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Boyanton BL, Zarate YA, Broadfoot BG, Kelly T, Crawford BD. NR3C2 microdeletions-an underrecognized cause of pseudohypoaldosteronism type 1A: a case report and literature review. Lab Med 2024:lmae005. [PMID: 38493321 DOI: 10.1093/labmed/lmae005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2024] Open
Abstract
OBJECTIVES Pseudohypoaldosteronism type 1A (PHA1A) is caused by haploinsufficiency of the mineralocorticoid receptor (MR). Heterozygous small insertions/deletions, transitions, and/or transversions within NR3C2 comprise the majority (85%-90%) of pathogenic copy number variants. Structural chromosomal abnormalities, contiguous gene deletion syndromes, and microdeletions are infrequent. We describe a neonate with PHA1A due to a novel NR3C2 microdeletion involving exons 1-2. METHODS Literature review identified 39 individuals with PHA1A due to NR3C2 microdeletions. Transmission modality, variant description(s), testing method(s), exon(s) deleted, and affected functional domain(s) were characterized. RESULTS In total, 40 individuals with NR3C2 microdeletions were described: 19 involved contiguous exons encoding a single MR domain; 21 involved contiguous exons encoding multiple MR domains. Transmission modality frequency was familial (65%), de novo (20%), or unknown (15%). Sequencing (Sanger or short-read next-generation) failed to detect microdeletions in 100% of tested individuals (n = 38). All were detected using deletion/duplication testing modalities. In 2 individuals, only microarray-based testing was performed; microdeletions were detected in both cases. CONCLUSION Initial testing for PHA1A should rely on sequencing to detect the most common genetic alterations. Deletion/duplication analysis should be performed when initial testing is nondiagnostic. Most NR3C2 microdeletions are parentally transmitted, thus highlighting the importance of familial genetic testing and counseling.
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Affiliation(s)
- Bobby L Boyanton
- Department of Pathology, University of Arkansas for Medical Sciences and Arkansas Children's Hospital, Little Rock, AR, US
| | - Yuri A Zarate
- Department of Pediatrics, Section of Genetics and Metabolism, University of Arkansas for Medical Sciences and Arkansas Children's Hospital, Little Rock, AR, US
- Division of Genetics and Metabolism, University of Kentucky, Lexington, KY, US
| | - Brannon G Broadfoot
- Department of Pathology, University of Arkansas for Medical Sciences and Arkansas Children's Hospital, Little Rock, AR, US
| | - Thomas Kelly
- Department of Pathology, University of Arkansas for Medical Sciences and Arkansas Children's Hospital, Little Rock, AR, US
| | - Brendan D Crawford
- Department of Medicine, Division of Pediatric Nephrology, University of Arkansas for Medical Sciences and Arkansas Children's Hospital, Little Rock, AR, US
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Mao M, Song S, Li X, Lu J, Li J, Zhao W, Liu H, Liu J, Zeng B. Advances in epigenetic modifications of autophagic process in pulmonary hypertension. Front Immunol 2023; 14:1206406. [PMID: 37398657 PMCID: PMC10313199 DOI: 10.3389/fimmu.2023.1206406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 05/30/2023] [Indexed: 07/04/2023] Open
Abstract
Pulmonary hypertension is characterized by pulmonary arterial remodeling that results in increased pulmonary vascular resistance, right ventricular failure, and premature death. It is a threat to public health globally. Autophagy, as a highly conserved self-digestion process, plays crucial roles with autophagy-related (ATG) proteins in various diseases. The components of autophagy in the cytoplasm have been studied for decades and multiple studies have provided evidence of the importance of autophagic dysfunction in pulmonary hypertension. The status of autophagy plays a dynamic suppressive or promotive role in different contexts and stages of pulmonary hypertension development. Although the components of autophagy have been well studied, the molecular basis for the epigenetic regulation of autophagy is less understood and has drawn increasing attention in recent years. Epigenetic mechanisms include histone modifications, chromatin modifications, DNA methylation, RNA alternative splicing, and non-coding RNAs, which control gene activity and the development of an organism. In this review, we summarize the current research progress on epigenetic modifications in the autophagic process, which have the potential to be crucial and powerful therapeutic targets against the autophagic process in pulmonary hypertension development.
