Publications by authors named "Silvia E Racedo"

9 Publications

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Dysregulation of TBX1 dosage in the anterior heart field results in congenital heart disease resembling the 22q11.2 duplication syndrome.

Hum Mol Genet 2018 06;27(11):1847-1857

Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA.

Non-allelic homologous recombination events on chromosome 22q11.2 during meiosis can result in either the deletion (22q11.2DS) or duplication (22q11.2DupS) syndrome. Although the spectrum and frequency of congenital heart disease (CHD) are known for 22q11.2DS, there is less known for 22q11.2DupS. We now evaluated cardiac phenotypes in 235 subjects with 22q11.2DupS including 102 subjects we collected and 133 subjects that were previously reported as a confirmation and found 25% have CHD, mostly affecting the cardiac outflow tract (OFT). Previous studies have shown that global loss or gain of function (LOF; GOF) of mouse Tbx1, encoding a T-box transcription factor mapping to the region of synteny to 22q11.2, results in similar OFT defects. To further evaluate Tbx1 function in the progenitor cells forming the cardiac OFT, termed the anterior heart field, Tbx1 was overexpressed using the Mef2c-AHF-Cre driver (Tbx1 GOF). Here we found that all resulting conditional GOF embryos had a persistent truncus arteriosus (PTA), similar to what was previously reported for conditional Tbx1 LOF mutant embryos. To understand the basis for the PTA in the conditional GOF embryos, we found that proliferation in the Mef2c-AHF-Cre lineage cells before migrating to the heart, was reduced and critical genes were oppositely changed in this tissue in Tbx1 GOF embryos versus conditional LOF embryos. These results suggest that a major function of TBX1 in the AHF is to maintain the normal balance of expression of key cardiac developmental genes required to form the aorta and pulmonary trunk, which is disrupted in 22q11.2DS and 22q11.2DupS.
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http://dx.doi.org/10.1093/hmg/ddy078DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5961083PMC
June 2018

Reduced dosage of β-catenin provides significant rescue of cardiac outflow tract anomalies in a Tbx1 conditional null mouse model of 22q11.2 deletion syndrome.

PLoS Genet 2017 03 27;13(3):e1006687. Epub 2017 Mar 27.

Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, United States of America.

The 22q11.2 deletion syndrome (22q11.2DS; velo-cardio-facial syndrome; DiGeorge syndrome) is a congenital anomaly disorder in which haploinsufficiency of TBX1, encoding a T-box transcription factor, is the major candidate for cardiac outflow tract (OFT) malformations. Inactivation of Tbx1 in the anterior heart field (AHF) mesoderm in the mouse results in premature expression of pro-differentiation genes and a persistent truncus arteriosus (PTA) in which septation does not form between the aorta and pulmonary trunk. Canonical Wnt/β-catenin has major roles in cardiac OFT development that may act upstream of Tbx1. Consistent with an antagonistic relationship, we found the opposite gene expression changes occurred in the AHF in β-catenin loss of function embryos compared to Tbx1 loss of function embryos, providing an opportunity to test for genetic rescue. When both alleles of Tbx1 and one allele of β-catenin were inactivated in the Mef2c-AHF-Cre domain, 61% of them (n = 34) showed partial or complete rescue of the PTA defect. Upregulated genes that were oppositely changed in expression in individual mutant embryos were normalized in significantly rescued embryos. Further, β-catenin was increased in expression when Tbx1 was inactivated, suggesting that there may be a negative feedback loop between canonical Wnt and Tbx1 in the AHF to allow the formation of the OFT. We suggest that alteration of this balance may contribute to variable expressivity in 22q11.2DS.
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http://dx.doi.org/10.1371/journal.pgen.1006687DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5386301PMC
March 2017

Genetic Drivers of Kidney Defects in the DiGeorge Syndrome.

N Engl J Med 2017 02 25;376(8):742-754. Epub 2017 Jan 25.

