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Vong KI, Lee S, Au KS, Crowley TB, Capra V, Martino J, Haller M, Araújo C, Machado HR, George R, Gerding B, James KN, Stanley V, Jiang N, Alu K, Meave N, Nidhiry AS, Jiwani F, Tang I, Nisal A, Jhamb I, Patel A, Patel A, McEvoy-Venneri J, Barrows C, Shen C, Ha YJ, Howarth R, Strain M, Ashley-Koch AE, Azam M, Mumtaz S, Bot GM, Finnell RH, Kibar Z, Marwan AI, Melikishvili G, Meltzer HS, Mutchinick OM, Stevenson DA, Mroczkowski HJ, Ostrander B, Schindewolf E, Moldenhauer J, Zackai EH, Emanuel BS, Garcia-Minaur S, Nowakowska BA, Stevenson RE, Zaki MS, Northrup H, McNamara HK, Aldinger KA, Phelps IG, Deng M, Glass IA, Morrow B, McDonald-McGinn DM, Sanna-Cherchi S, Lamb DJ, Gleeson JG. Risk of meningomyelocele mediated by the common 22q11.2 deletion. Science 2024; 384:584-590. [PMID: 38696583 DOI: 10.1126/science.adl1624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 03/27/2024] [Indexed: 05/04/2024]
Abstract
Meningomyelocele is one of the most severe forms of neural tube defects (NTDs) and the most frequent structural birth defect of the central nervous system. We assembled the Spina Bifida Sequencing Consortium to identify causes. Exome and genome sequencing of 715 parent-offspring trios identified six patients with chromosomal 22q11.2 deletions, suggesting a 23-fold increased risk compared with the general population. Furthermore, analysis of a separate 22q11.2 deletion cohort suggested a 12- to 15-fold increased NTD risk of meningomyelocele. The loss of Crkl, one of several neural tube-expressed genes within the minimal deletion interval, was sufficient to replicate NTDs in mice, where both penetrance and expressivity were exacerbated by maternal folate deficiency. Thus, the common 22q11.2 deletion confers substantial meningomyelocele risk, which is partially alleviated by folate supplementation.
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Affiliation(s)
- Keng Ioi Vong
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Sangmoon Lee
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Kit Sing Au
- Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth) and Children's Memorial Hermann Hospital, Houston, TX 77030, USA
| | - T Blaine Crowley
- 22q and You Center, Division of Human Genetics, Children's Hospital of Philadelphia and Department of Pediatrics, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Valeria Capra
- Genomics and Clinical Genetics Unit, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy
| | - Jeremiah Martino
- Division of Nephrology, Department of Medicine, Columbia University, NY 10027, USA
| | - Meade Haller
- Center for Reproductive Medicine, Department of Molecular and Cellular Biology and Scott Department of Urology, Baylor College of Medicine, TX 77030, USA
| | - Camila Araújo
- Department of Surgery and Anatomy, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14040-900, Brazil
| | - Hélio R Machado
- Department of Surgery and Anatomy, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14040-900, Brazil
| | - Renee George
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Bryn Gerding
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Kiely N James
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Valentina Stanley
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Nan Jiang
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Kameron Alu
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Naomi Meave
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Anna S Nidhiry
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Fiza Jiwani
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Isaac Tang
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Ashna Nisal
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Ishani Jhamb
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Arzoo Patel
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Aakash Patel
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Jennifer McEvoy-Venneri
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Chelsea Barrows
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Celina Shen
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Yoo-Jin Ha
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Robyn Howarth
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Madison Strain
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27710, USA
| | | | - Matloob Azam
- Pediatrics and Child Neurology, Wah Medical College, Wah Cantt, Punjab 47000, Pakistan
| | - Sara Mumtaz
- Department of Biological Sciences, National University of Medical Sciences (NUMS), Punjab 46000, Pakistan
| | - Gyang Markus Bot
- Neurosurgery Division, Department of Surgery, Jos University Teaching Hospital, Jos 930105, Nigeria
| | - Richard H Finnell
- Center for Precision Environmental Health, Departments of Molecular and Human Genetics, Molecular and Cellular Biology and Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zoha Kibar
- Department of Neurosciences, University of Montreal and CHU Sainte Justine Research Center, Montreal, QC H3T 1C5, Canada
| | - Ahmed I Marwan
- Division of Pediatric Surgery, University of Colorado School of Medicine, Children's Hospital of Colorado, Colorado Fetal Care Center, Aurora, CO 80045, USA
| | - Gia Melikishvili
- Department of Pediatrics, MediClubGeorgia Medical Center, Tbilisi 0160, Georgia
| | - Hal S Meltzer
- Department of Neurosurgery, University of California San Diego, Rady Children's Hospital, San Diego, CA 92123, USA
| | - Osvaldo M Mutchinick
- Department of Genetics, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, 14080 Mexico City, Mexico
| | - David A Stevenson
- Division of Medical Genetics, Stanford University, Palo Alto, CA 94305, USA
| | - Henry J Mroczkowski
- Division of Medical Genetics, University of Tennessee Health Science Campus, Memphis, TN 38163, USA
| | - Betsy Ostrander
- Division of Pediatric Neurology, Primary Children's Hospital, University of Utah, Salt Lake City, UT 84113, USA
| | - Erica Schindewolf
- Center for Fetal Diagnosis and Treatment, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Julie Moldenhauer
- Center for Fetal Diagnosis and Treatment, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Elaine H Zackai
- 22q and You Center, Division of Human Genetics, Children's Hospital of Philadelphia and Department of Pediatrics, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Beverly S Emanuel
- 22q and You Center, Division of Human Genetics, Children's Hospital of Philadelphia and Department of Pediatrics, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sixto Garcia-Minaur
- Clinical Genetics Section, Institute of Medical and Molecular Genetics, University Hospital La Paz, 28046 Madrid, Spain
| | - Beata A Nowakowska
- Department of Medical Genetics, Institute of Mother and Child, Kasprzaka, 01-211 Warsaw, Poland
| | - Roger E Stevenson
- JC Self Research Institute of Human Genetics, Greenwood Genetic Center, Greenwood, SC 29646, USA
| | - Maha S Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo 12311, Egypt
| | - Hope Northrup
- Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth) and Children's Memorial Hermann Hospital, Houston, TX 77030, USA
| | - Hanna K McNamara
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Kimberly A Aldinger
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
- Departments of Pediatrics, University of Washington, Seattle, WA 98105, USA
- Department of Neurology, University of Washington, Seattle, WA 98105, USA
| | - Ian G Phelps
- Departments of Pediatrics, University of Washington, Seattle, WA 98105, USA
| | - Mei Deng
- Departments of Pediatrics, University of Washington, Seattle, WA 98105, USA
| | - Ian A Glass
- Departments of Pediatrics, University of Washington, Seattle, WA 98105, USA
| | - Bernice Morrow
- Division of Translational Genetics, Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Donna M McDonald-McGinn
- 22q and You Center, Division of Human Genetics, Children's Hospital of Philadelphia and Department of Pediatrics, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Human Biology and Medical Genetics, Sapienza University, 00185-Rome RM, Italy
| | - Simone Sanna-Cherchi
- Division of Nephrology, Department of Medicine, Columbia University, NY 10027, USA
| | - Dolores J Lamb
- Center for Reproductive Medicine, Department of Molecular and Cellular Biology and Scott Department of Urology, Baylor College of Medicine, TX 77030, USA
- Department of Urology, Center for Reproductive Genomics, Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Joseph G Gleeson
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
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Greenberg D, Rosenblum ND, Tonelli M. The multifaceted links between hearing loss and chronic kidney disease. Nat Rev Nephrol 2024; 20:295-312. [PMID: 38287134 DOI: 10.1038/s41581-024-00808-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2024] [Indexed: 01/31/2024]
Abstract
Hearing loss affects nearly 1.6 billion people and is the third-leading cause of disability worldwide. Chronic kidney disease (CKD) is also a common condition that is associated with adverse clinical outcomes and high health-care costs. From a developmental perspective, the structures responsible for hearing have a common morphogenetic origin with the kidney, and genetic abnormalities that cause familial forms of hearing loss can also lead to kidney disease. On a cellular level, normal kidney and cochlea function both depend on cilial activities at the apical surface, and kidney tubular cells and sensory epithelial cells of the inner ear use similar transport mechanisms to modify luminal fluid. The two organs also share the same collagen IV basement membrane network. Thus, strong developmental and physiological links exist between hearing and kidney function. These theoretical considerations are supported by epidemiological data demonstrating that CKD is associated with a graded and independent excess risk of sensorineural hearing loss. In addition to developmental and physiological links between kidney and cochlear function, hearing loss in patients with CKD may be driven by specific medications or treatments, including haemodialysis. The associations between these two common conditions are not commonly appreciated, yet have important implications for research and clinical practice.
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Affiliation(s)
- Dina Greenberg
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, Toronto, Ontario, Canada
| | - Norman D Rosenblum
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, Toronto, Ontario, Canada
- Department of Paediatrics, Temerty Faculty of Medicine, Toronto, Ontario, Canada
| | - Marcello Tonelli
- Department of Medicine, University of Calgary, Calgary, Alberta, Canada.
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Goldmuntz E, Bassett AS, Boot E, Marino B, Moldenhauer JS, Óskarsdóttir S, Putotto C, Rychik J, Schindewolf E, McDonald-McGinn DM, Blagowidow N. Prenatal cardiac findings and 22q11.2 deletion syndrome: Fetal detection and evaluation. Prenat Diagn 2024. [PMID: 38593251 DOI: 10.1002/pd.6566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/11/2024]
Abstract
Clinical features of 22q11.2 microdeletion syndrome (22q11.2DS) are highly variable between affected individuals and frequently include a subset of conotruncal and aortic arch anomalies. Many are diagnosed with 22q11.2DS when they present as a fetus, newborn or infant with characteristic cardiac findings and subsequently undergo genetic testing. The presence of an aortic arch anomaly with characteristic intracardiac anomalies increases the likelihood that the patient has 22q11.2 DS, but those with an aortic arch anomaly and normal intracardiac anatomy are also at risk. It is particularly important to identify the fetus at risk for 22q11.2DS in order to prepare the expectant parents and plan postnatal care for optimal outcomes. Fetal anatomy scans now readily identify aortic arch anomalies (aberrant right subclavian artery, right sided aortic arch or double aortic arch) in the three-vessel tracheal view. Given the association of 22q11.2DS with aortic arch anomalies with and without intracardiac defects, this review highlights the importance of recognizing the fetus at risk for 22q11.2 deletion syndrome with an aortic arch anomaly and details current methods for genetic testing. To assist in the prenatal diagnosis of 22q11.2DS, this review summarizes the seminal features of 22q11.2DS, its prenatal presentation and current methods for genetic testing.
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Affiliation(s)
- Elizabeth Goldmuntz
- Division of Cardiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Anne S Bassett
- The Dalglish Family 22q Clinic, Toronto General Hospital, University Health Network, Toronto, Ontario, Canada
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
- Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
| | - Erik Boot
- The Dalglish Family 22q Clinic, Toronto General Hospital, University Health Network, Toronto, Ontario, Canada
- Advisium, 's Heeren Loo Zorggroep, Amersfoort, The Netherlands
- Department of Psychiatry and Neuropsychology, Maastricht University, Maastricht, The Netherlands
| | - Bruno Marino
- Department of Maternal Infantile and Urological Sciences, Sapienza University of Rome (Italy), Roma, Italy
| | - Julie S Moldenhauer
- Division of Human Genetics, 22q and You Center, Clinical Genetics Center, Section of Genetic Counseling, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Departments of Obstetrics and Gynecology and Surgery, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Sólveig Óskarsdóttir
- Department of Pediatrics, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Rheumatology and Immunology, Queen Silvia Children's Hospital, Gothenburg, Sweden
| | - Carolina Putotto
- Department of Maternal Infantile and Urological Sciences, Sapienza University of Rome (Italy), Roma, Italy
| | - Jack Rychik
- Division of Cardiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Erica Schindewolf
- Division of Human Genetics, 22q and You Center, Clinical Genetics Center, Section of Genetic Counseling, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Donna M McDonald-McGinn
- Department of Pediatrics, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Division of Human Genetics, 22q and You Center, Clinical Genetics Center, Section of Genetic Counseling, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Human Biology and Medical Genetics, Sapienza University, Rome, Italy
| | - Natalie Blagowidow
- The Harvey Institute for Human Genetics, Greater Baltimore Medical Center, Baltimore, Maryland, USA
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Dinges SS, Amini K, Notarangelo LD, Delmonte OM. Primary and secondary defects of the thymus. Immunol Rev 2024; 322:178-211. [PMID: 38228406 PMCID: PMC10950553 DOI: 10.1111/imr.13306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
The thymus is the primary site of T-cell development, enabling generation, and selection of a diverse repertoire of T cells that recognize non-self, whilst remaining tolerant to self- antigens. Severe congenital disorders of thymic development (athymia) can be fatal if left untreated due to infections, and thymic tissue implantation is the only cure. While newborn screening for severe combined immune deficiency has allowed improved detection at birth of congenital athymia, thymic disorders acquired later in life are still underrecognized and assessing the quality of thymic function in such conditions remains a challenge. The thymus is sensitive to injury elicited from a variety of endogenous and exogenous factors, and its self-renewal capacity decreases with age. Secondary and age-related forms of thymic dysfunction may lead to an increased risk of infections, malignancy, and autoimmunity. Promising results have been obtained in preclinical models and clinical trials upon administration of soluble factors promoting thymic regeneration, but to date no therapy is approved for clinical use. In this review we provide a background on thymus development, function, and age-related involution. We discuss disease mechanisms, diagnostic, and therapeutic approaches for primary and secondary thymic defects.
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Affiliation(s)
- Sarah S. Dinges
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Kayla Amini
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Luigi D. Notarangelo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ottavia M. Delmonte
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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AlAshgar TM, AlDawsari NH, AlSanea NY, AlSalamah NA, AlSugair NS, Ardah HI, Kabbani MS. The Outcomes of Cardiac Surgery in Children With DiGeorge Syndrome in a Single Center Experience: A Retrospective Cohort Study. Cureus 2024; 16:e55186. [PMID: 38562270 PMCID: PMC10983060 DOI: 10.7759/cureus.55186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/28/2024] [Indexed: 04/04/2024] Open
Abstract
Background DiGeorge syndrome, a common genetic microdeletion syndrome, is associated with multiple congenital anomalies, including congenital cardiac diseases. This study aims to identify the short and midterm outcomes of cardiac surgery performed on children with DiGeorge syndrome. Methods A retrospective cohort study was conducted between the period of 2018-2022, which included children divided into two groups with a 1:2 ratio. Group one included DiGeorge syndrome patients who were diagnosed using fluorescence in situ hybridization (FISH). Group two included the control group of patients who were clear of genetic syndromes. The two groups were matched based on similar cardiac surgery, age of surgery, and Risk Adjustment in Congenital Heart Surgery (RACHS-1) score. The two groups were compared based on the demographical data and postoperative complications. Results The study consisted of 81 children; 27 were DiGeorge syndrome patients, and 54 were in the control group. DiGeorge syndrome patients showed an increase in mechanical ventilation duration (p=0.0047), intensive care unit (ICU) length of stay (p=0.0012), and hospital length of stay (p=0.0391). Moreover, they showed an increased risk for bacteremia (p=0.0414), ventilator-associated pneumonia (VAP; p=0.0036), urinary tract infections (UTI; p=0.0064), and surgical site infection (SSI; p≤0.0001). They were also more susceptible to postoperative seizures (p=0.0049). Furthermore, patients with DiGeorge syndrome had a higher prevalence of congenital renal anomalies. However, there was no mortality in either group. Conclusion This study shows a variability in the postoperative outcomes between the two groups. The study demonstrates that patients with DiGeorge syndrome have higher risks of infections and longer hospital stay during the postoperative period. Further research with a larger sample is needed to confirm our findings.
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Affiliation(s)
- Tala M AlAshgar
- Medicine and Surgery, King Saud Bin Abdulaziz University for Health Sciences College of Medicine, Riyadh, SAU
| | - Norah H AlDawsari
- Medicine and Surgery, King Saud Bin Abdulaziz University for Health Sciences College of Medicine, Riyadh, SAU
| | - Nasreen Y AlSanea
- Medicine and Surgery, King Saud Bin Abdulaziz University for Health Sciences College of Medicine, Riyadh, SAU
| | - Noura A AlSalamah
- Medicine and Surgery, King Saud Bin Abdulaziz University for Health Sciences College of Medicine, Riyadh, SAU
| | - Nada S AlSugair
- Medicine and Surgery, King Saud Bin Abdulaziz University for Health Sciences College of Medicine, Riyadh, SAU
| | - Husam I Ardah
- Biostatistics and Epidemiology, King Abdullah International Medical Research Center, Riyadh, SAU
| | - Mohamed S Kabbani
- Pediatric Critical Care, Department of Cardiac Sciences, Ministry of the National Guard Health Affairs, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, SAU
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Ma C, Huang R, Fu F, Zhou H, Wang Y, Yan S, Guo F, Chen H, Li L, Jing X, Li F, Han J, Li D, Li R, Liao C. Prenatal diagnosis and outcomes in fetuses with duplex kidney. Int J Gynaecol Obstet 2024. [PMID: 38189110 DOI: 10.1002/ijgo.15344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 12/13/2023] [Accepted: 12/17/2023] [Indexed: 01/09/2024]
Abstract
OBJECTIVE Duplex kidney is a relatively frequent form of urinary system abnormality. This study aimed to elucidate the value of chromosomal microarray analysis (CMA) and whole exome sequencing (WES) for duplex kidney and the perinatal outcomes of duplex kidney fetuses. METHODS This retrospective cohort study included 63 patients with duplex kidney diagnosed using antenatal ultrasound between August 2013 and January 2023. We reviewed the clinical characteristics, genetic test results, and pregnancy outcomes of the patients. RESULTS Among the 63 cases based on the inclusion criteria, the CMA detected seven (11.1%) clinically significant variants and nine variants of uncertain significance (VUS), and the pathogenic/likely pathogenic (P/LP) copy number variations (CNVs) in the recurrent region that were associated with prenatal duplex kidney included 17q12, 17p13.3, and 22q11.2. No significant disparity was observed in the CMA detection rate between the unilateral and bilateral groups, or between the isolated and non-isolated groups. WES identified three (50%) P/LP single-gene variants in six fetuses with duplex kidney. We detected the following pathogenic genes in the duplex kidney fetuses: KMT2D, SMPD4, and FANCI. Pregnancy termination in cases where clinically significant variants were detected by genetic testing was different in statistical significance from that in cases with negative results (9/10, 90.0% vs 8/48, 16.7%, P < 0.001). CONCLUSION This study elucidated the value of CMA and WES for fetal duplex kidney, proving that CMA and WES may be useful tools in prenatal diagnosis and genetic counseling.
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Affiliation(s)
- Chunling Ma
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, China
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Ruibin Huang
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Fang Fu
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Hang Zhou
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - You Wang
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, China
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Shujuan Yan
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Fei Guo
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Huanyi Chen
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Lushan Li
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Xiangyi Jing
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Fucheng Li
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Jin Han
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Dongzhi Li
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Ru Li
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Can Liao
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, China
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
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Huang R, Fu F, Guo F, Zhou H, Yu Q, Yan S, Liu L, Lu J, Ma C, Wang Y, Chen H, Wang D, Zhang Y, Jing X, Li F, Han J, Li D, Li R, Liao C. Prenatal diagnosis of polycystic renal diseases: diagnostic yield, novel disease-causing variants, and genotype-phenotype correlations. Am J Obstet Gynecol MFM 2024; 6:101228. [PMID: 37984685 DOI: 10.1016/j.ajogmf.2023.101228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 11/04/2023] [Accepted: 11/15/2023] [Indexed: 11/22/2023]
Abstract
BACKGROUND Polycystic renal disease is a frequent congenital anomaly of the kidneys, but research using chromosomal microarray analysis and exome sequencing in fetuses with polycystic renal disease remains sparse, with most studies focusing on the multisystem or genitourinary system. OBJECTIVE This study aimed to assess the detection rate of detectable genetic causes of fetal polycystic renal disease at different levels, novel disease-causing variants, and genotype-phenotype correlations. STUDY DESIGN This study included 220 fetal polycystic renal disease cases from January 2014 to June 2022. Cases were divided into the following 3 groups: isolated multicystic dysplastic kidneys, nonisolated multicystic dysplastic kidneys, and suspected polycystic kidney disease group. We reviewed data on maternal demographics, ultrasonographic results, chromosomal microarray analysis/exome sequencing results, and pregnancy outcomes. RESULTS In our cohort, chromosomal microarray analysis identified 19 (8.6%) fetuses carrying chromosomal abnormalities, and the most common copy number variation was 17q12 microdeletion (7/220; 3.2%). Furthermore, 94 families chose to perform trio-exome sequencing testing, and 21 fetuses (22.3%) were found to harbor pathogenic/likely pathogenic variants. There was a significant difference in the live birth rate among the 3 groups (91/130 vs 46/80 vs 1/10; P<.001). Among 138 live birth cases, 106 (78.5%) underwent postnatal ultrasound review, of which 95 (89.6%) had a consistent prenatal-postnatal ultrasound diagnosis. CONCLUSION For both isolated and nonisolated polycystic renal disease, our data showed high detection efficiency with both testing tools. The detection of novel pathogenic variants expands the known disease spectrum of polycystic renal disease-associated genes while enriching our understanding of the genotype-phenotype correlation. Therefore, we consider it feasible to perform chromosomal microarray analysis+exome sequencing testing in fetal polycystic renal disease. Moreover, prenatal-postnatal ultrasound concordance was greater, the live birth rate was higher, and prognosis was better when known genetic disorders were excluded, indicating that genetic testing results significantly influenced pregnancy decisions.
