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Wolfe C, Jnah A. Tracheoesophageal Fistula With Esophageal Atresia: A Case Series. Neonatal Netw 2024; 43:65-75. [PMID: 38599775 DOI: 10.1891/nn-2023-0051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
Tracheoesophageal fistula (TEF) with or without esophageal atresia (EA) results from maldevelopment of the trachea and esophagus during maturation of the primitive foregut. EA/TEF commonly presents shortly after birth because of increased oral secretions and the inability to advance a nasogastric or orogastric tube to the proper depth. Given that prenatal diagnosis is uncommon and early intervention is important to reduce morbidity and mortality risk, early recognition and diagnosis are imperative. We present a case series of two neonates diagnosed with EA/TEF, type "C" and type "E," born at low-acuity centers, who required transport to a tertiary center for surgical support. The pathophysiology as well as types of TEFs, symptomology, stabilization goals, corrective treatment, and long-term implications will be examined. Finally, the educational needs of parents and caregivers will be discussed.
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2
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Ulhaq ZS, Soraya GV, Istifiani LA, Pamungkas SA, Arisanti D, Dini B, Astari LF, Hasan YTN, Ayudianti P, Kusuma MAS, Shodry S, Herawangsa S, Nurputra DK, Idaiani S, Tse WKF. A Brief Analysis on Clinical Severity of Mandibulofacial Dysostosis Guion-Almeida Type. Cleft Palate Craniofac J 2024; 61:688-696. [PMID: 36317361 DOI: 10.1177/10556656221136177] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024] Open
Abstract
OBJECTIVE Genetic variants in EFTUD2 were proven to influence variable phenotypic expressivity in mandibulofacial dysostosis Guion-Almeida type (MFDGA) or mandibulofacial dysostosis with microcephaly (MFDM). Yet, the association between the severity of clinical findings with variants within the EFTUD2 gene has not been established. Thus, we aim to elucidate a possible genotype-phenotype correlation in MFDM. METHODS Forty articles comprising 156 patients were evaluated. The genotype-phenotype correlation was analyzed using a chi-square or Fisher's exact test. RESULTS The proportion of patients with MFDM was higher in Caucasian relative to Asian populations. Although, in general, there was no apparent genotype-phenotype correlation in patients with MFDM, Asians tended to have more severe clinical manifestations than Caucasians. In addition, cardiac abnormality presented in patients with intronic variants located in canonical splice sites was a predisposing factor in affecting MFDM severity. CONCLUSION Altogether, this article provides the pathogenic variants observed in EFTUD2 and possible genotype-phenotype relationships in this disease.
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Affiliation(s)
- Zulvikar Syambani Ulhaq
- Laboratory of Developmental Disorders and Toxicology, Center for Promotion of International Education and Research, Kyushu University, Faculty of Agriculture, Fukuoka, Fukuoka, Japan
- Research Center for Pre-Clinical and Clinical Medicine, National Research and Innovation Agency Republic of Indonesia, Cibinong, Indonesia
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Maulana Malik Ibrahim State Islamic University, Malang, East Java, Indonesia
| | - Gita Vita Soraya
- Department of Biochemistry, Faculty of Medicine, Hasanuddin University, Makassar, Indonesia
- Department of Neurology, Faculty of Medicine, Hasanuddin University, Makassar, Indonesia
| | - Lola Ayu Istifiani
- Department of Nutrition, Faculty of Health Sciences, Brawijaya University, Malang, East Java, Indonesia
| | | | - Ditya Arisanti
- Department of Clinical Medicine, Faculty of Medicine and Health Science, Maulana Malik State Islamic University, Malang, Indonesia
| | - Badariyatud Dini
- Department of Clinical Medicine, Faculty of Medicine and Health Science, Maulana Malik State Islamic University, Malang, Indonesia
| | - Lina Fitria Astari
- Department of Clinical Medicine, Faculty of Medicine and Health Science, Maulana Malik State Islamic University, Malang, Indonesia
| | - Yuliono Trika Nur Hasan
- Department of Clinical Medicine, Faculty of Medicine and Health Science, Maulana Malik State Islamic University, Malang, Indonesia
| | - Prida Ayudianti
- Department of Clinical Medicine, Faculty of Medicine and Health Science, Maulana Malik State Islamic University, Malang, Indonesia
| | - Muhammad A'raaf Sirojan Kusuma
- Research Center for Pre-Clinical and Clinical Medicine, National Research and Innovation Agency Republic of Indonesia, Cibinong, Indonesia
| | - Syifaus Shodry
- Research Center for Pre-Clinical and Clinical Medicine, National Research and Innovation Agency Republic of Indonesia, Cibinong, Indonesia