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Affiliation(s)
- Min Mao
- Department of Pediatric Pulmonology and Immunology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
- National Health Commission (NHC) Key Laboratory of Chronobiology (Sichuan University), Chengdu, China
- The Joint Laboratory for Lung Development and Related Diseases of West China Second University Hospital, Sichuan University and School of Life Sciences of Fudan University, West China Institute of Women and Children’s Health, West China Second University Hospital, Sichuan University, Chengdu, China
- Sichuan Birth Defects Clinical Research Center, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Shasha Song
- College of Pharmacy, Shenzhen Technology University, Shenzhen, China
| | - Xin Li
- Department of Pediatric Pulmonology and Immunology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
- National Health Commission (NHC) Key Laboratory of Chronobiology (Sichuan University), Chengdu, China
- The Joint Laboratory for Lung Development and Related Diseases of West China Second University Hospital, Sichuan University and School of Life Sciences of Fudan University, West China Institute of Women and Children’s Health, West China Second University Hospital, Sichuan University, Chengdu, China
- Sichuan Birth Defects Clinical Research Center, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Jiayao Lu
- College of Pharmacy, Shenzhen Technology University, Shenzhen, China
| | - Jie Li
- Marketing Department, Shenzhen Reyson Biotechnology Co., Ltd, Shenzhen, China
- Nanjing Evertop Electronics Ltd., Nanjing, China
| | - Weifang Zhao
- Quality Management Department International Registration, North China Pharmaceutical Co., Ltd. (NCPC), Hebei Huamin Pharmaceutical Co., Ltd., Shijiazhuang, China
| | - Hanmin Liu
- Department of Pediatric Pulmonology and Immunology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
- National Health Commission (NHC) Key Laboratory of Chronobiology (Sichuan University), Chengdu, China
- The Joint Laboratory for Lung Development and Related Diseases of West China Second University Hospital, Sichuan University and School of Life Sciences of Fudan University, West China Institute of Women and Children’s Health, West China Second University Hospital, Sichuan University, Chengdu, China
- Sichuan Birth Defects Clinical Research Center, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Jingxin Liu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Bin Zeng
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
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3
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Miao ZY, Chen SF, Wu H, Liu XY, Shao HY. Analysis of genetic characteristics of 436 children with dysplasia and detailed analysis of rare karyotype. Open Life Sci 2022; 17:416-425. [PMID: 35582623 PMCID: PMC9055171 DOI: 10.1515/biol-2022-0046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 10/30/2021] [Accepted: 01/03/2022] [Indexed: 11/15/2022] Open
Abstract
Abstract
Chromosomal abnormality is one of the important causes of dysplasia in children. However, due to regional and ethnic differences, the reported rates of chromosomal abnormalities in patients with dysplasia vary greatly. Moreover, the clinical manifestations in children with rare chromosomal diseases were heterogeneous. So, we retrospectively analyzed the karyotype results of 436 children with dysplasia and conducted a detailed analysis of rare chromosomal diseases. The results showed that chromosomal abnormalities were present in 181 of 436 cases. Intellectual disability, dysmorphology, congenital malformations, the disorder of sexual development, and short stature were the main five clinical symptoms in children with chromosomal abnormalities. Moreover, 136 cases of Trisomy 21 (Tri21) were detected, of which 130 were standard Tri21, 5 were robertsonian Tri21, and 1 was chimera type. In addition, 16 cases of rare abnormal karyotype, including complex Tri21, complex Turner syndrome, 4p-syndrome, 18q-syndrome, and 5p-syndrome, were also detected. In summary, chromosome abnormality is one of the important causes of dysplasia in children. Furthermore, prenatal screening and diagnosis could play a great significance in preventing dysplasia in children. In addition, the retrospective analysis of rare cases is valuable for clinical diagnosis and risk assessment of recurrence.