From the Division of Nephrology (E.L.-R., M.V., V.P.C., Z.Y., A.M., J.M., N.J.S., D.A.F., R.D., M.W., G.S.M., M.B., J.M.B., K.K., A.G.G., S.S.-C.) and the Division of Nephrology in Medicine and Zuckerman Mind Brain Behavior Institute (B.H.), the Departments of Systems Biology (D.S.P., B.H.), Biochemistry and Molecular Biophysics (B.H.), and Pathology (V.D.), and the Howard Hughes Medical Institute (D.S.P., B.H.), Columbia University, and the Department of Genetics and Development, Columbia University Medical Center (Q.L., V.E.P.), New York, and the Department of Genetics, Albert Einstein College of Medicine, Bronx (S.E.R., B.E.M.) - all in New York; the Center for Human Disease Modeling, Duke University, Durham, NC (Y.P.L., B.R.A., N. Katsanis); the Departments of Internal Medicine-Nephrology (E.A.O.) and Pediatrics-Nephrology (M.G.S., C.E.G., V.V.-W.), University of Michigan School of Medicine, Ann Arbor; the Department of Anatomy, Histology, and Embryology, School of Medicine, University of Split (K.V., M.S.-B.), and the Departments of Pediatrics (A.A., M. Saraga) and Pathology (N. Kunac), University Hospital of Split, Split, Croatia; the Department of Pediatric Nephrology, VU University Medical Center, Amsterdam (R.W., J.A.E.W.); the Department of Medicine, Boston Children's Hospital (A.V., F.H.), and Harvard Medical School, Boston (A.V., F.H., I.A.D.), and the Nephrology Division, Massachusetts General Hospital, Charlestown (I.A.D.) - all in Massachusetts; the Division of Nephrology, Dialysis, Transplantation, and Laboratory on Pathophysiology of Uremia, Istituto G. Gaslini, Genoa (M.B., A.C., G.M.G.), the Department of Clinical and Experimental Medicine, University of Parma (M.B., M. Maiorana, L.A.), and the Pediatric Surgery Unit, University Hospital of Parma (E.C.), Parma, the Section of Nephrology, Department of Emergency and Organ Transplantation, University of Bari, Bari (L.G.), the Department of Medical Sciences, University of Milano, and Institute of Biomedical Technologies, Italian National Institute of Research ITB-CNR, Milan (D.C.), and Dipartimento Ostetrico-Ginecologico e Seconda Divisione di Nefrologia ASST Spedali Civili e Presidio di Montichiari (C.I.) and Cattedra di Nefrologia, Università di Brescia, Seconda Divisione di Nefrologia Azienda Ospedaliera Spedali Civili di Brescia Presidio di Montichiari (F.S.), Brescia - all in Italy; the Department of General and Transplant Surgery, University Hospital of Heidelberg, Germany (V.J.L.); the Department of Pediatric Nephrology, Centre de Référence des Maladies Rénales Héréditaires de l'Enfant et de l'Adulte (R.S., L.H., C.J.), INSERM UMR 1163, Laboratory of Hereditary Kidney Diseases (R.S.), Necker-Enfants Malades Hospital, Paris Descartes-Sorbonne Paris Cite University, Imagine Institute (R.S.), Sorbonne Universités, UPMC 06, Plateforme Post-génomique de la Pitié-Salpêtrière, UMS 2 Omique, Inserm US029 (W.C.), Paris, and the Department of Genetics, Centre Hospitalier Universitaire de Reims, Unité de Formation et de Recherche de Médecine, Reims (D.G.) - both in France; the Department of Neurology, University of Washington School of Medicine, and Northwest VA Parkinson's Disease Research, Education and Clinical Centers, Seattle (A. Samii); the Division of Human Genetics, Department of Pediatrics, 22q and You Center, Children's Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania (D.M.M.-M., T.B.C., E.H.Z., S.L.F.), Division of Nephrology, Children's Hospital of Philadelphia (S.L.F.), and the Department of Genetics, University of Pennsylvania (H.H.), Philadelphia; the Dialysis Unit, Jagiellonian University Medical College (D.D.), and the Department of Pediatric Nephrology, Jagiellonian University Medical College (M. Miklaszewska), Krakow, the Department of Pediatrics, Immunology and Nephrology, Polish Mother's Memorial Hospital Research Institute, Lodz (M.T.), the Department of Pediatric Nephrology Medical University of Lublin, Lublin (P.S.), the Department of Pediatrics, School of Medicine with the Division of Dentistry in Zabrze, Medical University of Silesia, Katowice (M. Szczepanska), the Department of Pediatrics and Nephrology, Medical University of Warsaw, Warsaw (M.M.-W., G.K., A. Szmigielska), and Krysiewicza Children's Hospital (M.Z.) and the Department of Medical Genetics, Poznan University of Medical Sciences, and Center for Medical Genetics GENESIS (A.L.-B., A.M.-K.), Poznań - all in Poland; the Department of Clinical Genetics (J.M.D., D.B.), National Children's Research Centre (J.M.D., P.P.), and University College Dublin School of Medicine (D.B.), Our Lady's Children's Hospital Crumlin, and the National Children's Hospital Tallaght (P.P.), Dublin, Ireland; the Division of Pediatric Nephrology, Children's Mercy Hospital, Kansas City, MO (B.A.W.); University Children's Hospital, Medical Faculty of Skopje, Skopje, Macedonia (Z.G., V.T.); Faculty of Medicine, Palacky University, Olomouc, Czech Republic (H.F.); the Division of Pediatric Nephrology, University of New Mexico Children's Hospital, Albuquerque (C.S.W.); Ben May Department for Cancer Research, University of Chicago, Chicago (A.I.); and the Department of Genetics, Howard Hughes Medical Institute, and Yale Center for Mendelian Genomics, Yale University, New Haven, CT (R.P.L.).