| | - Sarah Herawangsa
- Research Center for Pre-Clinical and Clinical Medicine, National Research and Innovation Agency Republic of Indonesia, Cibinong, Indonesia
| | - Dian Kesumapramudya Nurputra
- Department of Child Health, Faculty of Medicine, Public Health and Nursing, Gadjah Mada University, Yogyakarta, Indonesia
| | - Sri Idaiani
- Research Center for Pre-Clinical and Clinical Medicine, National Research and Innovation Agency Republic of Indonesia, Cibinong, Indonesia
| | - William Ka Fai Tse
- Laboratory of Developmental Disorders and Toxicology, Center for Promotion of International Education and Research, Kyushu University, Faculty of Agriculture, Fukuoka, Fukuoka, Japan
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Maj C, Eberts A, Schumacher J, Dasmeh P. Single-cell analysis reveals the spatial-temporal expression of genes associated with esophageal malformations. Sci Rep 2024; 14:3752. [PMID: 38355689 PMCID: PMC10866870 DOI: 10.1038/s41598-024-53098-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 01/27/2024] [Indexed: 02/16/2024] Open
Abstract
Understanding the molecular mechanisms of congenital diseases is challenging due to their occurrence within specific developmental stages. Esophageal malformations are examples of such conditions, characterized by abnormalities in the development of esophagus during embryogenesis. These developmental malformations encompass a range of anomalies, including esophageal atresia, and tracheoesophageal fistula. Here, we investigated the preferential expression of 29 genes that are implicated in such malformations and their immediate interactome (a total of 67 genes). We conducted our analyses across several single-cell atlases of embryonic development, encompassing approximately 150,000 cells from the mouse foregut, 180,000 cells from human embryos, and 500,000 cells from 24 human organs. Our study, spanning diverse mesodermal and endodermal cell populations and early developmental stages, shows that the genes associated with esophageal malformations show their highest cell-type specific expression in lateral plate mesoderm cells and at the developmental stage of E8.75-E9.0 days. In human embryos, these genes show a significant cell-type specific expression among subpopulations of epithelial cells, fibroblasts and progenitor cells including basal cells. Notably, members of the forkhead-box family of transcription factors, namely FOXF1, FOXC1, and FOXD1, as well as the SRY-box transcription factor, SOX2, demonstrate the most significant preferential expression in both mouse and human embryos. Overall, our findings provide insights into the temporal and cellular contexts contributing to esophageal malformations.
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Affiliation(s)
- Carlo Maj
- Center for Human Genetics, Marburg University and Marburg University Hospital, Marburg, Germany.
| | - Antonia Eberts
- Center for Human Genetics, Marburg University and Marburg University Hospital, Marburg, Germany
| | - Johannes Schumacher
- Center for Human Genetics, Marburg University and Marburg University Hospital, Marburg, Germany.
| | - Pouria Dasmeh
- Center for Human Genetics, Marburg University and Marburg University Hospital, Marburg, Germany.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, USA.
- Institute for Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.
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O'Shea D, Schmoke N, Porigow C, Murray LP, Chung WK, Kattan M, Jang M, Antosy A, Middlesworth W, Khlevner J. Recent Advances in the Genetic Pathogenesis, Diagnosis, and Management of Esophageal Atresia and Tracheoesophageal Fistula: A Review. J Pediatr Gastroenterol Nutr 2023; 77:703-712. [PMID: 37771007 DOI: 10.1097/mpg.0000000000003952] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/30/2023]
Abstract
Infants born with esophageal atresia and tracheoesophageal fistula, a complex congenital malformation occurring in 1/2500-4000 live births, may suffer threats to their cardiac, respiratory, and digestive health in addition to anomalies that may exist in the genitourinary and musculoskeletal systems. Optimal care for these patients throughout their lives is best achieved through a coordinated, multidisciplinary approach that our health care system is not always well-equipped to provide. This review, though not exhaustive, highlights the components of care that pertain to initial surgical reconstruction and subsequent diagnosis and management of the complications that are most frequently encountered. Authors from among the many specialties involved in the care of these patients summarize the current best practice with attention to the most recent advances. Assessment and improvement of quality of life and transition to adult specialists as children grow to adulthood is also reviewed.