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Affiliation(s)
- Zong-Yu Miao
- Medical Laboratory, Yantai Yu Huang Ding Hospital , 20#, The East Road of Yu Huang Ding, Zhifu District, Yantai, 264000 , Shandong , China
| | - Shi-Feng Chen
- Medical Laboratory, Yantai Yu Huang Ding Hospital , 20#, The East Road of Yu Huang Ding, Zhifu District, Yantai, 264000 , Shandong , China
| | - Hong Wu
- Medical Laboratory, Yantai Yu Huang Ding Hospital , 20#, The East Road of Yu Huang Ding, Zhifu District, Yantai, 264000 , Shandong , China
| | - Xiao-Yan Liu
- Medical Laboratory, Yantai Yu Huang Ding Hospital , 20#, The East Road of Yu Huang Ding, Zhifu District, Yantai, 264000 , Shandong , China
| | - Hui-Yuan Shao
- Medical Laboratory, Yantai Yu Huang Ding Hospital , 20#, The East Road of Yu Huang Ding, Zhifu District, Yantai, 264000 , Shandong , China
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Li D, Wang Q, Gong NN, Kurolap A, Feldman HB, Boy N, Brugger M, Grand K, McWalter K, Guillen Sacoto MJ, Wakeling E, Hurst J, March ME, Bhoj EJ, Nowaczyk MJM, Gonzaga-Jauregui C, Mathew M, Dava-Wala A, Siemon A, Bartholomew D, Huang Y, Lee H, Martinez-Agosto JA, Schwaibold EMC, Brunet T, Choukair D, Pais LS, White SM, Christodoulou J, Brown D, Lindstrom K, Grebe T, Tiosano D, Kayser MS, Tan TY, Deardorff MA, Song Y, Hakonarson H. Pathogenic variants in SMARCA5, a chromatin remodeler, cause a range of syndromic neurodevelopmental features. SCIENCE ADVANCES 2021; 7:7/20/eabf2066. [PMID: 33980485 PMCID: PMC8115915 DOI: 10.1126/sciadv.abf2066] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 03/23/2021] [Indexed: 05/17/2023]
Abstract
Intellectual disability encompasses a wide spectrum of neurodevelopmental disorders, with many linked genetic loci. However, the underlying molecular mechanism for more than 50% of the patients remains elusive. We describe pathogenic variants in SMARCA5, encoding the ATPase motor of the ISWI chromatin remodeler, as a cause of a previously unidentified neurodevelopmental disorder, identifying 12 individuals with de novo or dominantly segregating rare heterozygous variants. Accompanying phenotypes include mild developmental delay, frequent postnatal short stature and microcephaly, and recurrent dysmorphic features. Loss of function of the SMARCA5 Drosophila ortholog Iswi led to smaller body size, reduced sensory dendrite complexity, and tiling defects in larvae. In adult flies, Iswi neural knockdown caused decreased brain size, aberrant mushroom body morphology, and abnormal locomotor function. Iswi loss of function was rescued by wild-type but not mutant SMARCA5. Our results demonstrate that SMARCA5 pathogenic variants cause a neurodevelopmental syndrome with mild facial dysmorphia.
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Affiliation(s)
- Dong Li
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
| | - Qin Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Naihua N Gong
- Department of Psychiatry, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Alina Kurolap
- The Genetics Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Hagit Baris Feldman
- The Genetics Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Nikolas Boy
- Division of Child Neurology and Metabolic Medicine, Center for Child and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Melanie Brugger
- Institute of Human Genetics, Technical University Munich, Munich, Germany
- Institute of Human Genetics, University Hospital LMU Munich, Goethestr. 29, Munich, Germany
| | - Katheryn Grand
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | | | | | - Emma Wakeling
- North East Thames Regional Genetic Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Jane Hurst
- North East Thames Regional Genetic Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Michael E March
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Elizabeth J Bhoj
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Małgorzata J M Nowaczyk
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | | | - Mariam Mathew
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Ashita Dava-Wala
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Amy Siemon
- Department of Pediatrics and Clinical Genetics, Nationwide Children's Hospital, Columbus, OH, USA
| | - Dennis Bartholomew
- Department of Pediatrics and Clinical Genetics, Nationwide Children's Hospital, Columbus, OH, USA
| | - Yue Huang
- Department of Human Genetics; Division of Medical Genetics, Department of Pediatrics; David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Hane Lee
- Department of Pathology and Laboratory Medicine; Department of Human Genetics; David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Julian A Martinez-Agosto
- Department of Human Genetics; Division of Medical Genetics, Department of Pediatrics; David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Eva M C Schwaibold
- Department of Pathology and Laboratory Medicine; Department of Human Genetics; David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Theresa Brunet
- Institute of Human Genetics, Technical University Munich, Munich, Germany
| | - Daniela Choukair
- Division of Paediatric Endocrinology and Diabetes, Department of Paediatrics, University Hospital Heidelberg, Heidelberg, Germany
| | - Lynn S Pais
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Susan M White
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - John Christodoulou
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Dana Brown
- Division of Genetics and Metabolism, Phoenix Children's Hospital, Phoenix, AZ, USA
| | - Kristin Lindstrom
- Division of Genetics and Metabolism, Phoenix Children's Hospital, Phoenix, AZ, USA