Background: The DiGeorge syndrome, the most common of the microdeletion syndromes, affects multiple organs, including the heart, the nervous system, and the kidney. It is caused by deletions on chromosome 22q11.2; the genetic driver of the kidney defects is unknown.

Methods: We conducted a genomewide search for structural variants in two cohorts: 2080 patients with congenital kidney and urinary tract anomalies and 22,094 controls. We performed exome and targeted resequencing in samples obtained from 586 additional patients with congenital kidney anomalies. We also carried out functional studies using zebrafish and mice.

Results: We identified heterozygous deletions of 22q11.2 in 1.1% of the patients with congenital kidney anomalies and in 0.01% of population controls (odds ratio, 81.5; P=4.5×10). We localized the main drivers of renal disease in the DiGeorge syndrome to a 370-kb region containing nine genes. In zebrafish embryos, an induced loss of function in snap29, aifm3, and crkl resulted in renal defects; the loss of crkl alone was sufficient to induce defects. Five of 586 patients with congenital urinary anomalies had newly identified, heterozygous protein-altering variants, including a premature termination codon, in CRKL. The inactivation of Crkl in the mouse model induced developmental defects similar to those observed in patients with congenital urinary anomalies.

Conclusions: We identified a recurrent 370-kb deletion at the 22q11.2 locus as a driver of kidney defects in the DiGeorge syndrome and in sporadic congenital kidney and urinary tract anomalies. Of the nine genes at this locus, SNAP29, AIFM3, and CRKL appear to be critical to the phenotype, with haploinsufficiency of CRKL emerging as the main genetic driver. (Funded by the National Institutes of Health and others.).
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http://dx.doi.org/10.1056/NEJMoa1609009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5559731PMC
February 2017

LPA receptor activity is basal specific and coincident with early pregnancy and involution during mammary gland postnatal development.

Sci Rep 2016 11 3;6:35810. Epub 2016 Nov 3.

Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.

During pregnancy, luminal and basal epithelial cells of the adult mammary gland proliferate and differentiate resulting in remodeling of the adult gland. While pathways that control this process have been characterized in the gland as a whole, the contribution of specific cell subtypes, in particular the basal compartment, remains largely unknown. Basal cells provide structural and contractile support, however they also orchestrate the communication between the stroma and the luminal compartment at all developmental stages. Using RNA-seq, we show that basal cells are extraordinarily transcriptionally dynamic throughout pregnancy when compared to luminal cells. We identified gene expression changes that define specific basal functions acquired during development that led to the identification of novel markers. Enrichment analysis of gene sets from 24 mouse models for breast cancer pinpoint to a potential new function for insulin-like growth factor 1 (Igf1r) in the basal epithelium during lactogenesis. We establish that β-catenin signaling is activated in basal cells during early pregnancy, and demonstrate that this activity is mediated by lysophosphatidic acid receptor 3 (Lpar3). These findings identify novel pathways active during functional maturation of the adult mammary gland.
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http://dx.doi.org/10.1038/srep35810DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5093903PMC
November 2016

Rare copy number variants and congenital heart defects in the 22q11.2 deletion syndrome.

Hum Genet 2016 Mar 7;135(3):273-85. Epub 2016 Jan 7.

Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.