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Affiliation(s)
- Ruibin Huang
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China (Mr Huang, Dr Fu, Mr Guo, Mr Zhou, Ms Yu, Dr Yan, Ms Liu, Dr Lu, Ms Ma, Ms Y Wang, Ms Chen, Dr D Wang, Ms Zhang, Ms Jing, Dr F Li, Dr Han, Dr D Li, Dr R Li, and Ms Liao)
| | - Fang Fu
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China (Mr Huang, Dr Fu, Mr Guo, Mr Zhou, Ms Yu, Dr Yan, Ms Liu, Dr Lu, Ms Ma, Ms Y Wang, Ms Chen, Dr D Wang, Ms Zhang, Ms Jing, Dr F Li, Dr Han, Dr D Li, Dr R Li, and Ms Liao)
| | - Fei Guo
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China (Mr Huang, Dr Fu, Mr Guo, Mr Zhou, Ms Yu, Dr Yan, Ms Liu, Dr Lu, Ms Ma, Ms Y Wang, Ms Chen, Dr D Wang, Ms Zhang, Ms Jing, Dr F Li, Dr Han, Dr D Li, Dr R Li, and Ms Liao)
| | - Hang Zhou
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China (Mr Huang, Dr Fu, Mr Guo, Mr Zhou, Ms Yu, Dr Yan, Ms Liu, Dr Lu, Ms Ma, Ms Y Wang, Ms Chen, Dr D Wang, Ms Zhang, Ms Jing, Dr F Li, Dr Han, Dr D Li, Dr R Li, and Ms Liao)
| | - Qiuxia Yu
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China (Mr Huang, Dr Fu, Mr Guo, Mr Zhou, Ms Yu, Dr Yan, Ms Liu, Dr Lu, Ms Ma, Ms Y Wang, Ms Chen, Dr D Wang, Ms Zhang, Ms Jing, Dr F Li, Dr Han, Dr D Li, Dr R Li, and Ms Liao)
| | - Shujuan Yan
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China (Mr Huang, Dr Fu, Mr Guo, Mr Zhou, Ms Yu, Dr Yan, Ms Liu, Dr Lu, Ms Ma, Ms Y Wang, Ms Chen, Dr D Wang, Ms Zhang, Ms Jing, Dr F Li, Dr Han, Dr D Li, Dr R Li, and Ms Liao)
| | - Liyuan Liu
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China (Mr Huang, Dr Fu, Mr Guo, Mr Zhou, Ms Yu, Dr Yan, Ms Liu, Dr Lu, Ms Ma, Ms Y Wang, Ms Chen, Dr D Wang, Ms Zhang, Ms Jing, Dr F Li, Dr Han, Dr D Li, Dr R Li, and Ms Liao); The First Clinical Medical College, Southern Medical University, Guangzhou, China (Ms Liu and Ms Ma)
| | - Jianqin Lu
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China (Mr Huang, Dr Fu, Mr Guo, Mr Zhou, Ms Yu, Dr Yan, Ms Liu, Dr Lu, Ms Ma, Ms Y Wang, Ms Chen, Dr D Wang, Ms Zhang, Ms Jing, Dr F Li, Dr Han, Dr D Li, Dr R Li, and Ms Liao)
| | - Chunling Ma
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China (Mr Huang, Dr Fu, Mr Guo, Mr Zhou, Ms Yu, Dr Yan, Ms Liu, Dr Lu, Ms Ma, Ms Y Wang, Ms Chen, Dr D Wang, Ms Zhang, Ms Jing, Dr F Li, Dr Han, Dr D Li, Dr R Li, and Ms Liao); The First Clinical Medical College, Southern Medical University, Guangzhou, China (Ms Liu and Ms Ma)
| | - You Wang
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China (Mr Huang, Dr Fu, Mr Guo, Mr Zhou, Ms Yu, Dr Yan, Ms Liu, Dr Lu, Ms Ma, Ms Y Wang, Ms Chen, Dr D Wang, Ms Zhang, Ms Jing, Dr F Li, Dr Han, Dr D Li, Dr R Li, and Ms Liao)
| | - Huanyi Chen
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China (Mr Huang, Dr Fu, Mr Guo, Mr Zhou, Ms Yu, Dr Yan, Ms Liu, Dr Lu, Ms Ma, Ms Y Wang, Ms Chen, Dr D Wang, Ms Zhang, Ms Jing, Dr F Li, Dr Han, Dr D Li, Dr R Li, and Ms Liao)
| | - Dan Wang
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China (Mr Huang, Dr Fu, Mr Guo, Mr Zhou, Ms Yu, Dr Yan, Ms Liu, Dr Lu, Ms Ma, Ms Y Wang, Ms Chen, Dr D Wang, Ms Zhang, Ms Jing, Dr F Li, Dr Han, Dr D Li, Dr R Li, and Ms Liao)
| | - Yongling Zhang
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China (Mr Huang, Dr Fu, Mr Guo, Mr Zhou, Ms Yu, Dr Yan, Ms Liu, Dr Lu, Ms Ma, Ms Y Wang, Ms Chen, Dr D Wang, Ms Zhang, Ms Jing, Dr F Li, Dr Han, Dr D Li, Dr R Li, and Ms Liao)
| | - Xiangyi Jing
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China (Mr Huang, Dr Fu, Mr Guo, Mr Zhou, Ms Yu, Dr Yan, Ms Liu, Dr Lu, Ms Ma, Ms Y Wang, Ms Chen, Dr D Wang, Ms Zhang, Ms Jing, Dr F Li, Dr Han, Dr D Li, Dr R Li, and Ms Liao)
| | - Fucheng Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China (Mr Huang, Dr Fu, Mr Guo, Mr Zhou, Ms Yu, Dr Yan, Ms Liu, Dr Lu, Ms Ma, Ms Y Wang, Ms Chen, Dr D Wang, Ms Zhang, Ms Jing, Dr F Li, Dr Han, Dr D Li, Dr R Li, and Ms Liao)
| | - Jin Han
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China (Mr Huang, Dr Fu, Mr Guo, Mr Zhou, Ms Yu, Dr Yan, Ms Liu, Dr Lu, Ms Ma, Ms Y Wang, Ms Chen, Dr D Wang, Ms Zhang, Ms Jing, Dr F Li, Dr Han, Dr D Li, Dr R Li, and Ms Liao)
| | - Dongzhi Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China (Mr Huang, Dr Fu, Mr Guo, Mr Zhou, Ms Yu, Dr Yan, Ms Liu, Dr Lu, Ms Ma, Ms Y Wang, Ms Chen, Dr D Wang, Ms Zhang, Ms Jing, Dr F Li, Dr Han, Dr D Li, Dr R Li, and Ms Liao)
| | - Ru Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China (Mr Huang, Dr Fu, Mr Guo, Mr Zhou, Ms Yu, Dr Yan, Ms Liu, Dr Lu, Ms Ma, Ms Y Wang, Ms Chen, Dr D Wang, Ms Zhang, Ms Jing, Dr F Li, Dr Han, Dr D Li, Dr R Li, and Ms Liao)
| | - Can Liao
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China (Mr Huang, Dr Fu, Mr Guo, Mr Zhou, Ms Yu, Dr Yan, Ms Liu, Dr Lu, Ms Ma, Ms Y Wang, Ms Chen, Dr D Wang, Ms Zhang, Ms Jing, Dr F Li, Dr Han, Dr D Li, Dr R Li, and Ms Liao).
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8
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Martino J, Liu Q, Vukojevic K, Ke J, Lim TY, Khan A, Gupta Y, Perez A, Yan Z, Milo Rasouly H, Vena N, Lippa N, Giordano JL, Saraga M, Saraga-Babic M, Westland R, Bodria M, Piaggio G, Bendapudi PK, Iglesias AD, Wapner RJ, Tasic V, Wang F, Ionita-Laza I, Ghiggeri GM, Kiryluk K, Sampogna RV, Mendelsohn CL, D'Agati VD, Gharavi AG, Sanna-Cherchi S. Mouse and human studies support DSTYK loss of function as a low-penetrance and variable expressivity risk factor for congenital urinary tract anomalies. Genet Med 2023; 25:100983. [PMID: 37746849 DOI: 10.1016/j.gim.2023.100983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/14/2023] [Accepted: 09/17/2023] [Indexed: 09/26/2023] Open
Abstract
PURPOSE Previous work identified rare variants in DSTYK associated with human congenital anomalies of the kidney and urinary tract (CAKUT). Here, we present a series of mouse and human studies to clarify the association, penetrance, and expressivity of DSTYK variants. METHODS We phenotypically characterized Dstyk knockout mice of 3 separate inbred backgrounds and re-analyzed the original family segregating the DSTYK c.654+1G>A splice-site variant (referred to as "SSV" below). DSTYK loss of function (LOF) and SSVs were annotated in individuals with CAKUT, epilepsy, or amyotrophic lateral sclerosis vs controls. A phenome-wide association study analysis was also performed using United Kingdom Biobank (UKBB) data. RESULTS Results demonstrate ∼20% to 25% penetrance of obstructive uropathy, at least, in C57BL/6J and FVB/NJ Dstyk-/- mice. Phenotypic penetrance increased to ∼40% in C3H/HeJ mutants, with mild-to-moderate severity. Re-analysis of the original family segregating the rare SSV showed low penetrance (43.8%) and no alternative genetic causes for CAKUT. LOF DSTYK variants burden showed significant excess for CAKUT and epilepsy vs controls and an exploratory phenome-wide association study supported association with neurological disorders. CONCLUSION These data support causality for DSTYK LOF variants and highlights the need for large-scale sequencing studies (here >200,000 cases) to accurately assess causality for genes and variants to lowly penetrant traits with common population prevalence.
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Affiliation(s)
- Jeremiah Martino
- Department of Medicine, Columbia University Irving Medical Center, New York, NY
| | - Qingxue Liu
- Department of Medicine, Columbia University Irving Medical Center, New York, NY
| | - Katarina Vukojevic
- Department of Medicine, Columbia University Irving Medical Center, New York, NY; Department of Anatomy, Histology and Embryology, University of Split School of Medicine, Split, Croatia
| | - Juntao Ke
- Department of Medicine, Columbia University Irving Medical Center, New York, NY
| | - Tze Y Lim
- Department of Medicine, Columbia University Irving Medical Center, New York, NY; Unit of Genomic Variability and Complex Diseases, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Atlas Khan
- Department of Medicine, Columbia University Irving Medical Center, New York, NY
| | - Yask Gupta
- Department of Medicine, Columbia University Irving Medical Center, New York, NY; Institute for Inflammation Medicine, University of Lubeck, Germany
| | - Alejandra Perez
- Department of Medicine, Columbia University Irving Medical Center, New York, NY; Department of Urology, Mount Sinai Medical Center, Miami, FL
| | - Zonghai Yan
- Department of Medicine, Columbia University Irving Medical Center, New York, NY
| | - Hila Milo Rasouly
- Department of Medicine, Columbia University Irving Medical Center, New York, NY
| | - Natalie Vena
- Department of Medicine, Columbia University Irving Medical Center, New York, NY
| | - Natalie Lippa
- Department of Medicine, Columbia University Irving Medical Center, New York, NY
| | - Jessica L Giordano
- Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY
| | - Marijan Saraga
- Department of Pediatrics, University Hospital of Split, Split, Croatia; School of Medicine, University of Split, Split, Croatia
| | - Mirna Saraga-Babic
- Department of Anatomy, Histology and Embryology, University of Split School of Medicine, Split, Croatia
| | - Rik Westland
- Department of Pediatric Nephrology, Emma Children's Hospital, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Monica Bodria
- Division of Nephrology and Renal Transplantation, IRCCS Istituto Giannina Gaslini, Genoa, Italy; Laboratory on Molecular Nephrology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Giorgio Piaggio
- Division of Nephrology and Renal Transplantation, IRCCS Istituto Giannina Gaslini, Genoa, Italy; Laboratory on Molecular Nephrology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Pavan K Bendapudi
- Division of Hematology and Blood Transfusion Service, Massachusetts General Hospital, Boston, MA; Division of Hemostasis and Thrombosis, Beth Israel Deaconess Medical Center, Boston, MA; Harvard Medical School, Boston, MA
| | - Alejandro D Iglesias
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY
| | - Ronald J Wapner
- Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY
| | - Velibor Tasic
- Medical Faculty of Skopje, University Children's Hospital, Skopje, Macedonia
| | - Fan Wang
- Department of Biostatistics, Columbia University, New York, NY
| | | | - Gian Marco Ghiggeri
- Division of Nephrology and Renal Transplantation, IRCCS Istituto Giannina Gaslini, Genoa, Italy; Laboratory on Molecular Nephrology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Krzysztof Kiryluk
- Department of Medicine, Columbia University Irving Medical Center, New York, NY
| | - Rosemary V Sampogna
- Department of Medicine, Columbia University Irving Medical Center, New York, NY
| | - Cathy L Mendelsohn
- Department of Urology, Columbia University Irving Medical Center, New York, NY; Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY; Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY; Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY
| | - Vivette D D'Agati
- The Renal Pathology Laboratory of the Department of Pathology and Cell Biology, Columbia University, New York, NY
| | - Ali G Gharavi
- Department of Medicine, Columbia University Irving Medical Center, New York, NY
| | - Simone Sanna-Cherchi
- Department of Medicine, Columbia University Irving Medical Center, New York, NY.
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9
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Kabir M, Stuart HM, Lopes FM, Fotiou E, Keavney B, Doig AJ, Woolf AS, Hentges KE. Predicting congenital renal tract malformation genes using machine learning. Sci Rep 2023; 13:13204. [PMID: 37580336 PMCID: PMC10425350 DOI: 10.1038/s41598-023-38110-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 07/03/2023] [Indexed: 08/16/2023] Open
Abstract
Congenital renal tract malformations (RTMs) are the major cause of severe kidney failure in children. Studies to date have identified defined genetic causes for only a minority of human RTMs. While some RTMs may be caused by poorly defined environmental perturbations affecting organogenesis, it is likely that numerous causative genetic variants have yet to be identified. Unfortunately, the speed of discovering further genetic causes for RTMs is limited by challenges in prioritising candidate genes harbouring sequence variants. Here, we exploited the computer-based artificial intelligence methodology of supervised machine learning to identify genes with a high probability of being involved in renal development. These genes, when mutated, are promising candidates for causing RTMs. With this methodology, the machine learning classifier determines which attributes are common to renal development genes and identifies genes possessing these attributes. Here we report the validation of an RTM gene classifier and provide predictions of the RTM association status for all protein-coding genes in the mouse genome. Overall, our predictions, whilst not definitive, can inform the prioritisation of genes when evaluating patient sequence data for genetic diagnosis. This knowledge of renal developmental genes will accelerate the processes of reaching a genetic diagnosis for patients born with RTMs.
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Affiliation(s)
- Mitra Kabir
- CentreDivision of Evolution, Infection and Genomics, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Helen M Stuart
- CentreDivision of Evolution, Infection and Genomics, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Health Innovation Manchester, Manchester University Foundation NHS Trust, Manchester, M13 9WL, UK
| | - Filipa M Lopes
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PL, UK
| | - Elisavet Fotiou
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, M13 9PL, UK
- C.B.B Lifeline Biotech Ltd, 5 Propontidos Street, Strovolos, 2033, Nicosia, Cyprus
| | - Bernard Keavney
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, M13 9PL, UK
- Manchester Heart Institute, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, M13 9WL, UK
| | - Andrew J Doig
- Division of Neuroscience, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Stopford Building, Manchester, M13 9BL, UK
| | - Adrian S Woolf
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PL, UK
- Department of Nephrology, Royal Manchester Children's Hospital, Manchester Academic Health Science Centre, Manchester, M13 9WL, UK
| | - Kathryn E Hentges
- CentreDivision of Evolution, Infection and Genomics, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK.
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10
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Lu Y, Zhou Y, Guo J, Qi M, Lin Y, Zhang X, Xiang Y, Fu Q, Wang B. Integrated analysis of copy number variation-associated lncRNAs identifies candidates contributing to the etiologies of congenital kidney anomalies. Commun Biol 2023; 6:735. [PMID: 37460814 DOI: 10.1038/s42003-023-05101-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 07/05/2023] [Indexed: 07/20/2023] Open
Abstract
Congenital anomalies of the kidney and urinary tract (CAKUT) are disorders resulting from defects in the development of the kidneys and their outflow tract. Copy number variations (CNVs) have been identified as important genetic variations leading to CAKUT, whereas most CAKUT-associated CNVs cannot be attributed to a specific pathogenic gene. Here we construct coexpression networks involving long noncoding RNAs (lncRNAs) within these CNVs (CNV-lncRNAs) using human kidney developmental transcriptomic data. The results show that CNV-lncRNAs encompassed in recurrent CAKUT associated CNVs have highly correlated expression with CAKUT genes in the developing kidneys. The regulatory effects of two hub CNV-lncRNAs (HSALNG0134318 in 22q11.2 and HSALNG0115943 in 17q12) in the module most significantly enriched in known CAKUT genes (CAKUT_sig1, P = 1.150 × 10-6) are validated experimentally. Our results indicate that the reduction of CNV-lncRNAs can downregulate CAKUT genes as predicted by our computational analyses. Furthermore, knockdown of HSALNG0134318 would downregulate HSALNG0115943 and affect kidney development related pathways. The results also indicate that the CAKUT_sig1 module has function significance involving multi-organ development. Overall, our findings suggest that CNV-lncRNAs play roles in regulating CAKUT genes, and the etiologies of CAKUT-associated CNVs should take account of effects on the noncoding genome.
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Affiliation(s)
- Yibo Lu
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Yiyang Zhou
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Jing Guo
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Ming Qi
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Yuwan Lin
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Xingyu Zhang
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Ying Xiang
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai, 200127, China.
| | - Qihua Fu
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai, 200127, China.
| | - Bo Wang
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai, 200127, China.
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11
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Köllges R, Stegmann J, Schneider S, Waffenschmidt L, Fazaal J, Breuer K, Hilger AC, Dworschak GC, Mingardo E, Rösch W, Hofmann A, Neissner C, Ebert AK, Stein R, Younsi N, Hirsch-Koch K, Schmiedeke E, Zwink N, Jenetzky E, Thiele H, Ludwig KU, Reutter H. Exome Survey and Candidate Gene Re-Sequencing Identifies Novel Exstrophy Candidate Genes and Implicates LZTR1 in Disease Formation. Biomolecules 2023; 13:1117. [PMID: 37509153 PMCID: PMC10377188 DOI: 10.3390/biom13071117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 07/09/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
BACKGROUND The bladder exstrophy-epispadias complex (BEEC) is a spectrum of congenital abnormalities that involves the abdominal wall, the bony pelvis, the urinary tract, the external genitalia, and, in severe cases, the gastrointestinal tract as well. METHODS Herein, we performed an exome analysis of case-parent trios with cloacal exstrophy (CE), the most severe form of the BEEC. Furthermore, we surveyed the exome of a sib-pair presenting with classic bladder exstrophy (CBE) and epispadias (E) only. Moreover, we performed large-scale re-sequencing of CBE individuals for novel candidate genes that were derived from the current exome analysis, as well as for previously reported candidate genes within the CBE phenocritical region, 22q11.2. RESULTS The exome survey in the CE case-parent trios identified two candidate genes harboring de novo variants (NR1H2, GKAP1), four candidate genes with autosomal-recessive biallelic variants (AKR1B10, CLSTN3, NDST4, PLEKHB1) and one candidate gene with suggestive uniparental disomy (SVEP1). However, re-sequencing did not identify any additional variant carriers in these candidate genes. Analysis of the affected sib-pair revealed no candidate gene. Re-sequencing of the genes within the 22q11.2 CBE phenocritical region identified two highly conserved frameshift variants that led to early termination in two independent CBE males, in LZTR1 (c.978_985del, p.Ser327fster6) and in SLC7A4 (c.1087delC, p.Arg363fster68). CONCLUSIONS According to previous studies, our study further implicates LZTR1 in CBE formation. Exome analysis-derived candidate genes from CE individuals may not represent a frequent indicator for other BEEC phenotypes and warrant molecular analysis before their involvement in disease formation can be assumed.