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Affiliation(s)
- Delia O'Shea
- From the Division of Pediatric Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons/NewYork-Presbyterian Morgan Stanley Children's Hospital, New York, NY
| | - Nicholas Schmoke
- the Division of Pediatric Surgery, Department of Surgery, Columbia University Vagelos College of Physicians and Surgeons/NewYork-Presbyterian Morgan Stanley Children's Hospital, New York, NY
| | - Chloe Porigow
- the Division of Pediatric Surgery, Department of Surgery, Columbia University Vagelos College of Physicians and Surgeons/NewYork-Presbyterian Morgan Stanley Children's Hospital, New York, NY
| | - Laurie P Murray
- the Division of Pediatric Pulmonology, Department of Pediatrics, Columbia University Irving Medical Center/NewYork-Presbyterian Morgan Stanley Children's Hospital, New York, NY
| | - Wendy K Chung
- the Department of Pediatrics and Medicine, Columbia University Irving Medical Center, New York, NY
| | - Meyer Kattan
- the Division of Pediatric Pulmonology, Department of Pediatrics, Columbia University Irving Medical Center/NewYork-Presbyterian Morgan Stanley Children's Hospital, New York, NY
| | - Minyoung Jang
- the Department of Otolaryngology Head and Neck Surgery, Columbia University Vagelos College of Physicians and Surgeons/NewYork-Presbyterian Morgan Stanley Children's Hospital, New York, NY
| | - Alexandra Antosy
- From the Division of Pediatric Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons/NewYork-Presbyterian Morgan Stanley Children's Hospital, New York, NY
| | - William Middlesworth
- the Division of Pediatric Surgery, Department of Surgery, Columbia University Vagelos College of Physicians and Surgeons/NewYork-Presbyterian Morgan Stanley Children's Hospital, New York, NY
| | - Julie Khlevner
- From the Division of Pediatric Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons/NewYork-Presbyterian Morgan Stanley Children's Hospital, New York, NY
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Cai J, Li Y, Hu P, Xu R, Yuan H, Zhang W, Feng T, Liu R, Li W, Zhu C. Plerixafor and resatorvid inhibit hepatitis B virus in vitro by upregulating elongation factor Tu GTP-binding domain containing 2. Front Cell Infect Microbiol 2023; 13:1118801. [PMID: 36891156 PMCID: PMC9986551 DOI: 10.3389/fcimb.2023.1118801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 02/06/2023] [Indexed: 02/22/2023] Open
Abstract
Background An increase in the demand for a functional cure has accelerated research on new methods of therapy for chronic hepatitis B, which is mainly focused on restoring antiviral immunity for controlling viral infections. Previously, we had described elongation factor Tu GTP-binding domain containing 2 (EFTUD2) as an innate immune regulator and suggested that it might be an antiviral target. Methods In this study, we generated the Epro-LUC-HepG2 cell model for screening compounds that target EFTUD2. Plerixafor and resatorvid were screened from 261 immunity and inflammation-related compounds due to their ability to highly upregulate EFTUD2. The effects of plerixafor and resatorvid on hepatitis B virus (HBV) were examined in HepAD38 cells and HBV-infected HepG2-NTCP cells. Results The dual-luciferase reporter assays showed that the EFTUD2 promoter hEFTUD2pro-0.5 kb had the strongest activity. In Epro-LUC-HepG2 cells, plerixafor and resatorvid significantly upregulated the activity of the EFTUD2 promoter and the expression of the gene and protein. In HepAD38 cells and HBV-infected HepG2-NTCP cells, treatment with plerixafor and resatorvid strongly inhibited HBsAg, HBV DNA, HBV RNAs, and cccDNA in a dose-dependent manner. Furthermore, the anti-HBV effect was enhanced when entecavir was administered along with either of the previous two compounds, and the effect could be blocked by knocking down EFTUD2. Conclusion We established a convenient model for screening compounds that target EFTUD2 and further identified plerixafor and resatorvid as novel HBV inhibitors in vitro. Our findings provided information on the development of a new class of anti-HBV agents that act on host factors rather than viral enzymes.