The 22q11.2 deletion syndrome (22q11DS; velocardiofacial/DiGeorge syndrome; VCFS/DGS; MIM #192430; 188400) is the most common microdeletion syndrome. The phenotypic presentation of 22q11DS is highly variable; approximately 60-75 % of 22q11DS patients have been reported to have a congenital heart defect (CHD), mostly of the conotruncal type, and/or aortic arch defect. The etiology of the cardiac phenotypic variability is not currently known for the majority of patients. We hypothesized that rare copy number variants (CNVs) outside the 22q11.2 deleted region may modify the risk of being born with a CHD in this sensitized population. Rare CNV analysis was performed using Affymetrix SNP Array 6.0 data from 946 22q11DS subjects with CHDs (n = 607) or with normal cardiac anatomy (n = 339). Although there was no significant difference in the overall burden of rare CNVs, an overabundance of CNVs affecting cardiac-related genes was detected in 22q11DS individuals with CHDs. When the rare CNVs were examined with regard to gene interactions, specific cardiac networks, such as Wnt signaling, appear to be overrepresented in 22q11DS CHD cases but not 22q11DS controls with a normal heart. Collectively, these data suggest that CNVs outside the 22q11.2 region may contain genes that modify risk for CHDs in some 22q11DS patients.
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http://dx.doi.org/10.1007/s00439-015-1623-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4896312PMC
March 2016

Copy-Number Variation of the Glucose Transporter Gene SLC2A3 and Congenital Heart Defects in the 22q11.2 Deletion Syndrome.

Am J Hum Genet 2015 May 16;96(5):753-64. Epub 2015 Apr 16.

Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Electronic address:

The 22q11.2 deletion syndrome (22q11DS; velocardiofacial/DiGeorge syndrome; VCFS/DGS) is the most common microdeletion syndrome and the phenotypic presentation is highly variable. Approximately 65% of individuals with 22q11DS have a congenital heart defect (CHD), mostly of the conotruncal type, and/or an aortic arch defect. The etiology of this phenotypic variability is not currently known. We hypothesized that copy-number variants (CNVs) outside the 22q11.2 deleted region might increase the risk of being born with a CHD in this sensitized population. Genotyping with Affymetrix SNP Array 6.0 was performed on two groups of subjects with 22q11DS separated by time of ascertainment and processing. CNV analysis was completed on a total of 949 subjects (cohort 1, n = 562; cohort 2, n = 387), 603 with CHDs (cohort 1, n = 363; cohort 2, n = 240) and 346 with normal cardiac anatomy (cohort 1, n = 199; cohort 2, n = 147). Our analysis revealed that a duplication of SLC2A3 was the most frequent CNV identified in the first cohort. It was present in 18 subjects with CHDs and 1 subject without (p = 3.12 × 10(-3), two-tailed Fisher's exact test). In the second cohort, the SLC2A3 duplication was also significantly enriched in subjects with CHDs (p = 3.30 × 10(-2), two-tailed Fisher's exact test). The SLC2A3 duplication was the most frequent CNV detected and the only significant finding in our combined analysis (p = 2.68 × 10(-4), two-tailed Fisher's exact test), indicating that the SLC2A3 duplication might serve as a genetic modifier of CHDs and/or aortic arch anomalies in individuals with 22q11DS.
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http://dx.doi.org/10.1016/j.ajhg.2015.03.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4570279PMC
May 2015

Mouse and human CRKL is dosage sensitive for cardiac outflow tract formation.

Am J Hum Genet 2015 Feb;96(2):235-44

Department of Genetics, Albert Einstein College of Medicine, Yeshiva University, Bronx, NY 10461, USA. Electronic address:

The human chromosome 22q11.2 region is susceptible to rearrangements during meiosis leading to velo-cardio-facial/DiGeorge/22q11.2 deletion syndrome (22q11DS) characterized by conotruncal heart defects (CTDs) and other congenital anomalies. The majority of individuals have a 3 Mb deletion whose proximal region contains the presumed disease-associated gene TBX1 (T-box 1). Although a small subset have proximal nested deletions including TBX1, individuals with distal deletions that exclude TBX1 have also been identified. The deletions are flanked by low-copy repeats (LCR22A, B, C, D). We describe cardiac phenotypes in 25 individuals with atypical distal nested deletions within the 3 Mb region that do not include TBX1 including 20 with LCR22B to LCR22D deletions and 5 with nested LCR22C to LCR22D deletions. Together with previous reports, 12 of 37 (32%) with LCR22B-D deletions and 5 of 34 (15%) individuals with LCR22C-D deletions had CTDs including tetralogy of Fallot. In the absence of TBX1, we hypothesized that CRKL (Crk-like), mapping to the LCR22C-D region, might contribute to the cardiac phenotype in these individuals. We created an allelic series in mice of Crkl, including a hypomorphic allele, to test for gene expression effects on phenotype. We found that the spectrum of heart defects depends on Crkl expression, occurring with analogous malformations to that in human individuals, suggesting that haploinsufficiency of CRKL could be responsible for the etiology of CTDs in individuals with nested distal deletions and might act as a genetic modifier of individuals with the typical 3 Mb deletion.
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http://dx.doi.org/10.1016/j.ajhg.2014.12.025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4320261PMC
February 2015

Tbx1 is required autonomously for cell survival and fate in the pharyngeal core mesoderm to form the muscles of mastication.