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Affiliation(s)
- Ricarda Köllges
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; (R.K.)
| | - Jil Stegmann
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; (R.K.)
- Institute of Anatomy and Cell Biology, Medical Faculty, University of Bonn, 53127 Bonn, Germany
| | - Sophia Schneider
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; (R.K.)
| | - Lea Waffenschmidt
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; (R.K.)
| | - Julia Fazaal
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; (R.K.)
| | - Katinka Breuer
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; (R.K.)
| | - Alina C. Hilger
- Department of Pediatrics and Adolescent Medicine, University Hospital Erlangen, 91054 Erlangen, Germany
| | - Gabriel C. Dworschak
- Institute of Anatomy and Cell Biology, Medical Faculty, University of Bonn, 53127 Bonn, Germany
- Department of Neuropediatrics, University Hospital Bonn, 53127 Bonn, Germany
| | - Enrico Mingardo
- Institute of Anatomy and Cell Biology, Medical Faculty, University of Bonn, 53127 Bonn, Germany
| | - Wolfgang Rösch
- Department of Pediatric Urology, Clinic St. Hedwig, University Medical Center Regensburg, 93053 Regensburg, Germany
| | - Aybike Hofmann
- Department of Pediatric Urology, Clinic St. Hedwig, University Medical Center Regensburg, 93053 Regensburg, Germany
| | - Claudia Neissner
- Department of Pediatric Urology, Clinic St. Hedwig, University Medical Center Regensburg, 93053 Regensburg, Germany
| | - Anne-Karolin Ebert
- Department of Urology and Pediatric Urology, University Hospital Ulm, 89081 Ulm, Germany
| | - Raimund Stein
- Center for Pediatric, Adolescent and Reconstructive Urology, University Medical Center Mannheim, University Heidelberg, 69117 Mannheim, Germany
| | - Nina Younsi
- Center for Pediatric, Adolescent and Reconstructive Urology, University Medical Center Mannheim, University Heidelberg, 69117 Mannheim, Germany
| | - Karin Hirsch-Koch
- Division of Pediatric Urology, Department of Urology, University Hospital Erlangen, 91054 Erlangen, Germany
| | - Eberhard Schmiedeke
- Clinic for Pediatric Surgery and Pediatric Urology, Klinikum Bremen-Mitte, 28205 Bremen, Germany
| | - Nadine Zwink
- Department of Child and Adolescent Psychiatry, University Medical Center of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany
| | - Ekkehart Jenetzky
- Department of Child and Adolescent Psychiatry, University Medical Center of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany
| | - Holger Thiele
- Cologne Center for Genomics, University of Cologne, 50923 Cologne, Germany
| | - Kerstin U. Ludwig
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; (R.K.)
| | - Heiko Reutter
- Division of Neonatology and Pediatric Intensive Care, Department of Pediatrics and Adolescent Medicine, University Hospital Erlangen, 91054 Erlangen, Germany
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12
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Ahram DF, Lim TY, Ke J, Jin G, Verbitsky M, Bodria M, Kil BH, Chatterjee D, Piva SE, Marasa M, Zhang JY, Cocchi E, Caridi G, Gucev Z, Lozanovski VJ, Pisani I, Izzi C, Savoldi G, Gnutti B, Capone VP, Morello W, Guarino S, Esposito P, Lambert S, Radhakrishnan J, Appel GB, Uy NS, Rao MK, Canetta PA, Bomback AS, Nestor JG, Hays T, Cohen DJ, Finale C, van Wijk JA, La Scola C, Baraldi O, Tondolo F, Di Renzo D, Jamry-Dziurla A, Pezzutto A, Manca V, Mitrotti A, Santoro D, Conti G, Martino M, Giordano M, Gesualdo L, Zibar L, Masnata G, Bonomini M, Alberti D, La Manna G, Caliskan Y, Ranghino A, Marzuillo P, Kiryluk K, Krzemień G, Miklaszewska M, Lin F, Montini G, Scolari F, Fiaccadori E, Arapović A, Saraga M, McKiernan J, Alam S, Zaniew M, Szczepańska M, Szmigielska A, Sikora P, Drożdż D, Mizerska-Wasiak M, Mane S, Lifton RP, Tasic V, Latos-Bielenska A, Gharavi AG, Ghiggeri GM, Materna-Kiryluk A, Westland R, Sanna-Cherchi S. Rare Single Nucleotide and Copy Number Variants and the Etiology of Congenital Obstructive Uropathy: Implications for Genetic Diagnosis. J Am Soc Nephrol 2023; 34:1105-1119. [PMID: 36995132 PMCID: PMC10278788 DOI: 10.1681/asn.0000000000000132] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 01/18/2023] [Indexed: 03/31/2023] Open
Abstract
SIGNIFICANCE STATEMENT Congenital obstructive uropathy (COU) is a prevalent human developmental defect with highly heterogeneous clinical presentations and outcomes. Genetics may refine diagnosis, prognosis, and treatment, but the genomic architecture of COU is largely unknown. Comprehensive genomic screening study of 733 cases with three distinct COU subphenotypes revealed disease etiology in 10.0% of them. We detected no significant differences in the overall diagnostic yield among COU subphenotypes, with characteristic variable expressivity of several mutant genes. Our findings therefore may legitimize a genetic first diagnostic approach for COU, especially when burdening clinical and imaging characterization is not complete or available. BACKGROUND Congenital obstructive uropathy (COU) is a common cause of developmental defects of the urinary tract, with heterogeneous clinical presentation and outcome. Genetic analysis has the potential to elucidate the underlying diagnosis and help risk stratification. METHODS We performed a comprehensive genomic screen of 733 independent COU cases, which consisted of individuals with ureteropelvic junction obstruction ( n =321), ureterovesical junction obstruction/congenital megaureter ( n =178), and COU not otherwise specified (COU-NOS; n =234). RESULTS We identified pathogenic single nucleotide variants (SNVs) in 53 (7.2%) cases and genomic disorders (GDs) in 23 (3.1%) cases. We detected no significant differences in the overall diagnostic yield between COU sub-phenotypes, and pathogenic SNVs in several genes were associated to any of the three categories. Hence, although COU may appear phenotypically heterogeneous, COU phenotypes are likely to share common molecular bases. On the other hand, mutations in TNXB were more often identified in COU-NOS cases, demonstrating the diagnostic challenge in discriminating COU from hydronephrosis secondary to vesicoureteral reflux, particularly when diagnostic imaging is incomplete. Pathogenic SNVs in only six genes were found in more than one individual, supporting high genetic heterogeneity. Finally, convergence between data on SNVs and GDs suggest MYH11 as a dosage-sensitive gene possibly correlating with severity of COU. CONCLUSIONS We established a genomic diagnosis in 10.0% of COU individuals. The findings underscore the urgent need to identify novel genetic susceptibility factors to COU to better define the natural history of the remaining 90% of cases without a molecular diagnosis.
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Affiliation(s)
- Dina F. Ahram
- Department of Medicine, Division of Nephrology, Columbia University, New York, New York
| | - Tze Y. Lim
- Department of Medicine, Division of Nephrology, Columbia University, New York, New York
| | - Juntao Ke
- Department of Medicine, Division of Nephrology, Columbia University, New York, New York
| | - Gina Jin
- Department of Medicine, Division of Nephrology, Columbia University, New York, New York
| | - Miguel Verbitsky
- Department of Medicine, Division of Nephrology, Columbia University, New York, New York
| | - Monica Bodria
- Division of Nephrology and Renal Transplantation, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Byum Hee Kil
- Department of Medicine, Division of Nephrology, Columbia University, New York, New York
| | - Debanjana Chatterjee
- Department of Medicine, Division of Nephrology, Columbia University, New York, New York
| | - Stacy E. Piva
- Department of Medicine, Division of Nephrology, Columbia University, New York, New York
| | - Maddalena Marasa
- Department of Medicine, Division of Nephrology, Columbia University, New York, New York
| | - Jun Y. Zhang
- Department of Medicine, Division of Nephrology, Columbia University, New York, New York
| | - Enrico Cocchi
- Department of Medicine, Division of Nephrology, Columbia University, New York, New York
| | - Gianluca Caridi
- Division of Nephrology and Renal Transplantation, IRCCS Istituto Giannina Gaslini, Genoa, Italy
- Laboratory on Molecular Nephrology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Zoran Gucev
- Medical Faculty of Skopje, University Children's Hospital, Skopje, Macedonia
| | - Vladimir J. Lozanovski
- Medical Faculty of Skopje, University Children's Hospital, Skopje, Macedonia
- Department of General, Visceral and Transplant Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Isabella Pisani
- Unità Operativa Nefrologia, Azienda Ospedaliero-Universitaria di Parma, Dipartimento di Medicina e Chirurgia, Università di Parma, Parma, Italy
| | - Claudia Izzi
- Division of Nephrology, Department of Obstetrics and Gynecology, ASST Spedali Civili of Brescia, Brescia, Italy
| | | | - Barbara Gnutti
- Medical Genetics Laboratory, ASST-Spedali Civili, Brescia, Italy
| | - Valentina P. Capone
- Department of Medicine, Division of Nephrology, Columbia University, New York, New York
- Pediatric Nephrology, Dialysis and Transplant Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - William Morello
- Pediatric Nephrology, Dialysis and Transplant Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Stefano Guarino
- Department of Woman and Child and of General and Specialized Surgery, Università degli Studi della Campania “Luigi Vanvitelli,” Naples, Italy
| | - Pasquale Esposito
- Department of Internal Medicine, University of Genoa, Genova, Italy
- Unit of Nephrology, IRCCS San Martino Polyclinic Hospital, Genoa, Italy
| | - Sarah Lambert
- Yale School of Medicine/Yale New Haven Health System, New Haven, Connecticut
| | - Jai Radhakrishnan
- Department of Medicine, Division of Nephrology, Columbia University, New York, New York
| | - Gerald B. Appel
- Department of Medicine, Division of Nephrology, Columbia University, New York, New York
| | - Natalie S. Uy
- Division of Pediatric Nephrology, Department of Pediatric, NewYork-Presbyterian Morgan Stanley Children's Hospital, Columbia University Irving Medical Center, New York, New York
| | - Maya K. Rao
- Department of Medicine, Division of Nephrology, Columbia University, New York, New York
| | - Pietro A. Canetta
- Department of Medicine, Division of Nephrology, Columbia University, New York, New York
| | - Andrew S. Bomback
- Department of Medicine, Division of Nephrology, Columbia University, New York, New York
| | - Jordan G. Nestor
- Department of Medicine, Division of Nephrology, Columbia University, New York, New York
| | - Thomas Hays
- Department of Pediatrics, Division of Neonatology, Columbia University, New York, New York
| | - David J. Cohen
- Department of Medicine, Division of Nephrology, Columbia University, New York, New York
| | - Carolina Finale
- Nephrology, Dialysis and Renal Transplantation Unit, Azienda Ospedaliera Universitaria Ospedali Riuniti Umberto I, Lancisi, Salesi of Ancona, Ancona, Italy
| | - Joanna A.E. van Wijk
- Department of Pediatric Nephrology, Emma Children's Hospital, University of Amsterdam, Amsterdam, The Netherlands
| | - Claudio La Scola
- Nephrology and Dialysis Unit, Department of Pediatrics, Azienda Ospedaliero Universitaria Sant'Orsola-Malpighi, Bologna, Italy
| | - Olga Baraldi
- Nephrology, Dialysis and Renal Transplant Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Francesco Tondolo
- Nephrology, Dialysis and Renal Transplant Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Dacia Di Renzo
- “Spirito Santo” Hospital of Pescara, Pediatric Surgery of “G. d'Annunzio” University of Chieti-Pescara, Chieti, Italy
| | - Anna Jamry-Dziurla
- Polish Registry of Congenital Malformations, Chair and Department of Medical Genetics, University of Medical Sciences, Poznan, Poland
| | - Alessandro Pezzutto
- Nephrology and Dialysis Unit, Department of Medicine, SS Annunziata Hospital, “G. d'Annunzio” University, Chieti, Italy
| | - Valeria Manca
- Department of Pediatric Urology, Azienda Ospedaliera Brotzu, Cagliari, Italy
| | - Adele Mitrotti
- Department of Medicine, Division of Nephrology, Columbia University, New York, New York
- Section of Nephrology, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Domenico Santoro
- Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy
| | - Giovanni Conti
- Department of Pediatric Nephrology, Azienda Ospedaliera Universitaria “G. Martino,” Messina, Italy
| | - Marida Martino
- Pediatric Nephrology and Dialysis Unit, Pediatric Hospital “Giovanni XXIII,” Bari, Italy
| | - Mario Giordano
- Pediatric Nephrology and Dialysis Unit, Pediatric Hospital “Giovanni XXIII,” Bari, Italy
| | - Loreto Gesualdo
- Section of Nephrology, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Lada Zibar
- Department of Nephrology, University Hospital Merkur, Zagreb, Croatia
- Faculty of Medicine, University Josip Juraj Strossmayer in Osijek, Osijek, Croatia
| | - Giuseppe Masnata
- Department of Pediatric Urology, Azienda Ospedaliera Brotzu, Cagliari, Italy
| | - Mario Bonomini
- Nephrology and Dialysis Unit, Department of Medicine, SS Annunziata Hospital, “G. d'Annunzio” University, Chieti, Italy
| | | | - Gaetano La Manna
- IRCCS Azienda Ospedaliera di Bologna, Nephrology, Dialysis and Kidney Transplant Unit, St. Orsola University Hospital, Bologna, Italy
| | - Yasar Caliskan
- Division of Nephrology, Saint Louis University School of Medicine, Saint Louis, Missouri
| | - Andrea Ranghino
- Nephrology, Dialysis and Renal Transplantation Unit, Azienda Ospedaliera Universitaria Ospedali Riuniti Umberto I, Lancisi, Salesi of Ancona, Ancona, Italy
| | - Pierluigi Marzuillo
- Department of Woman and Child and of General and Specialized Surgery, Università degli Studi della Campania “Luigi Vanvitelli,” Naples, Italy
| | - Krzysztof Kiryluk
- Department of Medicine, Division of Nephrology, Columbia University, New York, New York
| | - Grażyna Krzemień
- Department of Pediatrics and Nephrology, Medical University of Warsaw, Warsaw, Poland
| | - Monika Miklaszewska
- Department of Pediatric Nephrology and Hypertension, Jagiellonian University Medical College, Krakow, Poland
| | - Fangming Lin
- Division of Pediatric Nephrology, Department of Pediatric, NewYork-Presbyterian Morgan Stanley Children's Hospital, Columbia University Irving Medical Center, New York, New York
| | - Giovanni Montini
- Pediatric Nephrology, Dialysis and Transplant Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
- Department of Clinical Sciences and Community Health, Giuliana and Bernardo Caprotti Chair of Pediatrics, University of Milano, Milano, Italy
| | - Francesco Scolari
- Division of Nephrology and Dialysis, Department of Medical and Surgical Specialties, Radiological Sciences, and Public Health, University of Brescia and ASST Spedali Civili of Brescia, Brescia, Italy
| | - Enrico Fiaccadori
- Unità Operativa Nefrologia, Azienda Ospedaliero-Universitaria di Parma, Dipartimento di Medicina e Chirurgia, Università di Parma, Parma, Italy
| | - Adela Arapović
- Department of Pediatrics, University Hospital of Split, Split, Croatia
- School of Medicine, University of Split, Split, Croatia
| | - Marijan Saraga
- Department of Pediatrics, University Hospital of Split, Split, Croatia
- School of Medicine, University of Split, Split, Croatia
| | - James McKiernan
- Department of Urology, Columbia University Irving Medical Center, New York, New York
| | - Shumyle Alam
- Department of Urology, Columbia University Irving Medical Center, New York, New York
- Division of Pediatric Urology, MUSC Health-University Medical Center, Charleston, South Carolina
| | - Marcin Zaniew
- Department of Pediatrics, University of Zielona Góra, Zielona Góra, Poland
| | - Maria Szczepańska
- Department of Pediatrics, FMS in Zabrze, Medical University of Silesia, Katowice, Poland
| | - Agnieszka Szmigielska
- Department of Pediatrics and Nephrology, Medical University of Warsaw, Warsaw, Poland
| | - Przemysław Sikora
- Department of Pediatric Nephrology, Medical University of Lublin, Lublin, Poland
| | - Dorota Drożdż
- Department of Pediatric Nephrology and Hypertension, Jagiellonian University Medical College, Krakow, Poland
| | | | - Shrikant Mane
- Yale Center for Mendelian Genomics (YCMG), New Haven, Connecticut
| | | | - Velibor Tasic
- Medical Faculty of Skopje, University Children's Hospital, Skopje, Macedonia
| | - Anna Latos-Bielenska
- Polish Registry of Congenital Malformations, Chair and Department of Medical Genetics, University of Medical Sciences, Poznan, Poland
| | - Ali G. Gharavi
- Department of Medicine, Division of Nephrology, Columbia University, New York, New York
| | - Gian Marco Ghiggeri
- Division of Nephrology and Renal Transplantation, IRCCS Istituto Giannina Gaslini, Genoa, Italy
- Laboratory on Molecular Nephrology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Anna Materna-Kiryluk
- Polish Registry of Congenital Malformations, Chair and Department of Medical Genetics, University of Medical Sciences, Poznan, Poland
| | - Rik Westland
- Department of Pediatric Nephrology, Emma Children's Hospital, University of Amsterdam, Amsterdam, The Netherlands
| | - Simone Sanna-Cherchi
- Department of Medicine, Division of Nephrology, Columbia University, New York, New York
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Paranjape N, Lin YHT, Flores-Ramirez Q, Sarin V, Johnson AB, Chu J, Paredes M, Wiita AP. A CRISPR-engineered isogenic model of the 22q11.2 A-B syndromic deletion. Sci Rep 2023; 13:7689. [PMID: 37169815 PMCID: PMC10175260 DOI: 10.1038/s41598-023-34325-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 04/27/2023] [Indexed: 05/13/2023] Open
Abstract
22q11.2 deletion syndrome, associated with congenital and neuropsychiatric anomalies, is the most common copy number variant (CNV)-associated syndrome. Patient-derived, induced pluripotent stem cell (iPS) models have provided insight into this condition. However, patient-derived iPS cells may harbor underlying genetic heterogeneity that can confound analysis. Furthermore, almost all available models reflect the commonly-found ~ 3 Mb "A-D" deletion at this locus. The ~ 1.5 Mb "A-B" deletion, a variant of the 22q11.2 deletion which may lead to different syndromic features, and is much more frequently inherited than the A-D deletion, remains under-studied due to lack of relevant models. Here we leveraged a CRISPR-based strategy to engineer isogenic iPS models of the 22q11.2 "A-B" deletion. Differentiation to excitatory neurons with subsequent characterization by transcriptomics and cell surface proteomics identified deletion-associated alterations in proliferation and adhesion. To illustrate in vivo applications of this model, we further implanted neuronal progenitor cells into the cortex of neonatal mice and found potential alterations in neuronal maturation. The isogenic models generated here will provide a unique resource to study this less-common variant of the 22q11.2 microdeletion syndrome.
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Affiliation(s)
- Neha Paranjape
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Yu-Hsiu T Lin
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Quetzal Flores-Ramirez
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Vishesh Sarin
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Amanda Brooke Johnson
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
- San Francisco State University, San Francisco, CA, USA
| | - Julia Chu
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Mercedes Paredes
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub-San Francisco, San Francisco, CA, USA.
| | - Arun P Wiita
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub-San Francisco, San Francisco, CA, USA.
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.
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14
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Cai M, Guo C, Wang X, Lin M, Xu S, Huang H, Lin N, Xu L. Classifying and evaluating fetuses with multicystic dysplastic kidney in etiologic studies. Exp Biol Med (Maywood) 2023; 248:858-865. [PMID: 37208928 PMCID: PMC10484196 DOI: 10.1177/15353702231164933] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 01/18/2023] [Indexed: 05/21/2023] Open
Abstract
Multicystic dysplastic kidney (MCDK) is one of the most common fetal malformations, but its etiology remains unclear. Identification of the molecular etiology could provide a basis for prenatal diagnosis, consultation, and prognosis evaluation for MCDK fetuses. We used chromosome microarray analysis (CMA) and whole-exome sequencing (WES) to conduct genetic tests on MCDK fetuses and explore their genetic etiology. A total of 108 MCDK fetuses with or without other extrarenal abnormalities were selected. Karyotype analysis of 108 MCDK fetuses showed an abnormal karyotype in 4 (3.7%, 4/108) of the fetuses. However, CMA detected 15 abnormal copy number variations (CNVs) (14 pathogenic CNVs, and one variant of unknown significance [VUS] CNVs), in addition to four cases that were consistent with the results of karyotype analysis. Out of the 14 pathogenic CNVs cases, three were of 17q12 microdeletion, two of 22q11.21 microdeletion, 22q11.21 microduplication uniparental disomy (UPD), and one case of 4q31.3q32.2 microdeletion, 7q11.23 microduplication, 15q11.2 microdeletion, 16p11.2 microdeletion, and 17p12 microdeletion. Of the 89 MCDK fetuses with normal karyotype analysis and CMA, 15 were tested by WES. Two (13.3%, 2/15) fetuses were identified by WES as Bardet-Biedl syndrome (BBS) 1 and BBS2. Combined application of CMA-WES to detect MCDK fetuses can significantly improve the detection rate of genetic etiology, providing a basis for consultation, and prognosis evaluation.
