Front Genet 2021; 12:749480. [PMID: 34804119 PMCID: PMC8602698 DOI: 10.3389/fgene.2021.749480] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 10/21/2021] [Indexed: 12/27/2022] Open
Abstract
People with Down syndrome have unique characteristics as a result of the presence of an extra chromosome 21. Regarding cancer, they present a unique pattern of tumors, which has not been fully explained to date. Globally, people with Down syndrome have a similar lifetime risk of developing cancer compared to the general population. However, they have a very increased risk of developing certain tumors (e.g., acute leukemia, germ cell tumors, testicular tumors and retinoblastoma) and, on the contrary, there are some other tumors which appear only exceptionally in this syndrome (e.g., breast cancer, prostate cancer, medulloblastoma, neuroblastoma and Wilms tumor). Various hypotheses have been developed to explain this situation. The genetic imbalance secondary to the presence of an extra chromosome 21 has molecular consequences at several levels, not only in chromosome 21 but also throughout the genome. In this review, we discuss the different proposed mechanisms that protect individuals with trisomy 21 from developing solid tumors: genetic dosage effect, tumor suppressor genes overexpression, disturbed metabolism, impaired neurogenesis and angiogenesis, increased apoptosis, immune system dysregulation, epigenetic aberrations and the effect of different microRNAs, among others. More research into the molecular pathways involved in this unique pattern of malignancies is still needed.
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Affiliation(s)
- Marta Pilar Osuna-Marco
- Biology of Ageing Group, Faculty of Experimental Sciences, Universidad Francisco de Vitoria, Madrid, Spain.,Pediatric Oncology and Hematology Unit, HM Hospitals, Madrid, Spain
| | | | | | - Águeda Mercedes Tejera
- Biology of Ageing Group, Faculty of Experimental Sciences, Universidad Francisco de Vitoria, Madrid, Spain
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Mégarbané A, Piquemal D, Rebillat AS, Stora S, Pierrat F, Bruno R, Noguier F, Mircher C, Ravel A, Vilaire-Meunier M, Durand S, Lefranc G. Transcriptomic study in women with trisomy 21 identifies a possible role of the GTPases of the immunity-associated proteins (GIMAP) in the protection of breast cancer. Sci Rep 2020; 10:9447. [PMID: 32523132 PMCID: PMC7286899 DOI: 10.1038/s41598-020-66469-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 05/22/2020] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND People with trisomy 21 (T21) are predisposed to developing hematological tumors, but have significantly lower-than-expected age-adjusted incidence rates of having a solid tumor. MATERIAL AND METHODS To identify novel genetic factors implicated in the lower breast cancer (BC) frequency observed in women with T21 than in the general population, we compared the transcriptome pattern of women with a homogeneous T21, aged more than 30 years, with or without BC, and tumoral BC tissue of control women with a normal karyotype from the study of Varley et al. (2014). RESULTS Differential analysis of gene expression between the 15 women in the T21 without BC group and BC patients in the other groups (two women with T21 and fifteen control women, respectively) revealed 154 differentially expressed genes, of which 63 were found to have similar expression profile (up- or downregulated). Of those 63 genes, four were in the same family, namely GIMAP4, GIMAP6, GIMAP7 and GIMAP8, and were strongly upregulated in the T21 without BC group compared to the other groups. A significant decrease in mRNA levels of these genes in BC tissues compared to non-tumor breast tissues was also noted. CONCLUSION We found that the expression of some GIMAPs is significantly higher in women with T21 without BC than in patients with sporadic BC. Our findings support the hypothesis that GIMAPs may play a tumor-suppressive role against BC, and open the possibility that they may also have the same role for other solid tumors in T21 patients. The search for new prognostic factors and hopefully new therapeutic or preventive strategies against BC are discussed.