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Affiliation(s)
- Jinyuan Cai
- 1Department of Infectious Disease, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Department of Infectious Disease, Zhongda Hospital, Southeast University, Nanjing, China
| | - Yuwen Li
- Department of Pediatrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Pingping Hu
- Department of Infectious Disease, Zhongda Hospital, Southeast University, Nanjing, China
| | - Ruirui Xu
- Department of Infectious Disease, Zhongda Hospital, Southeast University, Nanjing, China
| | - Hui Yuan
- Department of Infectious Disease, Zhongda Hospital, Southeast University, Nanjing, China
| | - Wen Zhang
- Department of Infectious Disease, Zhongda Hospital, Southeast University, Nanjing, China
| | - Tiantong Feng
- Department of Infectious Disease, Zhongda Hospital, Southeast University, Nanjing, China
| | - Rui Liu
- Department of Infectious and Tropical Diseases, The Second Affiliated Hospital of Hainan Medical University, Hainan, China
| | - Wenting Li
- Department of Infectious and Tropical Diseases, The Second Affiliated Hospital of Hainan Medical University, Hainan, China
| | - Chuanlong Zhu
- 1Department of Infectious Disease, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Department of Infectious and Tropical Diseases, The Second Affiliated Hospital of Hainan Medical University, Hainan, China
- *Correspondence: Chuanlong Zhu,
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Raad S, David A, Sagniez M, Paré B, Orfi Z, Dumont NA, Smith MA, Faure C. iPSCs derived from esophageal atresia patients reveal SOX2 dysregulation at the anterior foregut stage. Dis Model Mech 2022; 15:dmm049541. [PMID: 36317486 PMCID: PMC10655818 DOI: 10.1242/dmm.049541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 10/18/2022] [Indexed: 11/19/2023] Open
Abstract
A series of well-regulated cellular and molecular events result in the compartmentalization of the anterior foregut into the esophagus and trachea. Disruption of the compartmentalization process leads to esophageal atresia/tracheoesophageal fistula (EA/TEF). The cause of EA/TEF remains largely unknown. Therefore, to mimic the early development of the esophagus and trachea, we differentiated induced pluripotent stem cells (iPSCs) from EA/TEF patients, and iPSCs and embryonic stem cells from healthy individuals into mature three-dimensional esophageal organoids. CXCR4, SOX17 and GATA4 expression was similar in both patient-derived and healthy endodermal cells. The expression of the key transcription factor SOX2 was significantly lower in the patient-derived anterior foregut. We also observed an abnormal expression of NKX2.1 (or NKX2-1) in the patient-derived mature esophageal organoids. At the anterior foregut stage, RNA sequencing revealed the critical genes GSTM1 and RAB37 to be significantly lower in the patient-derived anterior foregut. We therefore hypothesize that a transient dysregulation of SOX2 and the abnormal expression of NKX2.1 in patient-derived cells could be responsible for the abnormal foregut compartmentalization.
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Affiliation(s)
- Suleen Raad
- Esophageal Development and Engineering Laboratory, CHU Sainte-Justine Research Center, 3175 Côte Sainte-Catherine, Montréal, Quebec H3T 1C5, Canada
| | - Anu David
- Esophageal Development and Engineering Laboratory, CHU Sainte-Justine Research Center, 3175 Côte Sainte-Catherine, Montréal, Quebec H3T 1C5, Canada
| | - Melanie Sagniez
- CHU Sainte-Justine Research Center, 3175 Côte Sainte-Catherine, Montréal, Quebec H3T 1C5, Canada
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, University of Montreal, Montréal, Quebec H3T 1J4, Canada
| | - Bastien Paré
- CHU Sainte-Justine Research Center, 3175 Côte Sainte-Catherine, Montréal, Quebec H3T 1C5, Canada
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, University of Montreal, Montréal, Quebec H3T 1J4, Canada
| | - Zakaria Orfi
- CHU Sainte-Justine Research Center, 3175 Côte Sainte-Catherine, Montréal, Quebec H3T 1C5, Canada
| | - Nicolas A. Dumont
- CHU Sainte-Justine Research Center, 3175 Côte Sainte-Catherine, Montréal, Quebec H3T 1C5, Canada
- School of Rehabilitation, Faculty of Medicine, Université de Montréal, Montréal, Quebec H3T 1J4, Canada
| | - Martin A. Smith
- CHU Sainte-Justine Research Center, 3175 Côte Sainte-Catherine, Montréal, Quebec H3T 1C5, Canada