Hum Mol Genet 2014 Aug 4;23(16):4215-31. Epub 2014 Apr 4.

Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY 10461, USA,

Velo-cardio-facial/DiGeorge syndrome, also known as 22q11.2 deletion syndrome, is a congenital anomaly disorder characterized by craniofacial anomalies including velo-pharyngeal insufficiency, facial muscle hypotonia and feeding difficulties, in part due to hypoplasia of the branchiomeric muscles. Inactivation of both alleles of mouse Tbx1, encoding a T-box transcription factor, deleted on chromosome 22q11.2, results in reduction or loss of branchiomeric muscles. To identify downstream pathways, we performed gene profiling of microdissected pharyngeal arch one (PA1) from Tbx1(+/+) and Tbx1(-/-) embryos at stages E9.5 (somites 20-25) and E10.5 (somites 30-35). Basic helix-loop-helix (bHLH) transcription factors were reduced, while secondary heart field genes were increased in expression early and were replaced by an increase in expression of cellular stress response genes later, suggesting a change in gene expression patterns or cell populations. Lineage tracing studies using Mesp1(Cre) and T-Cre drivers showed that core mesoderm cells within PA1 were present at E9.5 but were greatly reduced by E10.5 in Tbx1(-/-) embryos. Using Tbx1(Cre) knock-in mice, we found that cells are lost due to apoptosis, consistent with increase in expression of cellular stress response genes at E10.5. To determine whether Tbx1 is required autonomously in the core mesoderm, we used Mesp1(Cre) and T-Cre mesodermal drivers in combination with inactivate Tbx1 and found reduction or loss of branchiomeric muscles from PA1. These mechanistic studies inform us that Tbx1 is required upstream of key myogenic genes needed for core mesoderm cell survival and fate, between E9.5 and E10.5, resulting in formation of the branchiomeric muscles.
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http://dx.doi.org/10.1093/hmg/ddu140DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4103673PMC
August 2014

Effects of follicle size and stages of maturation on mRNA expression in bovine in vitro matured oocytes.

Mol Reprod Dev 2008 Jan;75(1):17-25

Department of Biotechnology, Institute for Animal Breeding (FAL), Mariensee, Neustadt, Germany.

Transcription in bovine oocytes: The goal of this study was to unravel the dynamics of transcripts thought to be critically involved in oocyte maturation. The relative abundance (RA) of DYNLL1 (cytoplasmic dynein light chain LC8), DYNC1I1 (cytoplasmic dynein 1 intermediate chain), DCTN1 (dynactin 1; pGlued homolog, the activator of the cytoplasmic dynein complex 1), PMSB1 (proteasome beta subunit 1), PMSA4 (proteasome alfa subunit 4), PAP (poly-A polymerase) and Cx43 (connexin 43) were determined by semi-quantitative endpoint RT-PCR at different stages of IVM, that is, GV, GVBD, MI and MII in oocytes collected from follicles of two different size categories, that is, <2 mm and 2-8 mm. The RA of DYNLL1 and DYNC1I1 were significantly higher in immature oocytes from bigger follicles than in oocytes from small follicles. Messenger RNA expression levels were similar for DCTN1, PMSB1, PMSA4, PAP, and Cx43 in the two groups during the maturation process. RA of DYNLL1, DYNC1I1 and PMSB1 decreased significantly during IVM in oocytes from follicles 2 to 8 mm. The RA for DYNLL1 was significantly higher in GVBD and MI in the oocytes from follicles 2 to 8 mm in size compared to the other group. The higher mRNA expression of DYNLL1 and DYNC1I1 and the diverging dynamics of DYNLL1, DYNC1I1, and PMSB1 mRNA expression during IVM in oocytes from the different follicle categories could be related to the developmental capacity, that is, development to blastocysts after IVF. The differences found between groups of oocytes could serve as a marker to assess the developmental capacity of bovine oocytes.
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http://dx.doi.org/10.1002/mrd.20770DOI Listing
January 2008