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Affiliation(s)
- Meiying Cai
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou 350001, China
| | - Chong Guo
- Child Healthcare Department, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou 350001, China
| | - Xinrui Wang
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou 350001, China
| | - Min Lin
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou 350001, China
| | - Shiyi Xu
- Guangxi Medical University, Guangxi 541000, China
| | - Hailong Huang
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou 350001, China
| | - Na Lin
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou 350001, China
| | - Liangpu Xu
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou 350001, China
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15
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Verbitsky M, Krishnamurthy S, Krithivasan P, Hughes D, Khan A, Marasà M, Vena N, Khosla P, Zhang J, Lim TY, Glessner JT, Weng C, Shang N, Shen Y, Hripcsak G, Hakonarson H, Ionita-Laza I, Levy B, Kenny EE, Loos RJ, Kiryluk K, Sanna-Cherchi S, Crosslin DR, Furth S, Warady BA, Igo RP, Iyengar SK, Wong CS, Parsa A, Feldman HI, Gharavi AG. Genomic Disorders in CKD across the Lifespan. J Am Soc Nephrol 2023; 34:607-618. [PMID: 36302597 PMCID: PMC10103259 DOI: 10.1681/asn.2022060725] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 09/15/2022] [Indexed: 01/24/2023] Open
Abstract
SIGNIFICANCE STATEMENT Pathogenic structural genetic variants, also known as genomic disorders, have been associated with pediatric CKD. This study extends those results across the lifespan, with genomic disorders enriched in both pediatric and adult patients compared with controls. In the Chronic Renal Insufficiency Cohort study, genomic disorders were also associated with lower serum Mg, lower educational performance, and a higher risk of death. A phenome-wide association study confirmed the link between kidney disease and genomic disorders in an unbiased way. Systematic detection of genomic disorders can provide a molecular diagnosis and refine prediction of risk and prognosis. BACKGROUND Genomic disorders (GDs) are associated with many comorbid outcomes, including CKD. Identification of GDs has diagnostic utility. METHODS We examined the prevalence of GDs among participants in the Chronic Kidney Disease in Children (CKiD) cohort II ( n =248), Chronic Renal Insufficiency Cohort (CRIC) study ( n =3375), Columbia University CKD Biobank (CU-CKD; n =1986), and the Family Investigation of Nephropathy and Diabetes (FIND; n =1318) compared with 30,746 controls. We also performed a phenome-wide association analysis (PheWAS) of GDs in the electronic MEdical Records and GEnomics (eMERGE; n =11,146) cohort. RESULTS We found nine out of 248 (3.6%) CKiD II participants carried a GD, replicating prior findings in pediatric CKD. We also identified GDs in 72 out of 6679 (1.1%) adult patients with CKD in the CRIC, CU-CKD, and FIND cohorts, compared with 199 out of 30,746 (0.65%) GDs in controls (OR, 1.7; 95% CI, 1.3 to 2.2). Among adults with CKD, we found recurrent GDs at the 1q21.1, 16p11.2, 17q12, and 22q11.2 loci. The 17q12 GD (diagnostic of renal cyst and diabetes syndrome) was most frequent, present in 1:252 patients with CKD and diabetes. In the PheWAS, dialysis and neuropsychiatric phenotypes were the top associations with GDs. In CRIC participants, GDs were associated with lower serum magnesium, lower educational achievement, and higher mortality risk. CONCLUSION Undiagnosed GDs are detected both in children and adults with CKD. Identification of GDs in these patients can enable a precise genetic diagnosis, inform prognosis, and help stratify risk in clinical studies. GDs could also provide a molecular explanation for nephropathy and comorbidities, such as poorer neurocognition for a subset of patients.
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Affiliation(s)
- Miguel Verbitsky
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | | | - Priya Krithivasan
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Daniel Hughes
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
| | - Atlas Khan
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Maddalena Marasà
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Natalie Vena
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Pavan Khosla
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Junying Zhang
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Tze Y. Lim
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Joseph T. Glessner
- Center for Applied Genomics and Department of Pediatrics, Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Chunhua Weng
- Department of Biomedical Informatics, Columbia University, New York, New York
| | - Ning Shang
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
- Department of Biomedical Informatics, Columbia University, New York, New York
| | - Yufeng Shen
- Department of Systems Biology and Columbia Genome Center, Columbia University, New York, New York
| | - George Hripcsak
- Department of Biomedical Informatics, Columbia University, New York, New York
| | - Hakon Hakonarson
- Center for Applied Genomics and Department of Pediatrics, Perelman School of Medicine, Philadelphia, Pennsylvania
| | | | - Brynn Levy
- Department of Pathology and Cell Biology, Columbia University, New York, New York
| | - Eimear E. Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ruth J.F. Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Simone Sanna-Cherchi
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - David R. Crosslin
- Division of Biomedical Informatics and Genomics, Tulane University School of Medicine, New Orleans, Louisiana
| | - Susan Furth
- Departments of Pediatrics and Epidemiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Bradley A. Warady
- Department of Pediatrics, University of Missouri-Kansas City School of Medicine, Kansas City, Missouri
| | - Robert P. Igo
- Department of Population and Quantitative Health Sciences, Case Western Reserve University and Louis Stoke, Cleveland, Ohio
| | - Sudha K. Iyengar
- Department of Population and Quantitative Health Sciences, Case Western Reserve University and Louis Stoke, Cleveland, Ohio
| | - Craig S. Wong
- Division of Pediatric Nephrology, University of New Mexico Children’s Hospital, Albuquerque, New Mexico
| | - Afshin Parsa
- Division of Kidney, Urologic, and Hematologic Diseases, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland
| | - Harold I. Feldman
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, Philadelphia, Pennsylvania
- Department of Medicine, Perelman School of Medicine, Philadelphia, Pennsylvania
- Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Ali G. Gharavi
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
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16
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Boot E, Óskarsdóttir S, Loo JCY, Crowley TB, Orchanian-Cheff A, Andrade DM, Arganbright JM, Castelein RM, Cserti-Gazdewich C, de Reuver S, Fiksinski AM, Klingberg G, Lang AE, Mascarenhas MR, Moss EM, Nowakowska BA, Oechslin E, Palmer L, Repetto GM, Reyes NGD, Schneider M, Silversides C, Sullivan KE, Swillen A, van Amelsvoort TAMJ, Van Batavia JP, Vingerhoets C, McDonald-McGinn DM, Bassett AS. Updated clinical practice recommendations for managing adults with 22q11.2 deletion syndrome. Genet Med 2023; 25:100344. [PMID: 36729052 DOI: 10.1016/j.gim.2022.11.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 11/15/2022] [Accepted: 11/15/2022] [Indexed: 02/03/2023] Open
Abstract
This review aimed to update the clinical practice guidelines for managing adults with 22q11.2 deletion syndrome (22q11.2DS). The 22q11.2 Society recruited expert clinicians worldwide to revise the original clinical practice guidelines for adults in a stepwise process according to best practices: (1) a systematic literature search (1992-2021), (2) study selection and synthesis by clinical experts from 8 countries, covering 24 subspecialties, and (3) formulation of consensus recommendations based on the literature and further shaped by patient advocate survey results. Of 2441 22q11.2DS-relevant publications initially identified, 2344 received full-text review, with 2318 meeting inclusion criteria (clinical care relevance to 22q11.2DS) including 894 with potential relevance to adults. The evidence base remains limited. Thus multidisciplinary recommendations represent statements of current best practice for this evolving field, informed by the available literature. These recommendations provide guidance for the recognition, evaluation, surveillance, and management of the many emerging and chronic 22q11.2DS-associated multisystem morbidities relevant to adults. The recommendations also address key genetic counseling and psychosocial considerations for the increasing numbers of adults with this complex condition.
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Affiliation(s)
- Erik Boot
- Advisium, 's Heeren Loo Zorggroep, Amersfoort, The Netherlands; The Dalglish Family 22q Clinic, Toronto General Hospital, University Health Network, Toronto, Ontario, Canada; Department of Psychiatry and Neuropsychology, Maastricht University, Maastricht, The Netherlands.
| | - Sólveig Óskarsdóttir
- Department of Pediatric Rheumatology and Immunology, Queen Silvia Children's Hospital, Sahlgrenska University Hospital, Gothenburg, Sweden; Department of Pediatrics, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
| | - Joanne C Y Loo
- The Dalglish Family 22q Clinic, Toronto General Hospital, University Health Network, Toronto, Ontario, Canada
| | - Terrence Blaine Crowley
- 22q and You Center, Clinical Genetics Center, and Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Ani Orchanian-Cheff
- Library and Information Services, and The Institute of Education Research (TIER), University Health Network, Toronto, Ontario, Canada
| | - Danielle M Andrade
- Adult Genetic Epilepsy Program, Toronto Western Hospital and University of Toronto, Toronto, Ontario, Canada
| | - Jill M Arganbright
- Division of Otolaryngology, Children's Mercy Hospital and University of Missouri Kansas City School of Medicine, Kansas City, MO
| | - René M Castelein
- Department of Orthopedic Surgery, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Steven de Reuver
- Department of Orthopedic Surgery, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Ania M Fiksinski
- Department of Psychiatry and Neuropsychology, Maastricht University, Maastricht, The Netherlands; Department of Pediatric Psychology, University Medical Centre, Wilhelmina Children's Hospital, Utrecht, The Netherlands
| | | | - Anthony E Lang
- The Edmond J. Safra Program in Parkinson's Disease and the Morton and Gloria Shulman Movement Disorders, Toronto Western Hospital, University Health Network, Toronto, Ontario, Canada
| | - Maria R Mascarenhas
- Division of Gastroenterology and 22q and You Center, Children's Hospital of Philadelphia, Philadelphia, PA; Department of Pediatrics, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA
| | | | | | - Erwin Oechslin
- Toronto Adult Congenital Heart Disease Program, Peter Munk Cardiac Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - Lisa Palmer
- The Dalglish Family 22q Clinic, Toronto General Hospital, University Health Network, Toronto, Ontario, Canada
| | - Gabriela M Repetto
- Rare Diseases Program, Institute for Sciences and Innovation in Medicine, Facultad de Medicina Clinica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Nikolai Gil D Reyes
- The Edmond J. Safra Program in Parkinson's Disease and the Morton and Gloria Shulman Movement Disorders, Toronto Western Hospital, University Health Network, Toronto, Ontario, Canada
| | - Maude Schneider
- Clinical Psychology Unit for Intellectual and Developmental Disabilities, Faculty of Psychology and Educational Sciences, University of Geneva, Geneva, Switzerland
| | - Candice Silversides
- Toronto ACHD Program, Mount Sinai and Toronto General Hospitals, University of Toronto, Toronto, Ontario, Canada
| | - Kathleen E Sullivan
- Department of Pediatrics, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA; Division of Allergy and Immunology and 22q and You Center, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Ann Swillen
- Center for Human Genetics, University Hospital UZ Leuven, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | | | - Jason P Van Batavia
- Department of Surgery, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA; Division of Urology and 22q and You Center, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Claudia Vingerhoets
- Advisium, 's Heeren Loo Zorggroep, Amersfoort, The Netherlands; Department of Psychiatry and Neuropsychology, Maastricht University, Maastricht, The Netherlands
| | - Donna M McDonald-McGinn
- 22q and You Center, Clinical Genetics Center, and Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA; Department of Pediatrics, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA; Department of Human Biology and Medical Genetics, Sapienza University, Rome, Italy.
| | - Anne S Bassett
- The Dalglish Family 22q Clinic, Toronto General Hospital, University Health Network, Toronto, Ontario, Canada; Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada; Clinical Genetics Research Program and Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Mental Health and Division of Cardiology, Department of Medicine, and Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada.
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17
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Blagowidow N, Nowakowska B, Schindewolf E, Grati FR, Putotto C, Breckpot J, Swillen A, Crowley TB, Loo JCY, Lairson LA, Óskarsdóttir S, Boot E, Garcia-Minaur S, Cristina Digilio M, Marino B, Coleman B, Moldenhauer JS, Bassett AS, McDonald-McGinn DM. Prenatal Screening and Diagnostic Considerations for 22q11.2 Microdeletions. Genes (Basel) 2023; 14. [PMID: 36672900 DOI: 10.3390/genes14010160] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/23/2022] [Accepted: 12/24/2022] [Indexed: 01/11/2023] Open
Abstract
Diagnosis of a chromosome 22q11.2 microdeletion and its associated deletion syndrome (22q11.2DS) is optimally made early. We reviewed the available literature to provide contemporary guidance and recommendations related to the prenatal period. Indications for prenatal diagnostic testing include a parent or child with the 22q11.2 microdeletion or suggestive prenatal screening results. Definitive diagnosis by genetic testing of chorionic villi or amniocytes using a chromosomal microarray will detect clinically relevant microdeletions. Screening options include noninvasive prenatal screening (NIPS) and imaging. The potential benefits and limitations of each screening method should be clearly conveyed. NIPS, a genetic option available from 10 weeks gestational age, has a 70-83% detection rate and a 40-50% PPV for most associated 22q11.2 microdeletions. Prenatal imaging, usually by ultrasound, can detect several physical features associated with 22q11.2DS. Findings vary, related to detection methods, gestational age, and relative specificity. Conotruncal cardiac anomalies are more strongly associated than skeletal, urinary tract, or other congenital anomalies such as thymic hypoplasia or cavum septi pellucidi dilatation. Among others, intrauterine growth restriction and polyhydramnios are additional associated, prenatally detectable signs. Preconception genetic counselling should be offered to males and females with 22q11.2DS, as there is a 50% risk of transmission in each pregnancy. A previous history of a de novo 22q11.2 microdeletion conveys a low risk of recurrence. Prenatal genetic counselling includes an offer of screening or diagnostic testing and discussion of results. The goal is to facilitate optimal perinatal care.
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18
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Lucà F, Colivicchi F, Parrini I, Russo MG, Di Fusco SA, Ceravolo R, Riccio C, Favilli S, Rossini R, Gelsomino S, Oliva F, Gulizia MM. The role of the pregnancy heart team in clinical practice. Front Cardiovasc Med 2023; 10:1135294. [PMID: 37139137 PMCID: PMC10150137 DOI: 10.3389/fcvm.2023.1135294] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 03/29/2023] [Indexed: 05/05/2023] Open
Abstract
Significant maternal and fetal morbidity and mortality risk has been shown to be associated with cardiovascular disease in pregnancy. Several determinants, such as the increasing number of females with corrected congenital heart disease in reproductive age, a more advanced maternal age associated with cardiovascular risk factors, and a greater prevalence of preexisting comorbidities related to cardiac disorders such as cancer and COVID-19), lead to a higher incidence of cardiac complications in pregnancy in the last few decades. However, adopting a multidisciplinary strategy may influence maternal and neonatal outcomes. This review aims at assessing the role of the Pregnancy Heart Team, which should ensure careful pre-pregnancy counseling, pregnancy monitoring, and delivery planning for both congenital and other cardiac or metabolic disorders, addressing several emerging aspects in the multidisciplinary team-based approach.
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Affiliation(s)
- Fabiana Lucà
- Cardiology Department, Grande Ospedale Metropolitano, GOM, AO Bianchi Melacrino Morelli, Reggio Calabria, Italy
- Correspondence: Fabiana Lucà
| | - Furio Colivicchi
- Clinical and Rehabilitation Cardiology Department, San Filippo Neri Hospital, ASL Roma 1, Roma, Italy
| | - Iris Parrini
- Cardiology Department, Mauriziano Hospital, Torino, Italy
| | - Maria Giovanna Russo
- U.O.C. Cardiologia e UTIC Pediatrica, AORN dei Colli, Ospedale Monaldi, Università Della Campania “L. Vanvitelli”, Napoli, Italy
| | - Stefania Angela Di Fusco
- Clinical and Rehabilitation Cardiology Department, San Filippo Neri Hospital, ASL Roma 1, Roma, Italy
| | | | - Carmine Riccio
- Cardiovascular Department, Sant'Anna e San Sebastiano Hospital, Caserta, Italy
| | - Silvia Favilli
- Department of Pediatric Cardiology, Meyer Hospital, Florence, Italy
| | | | - Sandro Gelsomino
- Cardiothoracic Department, Maastricht University Hospital, Maastricht, Netherlands
| | - Fabrizio Oliva
- Cardiology Unit, ASST Grande Ospedale Metropolitano Niguarda, Milano, Italy
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19
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Ruthig VA, Lamb DJ. Modeling development of genitourinary birth defects to understand disruption due to changes in gene dosage. Am J Clin Exp Urol 2022; 10:412-424. [PMID: 36636694 PMCID: PMC9831917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 12/25/2022] [Indexed: 01/14/2023]
Abstract
Genitourinary development is a delicately orchestrated process that begins in the embryo. Once complete, the genitourinary system is a collection of functionally disparate organs spread throughout the abdominal and pelvic regions. These distinct organs are interconnected through an elaborate duct system which aggregates the organs' products to a common exit point. The complicated nature of the genitourinary system makes it highly susceptible to developmental disruptions that produce anomalies. In fact, genitourinary anomalies are among the most common class of human birth defects. Aside from congenital anomalies of the kidney and urinary tract (CAKUT), for males, these birth defects can also occur in the penis (hypospadias) and testis (cryptorchism), which impact male fertility and male mental health. As genetic technology has advanced, it has become clear that a subset of cases of genitourinary birth defects are due to gene variation causing dosage changes in critical regulatory genes. Here we first review the parallels between human and mouse genitourinary development. We then demonstrate how translational research leverages mouse models of human gene variation cases to advance mechanistic understanding of causation in genitourinary birth defects. We close with a view to the future highlighting upcoming technologies that will provide a deeper understanding of gene variation affecting regulation of genitourinary development, which should ultimately advance treatment options for patients.
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Affiliation(s)
- Victor A Ruthig
- Department of Urology, Weill Cornell MedicineNew York, NY, USA,Sexual Medicine Laboratory, Weill Cornell MedicineNew York, NY, USA
| | - Dolores J Lamb
- Department of Urology, Weill Cornell MedicineNew York, NY, USA,Center for Reproductive Genomics, Weill Cornell MedicineNew York, NY, USA,Englander Institute for Precision Medicine, Weill Cornell MedicineNew York, NY, USA
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20
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Mannstadt M, Cianferotti L, Gafni RI, Giusti F, Kemp EH, Koch CA, Roszko KL, Yao L, Guyatt GH, Thakker RV, Xia W, Brandi ML. Hypoparathyroidism: Genetics and Diagnosis. J Bone Miner Res 2022; 37:2615-2629. [PMID: 36375809 DOI: 10.1002/jbmr.4667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 07/22/2022] [Accepted: 07/31/2022] [Indexed: 01/05/2023]
Abstract
This narrative report summarizes diagnostic criteria for hypoparathyroidism and describes the clinical presentation and underlying genetic causes of the nonsurgical forms. We conducted a comprehensive literature search from January 2000 to January 2021 and included landmark articles before 2000, presenting a comprehensive update of these topics and suggesting a research agenda to improve diagnosis and, eventually, the prognosis of the disease. Hypoparathyroidism, which is characterized by insufficient secretion of parathyroid hormone (PTH) leading to hypocalcemia, is diagnosed on biochemical grounds. Low albumin-adjusted calcium or ionized calcium with concurrent inappropriately low serum PTH concentration are the hallmarks of the disease. In this review, we discuss the characteristics and pitfalls in measuring calcium and PTH. We also undertook a systematic review addressing the utility of measuring calcium and PTH within 24 hours after total thyroidectomy to predict long-term hypoparathyroidism. A summary of the findings is presented here; results of the detailed systematic review are published separately in this issue of JBMR. Several genetic disorders can present with hypoparathyroidism, either as an isolated disease or as part of a syndrome. A positive family history and, in the case of complex diseases, characteristic comorbidities raise the clinical suspicion of a genetic disorder. In addition to these disorders' phenotypic characteristics, which include autoimmune diseases, we discuss approaches for the genetic diagnosis. © 2022 The Authors. Journal of Bone and Mineral Research published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research (ASBMR).