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, University of Montreal, Montréal, Quebec H3T 1J4, Canada
| | - Christophe Faure
- Esophageal Development and Engineering Laboratory, CHU Sainte-Justine Research Center, 3175 Côte Sainte-Catherine, Montréal, Quebec H3T 1C5, Canada
- Esophageal Atresia Clinic and Division of Pediatric Gastroenterology Hepatology and Nutrition, CHU Sainte-Justine, 3715 Côte Sainte-Catherine, Université de Montréal, Montréal, Quebec H3T1C5, Canada
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7
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Zhong G, Shen Y. Statistical models of the genetic etiology of congenital heart disease. Curr Opin Genet Dev 2022; 76:101967. [PMID: 35939966 PMCID: PMC10586490 DOI: 10.1016/j.gde.2022.101967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 06/29/2022] [Accepted: 07/08/2022] [Indexed: 11/03/2022]
Abstract
Congenital heart disease (CHD) is a collection of anatomically and clinically heterogeneous structure anomalies of heart at birth. Finding genetic causes of CHD can not only shed light on developmental biology of heart, but also provide basis for improving clinical care and interventions. The optimal study design and analytical approaches to identify genetic causes depend on the underlying genetic architecture. A few well-known syndromes with CHD as core conditions, such as Noonan and CHARGE, have known monogenic causes. The genetic causes of most of CHD patients, however, are unknown and likely to be complex. In this review, we highlight recent studies that assume a complex genetic architecture of CHD with two main approaches. One is genomic sequencing studies aiming for identifying rare or de novo risk variants with large genetic effect. The other is genome-wide association studies optimized for common variants with moderate genetic effect.
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Affiliation(s)
- Guojie Zhong
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA; Integrated Program in Cellular, Molecular, and Biological Studies, Columbia University Irving Medical Center, New York, NY, USA
| | - Yufeng Shen
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA; Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA; JP Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, NY, USA.
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8
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Zhong G, Ahimaz P, Edwards NA, Hagen JJ, Faure C, Lu Q, Kingma P, Middlesworth W, Khlevner J, El Fiky M, Schindel D, Fialkowski E, Kashyap A, Forlenza S, Kenny AP, Zorn AM, Shen Y, Chung WK. Identification and validation of candidate risk genes in endocytic vesicular trafficking associated with esophageal atresia and tracheoesophageal fistulas. HGG ADVANCES 2022; 3:100107. [PMID: 35519826 PMCID: PMC9065433 DOI: 10.1016/j.xhgg.2022.100107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 04/06/2022] [Indexed: 11/15/2022] Open
Abstract
Esophageal atresias/tracheoesophageal fistulas (EA/TEF) are rare congenital anomalies caused by aberrant development of the foregut. Previous studies indicate that rare or de novo genetic variants significantly contribute to EA/TEF risk, and most individuals with EA/TEF do not have pathogenic genetic variants in established risk genes. To identify the genetic contributions to EA/TEF, we performed whole genome sequencing of 185 trios (probands and parents) with EA/TEF, including 59 isolated and 126 complex cases with additional congenital anomalies and/or neurodevelopmental disorders. There was a significant burden of protein-altering de novo coding variants in complex cases (p = 3.3 × 10-4), especially in genes that are intolerant of loss-of-function variants in the population. We performed simulation analysis of pathway enrichment based on background mutation rate and identified a number of pathways related to endocytosis and intracellular trafficking that as a group have a significant burden of protein-altering de novo variants. We assessed 18 variants for disease causality using CRISPR-Cas9 mutagenesis in Xenopus and confirmed 13 with tracheoesophageal phenotypes. Our results implicate disruption of endosome-mediated epithelial remodeling as a potential mechanism of foregut developmental defects. Our results suggest significant genetic heterogeneity of EA/TEF and may have implications for the mechanisms of other rare congenital anomalies.