| | - Theresa Grebe
- Division of Genetics and Metabolism, Phoenix Children's Hospital, Phoenix, AZ, USA
- College of Medicine, University of Arizona, Phoenix, 475 N. 5th Street, Phoenix, AZ, USA
| | - Dov Tiosano
- Pediatric Endocrinology Unit, Ruth Rappaport Children's Hospital, Rambam Healthcare Campus, Haifa, Israel
- The Ruth and Bruce Rappaport Faculty of Medicine, Technion, Israel Institute of Technology, Haifa, Israel
| | - Matthew S Kayser
- Department of Psychiatry, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Tiong Yang Tan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Matthew A Deardorff
- Departments of Pathology and Pediatrics, Children's Hospital Los Angeles, and University of Southern California, Los Angeles, CA, USA
| | - Yuanquan Song
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
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5
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Xing J, Jie W. Methyltransferase SET domain family and its relationship with cardiovascular development and diseases. Zhejiang Da Xue Xue Bao Yi Xue Ban 2021; 51:251-260. [PMID: 35462466 DOI: 10.3724/zdxbyxb-2021-0192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Abnormal epigenetic modification is closely related to the occurrence and development of cardiovascular diseases. The SET domain (SETD) family is an important epigenetic modifying enzyme containing SETD. They mainly affect gene expression by methylating H3K4, H3K9, H3K36 and H4K20. Additionally, the SETD family catalyzes the methylation of non-histone proteins, thereby affects the signal transduction of signal transduction and activator of transcription (STAT) 1, Wnt/β-catenin, hypoxia-inducible factor (HIF)-1α and Hippo/YAP pathways. The SETD family has the following regulatory effects on cardiovascular development and diseases: regulating coronary artery formation and cardiac development; protecting cardiac tissue from ischemia reperfusion injury; regulating inflammation, oxidative stress and apoptosis in cardiovascular complications of diabetes; participating in the formation of pulmonary hypertension; regulating thrombosis, cardiac hypertrophy and arrhythmia. This article summarizes the basic structures, expression regulation mechanisms and the role of existing SETD family members in cardiovascular development and diseases, in order to provide a basis for understanding the molecular mechanism of cardiovascular disease and exploring the therapeutic targets.
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Affiliation(s)
- Jingci Xing
- 1. Department of Pathology, School of Basic Medicine Sciences, Guangdong Medical University, Zhanjiang 524023, Guangdong Province, China
| | - Wei Jie
- 1. Department of Pathology, School of Basic Medicine Sciences, Guangdong Medical University, Zhanjiang 524023, Guangdong Province, China.,Medical University, Key Laboratory of Emergency and Trauma, Ministry of Education, Hainan Provincial Key Laboratory of Tropical Cardiovascular Diseases Research, Haikou 571199, China
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Tan N, Zhang Y, Zhang Y, Li L, Zong Y, Han W, Liu L. Berberine ameliorates vascular dysfunction by a global modulation of lncRNA and mRNA expression profiles in hypertensive mouse aortae. PLoS One 2021; 16:e0247621. [PMID: 33621262 PMCID: PMC7901729 DOI: 10.1371/journal.pone.0247621] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 02/09/2021] [Indexed: 12/24/2022] Open
Abstract
Objective The current study investigated the mechanism underlying the therapeutic effects of berberine in the vasculature in hypertension. Methods Angiotensin II (Ang II)-loaded osmotic pumps were implanted in C57BL/6J mice with or without berberine administration. Mouse aortae were suspended in myograph for force measurement. Microarray technology were performed to analyze expression profiles of lncRNAs and mRNAs in the aortae. These dysregulated expressions were then validated by qRT-PCR. LncRNA-mRNA co-expression network was constructed to reveal the specific relationships. Results Ang Ⅱ resulted in a significant increase in the blood pressure of mice, which was suppressed by berberine. The impaired endothelium-dependent aortic relaxation was restored in hypertensive mice. Microarray data revealed that 578 lncRNAs and 554 mRNAs were up-regulated, while 320 lncRNAs and 377 mRNAs were down-regulated in the aortae by Ang Ⅱ; both were reversed by berberine treatment. qRT-PCR validation results of differentially expressed genes (14 lncRNAs and 6 mRNAs) were completely consistent with the microarray data. GO analysis showed that these verified differentially expressed genes were significantly enriched in terms of “cellular process”, “biological regulation” and “regulation of biological process”, whilst KEGG analysis identified vascular function-related pathways including cAMP signaling pathway, cGMP-PKG signaling pathway, and calcium signaling pathway etc. Importantly, we observed that lncRNA ENSMUST00000144849, ENSMUST00000155383, and AK041185 were majorly expressed in endothelial cells. Conclusion The present results suggest that the five lncRNAs ENSMUST00000144849, NR_028422, ENSMUST00000155383, AK041185, and uc.335+ might serve critical regulatory roles in hypertensive vasculature by targeting pivotal mRNAs and subsequently affecting vascular function-related pathways. Moreover, these lncRNAs were modulated by berberine, therefore providing the novel potential therapeutic targets of berberine in hypertension. Furthermore, lncRNA ENSMUST00000144849, ENSMUST00000155383, and AK041185 might be involved in the preservation of vascular endothelial cell function.