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Affiliation(s)
- Michael Mannstadt
- Endocrine Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Luisella Cianferotti
- Bone Metabolic Diseases Unit, Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence, Italy
| | - Rachel I Gafni
- National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | | | | | - Christian A Koch
- Department of Medicine/Endocrinology, Fox Chase Cancer Center, Philadelphia, PA, USA.,Department of Medicine/Endocrinology, The University of Tennessee Health Science Center, Memphis, TN, USA
| | - Kelly L Roszko
- National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Liam Yao
- Department of Health Research Methods, Evidence, and Impact, and Department of Medicine, McMaster University, Hamilton, Canada
| | - Gordon H Guyatt
- Department of Health Research Methods, Evidence, and Impact, and Department of Medicine, McMaster University, Hamilton, Canada
| | - Rajesh V Thakker
- Academic Endocrine Unit, Radcliffe Department of Medicine, University of Oxford, Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM), Churchill Hospital, Headington, Oxford, UK.,Oxford National Institute for Health Research (NIHR) Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Weibo Xia
- Department of Endocrinology, Peking Union Medical Collage Hospital, Beijing, China
| | - Maria-Luisa Brandi
- Fondazione Italiana sulla Ricerca sulle Malattie dell'Osso (F.I.R.M.O. Foundation), Florence, Italy
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21
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Gavril EC, Popescu R, Nucă I, Ciobanu CG, Butnariu LI, Rusu C, Pânzaru MC. Different Types of Deletions Created by Low-Copy Repeats Sequences Location in 22q11.2 Deletion Syndrome: Genotype-Phenotype Correlation. Genes (Basel) 2022; 13:2083. [PMID: 36360320 PMCID: PMC9690028 DOI: 10.3390/genes13112083] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/21/2022] [Accepted: 11/08/2022] [Indexed: 09/19/2023] Open
Abstract
The most frequent microdeletion, 22q11.2 deletion syndrome (22q11.2DS), has a wide and variable phenotype that causes difficulties in diagnosis. 22q11.2DS is a contiguous gene syndrome, but due to the existence of several low-copy-number repeat sequences (LCR) it displays a high variety of deletion types: typical deletions LCR A-D-the most common (~90%), proximal deletions LCR A-B, central deletions (LCR B, C-D) and distal deletions (LCR D-E, F). METHODS We conducted a retrospective study of 59 22q11.2SD cases, with the aim of highlighting phenotype-genotype correlations. All cases were tested using MLPA combined kits: SALSA MLPA KIT P245 and P250 (MRC Holland). RESULTS most cases (76%) presented classic deletion LCR A-D with various severity and phenotypic findings. A total of 14 atypical new deletions were identified: 2 proximal deletions LCR A-B, 1 CES (Cat Eye Syndrome region) to LCR B deletion, 4 nested deletions LCR B-D and 1 LCR C-D, 3 LCR A-E deletions, 1 LCR D-E, and 2 small single gene deletions: delDGCR8 and delTOP3B. CONCLUSIONS This study emphasizes the wide phenotypic variety and incomplete penetrance of 22q11.2DS. Our findings contribute to the genotype-phenotype data regarding different types of 22q11.2 deletions and illustrate the usefulness of MLPA combined kits in 22q11.2DS diagnosis.
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Affiliation(s)
- Eva-Cristiana Gavril
- Department of Medical Genetics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, University Street, No 16, 700115 Iasi, Romania
- Investigații Medicale Praxis, St. Moara de Vant No 35, 700376 Iasi, Romania
| | - Roxana Popescu
- Department of Medical Genetics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, University Street, No 16, 700115 Iasi, Romania
- Department of Medical Genetics “Saint Mary” Emergency Children’s Hospital, St. Vasile Lupu No 62, 700309 Iasi, Romania
| | - Irina Nucă
- Department of Medical Genetics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, University Street, No 16, 700115 Iasi, Romania
- Investigații Medicale Praxis, St. Moara de Vant No 35, 700376 Iasi, Romania
| | - Cristian-Gabriel Ciobanu
- Department of Medical Genetics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, University Street, No 16, 700115 Iasi, Romania
| | - Lăcrămioara Ionela Butnariu
- Department of Medical Genetics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, University Street, No 16, 700115 Iasi, Romania
- Department of Medical Genetics “Saint Mary” Emergency Children’s Hospital, St. Vasile Lupu No 62, 700309 Iasi, Romania
| | - Cristina Rusu
- Department of Medical Genetics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, University Street, No 16, 700115 Iasi, Romania
- Department of Medical Genetics “Saint Mary” Emergency Children’s Hospital, St. Vasile Lupu No 62, 700309 Iasi, Romania
| | - Monica-Cristina Pânzaru
- Department of Medical Genetics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, University Street, No 16, 700115 Iasi, Romania
- Department of Medical Genetics “Saint Mary” Emergency Children’s Hospital, St. Vasile Lupu No 62, 700309 Iasi, Romania
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22
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Kagan M, Pleniceanu O, Vivante A. The genetic basis of congenital anomalies of the kidney and urinary tract. Pediatr Nephrol 2022; 37:2231-2243. [PMID: 35122119 DOI: 10.1007/s00467-021-05420-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 12/02/2021] [Accepted: 12/03/2021] [Indexed: 10/19/2022]
Abstract
During the past decades, remarkable progress has been made in our understanding of the molecular basis of kidney diseases, as well as in the ability to pinpoint disease-causing genetic changes. Congenital anomalies of the kidney and urinary tract (CAKUT) are remarkably diverse, and may be either isolated to the kidney or involve other systems, and are notorious in their variable genotype-phenotype correlations. Genetic conditions underlying CAKUT are individually rare, but collectively contribute to disease etiology in ~ 16% of children with CAKUT. In this review, we will discuss basic concepts of kidney development and genetics, common causes of monogenic CAKUT, and the approach to diagnosing and managing a patient with suspected monogenic CAKUT. Altogether, the concepts presented herein represent an introduction to the emergence of nephrogenetics, a fast-growing multi-disciplinary field that is focused on deciphering the causes and manifestations of genetic kidney diseases as well as providing the framework for managing patients with genetic forms of CAKUT.
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Affiliation(s)
- Maayan Kagan
- Pediatric Department B and Pediatric Nephrology Unit, Edmond and Lily Safra Children's Hospital, Sackler Faculty of Medicine, Sheba Medical Center, Tel Hashomer, 5265601, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Oren Pleniceanu
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Kidney Research Lab, The Institute of Nephrology and Hypertension, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
| | - Asaf Vivante
- Pediatric Department B and Pediatric Nephrology Unit, Edmond and Lily Safra Children's Hospital, Sackler Faculty of Medicine, Sheba Medical Center, Tel Hashomer, 5265601, Ramat Gan, Israel. .,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel. .,Talpiot Medical Leadership Program, Tel HaShomer, Ramat Gan, Israel.
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23
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Abstract
BACKGROUND To assess multicystic dysplastic kidneys (MCDK) in children, their complications and associated congenital genitourinary anomalies. METHODS Children with unilateral MCDK, evaluated between 2012 and 2020, were analyzed. In this retrospective study, data were obtained from electronic and paper health care records. RESULTS There were 80 children included. Follow-up time was 8.0 +/- 5.2 years (mean +/- standard deviation). None of them had hypertension. In total, 43.8% of the children had associated congenital genitourinary anomalies, most commonly cryptorchidism and vesicoureteral reflux (VUR), and 6.3% of these children had chromosomopathy. All of them had normal kidney function except one child with dysplasia of the contralateral kidney. Urinalysis was normal in 90% of children. Extrarenal malformations occurred in 22.5% of them. We observed spontaneous involution of MCDK in 38.8% of children in the observed period. Nephrectomy was performed in 12.5% of children, at an average age of 2.0 years. CONCLUSIONS Children with a unilateral MCDK have a very good prognosis if the contralateral kidney is normal. Associated congenital genitourinary anomalies are common. Cryptorchidism was found to be the most common associated anomaly among boys, which is unique for this study. Most of these children do not suffer from hypertension, kidney dysfunction or other complications.
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Affiliation(s)
- Matjaž Kopač
- Division of Pediatrics, Department of Nephrology, University Medical Centre Ljubljana, Bohoričeva 20, 1000 Ljubljana, Slovenia
- Correspondence: ; Tel.: +386-1-522-9626; Fax: +386-1-522-9620
| | - Robert Kordič
- Division of Surgery, Department of Pediatric Surgery, University Medical Centre Ljubljana, Bohoričeva 20, 1000 Ljubljana, Slovenia
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24
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Collins RL, Glessner JT, Porcu E, Lepamets M, Brandon R, Lauricella C, Han L, Morley T, Niestroj LM, Ulirsch J, Everett S, Howrigan DP, Boone PM, Fu J, Karczewski KJ, Kellaris G, Lowther C, Lucente D, Mohajeri K, Nõukas M, Nuttle X, Samocha KE, Trinh M, Ullah F, Võsa U, Hurles ME, Aradhya S, Davis EE, Finucane H, Gusella JF, Janze A, Katsanis N, Matyakhina L, Neale BM, Sanders D, Warren S, Hodge JC, Lal D, Ruderfer DM, Meck J, Mägi R, Esko T, Reymond A, Kutalik Z, Hakonarson H, Sunyaev S, Brand H, Talkowski ME. A cross-disorder dosage sensitivity map of the human genome. Cell 2022; 185:3041-3055.e25. [PMID: 35917817 PMCID: PMC9742861 DOI: 10.1016/j.cell.2022.06.036] [Citation(s) in RCA: 99] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 03/17/2022] [Accepted: 06/20/2022] [Indexed: 02/06/2023]
Abstract
Rare copy-number variants (rCNVs) include deletions and duplications that occur infrequently in the global human population and can confer substantial risk for disease. In this study, we aimed to quantify the properties of haploinsufficiency (i.e., deletion intolerance) and triplosensitivity (i.e., duplication intolerance) throughout the human genome. We harmonized and meta-analyzed rCNVs from nearly one million individuals to construct a genome-wide catalog of dosage sensitivity across 54 disorders, which defined 163 dosage sensitive segments associated with at least one disorder. These segments were typically gene dense and often harbored dominant dosage sensitive driver genes, which we were able to prioritize using statistical fine-mapping. Finally, we designed an ensemble machine-learning model to predict probabilities of dosage sensitivity (pHaplo & pTriplo) for all autosomal genes, which identified 2,987 haploinsufficient and 1,559 triplosensitive genes, including 648 that were uniquely triplosensitive. This dosage sensitivity resource will provide broad utility for human disease research and clinical genetics.
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Affiliation(s)
- Ryan L Collins
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Division of Medical Sciences and Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.
| | - Joseph T Glessner
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pediatrics, Division of Human Genetics, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Eleonora Porcu
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Maarja Lepamets
- Estonian Genome Centre, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia; Institute of Molecular and Cell Biology, University of Tartu, 51010 Tartu, Estonia
| | | | | | - Lide Han
- Division of Genetic Medicine, Department of Medicine, and Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Theodore Morley
- Division of Genetic Medicine, Department of Medicine, and Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | | | - Jacob Ulirsch
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Division of Medical Sciences and Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Selin Everett
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Daniel P Howrigan
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Philip M Boone
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA
| | - Jack Fu
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Konrad J Karczewski
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Georgios Kellaris
- Advanced Center for Translational and Genetic Medicine, Stanley Manne Children's Research Institute, Lurie Children's Hospital, Chicago, IL 60611, USA; Departments of Pediatrics and Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Chelsea Lowther
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Diane Lucente
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Kiana Mohajeri
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Division of Medical Sciences and Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Margit Nõukas
- Estonian Genome Centre, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia; Institute of Molecular and Cell Biology, University of Tartu, 51010 Tartu, Estonia
| | - Xander Nuttle
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Kaitlin E Samocha
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Division of Medical Sciences and Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10, UK
| | - Mi Trinh
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10, UK
| | - Farid Ullah
- Advanced Center for Translational and Genetic Medicine, Stanley Manne Children's Research Institute, Lurie Children's Hospital, Chicago, IL 60611, USA; Departments of Pediatrics and Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Urmo Võsa
- Estonian Genome Centre, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
| | | | | | - Matthew E Hurles
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10, UK
| | | | - Erica E Davis
- Advanced Center for Translational and Genetic Medicine, Stanley Manne Children's Research Institute, Lurie Children's Hospital, Chicago, IL 60611, USA; Departments of Pediatrics and Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Hilary Finucane
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - James F Gusella
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | | | - Nicholas Katsanis
- Advanced Center for Translational and Genetic Medicine, Stanley Manne Children's Research Institute, Lurie Children's Hospital, Chicago, IL 60611, USA; Departments of Pediatrics and Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | | | - Benjamin M Neale
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | | | - Jennelle C Hodge
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Dennis Lal
- Cologne Center for Genomics, University of Cologne, 51149 Cologne, Germany; Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Douglas M Ruderfer
- Division of Genetic Medicine, Department of Medicine, and Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Center for Precision Medicine, Department of Biomedical Informatics, and Department of Psychiatry and Behavioral Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | | | - Reedik Mägi
- Estonian Genome Centre, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
| | - Tõnu Esko
- Estonian Genome Centre, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Zoltán Kutalik
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland; Center for Primary Care and Public Health, University of Lausanne, 1015 Lausanne, Switzerland; Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Hakon Hakonarson
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pediatrics, Division of Human Genetics, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Shamil Sunyaev
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Division of Medical Sciences and Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Harrison Brand
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, MA 02114, USA.
| | - Michael E Talkowski
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
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Kotcher RE, Chait DB, Heckert JM, Crowley TB, Forde KA, Ahuja NK, Mascarenhas MR, Emanuel BS, Zackai EH, McDonald-McGinn DM, Reynolds JC. Gastrointestinal Features of 22q11.2 Deletion Syndrome Include Chronic Motility Problems From Childhood to Adulthood. J Pediatr Gastroenterol Nutr 2022; 75:e8-e14. [PMID: 35641891 PMCID: PMC9329196 DOI: 10.1097/mpg.0000000000003491] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
OBJECTIVES 22q11.2 deletion syndrome (22q11.2DS) is the most common chromosomal microdeletion syndrome and has a multisystemic presentation including gastrointestinal features that have not yet been fully described. Our aim was to examine lifetime gastrointestinal problems in a large cohort of patients with 22q11.2DS. METHODS All patients followed in the 22q and You Center at the Children's Hospital of Philadelphia (n = 1421) were retrospectively screened for: 1) age ≥ 17 years, 2) documented chromosomal microdeletion within the 22q11.2 LCR22A-LCR22D region, and 3) sufficient clinical data to characterize the adult gastrointestinal phenotype. Gastrointestinal problems in childhood, adolescence, and adulthood were summarized. Statistical association testing of symptoms against other patient characteristics was performed. RESULTS Included patients (n = 206; 46% female; mean age, 27 years; median follow-up, 21 years) had similar clinical characteristics to the overall cohort. Genetic distribution was also similar, with 96% having deletions including the critical LCR22A-LCR22B segment (95% in the overall cohort). Most patients experienced chronic gastrointestinal symptoms in their lifetime (91%), but congenital gastrointestinal malformations (3.5%) and gastrointestinal autoimmune diseases (1.5%) were uncommon. Chronic symptoms without anatomic or pathologic abnormalities represented the vast burden of illness. Chronic symptoms in adulthood are associated with other chronic gastrointestinal symptoms and psychiatric comorbidities ( P < 0.01) but not with deletion size or physiologic comorbidities ( P > 0.05). One exception was increased nausea/vomiting in hypothyroidism ( P = 0.002). CONCLUSIONS Functional gastrointestinal disorders (FGIDs) are a common cause of ill health in children and adults with 22q11.2DS. Providers should consider screening for the deletion in patients presenting with FGIDs and associated comorbidities such as neuropsychiatric illness, congenital heart disease, and palatal abnormalities.
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Affiliation(s)
| | | | | | | | - Kimberly A. Forde
- Perelman School of Medicine, University of Pennsylvania
- Division of Gastroenterology, University of Pennsylvania
| | - Nitin K. Ahuja
- Perelman School of Medicine, University of Pennsylvania
- Division of Gastroenterology, University of Pennsylvania
| | - Maria R. Mascarenhas
- Perelman School of Medicine, University of Pennsylvania
- 22q and You Center, Children’s Hospital of Philadelphia
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia
| | - Beverly S. Emanuel
- Perelman School of Medicine, University of Pennsylvania
- 22q and You Center, Children’s Hospital of Philadelphia
- Division of Human Genetics, Children’s Hospital of Philadelphia
| | - Elaine H. Zackai
- Perelman School of Medicine, University of Pennsylvania
- 22q and You Center, Children’s Hospital of Philadelphia
- Division of Human Genetics, Children’s Hospital of Philadelphia
| | - Donna M. McDonald-McGinn
- Perelman School of Medicine, University of Pennsylvania
- 22q and You Center, Children’s Hospital of Philadelphia
- Division of Human Genetics, Children’s Hospital of Philadelphia
| | - James C. Reynolds
- Perelman School of Medicine, University of Pennsylvania
- Division of Gastroenterology, University of Pennsylvania
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26
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Pala F, Notarangelo LD, Bosticardo M. Inborn errors of immunity associated with defects of thymic development. Pediatr Allergy Immunol 2022; 33:e13832. [PMID: 36003043 PMCID: PMC11077434 DOI: 10.1111/pai.13832] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/29/2022] [Accepted: 07/07/2022] [Indexed: 12/18/2022]
Abstract
The main function of the thymus is to support the establishment of a wide repertoire of T lymphocytes capable of eliminating foreign pathogens, yet tolerant to self-antigens. Thymocyte development in the thymus is dependent on the interaction with thymic stromal cells, a complex mixture of cells comprising thymic epithelial cells (TEC), mesenchymal and endothelial cells. The exchange of signals between stromal cells and thymocytes is referred to as "thymic cross-talk". Genetic defects affecting either side of this interaction result in defects in thymic development that ultimately lead to a decreased output of T lymphocytes to the periphery. In the present review, we aim at providing a summary of inborn errors of immunity (IEI) characterized by T-cell lymphopenia due to defects of the thymic stroma, or to hematopoietic-intrinsic defects of T-cell development, with a special focus on recently discovered disorders. Additionally, we review the novel diagnostic tools developed to discover and study new genetic causes of IEI due to defects in thymic development. Finally, we discuss therapeutic approaches to correct thymic defects that are currently available, in addition to potential novel therapies that could be applied in the future.
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Affiliation(s)
- Francesca Pala
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Marita Bosticardo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
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27
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Beaman GM, Woolf AS, Lopes FM, Guo SA, Harkness JR, Cervellione RM, Keene D, Mushtaq I, Clatworthy MR, Newman WG. Narrowing the chromosome 22q11.2 locus duplicated in bladder exstrophy-epispadias complex. J Pediatr Urol 2022; 18:362.e1-362.e8. [PMID: 35491304 DOI: 10.1016/j.jpurol.2022.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 02/15/2022] [Accepted: 04/03/2022] [Indexed: 10/18/2022]
Abstract
INTRODUCTION Bladder exstrophy-epispadias complex (BEEC) comprises a spectrum of anterior midline congenital malformations, involving the lower urinary tract. BEEC is usually sporadic, but families with more than one affected member have been reported, and a twin concordance study supported a genetic contribution to pathogenesis. Moreover, diverse chromosomal aberrations have been reported in a small subset of individuals with BEEC. The commonest are 22q11.2 microduplications, identified in approximately 3% of BEEC index cases. OBJECTIVES We aimed to refine the chromosome 22q11.2 locus, and to determine whether the encompassed genes are expressed in normal developing and mature human urinary bladders. RESULTS Using DNA from an individual with CBE, the 22q11.2 duplicated locus was refined by identification of a maternally inherited 314 kb duplication (chr22:21,147,293-21,461,017), as depicted in this image. Moreover, the eight protein coding genes within the locus were found to be expressed during normal developing and mature bladders. To determine whether duplications in any of these individual genes were associated with CBE, we undertook copy number analyses in 115 individuals with CBE without duplications of the whole locus. No duplications of individual genes were found. DISCUSSION The current study has refined the 22q11.2 locus associated with BEEC and has shown that the eight protein coding genes are expressed in human bladders both during antenatal development and postnatally. Nevertheless, the precise biological explanation as to why duplication of the phenocritical region of 22q11 confers increased susceptibility to BEEC remains to be determined. The fact that individuals with CBE without duplications of the whole locus also lacked duplication of any of the individual genes suggests that in individuals with BEEC and duplication of the 22q11.2 locus altered dosage of more than one gene may be important in BEEC etiology. CONCLUSIONS The study has refined the 22q11.2 locus associated with BEEC and has shown that the eight protein coding genes within this locus are expressed in human bladders.