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Affiliation(s)
- Guojie Zhong
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University, New York, NY, USA
| | - Priyanka Ahimaz
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Nicole A. Edwards
- Center for Stem Cell & Organoid Medicine (CuSTOM), Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, USA
| | - Jacob J. Hagen
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Christophe Faure
- Division of Pediatric Gastroenterology, CHU Sainte-Justine, Montreal, QC, Canada
| | - Qiao Lu
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Paul Kingma
- Division of Neonatology, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - William Middlesworth
- Division of Pediatric Surgery, Columbia University Irving Medical Center, New York, NY, USA
| | - Julie Khlevner
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Columbia University Irving Medical Center, New York, NY, USA
| | - Mahmoud El Fiky
- Pediatric Surgery, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - David Schindel
- Division of Pediatric Surgery, UT Southwestern School of Medicine Dallas, Texas, USA
| | - Elizabeth Fialkowski
- Division of Pediatric Surgery, Oregon Health and Science University, Portland, OR, USA
| | - Adhish Kashyap
- Center for Stem Cell & Organoid Medicine (CuSTOM), Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, USA
| | - Sophia Forlenza
- Division of Neonatology, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Pulmonary Biology, Cincinnati Children’s Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | - Alan P. Kenny
- Division of Neonatology, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Pulmonary Biology, Cincinnati Children’s Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | - Aaron M. Zorn
- Center for Stem Cell & Organoid Medicine (CuSTOM), Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, USA
| | - Yufeng Shen
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA
| | - Wendy K. Chung
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
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9
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Brosens E, Brouwer RWW, Douben H, van Bever Y, Brooks AS, Wijnen RMH, van IJcken WFJ, Tibboel D, Rottier RJ, de Klein A. Heritability and De Novo Mutations in Oesophageal Atresia and Tracheoesophageal Fistula Aetiology. Genes (Basel) 2021; 12:genes12101595. [PMID: 34680991 PMCID: PMC8535313 DOI: 10.3390/genes12101595] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 10/03/2021] [Accepted: 10/05/2021] [Indexed: 01/12/2023] Open
Abstract
Tracheoesophageal Fistula (TOF) is a congenital anomaly for which the cause is unknown in the majority of patients. OA/TOF is a variable feature in many (often mono-) genetic syndromes. Research using animal models targeting genes involved in candidate pathways often result in tracheoesophageal phenotypes. However, there is limited overlap in the genes implicated by animal models and those found in OA/TOF-related syndromic anomalies. Knowledge on affected pathways in animal models is accumulating, but our understanding on these pathways in patients lags behind. If an affected pathway is associated with both animals and patients, the mechanisms linking the genetic mutation, affected cell types or cellular defect, and the phenotype are often not well understood. The locus heterogeneity and the uncertainty of the exact heritability of OA/TOF results in a relative low diagnostic yield. OA/TOF is a sporadic finding with a low familial recurrence rate. As parents are usually unaffected, de novo dominant mutations seems to be a plausible explanation. The survival rates of patients born with OA/TOF have increased substantially and these patients start families; thus, the detection and a proper interpretation of these dominant inherited pathogenic variants are of great importance for these patients and for our understanding of OA/TOF aetiology.
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Affiliation(s)
- Erwin Brosens
- Department of Clinical Genetics, Erasmus University Medical Center-Sophia Children’s Hospital, 3000 CA Rotterdam, The Netherlands; (H.D.); (Y.v.B.); (A.S.B.); (A.d.K.)
- Correspondence:
| | - Rutger W. W. Brouwer
- Department of Cell Biology, Center for Biomics, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands; (R.W.W.B.); (W.F.J.v.I.)
| | - Hannie Douben
- Department of Clinical Genetics, Erasmus University Medical Center-Sophia Children’s Hospital, 3000 CA Rotterdam, The Netherlands; (H.D.); (Y.v.B.); (A.S.B.); (A.d.K.)
| | - Yolande van Bever
- Department of Clinical Genetics, Erasmus University Medical Center-Sophia Children’s Hospital, 3000 CA Rotterdam, The Netherlands; (H.D.); (Y.v.B.); (A.S.B.); (A.d.K.)
| | - Alice S. Brooks
- Department of Clinical Genetics, Erasmus University Medical Center-Sophia Children’s Hospital, 3000 CA Rotterdam, The Netherlands; (H.D.); (Y.v.B.); (A.S.B.); (A.d.K.)
| | - Rene M. H. Wijnen
- Department of Pediatric Surgery, Erasmus University Medical Center-Sophia Children’s Hospital, 3000 CA Rotterdam, The Netherlands; (R.M.H.W.); (D.T.)
| | - Wilfred F. J. van IJcken
- Department of Cell Biology, Center for Biomics, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands; (R.W.W.B.); (W.F.J.v.I.)
| | - Dick Tibboel
- Department of Pediatric Surgery, Erasmus University Medical Center-Sophia Children’s Hospital, 3000 CA Rotterdam, The Netherlands; (R.M.H.W.); (D.T.)
| | - Robbert J. Rottier
- Departments of Pediatric Surgery & Cell Biology, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands;
| | - Annelies de Klein
- Department of Clinical Genetics, Erasmus University Medical Center-Sophia Children’s Hospital, 3000 CA Rotterdam, The Netherlands; (H.D.); (Y.v.B.); (A.S.B.); (A.d.K.)