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Affiliation(s)
- Na Tan
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Yi Zhang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Yan Zhang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Beijing, China
- Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, China
| | - Li Li
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Beijing, China
- Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, China
| | - Yi Zong
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Wenwen Han
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Limei Liu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Beijing, China
- Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, China
- * E-mail:
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Wu M, Zheng X, Wang X, Zhang G, Kuang J. 4q27 deletion and 7q36.1 microduplication in a patient with multiple malformations and hearing loss: a case report. BMC Med Genomics 2020; 13:31. [PMID: 32126996 PMCID: PMC7055054 DOI: 10.1186/s12920-020-0697-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Accepted: 02/18/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Chromosome deletions of the long arm of chromosome 4 in 4q syndrome are characterized by mild facial and digital dysmorphism, developmental delay, growth retardation, and skeletal and cardiac anomalies, which is regarded as an autism spectrum disorder. Moreover, some scarce reports indicate that patients with 4q interstitial deletion and 7p duplication may present symptoms associated with hearing loss. CASE PRESENTATION A boy with a severe developmental delay not only post-natal but also intrauterine and several dysmorphic features including microcephaly, ocular hypertelorism, exophthalmos, low-set ears, single palmar flexion crease, and overlapping toes presented discontinued cyanosis and recurrent respiratory infections. MRI, BAEP, echocardiogram and bronchoscopy revealed that he had persistent falcine sinus with a thin corpus callosum, left auditory pathway disorder, patent foramen ovale (2 mm), and tracheobronchomalacia with the right superior bronchus arising from the lateral posterior wall of the right main bronchus. Finally, the patient died with severe pneumonia at 10 months. Array CGH revealed a 23.62 Mb deletion at chromosome 4q27, arr [hg19] 4q27-q31.21 (121, 148, 089-144, 769, 263) × 1, and a 0.85 Mb duplication at chromosome 7q36.1, arr [hg19] 7q36.1-q36.2 (152, 510, 685-153, 363,5 98) × 3. It is rare for 4q syndrome cases or 7q duplications previously reported to have a hearing disorder, pulmonary dysplasia, and pulmonary arterial hypertension. CONCLUSIONS The phenotype of our patient mainly reflects the effects of haploinsufficiency of FGF2, SPATA5, NAA15, SMAD1, HHIP genes combined with a microduplication of 7q36.1.
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Affiliation(s)
- Maolan Wu
- Department of Pediatrics, XiangYa Hospital, Central South University, Changsha, China
| | - Xiangrong Zheng
- Department of Pediatrics, XiangYa Hospital, Central South University, Changsha, China.
| | - Xia Wang
- Department of Pediatrics, XiangYa Hospital, Central South University, Changsha, China
| | - Guoyuan Zhang
- Department of Pediatrics, XiangYa Hospital, Central South University, Changsha, China
| | - Jian Kuang
- Department of Pediatrics, XiangYa Hospital, Central South University, Changsha, China
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8
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Barone Pritchard A, Ritter A, Kearney HM, Izumi K. Interstitial 4q Deletion Syndrome Including NR3C2 Causing Pseudohypoaldosteronism. Mol Syndromol 2020; 10:327-331. [PMID: 32021607 DOI: 10.1159/000505279] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2019] [Indexed: 11/19/2022] Open
Abstract
Interstitial and terminal deletions of chromosome 4q have been described for many years and have variable phenotypes depending on the size of the deletion present. Clinical features can include developmental delay, growth difficulty, digital differences, dysmorphic features, and cardiac anomalies. Here, we present an infant with pseudohypoaldosteronism found to have a deletion of 4q31.21q31.23, including NR3C2. Heterozygous mutations in NR3C2 have been reported to cause autosomal dominant pseudohypoaldosteronism type 1 (PHA1A). This represents a rare case of PHA1A due to a contiguous interstitial deletion and highlights the importance of evaluating patients with overlapping deletions for PHA1A.