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Affiliation(s)
- Glenda M Beaman
- Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK; Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK
| | - Adrian S Woolf
- Division of Cell Matrix Biology & Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK; Royal Manchester Children's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Filipa M Lopes
- Division of Cell Matrix Biology & Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Shuang Andrew Guo
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge CB2 0QH, United Kingdom; Cambridge Institute of Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge CB2 0AW, United Kingdom; Cellular Genetics, Wellcome Sanger Institute, Hinxton CB10 1RQ, United Kingdom
| | - J Robert Harkness
- Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK; Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK
| | - Raimondo M Cervellione
- Royal Manchester Children's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - David Keene
- Royal Manchester Children's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Imran Mushtaq
- Department of Paediatric Urology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Menna R Clatworthy
- Cambridge Institute of Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge CB2 0AW, United Kingdom; Cellular Genetics, Wellcome Sanger Institute, Hinxton CB10 1RQ, United Kingdom; Department of Paediatric Urology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - William G Newman
- Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK; Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK.
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28
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Abstract
The 22q11.2 deletion is one of the most common genetic microdeletions, affecting approximately 1 in 4000 live births in humans. A 1.5 to 2.5 Mb hemizygous deletion of chromosome 22q11.2 causes DiGeorge syndrome (DGS) and velocardiofacial syndrome (VCFS). DGS/VCFS are associated with prevalent cardiac malformations, thymic and parathyroid hypoplasia, and craniofacial defects. Patients with DGS/VCFS manifest craniofacial anomalies involving the cranium, cranial base, jaws, pharyngeal muscles, ear-nose-throat, palate, teeth, and cervical spine. Most craniofacial phenotypes of DGS/VCFS are caused by proximal 1.5 Mb microdeletions, resulting in a hemizygosity of coding genes, microRNAs, and long noncoding RNAs. TBX1, located on chromosome 22q11.21, encodes a T-box transcription factor and is a candidate gene for DGS/VCFS. TBX1 regulates the fate of progenitor cells in the cranial and pharyngeal apparatus during embryogenesis. Tbx1-null mice exhibit the most clinical features of DGS/VCFS, including craniofacial phenotypes. Despite the frequency of DGS/VCFS, there has been a limited review of the craniofacial phenotypes of DGC/VCFS. This review focuses on these phenotypes and summarizes the current understanding of the genetic factors that impact DGS/VCFS-related phenotypes. We also review DGS/VCFS mouse models that have been designed to better understand the pathogenic processes of DGS/VCFS.
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Affiliation(s)
- Noriko Funato
- Department of Signal Gene Regulation, Advanced Therapeutic Sciences, Medical and Dental Sciences, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan
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29
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Handel AE, Cheuk S, Dhalla F, Maio S, Hübscher T, Rota I, Deadman ME, Ekwall O, Lütolf M, Weinberg K, Holländer G. Developmental dynamics of the neural crest-mesenchymal axis in creating the thymic microenvironment. Sci Adv 2022; 8:eabm9844. [PMID: 35559672 PMCID: PMC9106291 DOI: 10.1126/sciadv.abm9844] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 03/28/2022] [Indexed: 06/15/2023]
Abstract
The thymic stroma is composed of epithelial and nonepithelial cells providing separate microenvironments controlling homing, differentiation, and selection of hematopoietic precursor cells to functional T cells. Here, we explore at single-cell resolution the complex composition and dynamic changes of the nonepithelial stromal compartment across different developmental stages in the human and mouse thymus, and in an experimental model of the DiGeorge syndrome, the most common form of human thymic hypoplasia. The detected gene expression signatures identify previously unknown stromal subtypes and relate their individual molecular profiles to separate differentiation trajectories and functions, revealing an unprecedented heterogeneity of different cell types that emerge at discrete developmental stages and vary in their expression of key regulatory signaling circuits and extracellular matrix components. Together, these findings highlight the dynamic complexity of the nonepithelial thymus stroma and link this to separate instructive roles essential for normal thymus organogenesis and tissue maintenance.
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Affiliation(s)
- Adam E. Handel
- Department of Paediatrics and the Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Stanley Cheuk
- Department of Paediatrics and the Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Rheumatology and Inflammation Research, University of Gothenburg, Gothenburg, Sweden
| | - Fatima Dhalla
- Department of Paediatrics and the Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Stefano Maio
- Department of Paediatrics and the Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Tania Hübscher
- Laboratory of Stem Cell Bioengineering, Swiss Federal Institute of Technology in Lausanne, Lausanne, Switzerland
| | - Ioanna Rota
- Department of Paediatrics and the Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Mary E. Deadman
- Department of Paediatrics and the Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Olov Ekwall
- Department of Rheumatology and Inflammation Research, University of Gothenburg, Gothenburg, Sweden
- Department of Pediatrics, University of Gothenburg, Gothenburg, Sweden
| | - Matthias Lütolf
- Laboratory of Stem Cell Bioengineering, Swiss Federal Institute of Technology in Lausanne, Lausanne, Switzerland
| | - Kenneth Weinberg
- Division of Stem Cell Transplantation and Regenerative Medicine Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Georg Holländer
- Department of Paediatrics and the Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Paediatric Immunology, Department of Biomedicine, University of Basel and University Children’s Hospital Basel, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
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30
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Khan K, Ahram DF, Liu YP, Westland R, Sampogna RV, Katsanis N, Davis EE, Sanna-Cherchi S. Multidisciplinary approaches for elucidating genetics and molecular pathogenesis of urinary tract malformations. Kidney Int 2022; 101:473-484. [PMID: 34780871 PMCID: PMC8934530 DOI: 10.1016/j.kint.2021.09.034] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 09/15/2021] [Accepted: 09/30/2021] [Indexed: 12/28/2022]
Abstract
Advances in clinical diagnostics and molecular tools have improved our understanding of the genetically heterogeneous causes underlying congenital anomalies of kidney and urinary tract (CAKUT). However, despite a sharp incline of CAKUT reports in the literature within the past 2 decades, there remains a plateau in the genetic diagnostic yield that is disproportionate to the accelerated ability to generate robust genome-wide data. Explanations for this observation include (i) diverse inheritance patterns with incomplete penetrance and variable expressivity, (ii) rarity of single-gene drivers such that large sample sizes are required to meet the burden of proof, and (iii) multigene interactions that might produce either intra- (e.g., copy number variants) or inter- (e.g., effects in trans) locus effects. These challenges present an opportunity for the community to implement innovative genetic and molecular avenues to explain the missing heritability and to better elucidate the mechanisms that underscore CAKUT. Here, we review recent multidisciplinary approaches at the intersection of genetics, genomics, in vivo modeling, and in vitro systems toward refining a blueprint for overcoming the diagnostic hurdles that are pervasive in urinary tract malformation cohorts. These approaches will not only benefit clinical management by reducing age at molecular diagnosis and prompting early evaluation for comorbid features but will also serve as a springboard for therapeutic development.
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Affiliation(s)
- Kamal Khan
- Center for Human Disease Modeling, Duke University, Durham, North Carolina, USA.,Stanley Manne Children’s Research Institute, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, USA (current address)
| | - Dina F. Ahram
- Division of Nephrology, Columbia University, New York, USA
| | - Yangfan P. Liu
- Center for Human Disease Modeling, Duke University, Durham, North Carolina, USA
| | - Rik Westland
- Division of Nephrology, Columbia University, New York, USA.,Department of Pediatric Nephrology, Amsterdam UMC- Emma Children’s Hospital, Amsterdam, NL
| | | | - Nicholas Katsanis
- Center for Human Disease Modeling, Duke University, Durham, North Carolina, USA; Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA (current address); Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA; Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.
| | - Erica E. Davis
- Center for Human Disease Modeling, Duke University, Durham, North Carolina, USA.,Stanley Manne Children’s Research Institute, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, USA (current address).,Department of Pediatrics and Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.,To whom correspondence should be addressed: ADDRESS CORRESPONDENCE TO: Simone Sanna-Cherchi, MD, Division of Nephrology, Columbia University, College of Physicians and Surgeons, New York, NY 10032, USA; Phone: 212-851-4925; Fax: 212-851-5461; . Erica E. Davis, PhD, Stanley Manne Children’s Research Institute, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL 60611, USA; Phone: 312-503-7662; Fax: 312-503-7343; , Nicholas Katsanis, PhD, Stanley Manne Children’s Research Institute, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL 60611, USA; Phone: 312-503-7339; Fax: 312-503-7343;
| | - Simone Sanna-Cherchi
- Department of Medicine, Division of Nephrology, Columbia University Irving Medical Center, New York, New York, USA.
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31
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Callahan KP, Feudtner C. Genetic Testing Is Messier in Practice than in Theory: Lessons from Neonatology. Am J Bioeth 2022; 22:37-39. [PMID: 35089833 PMCID: PMC8936853 DOI: 10.1080/15265161.2021.2013978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Affiliation(s)
- Katharine Press Callahan
- The Children's Hospital of Philadelphia; Philadelphia, Pennsylvania
- Department of Medical Ethics and Health Policy, The Perelman School of Medicine at the University of Pennsylvania; Philadelphia, Pennsylvania
| | - Chris Feudtner
- The Children's Hospital of Philadelphia; Philadelphia, Pennsylvania
- Department of Medical Ethics and Health Policy, The Perelman School of Medicine at the University of Pennsylvania; Philadelphia, Pennsylvania
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Mary L, Lavillaureix A, Perrot A, Loget P, Launay E, Leborgne AS, Demurger F, Fradin M, Le Bouar G, Quélin C, Dubourg C, Pasquier L, Odent S, Belaud-Rotureau MA, Jaillard S. Prenatal phenotype of 22q11 micro-duplications: A systematic review and report on 12 new cases. Eur J Med Genet 2022; 65:104422. [PMID: 35026468 DOI: 10.1016/j.ejmg.2022.104422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 01/05/2022] [Accepted: 01/07/2022] [Indexed: 11/23/2022]
Abstract
The 22q11 region is prone to generating recurring Copy Number Variations (CNVs) as a result of the large numbers of Low Copy Repeats (LCRs). Typical duplications encompass the LCR-A-to-D region but atypical duplications of various sizes have also been reported. These duplications are responsible for highly variable phenotypes with incomplete penetrance and expressivity, which is challenging for adequate genetic counselling, especially in the prenatal period. To better delineate prenatal phenotypes associated with these CNVs, we report here a clinical and molecular description of twelve cases (9 foetuses and 3 deceased new-borns babies) carrying recurrent 22q11 duplications (diagnosed via aCGH), along with a review of the existing literature. 22q11 duplications were inherited from an apparently healthy parent in almost 60% of the cases. Other CNVs were diagnosed for 8% of the cases. Increased nuchal translucency and cardiac anomalies (CHD) were the most prominent phenotypes observed, along with mild renal and skeletal anomalies. Duplications encompassing the LCR-C-to-D region (and the CRKL gene) seemed more likely to generate CHDs and renal malformations. Cleft lip/palate were observed in foetuses with duplications encompassing the LCR-A-to-B region or the SPECC1L gene, as previously suggested. However, genotype-phenotype correlations remain difficult to ascertain. Second-hit point variants, epigenetic or environmental variations could play a role in the phenotypic variability of 22q11 duplications, but remain a challenge for assessment in the short period of pregnancy.
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Affiliation(s)
- Laura Mary
- Service de Cytogénétique et Biologie Cellulaire, CHU Rennes, Rennes, France; INSERM, EHESP, IRSET - UMR_S, 1085, Université Rennes 1, Rennes, France.
| | - Alinoë Lavillaureix
- Service de Génétique Clinique, CHU Rennes, CLAD Ouest, Rennes, France; ERN ITHACA, Hôpital Sud Rennes France, Université de Rennes, CNRS, IGDR, UMR 6290, F-35000, Rennes, France
| | - Adélie Perrot
- Service de Cytogénétique et Biologie Cellulaire, CHU Rennes, Rennes, France
| | - Philippe Loget
- Service d'Anatomie Pathologique, Hôpital Pontchaillou, CHU Rennes, Rennes, France
| | - Erika Launay
- Service de Cytogénétique et Biologie Cellulaire, CHU Rennes, Rennes, France
| | | | | | - Mélanie Fradin
- Service de Génétique Clinique, CHU Rennes, CLAD Ouest, Rennes, France
| | - Gwenaelle Le Bouar
- Unité de Médecine fœtale, Service de Gynécologie-Obstétrique, CHU Rennes, Rennes, France
| | - Chloé Quélin
- Service de Génétique Clinique, CHU Rennes, CLAD Ouest, Rennes, France; Service d'Anatomie Pathologique, Hôpital Pontchaillou, CHU Rennes, Rennes, France
| | - Christèle Dubourg
- Laboratoire de Génétique Moléculaire et Génomique, Centre Hospitalier Universitaire de Rennes, Rennes, 35033, France
| | - Laurent Pasquier
- Service de Génétique Clinique, CHU Rennes, CLAD Ouest, Rennes, France; ERN ITHACA, Hôpital Sud Rennes France, Université de Rennes, CNRS, IGDR, UMR 6290, F-35000, Rennes, France
| | - Sylvie Odent
- Service de Génétique Clinique, CHU Rennes, CLAD Ouest, Rennes, France; ERN ITHACA, Hôpital Sud Rennes France, Université de Rennes, CNRS, IGDR, UMR 6290, F-35000, Rennes, France
| | - Marc-Antoine Belaud-Rotureau
- Service de Cytogénétique et Biologie Cellulaire, CHU Rennes, Rennes, France; INSERM, EHESP, IRSET - UMR_S, 1085, Université Rennes 1, Rennes, France
| | - Sylvie Jaillard
- Service de Cytogénétique et Biologie Cellulaire, CHU Rennes, Rennes, France; INSERM, EHESP, IRSET - UMR_S, 1085, Université Rennes 1, Rennes, France
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Lanham KA, Nedden ML, Wise VE, Taylor MR. Genetically inducible and reversible zebrafish model of systemic inflammation. Biol Open 2022; 11:274172. [PMID: 35099005 PMCID: PMC8918989 DOI: 10.1242/bio.058559] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 01/20/2022] [Indexed: 11/20/2022] Open
Abstract
The inflammatory response is a vital defense mechanism against trauma and pathogen induced damage, but equally important is its appropriate resolution. In some instances of severe trauma or sustained infection, inappropriate and persistent activation of the immune response can occur resulting in a dangerous systemic inflammatory response. Untreated, this systemic inflammatory response can lead to tissue damage, organ shutdown, and death. Replicating this condition in tractable model organisms can provide insight into the mechanisms involved in the induction, maintenance, and resolution of inflammation. To that end, we developed a non-invasive, inducible, and reversible model of systemic inflammation in zebrafish. Using the Gal4-EcR/UAS system activated by the ecdysone analog tebufenozide, we generated transgenic zebrafish that allow for chemically-induced, ubiquitous secretion of the mature form of zebrafish interleukin-1β (Il-1βmat) in both larval and adult developmental stages. To ensure a robust immune response, we attached a strong signal peptide from the Gaussia princeps luciferase enzyme to promote active secretion of the cytokine. We observe a dose-dependent inflammatory response involving neutrophil expansion accompanied by tissue damage and reduced survival. Washout of tebufenozide permits inflammation resolution. We also establish the utility of this model for the identification of small molecule anti-inflammatory compounds by treatment with the immunosuppressant rapamycin. Taken together, these features make this model a valuable new tool that can aid in identifying potential new therapies while broadening our understanding of systemic inflammation, its impact on the immune system and its resolution.
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Affiliation(s)
- Kevin A Lanham
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, Madison, WI, USA
| | - Megan L Nedden
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, Madison, WI, USA
| | - Virginia E Wise
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, Madison, WI, USA
| | - Michael R Taylor
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, Madison, WI, USA
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Cai M, Lin N, Fan X, Chen X, Xu S, Fu X, Xu L, Huang H. Fetal Aberrant Right Subclavian Artery: Associated Anomalies, Genetic Etiology, and Postnatal Outcomes in a Retrospective Cohort Study. Front Pediatr 2022; 10:895562. [PMID: 35722491 PMCID: PMC9203729 DOI: 10.3389/fped.2022.895562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 05/06/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Aberrant right subclavian artery (ARSA) is becoming increasingly common in fetuses. However, there are relatively fewer studies regarding the genetic etiology of ARSA. We performed a genetic analysis of fetuses with ARSA and followed up on the pregnancy outcomes to evaluate the prognosis of the fetuses, providing information for prenatal and eugenic consultations. METHODS This retrospective study included 112 pregnant females whose fetuses were diagnosed with ARSA from December 2016 to February 2021. Fetal karyotype analysis and single-nucleotide polymorphism (SNP) array were performed. RESULTS The 112 fetuses were divided into two groups: the isolated ARSA group (n = 48, 42.9%) and the non-isolated ARSA group (ARSA with other ultrasound abnormalities, n = 64, 57.1%). The total rate of pathogenic copy number variation (CNV) observed using karyotype analysis (3/8) and SNP array (5/8) was 7.1% (8/112). The rates of pathogenic CNV in the isolated and non-isolated ARSA groups were 4.2% (2/48) and 9.4% (6/64), respectively. No significant difference was observed between the two groups (P = 0.463). The results of genetic analysis influenced the parents' decision to terminate the pregnancy. During the follow-up examination, fetuses with ARSA without pathogenic CNV were found to have normal growth and development after birth. CONCLUSION Fetuses with isolated ARSA have a low probability of being diagnosed with pathogenic CNV. However, when ARSA is complicated with other ultrasound abnormalities, the risk of pathogenic CNV remarkably increases. Prenatal genetic counseling and SNP-array should be recommended for better assessment of fetal prognosis.
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Affiliation(s)
- Meiying Cai
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Na Lin
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Xiangqun Fan
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Xuemei Chen
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Shiyi Xu
- Guangxi Medical University, Guangxi, China
| | - Xianguo Fu
- Department of Prenatal Diagnosis, Ningde Municipal Hospital, Ningde Normal University, Ningde, China
| | - Liangpu Xu
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Hailong Huang
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
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Nissan E, Katz U, Levy-Shraga Y, Frizinsky S, Carmel E, Gothelf D, Somech R. Clinical Features in a Large Cohort of Patients With 22q11.2 Deletion Syndrome. J Pediatr 2021; 238:215-220.e5. [PMID: 34284033 DOI: 10.1016/j.jpeds.2021.07.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 07/09/2021] [Accepted: 07/13/2021] [Indexed: 12/28/2022]
Abstract
OBJECTIVES To evaluate various clinical aspects, specifically regarding immune status, in a large cohort of patients with DiGeorge syndrome. STUDY DESIGN Data were collected for 98 patients with DiGeorge syndrome treated at a tertiary medical center. This included general information, laboratory results, and clinical features. RESULTS The median age at diagnosis was 2.0 years (range, 0.0-36.5 years). The most common symptoms that led to diagnosis were congenital heart defect, speech delay, palate anomalies, and developmental delay. Common clinical features included recurrent infections (76 patients), congenital heart diseases (61 patients), and otorhinolaryngology disorders (61 patients). Twenty patients had anemia; the incidence was relatively high among patients aged 6-59 months. Thrombocytopenia was present in 20 patients. Recurrent chest infections were significantly higher in patients with T cell and T cell subset deficiencies. Decreased T cell receptor excision circles were more common with increasing age (P < .001). Of the 27 patients hospitalized due to infection, pneumonia was a leading cause in 13. CONCLUSIONS Awareness of DiGeorge syndrome's typical and uncommon characteristics is important to improve diagnosis, treatment, surveillance, and follow-up.
