23 results on '"Urraca N"'
Search Results
2. Increased copy number for methylated maternal 15q duplications leads to changes in gene and protein expression in human cortical samples
- Author
-
Scoles Haley A, Urraca Nora, Chadwick Samuel W, Reiter Lawrence T, and LaSalle Janine M
- Subjects
autism ,imprinting ,copy number variation ,15q ,duplication ,methylation ,epigenetic ,Neurology. Diseases of the nervous system ,RC346-429 - Abstract
Abstract Background Duplication of chromosome 15q11-q13 (dup15q) accounts for approximately 3% of autism cases. Chromosome 15q11-q13 contains imprinted genes necessary for normal mammalian neurodevelopment controlled by a differentially methylated imprinting center (imprinting center of the Prader-Willi locus, PWS-IC). Maternal dup15q occurs as both interstitial duplications and isodicentric chromosome 15. Overexpression of the maternally expressed gene UBE3A is predicted to be the primary cause of the autistic features associated with dup15q. Previous analysis of two postmortem dup15q frontal cortical samples showed heterogeneity between the two cases, with one showing levels of the GABAA receptor genes, UBE3A and SNRPN in a manner not predicted by copy number or parental imprint. Methods Postmortem human brain tissue (Brodmann area 19, extrastriate visual cortex) was obtained from 8 dup15q, 10 idiopathic autism and 21 typical control tissue samples. Quantitative PCR was used to confirm duplication status. Quantitative RT-PCR and Western blot analyses were performed to measure 15q11-q13 transcript and protein levels, respectively. Methylation-sensitive high-resolution melting-curve analysis was performed on brain genomic DNA to identify the maternal:paternal ratio of methylation at PWS-IC. Results Dup15q brain samples showed a higher level of PWS-IC methylation than control or autism samples, indicating that dup15q was maternal in origin. UBE3A transcript and protein levels were significantly higher than control and autism in dup15q, as expected, although levels were variable and lower than expected based on copy number in some samples. In contrast, this increase in copy number did not result in consistently increased GABRB3 transcript or protein levels for dup15q samples. Furthermore, SNRPN was expected to be unchanged in expression in dup15q because it is expressed from the single unmethylated paternal allele, yet SNRPN levels were significantly reduced in dup15q samples compared to controls. PWS-IC methylation positively correlated with UBE3A and GABRB3 levels but negatively correlated with SNRPN levels. Idiopathic autism samples exhibited significantly lower GABRB3 and significantly more variable SNRPN levels compared to controls. Conclusions Although these results show that increased UBE3A/UBE3A is a consistent feature of dup15q syndrome, they also suggest that gene expression within 15q11-q13 is not based entirely on copy number but can be influenced by epigenetic mechanisms in brain.
- Published
- 2011
- Full Text
- View/download PDF
3. The impact of clinical genome sequencing in a global population with suspected rare genetic disease.
- Author
-
Thorpe E, Williams T, Shaw C, Chekalin E, Ortega J, Robinson K, Button J, Jones MC, Campo MD, Basel D, McCarrier J, Keppen LD, Royer E, Foster-Bonds R, Duenas-Roque MM, Urraca N, Bosfield K, Brown CW, Lydigsen H, Mroczkowski HJ, Ward J, Sirchia F, Giorgio E, Vaux K, Salguero HP, Lumaka A, Mubungu G, Makay P, Ngole M, Lukusa PT, Vanderver A, Muirhead K, Sherbini O, Lah MD, Anderson K, Bazalar-Montoya J, Rodriguez RS, Cornejo-Olivas M, Milla-Neyra K, Shinawi M, Magoulas P, Henry D, Gibson K, Wiafe S, Jayakar P, Salyakina D, Masser-Frye D, Serize A, Perez JE, Taylor A, Shenbagam S, Abou Tayoun A, Malhotra A, Bennett M, Rajan V, Avecilla J, Warren A, Arseneault M, Kalista T, Crawford A, Ajay SS, Perry DL, Belmont J, and Taft RJ
- Subjects
- Humans, Male, Female, Child, Child, Preschool, Adolescent, Adult, Infant, Genetic Diseases, Inborn genetics, Genetic Diseases, Inborn diagnosis, Rare Diseases genetics, Rare Diseases diagnosis, Genetic Testing methods, Whole Genome Sequencing
- Abstract