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Affiliation(s)
- André Mégarbané
- Institut Jérôme Lejeune, CRB BioJeL, Paris, France. .,Faculty of Medical Sciences, Lebanese University, Beirut, Lebanon.
| | | | | | | | | | | | | | | | - Aimé Ravel
- Institut Jérôme Lejeune, CRB BioJeL, Paris, France
| | | | | | - Gérard Lefranc
- Institut de Génétique Humaine, UMR 9002 CNRS-Université de Montpellier, Montpellier, France
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de Aguiar Greca SC, Kyrou I, Pink R, Randeva H, Grammatopoulos D, Silva E, Karteris E. Involvement of the Endocrine-Disrupting Chemical Bisphenol A (BPA) in Human Placentation. J Clin Med 2020; 9:jcm9020405. [PMID: 32028606 PMCID: PMC7074564 DOI: 10.3390/jcm9020405] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 01/22/2020] [Accepted: 01/23/2020] [Indexed: 12/16/2022] Open
Abstract
Background: Endocrine-disrupting chemicals (EDCs) are environmental chemicals/toxicants that humans are exposed to, interfering with the action of multiple hormones. Bisphenol A (BPA) is classified as an EDC with xenoestrogenic activity with potentially adverse effects in reproduction. Currently, a significant knowledge gap remains regarding the complete spectrum of BPA-induced effects on the human placenta. As such, the present study examined the effects of physiologically relevant doses of BPA in vitro. Methods: qRT-PCR, Western blotting, immunofluorescence, ELISA, microarray analyses, and bioinformatics have been employed to study the effects of BPA using nonsyncytialised (non-ST) and syncytialised (ST) BeWo cells. Results: Treatment with 3 nM BPA led to an increase in cell number and altered the phosphorylation status of p38, an effect mediated primarily via the membrane-bound estrogen receptor (GPR30). Nonbiased microarray analysis identified 1195 and 477 genes that were differentially regulated in non-ST BeWo cells, whereas in ST BeWo cells, 309 and 158 genes had altered expression when treated with 3 and 10 nM, respectively. Enriched pathway analyses in non-ST BeWo identified a leptin and insulin overlap (3 nM), methylation pathways (10 nM), and differentiation of white and brown adipocytes (common). In the ST model, most significantly enriched were the nuclear factor erythroid 2-related factor 2 (NRF2) pathway (3 nM) and mir-124 predicted interactions with cell cycle and differentiation (10 nM). Conclusion: Collectively, our data offer a new insight regarding BPA effects at the placental level, and provide a potential link with metabolic changes that can have an impact on the developing fetus.
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Affiliation(s)
| | - Ioannis Kyrou
- Aston Medical Research Institute, Aston Medical School, Aston University, Birmingham B4 7ET, UK;
- Warwickshire Institute for the Study of Diabetes, Endocrinology and Metabolism (WISDEM), University Hospitals Coventry and Warwickshire NHS Trust, Coventry CV2 2DX, UK
- Institute of Precision Diagnostics and Translational Medicine, UHCW NHS Trust, Coventry CV4 7AL, UK; (H.R.); (D.G.)
- Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK
| | - Ryan Pink
- Dept of Bio. & Med. Sci., Oxford Brookes University, Oxford OX3 0BP, UK;
| | - Harpal Randeva
- Institute of Precision Diagnostics and Translational Medicine, UHCW NHS Trust, Coventry CV4 7AL, UK; (H.R.); (D.G.)
- Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK
| | - Dimitris Grammatopoulos
- Institute of Precision Diagnostics and Translational Medicine, UHCW NHS Trust, Coventry CV4 7AL, UK; (H.R.); (D.G.)
- Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK
| | - Elisabete Silva
- College of Health and Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK;
- Correspondence: (E.S.); (E.K.)
| | - Emmanouil Karteris
- College of Health and Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK;
- Correspondence: (E.S.); (E.K.)