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Affiliation(s)
- Ella Nissan
- Pediatric Department A and Immunology Service, Edmond and Lily Safra Children's Hospital, Jeffrey Modell Foundation Center, Tel Hashomer, Israel; Sheba Medical Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
| | - Uriel Katz
- Sheba Medical Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Edmond Safra International Congenital Heart Center, Edmond and Lily Safra Children's Hospital, Ramat Gan, Israel
| | - Yael Levy-Shraga
- Sheba Medical Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Pediatric Endocrinology Unit, Edmond and Lily Safra Children's Hospital, Ramat Gan, Israel
| | - Shirly Frizinsky
- Pediatric Department A and Immunology Service, Edmond and Lily Safra Children's Hospital, Jeffrey Modell Foundation Center, Tel Hashomer, Israel; Sheba Medical Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Eldar Carmel
- Sheba Medical Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Otorhinolaryngology Head and Neck Surgery Department, Edmond and Lily Safra Children's Hospital, Ramat Gan, Israel
| | - Doron Gothelf
- Sheba Medical Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Child and Adolescent Psychiatry Division, Edmond and Lily Safra Children's Hospital, Ramat Gan, Israel; Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Raz Somech
- Pediatric Department A and Immunology Service, Edmond and Lily Safra Children's Hospital, Jeffrey Modell Foundation Center, Tel Hashomer, Israel; Sheba Medical Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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Vysotskiy M, Zhong X, Miller-Fleming TW, Zhou D, Cox NJ, Weiss LA. Integration of genetic, transcriptomic, and clinical data provides insight into 16p11.2 and 22q11.2 CNV genes. Genome Med 2021; 13:172. [PMID: 34715901 PMCID: PMC8557010 DOI: 10.1186/s13073-021-00972-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 09/16/2021] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Deletions and duplications of the multigenic 16p11.2 and 22q11.2 copy number variant (CNV) regions are associated with brain-related disorders including schizophrenia, intellectual disability, obesity, bipolar disorder, and autism spectrum disorder (ASD). The contribution of individual CNV genes to each of these identified phenotypes is unknown, as well as the contribution of these CNV genes to other potentially subtler health implications for carriers. Hypothesizing that DNA copy number exerts most effects via impacts on RNA expression, we attempted a novel in silico fine-mapping approach in non-CNV carriers using both GWAS and biobank data. METHODS We first asked whether gene expression level in any individual gene in the CNV region alters risk for a known CNV-associated behavioral phenotype(s). Using transcriptomic imputation, we performed association testing for CNV genes within large genotyped cohorts for schizophrenia, IQ, BMI, bipolar disorder, and ASD. Second, we used a biobank containing electronic health data to compare the medical phenome of CNV carriers to controls within 700,000 individuals in order to investigate the full spectrum of health effects of the CNVs. Third, we used genotypes for over 48,000 individuals within the biobank to perform phenome-wide association studies between imputed expressions of individual 16p11.2 and 22q11.2 genes and over 1500 health traits. RESULTS Using large genotyped cohorts, we found individual genes within 16p11.2 associated with schizophrenia (TMEM219, INO80E, YPEL3), BMI (TMEM219, SPN, TAOK2, INO80E), and IQ (SPN), using conditional analysis to identify upregulation of INO80E as the driver of schizophrenia, and downregulation of SPN and INO80E as increasing BMI. We identified both novel and previously observed over-represented traits within the electronic health records of 16p11.2 and 22q11.2 CNV carriers. In the phenome-wide association study, we found seventeen significant gene-trait pairs, including psychosis (NPIPB11, SLX1B) and mood disorders (SCARF2), and overall enrichment of mental traits. CONCLUSIONS Our results demonstrate how integration of genetic and clinical data aids in understanding CNV gene function and implicates pleiotropy and multigenicity in CNV biology.
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Affiliation(s)
- Mikhail Vysotskiy
- Department of Psychiatry and Behavioral Sciences, University of California San Francisco, 513 Parnassus Ave., Health Sciences East 9th floor HSE901E, San Francisco, CA, 94143, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, 94143, USA
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, 94143, USA
- Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Xue Zhong
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Vanderbilt Genetics Institute, Nashville, TN, 37232, USA
| | - Tyne W Miller-Fleming
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Vanderbilt Genetics Institute, Nashville, TN, 37232, USA
| | - Dan Zhou
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Vanderbilt Genetics Institute, Nashville, TN, 37232, USA
| | - Nancy J Cox
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Vanderbilt Genetics Institute, Nashville, TN, 37232, USA
| | - Lauren A Weiss
- Department of Psychiatry and Behavioral Sciences, University of California San Francisco, 513 Parnassus Ave., Health Sciences East 9th floor HSE901E, San Francisco, CA, 94143, USA.
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, 94143, USA.
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, 94143, USA.
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Lozic M, Minarik L, Racetin A, Filipovic N, Saraga Babic M, Vukojevic K. CRKL, AIFM3, AIF, BCL2, and UBASH3A during Human Kidney Development. Int J Mol Sci 2021; 22:ijms22179183. [PMID: 34502088 PMCID: PMC8431184 DOI: 10.3390/ijms22179183] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 08/20/2021] [Accepted: 08/23/2021] [Indexed: 11/16/2022] Open
Abstract
We aimed to investigate the spatio-temporal expression of possible CAKUT candidate genes CRKL, AIFM3, and UBASH3A, as well as AIF and BCL2 during human kidney development. Human fetal kidney tissue was stained with antibodies and analyzed by fluorescence microscopy and RT-PCR. Quantification of positive cells was assessed by calculation of area percentage and counting cells in nephron structures. Results showed statistically significant differences in the temporal expression patterns of the examined markers, depending on the investigated developmental stage. Limited but strong expression of CRKL was seen in developing kidneys, with increasing expression up to the period where the majority of nephrons are formed. Results also lead us to conclude that AIFM3 and AIF are important for promoting cell survival, but only AIFM3 is considered a CAKUT candidate gene due to the lack of AIF in nephron developmental structures. Our findings imply great importance of AIFM3 in energy production in nephrogenesis and tubular maturation. UBASH3A raw scores showed greater immunoreactivity in developing structures than mature ones which would point to a meaningful role in nephrogenesis. The fact that mRNA and proteins of CRKL, UBASH3A, and AIFM3 were detected in all phases of kidney development implies their role as renal development control genes.
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Affiliation(s)
- Mirela Lozic
- Department of Anatomy, Histology and Embryology, School of Medicine, University of Split, Šoltanska 2, 21 000 Split, Croatia; (M.L.); (L.M.); (A.R.); (N.F.); (M.S.B.)
| | - Luka Minarik
- Department of Anatomy, Histology and Embryology, School of Medicine, University of Split, Šoltanska 2, 21 000 Split, Croatia; (M.L.); (L.M.); (A.R.); (N.F.); (M.S.B.)
| | - Anita Racetin
- Department of Anatomy, Histology and Embryology, School of Medicine, University of Split, Šoltanska 2, 21 000 Split, Croatia; (M.L.); (L.M.); (A.R.); (N.F.); (M.S.B.)
- Department of Medical Genetics, School of Medicine, University of Mostar, 88 000 Mostar, Bosnia and Herzegovina
| | - Natalija Filipovic
- Department of Anatomy, Histology and Embryology, School of Medicine, University of Split, Šoltanska 2, 21 000 Split, Croatia; (M.L.); (L.M.); (A.R.); (N.F.); (M.S.B.)
| | - Mirna Saraga Babic
- Department of Anatomy, Histology and Embryology, School of Medicine, University of Split, Šoltanska 2, 21 000 Split, Croatia; (M.L.); (L.M.); (A.R.); (N.F.); (M.S.B.)
| | - Katarina Vukojevic
- Department of Anatomy, Histology and Embryology, School of Medicine, University of Split, Šoltanska 2, 21 000 Split, Croatia; (M.L.); (L.M.); (A.R.); (N.F.); (M.S.B.)
- Department of Medical Genetics, School of Medicine, University of Mostar, 88 000 Mostar, Bosnia and Herzegovina
- Correspondence: ; Tel.: +385-21-557-807; Fax: +385-21-557-811
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Beaman GM, Cervellione RM, Keene D, Reutter H, Newman WG. The Genomic Architecture of Bladder Exstrophy Epispadias Complex. Genes (Basel) 2021; 12:genes12081149. [PMID: 34440323 PMCID: PMC8391660 DOI: 10.3390/genes12081149] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 07/21/2021] [Indexed: 11/16/2022] Open
Abstract
The bladder exstrophy-epispadias complex (BEEC) is an abdominal midline malformation comprising a spectrum of congenital genitourinary abnormalities of the abdominal wall, pelvis, urinary tract, genitalia, anus, and spine. The vast majority of BEEC cases are classified as non-syndromic and the etiology of this malformation is still unknown. This review presents the current knowledge on this multifactorial disorder, including phenotypic and anatomical characterization, epidemiology, proposed developmental mechanisms, existing animal models, and implicated genetic and environmental components.
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Affiliation(s)
- Glenda M. Beaman
- Division of Evolution and Genomic Sciences, Faculty of Biology, School of Biological Sciences, Medicine and Health, University of Manchester, Manchester M13 9PL, UK;
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester M13 9WL, UK
| | - Raimondo M. Cervellione
- Royal Manchester Children’s Hospital, Manchester University NHS Foundation Trust, Manchester M13 9WL, UK; (R.M.C.); (D.K.)
| | - David Keene
- Royal Manchester Children’s Hospital, Manchester University NHS Foundation Trust, Manchester M13 9WL, UK; (R.M.C.); (D.K.)
| | - Heiko Reutter
- Department of Neonatology and Paediatric Intensive Care, University Hospital Erlangen, 91054 Erlangen, Germany;
| | - William G. Newman
- Division of Evolution and Genomic Sciences, Faculty of Biology, School of Biological Sciences, Medicine and Health, University of Manchester, Manchester M13 9PL, UK;
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester M13 9WL, UK
- Correspondence:
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Friedrich S, Müller H, Riesterer C, Schüller H, Friedrich K, Wörner CL, Busch T, Viau A, Kuehn EW, Köttgen M, Hofherr A. Identification of pathological transcription in autosomal dominant polycystic kidney disease epithelia. Sci Rep 2021; 11:15139. [PMID: 34301992 DOI: 10.1038/s41598-021-94442-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 07/08/2021] [Indexed: 11/09/2022] Open
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) affects more than 12 million people worldwide. Mutations in PKD1 and PKD2 cause cyst formation through unknown mechanisms. To unravel the pathogenic mechanisms in ADPKD, multiple studies have investigated transcriptional mis-regulation in cystic kidneys from patients and mouse models, and numerous dysregulated genes and pathways have been described. Yet, the concordance between studies has been rather limited. Furthermore, the cellular and genetic diversity in cystic kidneys has hampered the identification of mis-expressed genes in kidney epithelial cells with homozygous PKD mutations, which are critical to identify polycystin-dependent pathways. Here we performed transcriptomic analyses of Pkd1- and Pkd2-deficient mIMCD3 kidney epithelial cells followed by a meta-analysis to integrate all published ADPKD transcriptomic data sets. Based on the hypothesis that Pkd1 and Pkd2 operate in a common pathway, we first determined transcripts that are differentially regulated by both genes. RNA sequencing of genome-edited ADPKD kidney epithelial cells identified 178 genes that are concordantly regulated by Pkd1 and Pkd2. Subsequent integration of existing transcriptomic studies confirmed 31 previously described genes and identified 61 novel genes regulated by Pkd1 and Pkd2. Cluster analyses then linked Pkd1 and Pkd2 to mRNA splicing, specific factors of epithelial mesenchymal transition, post-translational protein modification and epithelial cell differentiation, including CD34, CDH2, CSF2RA, DLX5, HOXC9, PIK3R1, PLCB1 and TLR6. Taken together, this model-based integrative analysis of transcriptomic alterations in ADPKD annotated a conserved core transcriptomic profile and identified novel candidate genes for further experimental studies.
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Gupton SE, McCarthy EA, Markert ML. Care of Children with DiGeorge Before and After Cultured Thymus Tissue Implantation. J Clin Immunol 2021; 41:896-905. [PMID: 34003433 DOI: 10.1007/s10875-021-01044-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 04/14/2021] [Indexed: 12/02/2022]
Abstract
Background Children with complete DiGeorge anomaly (cDGA) have congenital athymia plus a myriad of other challenging clinical conditions. The term cDGA encompasses children with congenital athymia secondary to 22q11.2DS, CHARGE syndrome (coloboma, heart defects, choanal atresia, growth or mental retardation, genital abnormalities, and ear abnormalities and/or deafness), and other genetic abnormalities. Some children have no known genetic defects. Since 1993, more than 100 children with congenital athymia have been treated with cultured thymus tissue implantation (CTTI). Naïve T cells develop approximately 6 to 12 months after CTTI. Most of the children had significant comorbidities such as heart disease, hypoparathyroidism, and infections requiring complex clinical care post cultured thymus tissue implantation (CTTI). Objective The purpose of this guidance is to assist multidisciplinary teams in caring for children with cDGA both before and after CTTI. Methods Thirty-one specialists, in addition to the authors, were asked to share their experience in caring for children with cDGA at Duke University Health System, before and after CTTI. These specialists included physicians, nurses, dentists, therapists, and dieticians. Results The goal of a multidisciplinary approach is to have children in the best possible condition for receiving CTTI and provide optimal care post CTTI through development of naïve T cells and beyond. The CTT (cultured thymus tissue) must be protected from high doses of steroids which can damage CTT. Organs must be protected from adverse effects of immunosuppression. Conclusion Creating a multidisciplinary team and a detailed plan of care for children with cDGA is important for optimal outcomes.
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Saito R, Miyoshi C, Koebis M, Kushima I, Nakao K, Mori D, Ozaki N, Funato H, Yanagisawa M, Aiba A. Two novel mouse models mimicking minor deletions in 22q11.2 deletion syndrome revealed the contribution of each deleted region to psychiatric disorders. Mol Brain 2021; 14:68. [PMID: 33845872 PMCID: PMC8042712 DOI: 10.1186/s13041-021-00778-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 04/03/2021] [Indexed: 12/02/2022] Open
Abstract
22q11.2 deletion syndrome (22q11.2DS) is a disorder caused by the segmental deletion of human chromosome 22. This chromosomal deletion is known as high genetic risk factors for various psychiatric disorders. The different deletion types are identified in 22q11.2DS patients, including the most common 3.0-Mb deletion, and the less-frequent 1.5-Mb and 1.4-Mb deletions. In previous animal studies of psychiatric disorders associated with 22q11.2DS mainly focused on the 1.5-Mb deletion and model mice mimicking the human 1.5-Mb deletion have been established with diverse genetic backgrounds, which resulted in the contradictory phenotypes. On the other hand, the contribution of the genes in 1.4-Mb region to psychiatric disorders is poorly understood. In this study, we generated two mouse lines that reproduced the 1.4-Mb and 1.5-Mb deletions of 22q11.2DS [Del(1.4 Mb)/+ and Del(1.5 Mb)/+] on the pure C57BL/6N genetic background. These mutant mice were analyzed comprehensively by behavioral tests, such as measurement of locomotor activity, sociability, prepulse inhibition and fear-conditioning memory. Del(1.4 Mb)/+ mice displayed decreased locomotor activity, but no abnormalities were observed in all other behavioral tests. Del(1.5 Mb)/+ mice showed reduction of prepulse inhibition and impairment of contextual- and cued-dependent fear memory, which is consistent with previous reports. Furthermore, apparently intact social recognition in Del(1.4 Mb)/+ and Del(1.5 Mb)/+ mice suggests that the impaired social recognition observed in Del(3.0 Mb)/+ mice mimicking the human 3.0-Mb deletion requires mutations both in 1.4-Mb and 1.5 Mb regions. Our previous study has shown that Del(3.0 Mb)/+ mice presented disturbance of behavioral circadian rhythm. Therefore, we further evaluated sleep/wakefulness cycles in Del(3.0 Mb)/+ mice by electroencephalogram (EEG) and electromyogram (EMG) recording. EEG/EMG analysis revealed the disturbed wakefulness and non-rapid eye moving sleep (NREMS) cycles in Del(3.0 Mb)/+ mice, suggesting that Del(3.0 Mb)/+ mice may be unable to maintain their wakefulness. Together, our mouse models deepen our understanding of genetic contributions to schizophrenic phenotypes related to 22q11.2DS.
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Affiliation(s)
- Ryo Saito
- Laboratory of Animal Resources, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Chika Miyoshi
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8575 Japan
| | - Michinori Koebis
- Laboratory of Animal Resources, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Itaru Kushima
- Department of Psychiatry, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550 Japan
- Medical Genomics Center, Nagoya University Hospital, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550 Japan
| | - Kazuki Nakao
- Laboratory of Animal Resources, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
- Institute of Experimental Animal Sciences, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871 Japan
| | - Daisuke Mori
- Department of Psychiatry, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550 Japan
- Brain and Mind Research Center, Nagoya University, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550 Japan
| | - Norio Ozaki
- Department of Psychiatry, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550 Japan
| | - Hiromasa Funato
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8575 Japan
| | - Masashi Yanagisawa
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8575 Japan
| | - Atsu Aiba
- Laboratory of Animal Resources, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
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Verbitsky M, Krithivasan P, Batourina E, Khan A, Graham SE, Marasà M, Kim H, Lim TY, Weng PL, Sánchez-Rodríguez E, Mitrotti A, Ahram DF, Zanoni F, Fasel DA, Westland R, Sampson MG, Zhang JY, Bodria M, Kil BH, Shril S, Gesualdo L, Torri F, Scolari F, Izzi C, van Wijk JA, Saraga M, Santoro D, Conti G, Barton DE, Dobson MG, Puri P, Furth SL, Warady BA, Pisani I, Fiaccadori E, Allegri L, Degl'Innocenti ML, Piaggio G, Alam S, Gigante M, Zaza G, Esposito P, Lin F, Simões-e-Silva AC, Brodkiewicz A, Drozdz D, Zachwieja K, Miklaszewska M, Szczepanska M, Adamczyk P, Tkaczyk M, Tomczyk D, Sikora P, Mizerska-Wasiak M, Krzemien G, Szmigielska A, Zaniew M, Lozanovski VJ, Gucev Z, Ionita-Laza I, Stanaway IB, Crosslin DR, Wong CS, Hildebrandt F, Barasch J, Kenny EE, Loos RJ, Levy B, Ghiggeri GM, Hakonarson H, Latos-Bieleńska A, Materna-Kiryluk A, Darlow JM, Tasic V, Willer C, Kiryluk K, Sanna-Cherchi S, Mendelsohn CL, Gharavi AG. Copy Number Variant Analysis and Genome-wide Association Study Identify Loci with Large Effect for Vesicoureteral Reflux. J Am Soc Nephrol 2021; 32:805-820. [PMID: 33597122 PMCID: PMC8017540 DOI: 10.1681/asn.2020050681] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 12/04/2020] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Vesicoureteral reflux (VUR) is a common, familial genitourinary disorder, and a major cause of pediatric urinary tract infection (UTI) and kidney failure. The genetic basis of VUR is not well understood. METHODS A diagnostic analysis sought rare, pathogenic copy number variant (CNV) disorders among 1737 patients with VUR. A GWAS was performed in 1395 patients and 5366 controls, of European ancestry. RESULTS Altogether, 3% of VUR patients harbored an undiagnosed rare CNV disorder, such as the 1q21.1, 16p11.2, 22q11.21, and triple X syndromes ((OR, 3.12; 95% CI, 2.10 to 4.54; P=6.35×10-8) The GWAS identified three study-wide significant and five suggestive loci with large effects (ORs, 1.41-6.9), containing canonical developmental genes expressed in the developing urinary tract (WDPCP, OTX1, BMP5, VANGL1, and WNT5A). In particular, 3.3% of VUR patients were homozygous for an intronic variant in WDPCP (rs13013890; OR, 3.65; 95% CI, 2.39 to 5.56; P=1.86×10-9). This locus was associated with multiple genitourinary phenotypes in the UK Biobank and eMERGE studies. Analysis of Wnt5a mutant mice confirmed the role of Wnt5a signaling in bladder and ureteric morphogenesis. CONCLUSIONS These data demonstrate the genetic heterogeneity of VUR. Altogether, 6% of patients with VUR harbored a rare CNV or a common variant genotype conferring an OR >3. Identification of these genetic risk factors has multiple implications for clinical care and for analysis of outcomes in VUR.