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10
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Zhao H, Pan S, Duan J, Liu F, Li G, Liu D, Liu Z. Integrative Analysis of m 6A Regulator-Mediated RNA Methylation Modification Patterns and Immune Characteristics in Lupus Nephritis. Front Cell Dev Biol 2021; 9:724837. [PMID: 34557492 PMCID: PMC8454410 DOI: 10.3389/fcell.2021.724837] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 08/05/2021] [Indexed: 12/28/2022] Open
Abstract
Background There is growing evidence to demonstrate that the epigenetic regulation of immune characteristics, especially for N6-methyladenosine (m6A) RNA methylation. However, how m6A methylation is involved in lupus nephritis (LN) is still unclear. This study aimed to determine the role of m6A RNA methylation and their association with the immune microenvironment in LN. Methods In total, 87 glomeruli (73 LN, 14 living healthy donors), 110 tubulointerstitium (95 LN, 15 living healthy donors), and 21 kidney whole tissue samples (14 LN, 7 controls) were included in our research to evaluate the expression levels of m6A regulators. CIBERSORT was used to assess the abundance of infiltrating immunocytes. The m6A regulator gene signature for LN was identified using LASSO-logistic regression and verified with external data. Consensus clustering algorithms were used for the unsupervised cluster analysis of m6A modification patterns in LN. Single-sample gene-set enrichment analysis and gene set variation analysis algorithms were employed to assess the activity of immune responses and other functional pathways. Weighted gene co-expression network analysis and protein-protein interaction networks were used to identify m6A methylation markers. Lastly, the Nephroseq V5 tool was used to analyze the correlation between m6A markers and renal function. Results We found that the expression of m6A regulators was more significantly different in the glomeruli in LN compared with tubulointerstitium and whole kidney tissue. We established an m6A regulator signature, comprised of METTL3, WTAP, YTHDC2, YTHDF1, FMR1, and FTO, that can easily distinguish LN and healthy individuals. Two distinct m6A modification patterns based on 18 m6A regulators were determined, with significant differences in m6A regulator expression, immune microenvironment, biological functional pathways, and clinical characteristics. Activated NK cells, most immune responses, and HLA genes had strong correlations with m6A regulators. Seven m6A markers were identified and demonstrated a meaningful correlation with GFR, indicating that they are potential prognostic biomarkers. Conclusion This study emphasized that m6A RNA methylation and the immune microenvironment are closely linked in LN. A better understanding of m6A modification patterns provide a basis for the development of novel therapeutic options for LN.
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Affiliation(s)
- Huanhuan Zhao
- Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Research Institute of Nephrology, Zhengzhou University, Zhengzhou, China.,Research Center for Kidney Disease, Zhengzhou, China.,Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, China.,Core Unit of National Clinical Medical Research Center of Kidney Disease, Zhengzhou, China
| | - Shaokang Pan
- Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Research Institute of Nephrology, Zhengzhou University, Zhengzhou, China.,Research Center for Kidney Disease, Zhengzhou, China.,Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, China.,Core Unit of National Clinical Medical Research Center of Kidney Disease, Zhengzhou, China
| | - Jiayu Duan
- Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Research Institute of Nephrology, Zhengzhou University, Zhengzhou, China.,Research Center for Kidney Disease, Zhengzhou, China.,Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, China.,Core Unit of National Clinical Medical Research Center of Kidney Disease, Zhengzhou, China
| | - Fengxun Liu
- Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Research Institute of Nephrology, Zhengzhou University, Zhengzhou, China.,Research Center for Kidney Disease, Zhengzhou, China.,Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, China.,Core Unit of National Clinical Medical Research Center of Kidney Disease, Zhengzhou, China
| | - Guangpu Li
- Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Research Institute of Nephrology, Zhengzhou University, Zhengzhou, China.,Research Center for Kidney Disease, Zhengzhou, China.,Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, China.,Core Unit of National Clinical Medical Research Center of Kidney Disease, Zhengzhou, China
| | - Dongwei Liu
- Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Research Institute of Nephrology, Zhengzhou University, Zhengzhou, China.,Research Center for Kidney Disease, Zhengzhou, China.,Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, China.,Core Unit of National Clinical Medical Research Center of Kidney Disease, Zhengzhou, China
| | - Zhangsuo Liu
- Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Research Institute of Nephrology, Zhengzhou University, Zhengzhou, China.,Research Center for Kidney Disease, Zhengzhou, China.,Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, China.,Core Unit of National Clinical Medical Research Center of Kidney Disease, Zhengzhou, China
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11