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Affiliation(s)
- Amanda Barone Pritchard
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Division of Pediatric Genetics, Metabolism, and Genomic Medicine, Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA
| | - Alyssa Ritter
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Hutton M Kearney
- Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, USA
| | - Kosuke Izumi
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
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9
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Sporadic PCDH18 somatic mutations in EpCAM-positive hepatocellular carcinoma. Cancer Cell Int 2017; 17:94. [PMID: 29075151 PMCID: PMC5654054 DOI: 10.1186/s12935-017-0467-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 10/16/2017] [Indexed: 12/16/2022] Open
Abstract
Background The relationship between specific genome alterations and hepatocellular carcinoma (HCC) cancer stem cells (CSCs) remains unclear. In this study, we evaluated the relationship between somatic mutations and epithelial cell adhesion molecule positive (EpCAM+) CSCs. Methods Two patient-derived HCC samples (HCC1 and HCC2) were sorted by EpCAM expression and analyzed by whole exome sequence. We measured PCDH18 expression level in eight HCC cell lines as well as HCC1 and HCC2 by real-time quantitative RT-PCR. We validated the identified gene mutations in 57 paired of HCC and matched non-cancerous liver tissues by Sanger sequence. Results Whole exome sequencing on the sorted EpCAM+ and EpCAM− HCC1 and HCC2 cells revealed 19,263 nonsynonymous mutations in the cording region. We selected mutations that potentially impair the function of the encoded protein. Ultimately, 60 mutations including 13 novel nonsense and frameshift mutations were identified. Among them, PCDH18 mutation was more frequently detected in sorted EpCAM+ cells than in EpCAM− cells in HCC1 by whole exome sequences. However, we could not confirm the difference of PCDH18 mutation frequency between sorted EpCAM+ and EpCAM− cells by Sanger sequencing, indicating that PCDH18 mutation could not explain intracellular heterogeneity. In contrast, we found novel PCDH18 mutations, including c.2556_2557delTG, c.1474C>G, c.2337A>G, and c.2976G>T, were detected in HCC1 and 3/57 (5.3%) additional HCC surgical specimens. All four HCCs with PCDH18 mutations were EpCAM-positive, suggesting that PCDH18 somatic mutations might explain the intertumor heterogeneity of HCCs in terms of the expression status of EpCAM. Furthermore, EpCAM-positive cell lines (Huh1, Huh7, HepG2, and Hep3B) had lower PCDH18 expression than EpCAM-negative cell lines (PLC/PRL/5, HLE, HLF, and SK-Hep-1), and PCDH18 knockdown in HCC2 cells slightly enhanced cell proliferation. Conclusions Our data suggest that PCDH18 is functionally suppressed in a subset of EpCAM-positive HCCs through somatic mutations, and may play a role in the development of EpCAM-positive HCCs. Electronic supplementary material The online version of this article (doi:10.1186/s12935-017-0467-x) contains supplementary material, which is available to authorized users.
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Zhou D, Tang W, Su G, Cai M, An HX, Zhang Y. PCDH18 is frequently inactivated by promoter methylation in colorectal cancer. Sci Rep 2017; 7:2819. [PMID: 28588296 PMCID: PMC5460281 DOI: 10.1038/s41598-017-03133-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 04/25/2017] [Indexed: 12/23/2022] Open
Abstract
Protocadherin18 (PCDH18) was found to be preferentially methylated and inactivated in colorectal cancer (CRC) using bioinformatics tools. However, its biologic role in tumorgenesis remains unclear. Herein, we aimed to elucidate its epigenetic regulation and biological functions in CRC. The methylation status of PCDH18 was significant higher in CRC tissues than in adjacent non-tumor tissues (median, 15.17% vs. median, 0.4438%). Expression level of PCDH18 was significantly lower in primary CRCs than in nonmalignant tissues. Importantly, methylation status of PCDH18 in cell-free DNA of CRC patients was also significantly higher than in healthy subjects. PCDH18 was readily expressed in NCM460 cells, but downregulated in 100% (4/4) of CRC cell lines by promoter methylation, despite its expression could be restored through demethylation treatment. Overexpression of PCDH18 suppressed CRC cell viability, colony formation and migration. Meanwhile, the depletion of PCDH18 by siRNA in NCM460 cells enhanced the colonogenicity and migration ability and promoted β-catenin nuclear accumulation, whereas it inhibited cell cycle arrest. These effects were associated with upregulation of phospho-GSK-3β and cyclin D1, and downregulation of caspase3 and p21. Our results suggested that PCDH18 was a putative tumor suppressor with epigenetic silencing in CRC and a potential biomarker for CRC diagnosis.