There is mounting evidence of the value of clinical genome sequencing (cGS) in individuals with suspected rare genetic disease (RGD), but cGS performance and impact on clinical care in a diverse population drawn from both high-income countries (HICs) and low- and middle-income countries (LMICs) has not been investigated. The iHope program, a philanthropic cGS initiative, established a network of 24 clinical sites in eight countries through which it provided cGS to individuals with signs or symptoms of an RGD and constrained access to molecular testing. A total of 1,004 individuals (median age, 6.5 years; 53.5% male) with diverse ancestral backgrounds (51.8% non-majority European) were assessed from June 2016 to September 2021. The diagnostic yield of cGS was 41.4% (416/1,004), with individuals from LMIC sites 1.7 times more likely to receive a positive test result compared to HIC sites (LMIC 56.5% [195/345] vs. HIC 33.5% [221/659], OR 2.6, 95% CI 1.9-3.4, p < 0.0001). A change in diagnostic evaluation occurred in 76.9% (514/668) of individuals. Change of management, inclusive of specialty referrals, imaging and testing, therapeutic interventions, and palliative care, was reported in 41.4% (285/694) of individuals, which increased to 69.2% (480/694) when genetic counseling and avoidance of additional testing were also included. Individuals from LMIC sites were as likely as their HIC counterparts to experience a change in diagnostic evaluation (OR 6.1, 95% CI 1.1-∞, p = 0.05) and change of management (OR 0.9, 95% CI 0.5-1.3, p = 0.49). Increased access to genomic testing may support diagnostic equity and the reduction of global health care disparities., Competing Interests: Declaration of interests E.T., E.C., K.R., J. Button, A.M., M.B., J.A., A.W., M.A., T.K., A.C., S.S.A., D.L.P., and R.J.T. were employees of and stockholders in Illumina, Inc. at the time of this investigation. V.R. is a stockholder in Illumina, Inc. J.O. is a stockholder in Illumina, Inc. and employee of C2N Diagnostics. J. Belmont and T.W. are stockholders in Illumina, Inc. and were compensated as research advisors through Genetics & Genomics Services Inc. C.S. was compensated as a consultant through Genetics & Genomics Services Inc. for statistical analysis. K.M. is an employee of Ambry Genetics., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)
- Published
- 2024
- Full Text
- View/download PDF
4. Genome sequencing detects a balanced pericentric inversion with breakpoints that impact the DMD and upstream region of POU3F4 genes.
- Author
-
Chandrasekhar A, Mroczkowski HJ, Urraca N, Gross A, Bluske K, Thorpe E, Hagelstrom RT, Schonberg SA, Perry DL, Taft RJ, and Kesari A
- Subjects
- Child, Preschool, Female, Humans, Male, Base Sequence, Chromosome Inversion genetics, Dystrophin genetics, POU Domain Factors genetics, Autism Spectrum Disorder genetics, Muscular Dystrophies genetics, Muscular Dystrophy, Duchenne genetics
- Abstract
We describe a family with two maternal half-brothers both of whom presented with muscular dystrophy, autism spectrum disorder, developmental delay, and sensorineural hearing loss. The elder brother had onset of features at ~3 months of age, followed by clinical confirmation of muscular dystrophy at 3 years. Skeletal biopsy staining at 4.7 years showed an absence of dystrophin protein which prompted extensive molecular testing over 4 years that included gene panels, targeted single-gene assays, arrays, and karyotyping, all of which failed to identify a clinically significant variant in the DMD gene. At 10 years of age, clinical whole-genome sequencing (cWGS) was performed, which revealed a novel hemizygous ~50.7 Mb balanced pericentric inversion on chromosome X that disrupts the DMD gene in both siblings, consistent with the muscular dystrophy phenotype. This inversion also impacts the upstream regulatory region of POU3F4, structural rearrangements which are known to cause hearing loss. The unaffected mother is a heterozygous carrier for the pericentric inversion. This finding illustrates the ability of cWGS to detect a wide breadth of disease-causing genomic variations including large genomic rearrangements., (© 2023 Wiley Periodicals LLC.)
- Published
- 2024
- Full Text
- View/download PDF
5. Effect of Whole-Genome Sequencing on the Clinical Management of Acutely Ill Infants With Suspected Genetic Disease: A Randomized Clinical Trial.