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Edwards NA, Shacham-Silverberg V, Weitz L, Kingma PS, Shen Y, Wells JM, Chung WK, Zorn AM. Developmental basis of trachea-esophageal birth defects. Dev Biol 2021; 477:85-97. [PMID: 34023332 DOI: 10.1016/j.ydbio.2021.05.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/13/2021] [Accepted: 05/16/2021] [Indexed: 02/07/2023]
Abstract
Trachea-esophageal defects (TEDs), including esophageal atresia (EA), tracheoesophageal fistula (TEF), and laryngeal-tracheoesophageal clefts (LTEC), are a spectrum of life-threatening congenital anomalies in which the trachea and esophagus do not form properly. Up until recently, the developmental basis of these conditions and how the trachea and esophagus arise from a common fetal foregut was poorly understood. However, with significant advances in human genetics, organoids, and animal models, and integrating single cell genomics with high resolution imaging, we are revealing the molecular and cellular mechanisms that orchestrate tracheoesophageal morphogenesis and how disruption in these processes leads to birth defects. Here we review the current understanding of the genetic and developmental basis of TEDs. We suggest future opportunities for integrating developmental mechanisms elucidated from animals and organoids with human genetics and clinical data to gain insight into the genotype-phenotype basis of these heterogeneous birth defects. Finally, we envision how this will enhance diagnosis, improve treatment, and perhaps one day, lead to new tissue replacement therapy.
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Affiliation(s)
- Nicole A Edwards
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Center for Stem Cell & Organoid Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Vered Shacham-Silverberg
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Center for Stem Cell & Organoid Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Leelah Weitz
- Department of Pediatrics, Columbia University Medical Center, New York, NY, USA; Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Paul S Kingma
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Yufeng Shen
- Department of Systems Biology, Columbia University Medical Center, New York, NY, USA; Department of Biomedical Informatics, Columbia University Medical Center, New York, NY, USA
| | - James M Wells
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Center for Stem Cell & Organoid Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Wendy K Chung
- Department of Pediatrics, Columbia University Medical Center, New York, NY, USA; Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Aaron M Zorn
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Center for Stem Cell & Organoid Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
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12
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Trisno SL, Higano NS, Kechele D, Nasr T, Chung W, Zorn AM, Woods JC, Wells JM, Kingma PS. Case Report: Esophageal Bronchus in a Neonate, With Image, Histological, and Molecular Analysis. Front Pediatr 2021; 9:707822. [PMID: 34307264 PMCID: PMC8298819 DOI: 10.3389/fped.2021.707822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 06/02/2021] [Indexed: 11/13/2022] Open
Abstract
In this case report, we describe the clinical course of a neonate who presented initially with respiratory distress and later with choking during feeding. He was subsequently found to have an esophageal bronchus to the right upper lung lobe, a rare communicating bronchopulmonary foregut malformation. Histological and molecular analysis of the fistula and distal tissues revealed that the proximal epithelium from the esophageal bronchus has characteristics of both esophageal and respiratory epithelia. Using whole exome sequencing of the patient's and parent's DNA, we identified gene variants that are predicted to impact protein function and thus could potentially contribute to the phenotype. These will be the subject of future functional analysis.
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Affiliation(s)
- Stephen L Trisno
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Nara S Higano
- Center for Pulmonary Imaging Research, Imaging Research Center and Department of Pulmonary Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Dan Kechele
- Division of Developmental Biology, Center for Stem Cell and Organoid Medicine (CuSTOM), Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Talia Nasr
- Division of Developmental Biology, Center for Stem Cell and Organoid Medicine (CuSTOM), Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Wendy Chung
- Departments of Pediatrics and Medicine, Columbia University Irving Medical Center, New York, NY, United States
| | - Aaron M Zorn
- Division of Developmental Biology, Center for Stem Cell and Organoid Medicine (CuSTOM), Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Jason C Woods
- Center for Pulmonary Imaging Research, Imaging Research Center and Department of Pulmonary Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - James M Wells
- Division of Developmental Biology, Center for Stem Cell and Organoid Medicine (CuSTOM), Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States.,Division of Endocrinology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Paul S Kingma
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Center for Pulmonary Imaging Research, Imaging Research Center and Department of Pulmonary Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
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