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Affiliation(s)
- Miguel Verbitsky
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Priya Krithivasan
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | | | - Atlas Khan
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Sarah E. Graham
- Department of Internal Medicine, Cardiology, University of Michigan, Ann Arbor, Michigan
| | - Maddalena Marasà
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Hyunwoo Kim
- Department of Urology, Columbia University, New York, New York
| | - Tze Y. Lim
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Patricia L. Weng
- Department of Pediatric Nephrology, University of California, Los Angeles Medical Center and University of California, Los Angeles Medical Center-Santa Monica, Los Angeles, California
| | | | - Adele Mitrotti
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
- Section of Nephrology, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Dina F. Ahram
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Francesca Zanoni
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - David A. Fasel
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Rik Westland
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
- Department of Pediatric Nephrology, Vrije Universiteit University Medical Center, Amsterdam, The Netherlands
| | - Matthew G. Sampson
- Division of Nephrology, Boston Children’s Hospital, Boston, Massachusetts
| | - Jun Y. Zhang
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Monica Bodria
- Division of Nephrology, Dialysis, Transplantation, and Laboratory on Pathophysiology of Uremia, Istituto G. Gaslini, Genoa, Italy
| | - Byum Hee Kil
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Shirlee Shril
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Loreto Gesualdo
- Section of Nephrology, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Fabio Torri
- Department of Pediatric Surgery, Spedali Civili Children’s Hospital of Brescia, Brescia, Italy
| | - Francesco Scolari
- Chair and Division of Nephrology, University and Spedali Civili Hospital, Brescia, Italy
| | - Claudia Izzi
- Division of Nephrology and Department of Obstetrics and Gynecology, ASST Spedali Civili of Brescia, Brescia, Italy
| | - Joanna A.E. van Wijk
- Department of Pediatric Nephrology, Vrije Universiteit University Medical Center, Amsterdam, The Netherlands
| | - Marijan Saraga
- Department of Pediatrics, University Hospital of Split, Split, Croatia
- School of Medicine, University of Split, Split, Croatia
| | - Domenico Santoro
- Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy
| | - Giovanni Conti
- Department of Pediatric Nephrology, Azienda Ospedaliera Universitaria “G. Martino,” Messina, Italy
| | - David E. Barton
- University College Dublin School of Medicine, Our Lady’s Children’s Hospital Crumlin, Dublin, Ireland
- Department of Clinical Genetics, Our Lady’s Children’s Hospital Crumlin, Dublin, Ireland
| | - Mark G. Dobson
- Department of Clinical Genetics, Our Lady’s Children’s Hospital Crumlin, Dublin, Ireland
- National Children’s Research Centre, Our Lady’s Children’s Hospital Crumlin, Dublin, Ireland
| | - Prem Puri
- National Children’s Research Centre, Our Lady’s Children’s Hospital Crumlin, Dublin, Ireland
- Department of Pediatric Surgery, Beacon Hospital, University College Dublin, Dublin, Ireland
| | - Susan L. Furth
- Division of Nephrology, Departments of Pediatrics and Epidemiology, Perelman School of Medicine at the University of Pennsylvania, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Bradley A. Warady
- Division of Nephrology, Department of Pediatrics, University of Missouri-Kansas City School of Medicine, Children’s Mercy Kansas City, Kansas City, Missouri
| | - Isabella Pisani
- Nephrology Unit, Parma University Hospital and Department of Medicine and Surgery, Parma University Medical School, Parma, Italy
| | - Enrico Fiaccadori
- Nephrology Unit, Parma University Hospital and Department of Medicine and Surgery, Parma University Medical School, Parma, Italy
| | - Landino Allegri
- Nephrology Unit, Parma University Hospital and Department of Medicine and Surgery, Parma University Medical School, Parma, Italy
| | - Maria Ludovica Degl'Innocenti
- Division of Nephrology, Dialysis, Transplantation, and Laboratory on Pathophysiology of Uremia, Istituto G. Gaslini, Genoa, Italy
| | - Giorgio Piaggio
- Division of Nephrology, Dialysis, Transplantation, and Laboratory on Pathophysiology of Uremia, Istituto G. Gaslini, Genoa, Italy
| | - Shumyle Alam
- Department of Pediatric Urology, Columbia University College of Physicians and Surgeons, New York, New York
| | - Maddalena Gigante
- Section of Nephrology, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Gianluigi Zaza
- Renal and Dialysis Unit, Department of Medicine, School of Medicine, University of Verona, Verona, Italy
| | - Pasquale Esposito
- Department of Internal Medicine, Nephrology, Dialysis and Transplantation Clinics, Genoa University and IRCCS Policlinico San Martino, Genova, Italy
| | - Fangming Lin
- Division of Pediatric Nephrology, Department of Pediatrics, Columbia University, New York, New York
| | - Ana Cristina Simões-e-Silva
- Department of Pediatrics, Unit of Pediatric Nephrology, Interdisciplinary Laboratory of Medical Investigation, Faculty of Medicine, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Andrzej Brodkiewicz
- Department of Pediatrics, Child Nephrology, Dialysotheraphy and Management of Acute Poisoning, Pomeranian Medical University, Szczecin, Poland
| | - Dorota Drozdz
- Department of Pediatric Nephrology and Hypertension, Jagiellonian University Medical College, Krakow, Poland
| | - Katarzyna Zachwieja
- Department of Pediatric Nephrology and Hypertension, Jagiellonian University Medical College, Krakow, Poland
| | - Monika Miklaszewska
- Department of Pediatric Nephrology and Hypertension, Jagiellonian University Medical College, Krakow, Poland
| | - Maria Szczepanska
- Department of Pediatrics, Faculty of Medical Sciences in Zabrze, Medical University of Silesia in Katowice, Katowice, Poland
| | - Piotr Adamczyk
- Department of Pediatrics, Faculty of Medical Sciences in Zabrze, Medical University of Silesia in Katowice, Katowice, Poland
| | - Marcin Tkaczyk
- Department of Pediatrics, Immunology and Nephrology, Polish Mother’s Memorial Hospital Research Institute, Lodz, Poland
| | - Daria Tomczyk
- Department of Pediatrics, Immunology and Nephrology, Polish Mother’s Memorial Hospital Research Institute, Lodz, Poland
| | - Przemyslaw Sikora
- Department of Pediatric Nephrology, Medical University of Lublin, Lublin, Poland
| | | | - Grazyna Krzemien
- Department of Pediatrics and Nephrology, Medical University of Warsaw, Poland
| | | | - Marcin Zaniew
- Department of Pediatrics, University of Zielona Góra, Zielona Góra, Poland
| | - Vladimir J. Lozanovski
- University Clinic for General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
- University Children’s Hospital, Medical Faculty of Skopje, Skopje, Macedonia
| | - Zoran Gucev
- University Children’s Hospital, Medical Faculty of Skopje, Skopje, Macedonia
| | | | - Ian B. Stanaway
- Department of Biomedical Informatics and Medical Education, University of Washington School of Medicine, Seattle, Washington
| | - David R. Crosslin
- Department of Biomedical Informatics and Medical Education, University of Washington School of Medicine, Seattle, Washington
| | - Craig S. Wong
- Division of Pediatric Nephrology, University of New Mexico Children’s Hospital, Albuquerque, New Mexico
| | - Friedhelm Hildebrandt
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jonathan Barasch
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
- Department of Urology, Columbia University, New York, New York
| | - Eimear E. Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ruth J.F. Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York
| | - Brynn Levy
- Department of Pathology and Cell Biology, Columbia University, New York, New York
| | - Gian Marco Ghiggeri
- Division of Nephrology, Dialysis, Transplantation, and Laboratory on Pathophysiology of Uremia, Istituto G. Gaslini, Genoa, Italy
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children’s Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Anna Latos-Bieleńska
- Department of Medical Genetics, Poznan University of Medical Sciences, and NZOZ Center for Medical Genetics GENESIS, Poznan, Poland
| | - Anna Materna-Kiryluk
- Department of Medical Genetics, Poznan University of Medical Sciences, and NZOZ Center for Medical Genetics GENESIS, Poznan, Poland
| | - John M. Darlow
- Department of Clinical Genetics, Our Lady’s Children’s Hospital Crumlin, Dublin, Ireland
- National Children’s Research Centre, Our Lady’s Children’s Hospital Crumlin, Dublin, Ireland
| | - Velibor Tasic
- University Children’s Hospital, Medical Faculty of Skopje, Skopje, Macedonia
| | - Cristen Willer
- Department of Internal Medicine, Cardiology, University of Michigan, Ann Arbor, Michigan
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan
- Department of Computational Medicine and Bioinformatics, Ann Arbor, Michigan
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Simone Sanna-Cherchi
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | | | - Ali G. Gharavi
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
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Stefekova A, Capkova P, Capkova Z, Curtisova V, Srovnal J, Mracka E, Klaskova E, Prochazka M. MLPA analysis of 32 foetuses with a congenital heart defect and 1 foetus with renal defects - pilot study. The significant frequency rate of presented pathological CNV. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub 2021; 166:187-194. [PMID: 33824538 DOI: 10.5507/bp.2021.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 03/17/2021] [Indexed: 11/23/2022] Open
Abstract
AIMS The aim of this retrospective study was to determine the detection rate of the pathogenic copy number variants (CNVs) in a cohort of 33 foetuses - 32 with CHD (congenital heart defects) and 1 with kidney defect, after exclusion of common aneuploidies (trisomy 13, 18, 21, and monosomy X) by karyotyping, Multiplex ligation - dependent probe amplification (MLPA) and chromosomal microarray analysis (CMA). We also assess the effectivity of MLPA as a method of the first tier for quick and inexpensive detection of mutations, causing congenital malformations in foetuses. METHODS MLPA with probe mixes P070, P036 - Telomere 3 and 5, P245 - microdeletions, P250 - DiGeorge syndrome, and P311 - CHD (Congenital heart defects) was performed in 33 samples of amniotic fluid and chorionic villi. CMA was performed in 10 relevant cases. RESULTS Pathogenic CNVs were found in 5 samples: microdeletions in region 22q11.2 (≈2 Mb) in two foetuses, one distal microdeletion of the 22q11.2 region containing genes LZTR1, CRKL, AIFM3 and SNAP29 (≈416 kb) in the foetus with bilateral renal agenesis, 8p23.1 (3.8 Mb) microdeletion syndrome and microdeletion in area 9q34.3 (1.7 Mb, Kleefstra syndrome). MLPA as an initial screening method revealed unambiguously pathogenic CNVs in 15.2 % of samples. CONCLUSION Our study suggests that MLPA and CMA are a reliable and high-resolution technology and should be used as the first-tier test for prenatal diagnosis of congenital heart disease. Determination of the cause of the abnormality is crucial for genetic counselling and further management of the pregnancy.
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Affiliation(s)
- Andrea Stefekova
- Department of Medical Genetics, University Hospital Olomouc, Czech Republic.,Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
| | - Pavlina Capkova
- Department of Medical Genetics, University Hospital Olomouc, Czech Republic.,Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
| | - Zuzana Capkova
- Department of Medical Genetics, University Hospital Olomouc, Czech Republic.,Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
| | - Vaclava Curtisova
- Department of Medical Genetics, University Hospital Olomouc, Czech Republic
| | - Josef Srovnal
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University Olomouc, Czech Republic.,Department of Pediatrics, University Hospital Olomouc, Czech Republic
| | - Enkhjargalan Mracka
- Department of Medical Genetics, University Hospital Olomouc, Czech Republic.,Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
| | - Eva Klaskova
- Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic.,Department of Pediatrics, University Hospital Olomouc, Czech Republic
| | - Martin Prochazka
- Department of Medical Genetics, University Hospital Olomouc, Czech Republic.,Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
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Yusuff T, Kellaris G, Girirajan S, Katsanis N. Dissecting the complexity of CNV pathogenicity: insights from Drosophila and zebrafish models. Curr Opin Genet Dev 2021; 68:79-87. [PMID: 33812298 DOI: 10.1016/j.gde.2021.02.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 02/21/2021] [Accepted: 02/26/2021] [Indexed: 11/20/2022]
Abstract
Genetic architecture predisposes regions of the human genome to copy-number variants, which confer substantial disease risk, most prominently towards neurodevelopmental disorders. These variants typically contain multiple genes and are often associated with extensive pleiotropy and variable phenotypic expressivity. Despite the expansion of the fidelity of CNV detection, and the study of such lesions at the population level, understanding causal mechanisms for CNV phenotypes will require biological testing of constituent genes and their interactions. In this regard, model systems amenable to high-throughput phenotypic analysis of dosage-sensitive genes (and combinations thereof) are beginning to offer improved granularity of CNV-driven pathology. Here, we review the utility of Drosophila and zebrafish models for pathogenic CNV regions, highlight the advances made in discovery of single gene drivers and genetic interactions that determine specific CNV phenotypes, and argue for their validity in dissecting conserved developmental mechanisms associated with CNVs.
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Abstract
Crk and CrkL are cellular counterparts of the viral oncoprotein v-Crk. Crk and CrkL are overexpressed in many types of human cancer, correlating with poor prognosis. Furthermore, gene knockdown and knockout of Crk and CrkL in tumor cell lines suppress tumor cell functions, including cell proliferation, transformation, migration, invasion, epithelial-mesenchymal transition, resistance to chemotherapy drugs, and in vivo tumor growth and metastasis. Conversely, overexpression of tumor cells with Crk or CrkL enhances tumor cell functions. Therefore, Crk and CrkL have been proposed as therapeutic targets for cancer treatment. However, it is unclear whether Crk and CrkL make distinct or overlapping contributions to tumor cell functions in various cancer types because Crk or CrkL have been examined independently in most studies. Two recent studies using colorectal cancer and glioblastoma cells clearly demonstrated that Crk and CrkL need to be ablated individually and combined to understand distinct and overlapping roles of the two proteins in cancer. A comprehensive understanding of individual and overlapping roles of Crk and CrkL in tumor cell functions is necessary to develop effective therapeutic strategies. This review systematically discusses crucial functions of Crk and CrkL in tumor cell functions and provides new perspectives on targeting Crk and CrkL in cancer therapy.
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Affiliation(s)
- Taeju Park
- Children's Mercy Research Institute, Children's Mercy Kansas City, Department of Pediatrics, University of Missouri Kansas City School of Medicine, Kansas City, MO 64108, USA
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Zhou X, Chen X, Jiang Y, Qi Q, Hao N, Liu C, Xu M, Cram DS, Liu J. A Rapid PCR-Free Next-Generation Sequencing Method for the Detection of Copy Number Variations in Prenatal Samples. Life (Basel) 2021; 11:98. [PMID: 33525582 DOI: 10.3390/life11020098] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/15/2021] [Accepted: 01/25/2021] [Indexed: 11/17/2022] Open
Abstract
Next-generation sequencing (NGS) is emerging as a new method for the detection of clinically significant copy number variants (CNVs). In this study, we developed and validated rapid CNV-sequencing (rCNV-seq) for clinical application in prenatal diagnosis. Low-pass whole-genome sequencing was performed on PCR libraries prepared from amniocyte genomic DNA. From 10-40 ng of input DNA, PCR-free libraries consistently produced sequencing data with high unique read mapping ratios, low read redundancy, low coefficient of variation for all chromosomes and high genomic coverage. In validation studies, reliable and accurate CNV detection using PCR-free-based rCNV-seq was demonstrated for a range of common trisomies and sex chromosome aneuploidies as well as microdeletion and duplication syndromes. In reproducibility studies, CNV copy number and genomic intervals closely matched those defined by chromosome microarray analysis. Clinical testing of genomic DNA samples from 217 women referred for prenatal diagnosis identified eight samples (3.7%) with known chromosome disorders. We conclude that PCR-free-based rCNV-seq is a sensitive, specific, reproducible and efficient method that can be used in any NGS-based diagnostic laboratory for detection of clinically significant CNVs.
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Westland R, Renkema KY, Knoers NV. Clinical Integration of Genome Diagnostics for Congenital Anomalies of the Kidney and Urinary Tract. Clin J Am Soc Nephrol 2021; 16:128-137. [PMID: 32312792 PMCID: PMC7792653 DOI: 10.2215/cjn.14661119] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Revolutions in genetics, epigenetics, and bioinformatics are currently changing the outline of diagnostics and clinical medicine. From a nephrologist's perspective, individuals with congenital anomalies of the kidney and urinary tract (CAKUT) are an important patient category: not only is CAKUT the predominant cause of kidney failure in children and young adults, but the strong phenotypic and genotypic heterogeneity of kidney and urinary tract malformations has hampered standardization of clinical decision making until now. However, patients with CAKUT may benefit from precision medicine, including an integrated diagnostics trajectory, genetic counseling, and personalized management to improve clinical outcomes of developmental kidney and urinary tract defects. In this review, we discuss the present understanding of the molecular etiology of CAKUT and the currently available genome diagnostic modalities in the clinical care of patients with CAKUT. Finally, we discuss how clinical integration of findings from large-scale genetic, epigenetic, and gene-environment interaction studies may improve the prognosis of all individuals with CAKUT.
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Affiliation(s)
- Rik Westland
- Department of Pediatric Nephrology, Amsterdam UMC, Amsterdam, The Netherlands
| | - Kirsten Y. Renkema
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Nine V.A.M. Knoers
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands,Department of Genetics, University Medical Centre Groningen, Groningen, The Netherlands
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Hilger AC, Dworschak GC, Reutter HM. Lessons Learned from CNV Analysis of Major Birth Defects. Int J Mol Sci 2020; 21:ijms21218247. [PMID: 33153233 PMCID: PMC7663563 DOI: 10.3390/ijms21218247] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 10/31/2020] [Accepted: 11/02/2020] [Indexed: 12/25/2022] Open
Abstract
The treatment of major birth defects are key concerns for child health. Hitherto, for the majority of birth defects, the underlying cause remains unknown, likely to be heterogeneous. The implicated mortality and/or reduced fecundity in major birth defects suggest a significant fraction of mutational de novo events among the affected individuals. With the advent of systematic array-based molecular karyotyping, larger cohorts of affected individuals have been screened over the past decade. This review discusses the identification of disease-causing copy-number variations (CNVs) among individuals with different congenital malformations. It highlights the differences in findings depending on the respective congenital malformation. It looks at the differences in findings of CNV analysis in non-isolated complex congenital malformations, associated with central nervous system malformations or intellectual disabilities, compared to isolated single organ-system malformations. We propose that the more complex an organ system is, and the more genes involved during embryonic development, the more likely it is that mutational de novo events, comprising CNVs, will confer to the expression of birth defects of this organ system.
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Affiliation(s)
- Alina Christine Hilger
- Department of Pediatrics, Children’s Hospital Medical Center, University Hospital Bonn, 53127 Bonn, Germany
- Institute of Human Genetics, University Hospital Bonn, 53127 Bonn, Germany
- Institute for Anatomy and Cell Biology, University Hospital Bonn, University of Bonn, 53115 Bonn, Germany
- Correspondence: (A.C.H.); (G.C.D.); (H.M.R.); Tel.: +49-228-6885-419 (A.C.H. & G.C.D. & H.M.R.)
| | - Gabriel Clemens Dworschak
- Department of Pediatrics, Children’s Hospital Medical Center, University Hospital Bonn, 53127 Bonn, Germany
- Institute of Human Genetics, University Hospital Bonn, 53127 Bonn, Germany
- Institute for Anatomy and Cell Biology, University Hospital Bonn, University of Bonn, 53115 Bonn, Germany
- Correspondence: (A.C.H.); (G.C.D.); (H.M.R.); Tel.: +49-228-6885-419 (A.C.H. & G.C.D. & H.M.R.)
| | - Heiko Martin Reutter
- Institute of Human Genetics, University Hospital Bonn, 53127 Bonn, Germany
- Department of Neonatology and Pediatric Intensive Care, Children’s Hospital Medical Center, University Hospital Bonn, 53127 Bonn, Germany
- Correspondence: (A.C.H.); (G.C.D.); (H.M.R.); Tel.: +49-228-6885-419 (A.C.H. & G.C.D. & H.M.R.)
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Abstract
Although often considered a single-entity, chronic kidney disease (CKD) comprises many pathophysiologically distinct disorders that result in persistently abnormal kidney structure and/or function, and encompass both monogenic and polygenic aetiologies. Rare inherited forms of CKD frequently span diverse phenotypes, reflecting genetic phenomena including pleiotropy, incomplete penetrance and variable expressivity. Use of chromosomal microarray and massively parallel sequencing technologies has revealed that genomic disorders and monogenic aetiologies contribute meaningfully to seemingly complex forms of CKD across different clinically defined subgroups and are characterized by high genetic and phenotypic heterogeneity. Investigations of prevalent genomic disorders in CKD have integrated genetic, bioinformatic and functional studies to pinpoint the genetic drivers underlying their renal and extra-renal manifestations, revealing both monogenic and polygenic mechanisms. Similarly, massively parallel sequencing-based analyses have identified gene- and allele-level variation that contribute to the clinically diverse phenotypes observed for many monogenic forms of nephropathy. Genome-wide sequencing studies suggest that dual genetic diagnoses are found in at least 5% of patients in whom a genetic cause of disease is identified, highlighting the fact that complex phenotypes can also arise from multilocus variation. A multifaceted approach that incorporates genetic and phenotypic data from large, diverse cohorts will help to elucidate the complex relationships between genotype and phenotype for different forms of CKD, supporting personalized medicine for individuals with kidney disease.
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Affiliation(s)
- Emily E Groopman
- Division of Nephrology, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Gundula Povysil
- Institute for Genomic Medicine, Columbia University, New York, NY, USA
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University, New York, NY, USA
| | - Ali G Gharavi
- Division of Nephrology, Columbia University College of Physicians and Surgeons, New York, NY, USA.
- Institute for Genomic Medicine, Columbia University, New York, NY, USA.
- Center for Precision Medicine and Genomics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA.
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Borowicz P, Chan H, Hauge A, Spurkland A. Adaptor proteins: Flexible and dynamic modulators of immune cell signalling. Scand J Immunol 2020; 92:e12951. [DOI: 10.1111/sji.12951] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/22/2020] [Accepted: 07/26/2020] [Indexed: 12/16/2022]
Affiliation(s)
- Paweł Borowicz
- Department of Molecular Medicine Institute of Basic Medical Sciences University of Oslo Oslo Norway
| | - Hanna Chan
- Department of Molecular Medicine Institute of Basic Medical Sciences University of Oslo Oslo Norway
| | - Anette Hauge
- Department of Molecular Medicine Institute of Basic Medical Sciences University of Oslo Oslo Norway
| | - Anne Spurkland
- Department of Molecular Medicine Institute of Basic Medical Sciences University of Oslo Oslo Norway
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