- Author
-
Krantz ID, Medne L, Weatherly JM, Wild KT, Biswas S, Devkota B, Hartman T, Brunelli L, Fishler KP, Abdul-Rahman O, Euteneuer JC, Hoover D, Dimmock D, Cleary J, Farnaes L, Knight J, Schwarz AJ, Vargas-Shiraishi OM, Wigby K, Zadeh N, Shinawi M, Wambach JA, Baldridge D, Cole FS, Wegner DJ, Urraca N, Holtrop S, Mostafavi R, Mroczkowski HJ, Pivnick EK, Ward JC, Talati A, Brown CW, Belmont JW, Ortega JL, Robinson KD, Brocklehurst WT, Perry DL, Ajay SS, Hagelstrom RT, Bennett M, Rajan V, and Taft RJ
- Subjects
- Female, Humans, Infant, Infant, Newborn, Male, Outcome Assessment, Health Care, Acute Disease, Genetic Diseases, Inborn, Whole Genome Sequencing
- Abstract
Importance: Whole-genome sequencing (WGS) shows promise as a first-line genetic test for acutely ill infants, but widespread adoption and implementation requires evidence of an effect on clinical management., Objective: To determine the effect of WGS on clinical management in a racially and ethnically diverse and geographically distributed population of acutely ill infants in the US., Design, Setting, and Participants: This randomized, time-delayed clinical trial enrolled participants from September 11, 2017, to April 30, 2019, with an observation period extending to July 2, 2019. The study was conducted at 5 US academic medical centers and affiliated children's hospitals. Participants included infants aged between 0 and 120 days who were admitted to an intensive care unit with a suspected genetic disease. Data were analyzed from January 14 to August 20, 2020., Interventions: Patients were randomized to receive clinical WGS results 15 days (early) or 60 days (delayed) after enrollment, with the observation period extending to 90 days. Usual care was continued throughout the study., Main Outcomes and Measures: The main outcome was the difference in the proportion of infants in the early and delayed groups who received a change of management (COM) 60 days after enrollment. Additional outcome measures included WGS diagnostic efficacy, within-group COM at 90 days, length of hospital stay, and mortality., Results: A total of 354 infants were randomized to the early (n = 176) or delayed (n = 178) arms. The mean participant age was 15 days (IQR, 7-32 days); 201 participants (56.8%) were boys; 19 (5.4%) were Asian; 47 (13.3%) were Black; 250 (70.6%) were White; and 38 (10.7%) were of other race. At 60 days, twice as many infants in the early group vs the delayed group received a COM (34 of 161 [21.1%; 95% CI, 15.1%-28.2%] vs 17 of 165 [10.3%; 95% CI, 6.1%-16.0%]; P = .009; odds ratio, 2.3; 95% CI, 1.22-4.32) and a molecular diagnosis (55 of 176 [31.0%; 95% CI, 24.5%-38.7%] vs 27 of 178 [15.0%; 95% CI, 10.2%-21.3%]; P < .001). At 90 days, the delayed group showed a doubling of COM (to 45 of 161 [28.0%; 95% CI, 21.2%-35.6%]) and diagnostic efficacy (to 56 of 178 [31.0%; 95% CI, 24.7%-38.8%]). The most frequent COMs across the observation window were subspecialty referrals (39 of 354; 11%), surgery or other invasive procedures (17 of 354; 4%), condition-specific medications (9 of 354; 2%), or other supportive alterations in medication (12 of 354; 3%). No differences in length of stay or survival were observed., Conclusions and Relevance: In this randomized clinical trial, for acutely ill infants in an intensive care unit, introduction of WGS was associated with a significant increase in focused clinical management compared with usual care. Access to first-line WGS may reduce health care disparities by enabling diagnostic equity. These data support WGS adoption and implementation in this population., Trail Registration: ClinicalTrials.gov Identifier: NCT03290469.