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Jackson RA, Nguyen ML, Barrett AN, Tan YY, Choolani MA, Chen ES. Synthetic combinations of missense polymorphic genetic changes underlying Down syndrome susceptibility. Cell Mol Life Sci 2016; 73:4001-17. [PMID: 27245382 PMCID: PMC11108497 DOI: 10.1007/s00018-016-2276-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 05/10/2016] [Accepted: 05/12/2016] [Indexed: 02/08/2023]
Abstract
Single nucleotide polymorphisms (SNPs) are important biomolecular markers in health and disease. Down syndrome, or Trisomy 21, is the most frequently occurring chromosomal abnormality in live-born children. Here, we highlight associations between SNPs in several important enzymes involved in the one-carbon folate metabolic pathway and the elevated maternal risk of having a child with Down syndrome. Our survey highlights that the combination of SNPs may be a more reliable predictor of the Down syndrome phenotype than single SNPs alone. We also describe recent links between SNPs in p53 and its related pathway proteins and Down syndrome, as well as highlight several proteins that help to associate apoptosis and p53 signaling with the Down syndrome phenotype. In addition to a comprehensive review of the literature, we also demonstrate that several SNPs reside within the same regions as these Down syndrome-linked SNPs, and propose that these closely located nucleotide changes may provide new candidates for future exploration.
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Affiliation(s)
- Rebecca A Jackson
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, #05-05, MD7, 8 Medical Drive, Singapore, 117597, Singapore
| | - Mai Linh Nguyen
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, #05-05, MD7, 8 Medical Drive, Singapore, 117597, Singapore
| | - Angela N Barrett
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, #05-05, MD7, 8 Medical Drive, Singapore, 117597, Singapore
| | - Yuan Yee Tan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, #05-05, MD7, 8 Medical Drive, Singapore, 117597, Singapore
| | - Mahesh A Choolani
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, #05-05, MD7, 8 Medical Drive, Singapore, 117597, Singapore.
- National University Health System, Singapore, Singapore.
| | - Ee Sin Chen
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, #05-05, MD7, 8 Medical Drive, Singapore, 117597, Singapore.
- National University Health System, Singapore, Singapore.
- NUS Graduate School of Science and Engineering, National University of Singapore, Singapore, Singapore.
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Cortical Folding of the Primate Brain: An Interdisciplinary Examination of the Genetic Architecture, Modularity, and Evolvability of a Significant Neurological Trait in Pedigreed Baboons (Genus Papio). Genetics 2015; 200:651-65. [PMID: 25873632 DOI: 10.1534/genetics.114.173443] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2014] [Accepted: 04/08/2015] [Indexed: 01/24/2023] Open
Abstract
Folding of the primate brain cortex allows for improved neural processing power by increasing cortical surface area for the allocation of neurons. The arrangement of folds (sulci) and ridges (gyri) across the cerebral cortex is thought to reflect the underlying neural network. Gyrification, an adaptive trait with a unique evolutionary history, is affected by genetic factors different from those affecting brain volume. Using a large pedigreed population of ∼1000 Papio baboons, we address critical questions about the genetic architecture of primate brain folding, the interplay between genetics, brain anatomy, development, patterns of cortical-cortical connectivity, and gyrification's potential for future evolution. Through Mantel testing and cluster analyses, we find that the baboon cortex is quite evolvable, with high integration between the genotype and phenotype. We further find significantly similar partitioning of variation between cortical development, anatomy, and connectivity, supporting the predictions of tension-based models for sulcal development. We identify a significant, moderate degree of genetic control over variation in sulcal length, with gyrus-shape features being more susceptible to environmental effects. Finally, through QTL mapping, we identify novel chromosomal regions affecting variation in brain folding. The most significant QTL contain compelling candidate genes, including gene clusters associated with Williams and Down syndromes. The QTL distribution suggests a complex genetic architecture for gyrification with both polygeny and pleiotropy. Our results provide a solid preliminary characterization of the genetic basis of primate brain folding, a unique and biomedically relevant phenotype with significant implications in primate brain evolution.
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