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Affiliation(s)
- Dan Zhou
- Key Laboratory of Design and Assembly of Functional Nanostructures, Fujian Provincial Key Laboratory of Nanomaterials, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fujian, China.,Department of Medical Oncology, Xiamen Cancer Hospital, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, China.,Xiamen Institute of Rare Earth Materials, Chinese Academy of Sciences, Xiamen, Fujian, China
| | - Weiwei Tang
- Department of Medical Oncology, Xiamen Cancer Hospital, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, China
| | - Guoqiang Su
- Department of Gastrointestinal surgery, Xiamen Cancer Hospital, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, China
| | - Mingquan Cai
- Department of Medical Oncology, Xiamen Cancer Hospital, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, China
| | - Han-Xiang An
- Department of Medical Oncology, Xiamen Cancer Hospital, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, China.
| | - Yun Zhang
- Key Laboratory of Design and Assembly of Functional Nanostructures, Fujian Provincial Key Laboratory of Nanomaterials, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fujian, China. .,Department of Medical Oncology, Xiamen Cancer Hospital, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, China. .,Xiamen Institute of Rare Earth Materials, Chinese Academy of Sciences, Xiamen, Fujian, China.
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11
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Scott M, Vallania F, Khatri P. META-ANALYSIS OF CONTINUOUS PHENOTYPES IDENTIFIES A GENE SIGNATURE THAT CORRELATES WITH COPD DISEASE STATUS. PACIFIC SYMPOSIUM ON BIOCOMPUTING. PACIFIC SYMPOSIUM ON BIOCOMPUTING 2017; 22:266-275. [PMID: 27896981 PMCID: PMC5464998 DOI: 10.1142/9789813207813_0026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The utility of multi-cohort two-class meta-analysis to identify robust differentially expressed gene signatures has been well established. However, many biomedical applications, such as gene signatures of disease progression, require one-class analysis. Here we describe an R package, MetaCorrelator, that can identify a reproducible transcriptional signature that is correlated with a continuous disease phenotype across multiple datasets. We successfully applied this framework to extract a pattern of gene expression that can predict lung function in patients with chronic obstructive pulmonary disease (COPD) in both peripheral blood mononuclear cells (PBMCs) and tissue. Our results point to a disregulation in the oxidation state of the lungs of patients with COPD, as well as underscore the classically recognized inammatory state that underlies this disease.
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Affiliation(s)
- Madeleine Scott
- Stanford Medical School, Stanford University, Stanford, California, USA
| | - Francesco Vallania
- Stanford Institute for Immunity, Transplantation, and Infection, Stanford University, Stanford, California, USA
| | - Purvesh Khatri
- Stanford Institute for Immunity, Transplantation, and Infection, Stanford University, Stanford, California, USA
- Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, California, USA
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12
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Rim JH, Kim SW, Han SH, Yoo J. Clinical and Molecular Delineation of a Novel De Novo 4q28.3-31.21 Interstitial Deletion in a Patient with Developmental Delay. Yonsei Med J 2015; 56:1742-4. [PMID: 26446663 PMCID: PMC4630069 DOI: 10.3349/ymj.2015.56.6.1742] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 05/11/2015] [Indexed: 11/27/2022] Open
Affiliation(s)
- John Hoon Rim
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Seong Woo Kim
- Department of Rehabilitation Medicine, National Health Insurance Service Ilsan Hospital, Goyang, Korea
| | - Sung-Hee Han
- Department of Laboratory Medicine, Seoul Clinical Laboratories, Yongin, Korea.
- Department of Laboratory Medicine, BioCore, Yongin, Korea
| | - Jongha Yoo
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
- Department of Laboratory Medicine, National Health Insurance Service Ilsan Hospital, Goyang, Korea.
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