- Published
- 2021
- Full Text
- View/download PDF
6. HIV Prevention for Black Heterosexual Men: The Barbershop Talk with Brothers Cluster Randomized Trial.
- Author
-
Wilson TE, Gousse Y, Joseph MA, Browne RC, Camilien B, McFarlane D, Mitchell S, Brown H, Urraca N, Romeo D, Johnson S, Salifu M, Stewart M, Vavagiakis P, and Fraser M
- Subjects
- Adult, Humans, Male, New York City, Black or African American psychology, Community-Based Participatory Research methods, HIV Infections prevention & control, Health Promotion methods, Heterosexuality psychology, Risk Reduction Behavior
- Abstract
Objectives. To identify the impact of a strengths-focused HIV prevention program among high-risk heterosexual Black men. Methods. Barbershops in Brooklyn, New York, neighborhoods with high rates of heterosexually transmitted HIV were randomized to the intervention or an attention control program. Men were recruited from barbershops between 2012 and 2016 and participated in a single small group, peer-led session focused on HIV risk reduction skills and motivation, community health empowerment, and identification of personal strengths and communication skills. The outcome was defined as 1 or more acts of condomless anal or vaginal sex in the preceding 90 days at a 6-month interview. Results. Fifty-three barbershops (24 intervention, 29 control) and 860 men (436 intervention, 424 control) were recruited; follow-up was completed by 657 participants (352 intervention, 305 control). Intervention exposure was associated with a greater likelihood of no condomless sex (64.4%) than control group participation (54.1%; adjusted odds ratio = 1.61; 95% confidence interval = 1.05, 2.47). Conclusions. Program exposure resulted in reduced sexual risk behaviors, and the program was acceptable for administration in partnership with barbershops. Public Health Implications. Dissemination of similar programs could improve public health in communities with high rates of HIV attributable to heterosexual transmission.
- Published
- 2019
- Full Text
- View/download PDF
7. Significant transcriptional changes in 15q duplication but not Angelman syndrome deletion stem cell-derived neurons.
- Author
-
Urraca N, Hope K, Victor AK, Belgard TG, Memon R, Goorha S, Valdez C, Tran QT, Sanchez S, Ramirez J, Donaldson M, Bridges D, and Reiter LT
- Subjects
- Angelman Syndrome metabolism, Basic Helix-Loop-Helix Transcription Factors genetics, Basic Helix-Loop-Helix Transcription Factors metabolism, Cells, Cultured, Chromosomes, Human, Pair 15 genetics, Chromosomes, Human, Pair 15 metabolism, Dental Pulp cytology, Forkhead Box Protein O1 genetics, Forkhead Box Protein O1 metabolism, Guanine Nucleotide Exchange Factors genetics, Guanine Nucleotide Exchange Factors metabolism, Humans, Nuclear Receptor Subfamily 1, Group F, Member 1 genetics, Nuclear Receptor Subfamily 1, Group F, Member 1 metabolism, Ubiquitin-Protein Ligases genetics, Ubiquitin-Protein Ligases metabolism, Angelman Syndrome genetics, Chromosome Deletion, Neural Stem Cells metabolism, Transcriptome, Trisomy genetics
- Abstract
Background: The inability to analyze gene expression in living neurons from Angelman (AS) and Duplication 15q (Dup15q) syndrome subjects has limited our understanding of these disorders at the molecular level., Method: Here, we use dental pulp stem cells (DPSC) from AS deletion, 15q Duplication, and neurotypical control subjects for whole transcriptome analysis. We identified 20 genes unique to AS neurons, 120 genes unique to 15q duplication, and 3 shared transcripts that were differentially expressed in DPSC neurons vs controls., Results: Copy number correlated with gene expression for most genes across the 15q11.2-q13.1 critical region. Two thirds of the genes differentially expressed in 15q duplication neurons were downregulated compared to controls including several transcription factors, while in AS differential expression was restricted primarily to the 15q region. Here, we show significant downregulation of the transcription factors FOXO1 and HAND2 in neurons from 15q duplication, but not AS deletion subjects suggesting that disruptions in transcriptional regulation may be a driving factor in the autism phenotype in Dup15q syndrome. Downstream analysis revealed downregulation of the ASD associated genes EHPB2 and RORA , both genes with FOXO1 binding sites. Genes upregulated in either Dup15q cortex or idiopathic ASD cortex both overlapped significantly with the most upregulated genes in Dup15q DPSC-derived neurons., Conclusions: Finding a significant increase in both HERC2 and UBE3A in Dup15q neurons and significant decrease in these two genes in AS deletion neurons may explain differences between AS deletion class and UBE3A specific classes of AS mutation where HERC2 is expressed at normal levels. Also, we identified an enrichment for FOXO1-regulated transcripts in Dup15q neurons including ASD-associated genes EHPB2 and RORA indicating a possible connection between this syndromic form of ASD and idiopathic cases., Competing Interests: The UTHSC Institutional Review Board (IRB) approved this study, and informed consent was obtained for both participation and publication of results in accordance with IRB policy.The authors declare that they have no competing interests.Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
