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Leid J, Gray R, Rakita P, Koenig AL, Tripathy R, Fitzpatrick JAJ, Kaufman C, Solnica-Krezel L, Lavine KJ. Deletion of taf1 and taf5 in zebrafish capitulate cardiac and craniofacial abnormalities associated with TAFopathies through perturbations in metabolism. Biol Open 2023; 12:bio059905. [PMID: 37746814 PMCID: PMC10354717 DOI: 10.1242/bio.059905] [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: 02/27/2023] [Accepted: 05/16/2023] [Indexed: 09/26/2023] Open
Abstract
Intellectual disability is a neurodevelopmental disorder that affects 2-3% of the general population. Syndromic forms of intellectual disability frequently have a genetic basis and are often accompanied by additional developmental anomalies. Pathogenic variants in components of TATA-binding protein associated factors (TAFs) have recently been identified in a subset of patients with intellectual disability, craniofacial hypoplasia, and congenital heart disease. This syndrome has been termed as a TAFopathy and includes mutations in TATA binding protein (TBP), TAF1, TAF2, and TAF6. The underlying mechanism by which TAFopathies give rise to neurodevelopmental, craniofacial, and cardiac abnormalities remains to be defined. Through a forward genetic screen in zebrafish, we have recovered a recessive mutant phenotype characterized by craniofacial hypoplasia, ventricular hypoplasia, heart failure at 96 h post-fertilization and lethality, and show it is caused by a nonsense mutation in taf5. CRISPR/CAS9 mediated gene editing revealed that these defects where phenocopied by mutations in taf1 and taf5. Mechanistically, taf5-/- zebrafish displayed misregulation in metabolic gene expression and metabolism as evidenced by RNA sequencing, respiration assays, and metabolite studies. Collectively, these findings suggest that the TAF complex may contribute to neurologic, craniofacial, and cardiac development through regulation of metabolism.
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Affiliation(s)
- Jamison Leid
- Center for Cardiovascular Research, Division of Cardiology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ryan Gray
- Departments of Nutritional Sciences, Dell Pediatrics Research Institute, University of Texas at Austin, Austin, TX 78723, USA
| | - Peter Rakita
- Center for Cardiovascular Research, Division of Cardiology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Andrew L. Koenig
- Center for Cardiovascular Research, Division of Cardiology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Rohan Tripathy
- Center for Cardiovascular Research, Division of Cardiology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - James A. J. Fitzpatrick
- Departments of Neuroscience and Cell Biology, Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Charles Kaufman
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Lilianna Solnica-Krezel
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kory J. Lavine
- Center for Cardiovascular Research, Division of Cardiology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Immunology and Pathology, Washington University School of Medicine, St. Louis, MO 63110, USA
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Ordiz MI, Janssen S, Humphrey G, Ackermann G, Stephenson K, Agapova S, Divala O, Kaimila Y, Maleta K, Zhong C, Knight R, Trehan I, Tarr PI, Rusconi B, Manary MJ. The effect of legume supplementation on the gut microbiota in rural Malawian infants aged 6 to 12 months. Am J Clin Nutr 2020; 111:884-892. [PMID: 32047925 PMCID: PMC8287943 DOI: 10.1093/ajcn/nqaa011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 09/14/2019] [Accepted: 01/21/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Common bean and cowpea contain about 25% protein and 25% fiber, and are recommended as complementary foods in sub-Saharan Africa. OBJECTIVE The objective of this study was to determine if a daily legume supplement given to Malawian infants aged 6 to 12 mo alters the 16S configuration of the fecal microbiota as read out by amplicon sequence variants (ASVs). METHODS This study was conducted within the context of a randomized, double-blind, controlled clinical trial to assess whether cowpea or common bean supplementation reduced intestinal permeability or increased linear growth. There were 2 village clusters in which the study was conducted. Fresh stool collections were flash frozen from 236 infants at ≤6 time points. The stools were sequenced using Earth Microbiome project protocols and data were processed using Qiime and Qiita, open-source, validated software packages. α-diversity was measured using the Faith's test. The 16S configuration was characterized by determining the weighted UniFrac distances of the ASVs and comparing them using permutational multivariate ANOVA. RESULTS Among the 1249 samples analyzed, the α-diversity of the fecal microbiome was unchanged among subjects after initiation of legume supplementation. Neither cowpea nor common bean altered the overall 16S configuration at any age. The 16S configuration differed between children with adequate and poor linear growth aged from 6 to 9 mo, but no specific ASVs differed in relative abundance. The 16S configuration differed between children with normal and abnormal intestinal permeability at 9 mo, but no specific ASVs differed in relative abundance. Among categorical characteristics of the population associated with different 16S configurations, village cluster was most pronounced. CONCLUSION Legume supplementation in breastfed, rural African infants did not affect the structure of the gut microbial communities until the children were aged 9 mo. This trial was registered at clinicaltrials.gov as NCT02472262.
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Affiliation(s)
- M Isabel Ordiz
- Department of Pediatrics, Washington University at St. Louis, St.
Louis, MO, USA
| | - Stefan Janssen
- Department of Pediatrics, University of California San Diego, La
Jolla, CA, USA
| | - Greg Humphrey
- Department of Pediatrics, University of California San Diego, La
Jolla, CA, USA
| | - Gail Ackermann
- Department of Pediatrics, University of California San Diego, La
Jolla, CA, USA
| | - Kevin Stephenson
- Department of Pediatrics, Washington University at St. Louis, St.
Louis, MO, USA
| | - Sophia Agapova
- Department of Pediatrics, Washington University at St. Louis, St.
Louis, MO, USA
| | - Oscar Divala
- Department of Community Health, College of Medicine, University of
Malawi, Malawi
| | - Yankho Kaimila
- Department of Community Health, College of Medicine, University of
Malawi, Malawi
| | - Ken Maleta
- Department of Community Health, College of Medicine, University of
Malawi, Malawi
| | - Caroline Zhong
- Department of Pediatrics, Washington University at St. Louis, St.
Louis, MO, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La
Jolla, CA, USA
- Department of Computer Science and Engineering, University of
California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego,
La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San
Diego, La Jolla, CA, USA
| | - Indi Trehan
- Department of Pediatrics, Washington University at St. Louis, St.
Louis, MO, USA
- Department of Paediatrics and Child Health, University of Malawi,
Blantyre, Malawi
| | - Phillip I Tarr
- Department of Pediatrics, Washington University at St. Louis, St.
Louis, MO, USA
| | - Brigida Rusconi
- Department of Pediatrics, Washington University at St. Louis, St.
Louis, MO, USA
| | - Mark J Manary
- Department of Pediatrics, Washington University at St. Louis, St.
Louis, MO, USA
- Department of Community Health, College of Medicine, University of
Malawi, Malawi
- USDA/Agricultural Research Service Children's Nutrition Research
Center, Houston, TX, USA
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