- Published
- 2018
- Full Text
- View/download PDF
8. Lessons Learned from the Implementation of a Shared Community-Academic HIV Prevention Intervention.
- Author
-
Gousse Y, McFarlane D, Fraser M, Joseph M, Alli B, Council-George M, Fraser H, Romeo D, Urraca N, Wellington P, Stewart M, Browne RC, Salifu MO, Vavagiakis P, and Wilson TE
- Subjects
- Barbering, Community-Based Participatory Research organization & administration, Humans, Male, Program Development, Universities organization & administration, Community-Based Participatory Research methods, Community-Institutional Relations, HIV Infections prevention & control
- Abstract
Background: Community-based participatory research (CBPR) is used to guide the design and evaluation of programs aimed at addressing complex health issues. Effective administrative management of CBPR projects is essential to ensuring the success and fidelity of these programs., Objective: We identify an administrative framework to support the implementation and management of a community- academic CBPR initiative., Methods: The Barbershop Talk with Brothers (BTWB) project was a cluster randomized CBPR intervention designed to reduce HIV among high-risk heterosexual men. Eight-hundred sixty men, representing 53 barbershops, participated in the project., Results: The 3Ps framework is defined by 1) partnership, 2) product, and 3) process. We describe the implementation of the 3Ps through applied examples including partnership management strategies, planning of shared resources, and flexible budgeting that can support the unique infrastructure of a shared community-academic project., Conclusions: The 3Ps are a translatable framework for comparable shared community-academic research projects to adopt.
- Published
- 2018
- Full Text
- View/download PDF
9. Multisite Semiautomated Clinical Data Repository for Duplication 15q Syndrome: Study Protocol and Early Uses.
- Author
-
Ajayi OJ, Smith EJ, Viangteeravat T, Huang EY, Nagisetty NSVR, Urraca N, Lusk L, Finucane B, Arkilo D, Young J, Jeste S, Thibert R, and Reiter LT
- Abstract
Background: Chromosome 15q11.2-q13.1 duplication syndrome (Dup15q syndrome) is a rare disorder caused by duplications of chromosome 15q11.2-q13.1, resulting in a wide range of developmental disabilities in affected individuals. The Dup15q Alliance is an organization that provides family support and promotes research to improve the quality of life of patients living with Dup15q syndrome. Because of the low prevalence of this condition, the establishment of a single research repository would have been difficult and more time consuming without collaboration across multiple institutions., Objective: The goal of this project is to establish a national deidentified database with clinical and survey information on individuals diagnosed with Dup15q syndrome., Methods: The development of a multiclinic site repository for clinical and survey data on individuals with Dup15q syndrome was initiated and supported by the Dup15q Alliance. Using collaborative workflows, communication protocols, and stakeholder engagement tools, a comprehensive database of patient-centered information was built., Results: We successfully established a self-report populating, centralized repository for Dup15q syndrome research. This repository also resulted in the development of standardized instruments that can be used for other studies relating to developmental disorders. By standardizing the data collection instruments, it allows us integrate our data with other national databases, such as the National Database for Autism Research. A substantial portion of the data collected from the questionnaires was facilitated through direct engagement of participants and their families. This allowed for a more complete set of information to be collected with a minimal turnaround time., Conclusions: We developed a repository that can efficiently be mined for shared clinical phenotypes observed at multiple clinic sites and used as a springboard for future clinical and basic research studies., (©Oluwaseun Jessica Ajayi, Ebony Jeannae Smith, Teeradache Viangteeravat, Eunice Y Huang, Naga Satya V Rao Nagisetty, Nora Urraca, Laina Lusk, Brenda Finucane, Dimitrios Arkilo, Jennifer Young, Shafali Jeste, Ronald Thibert, The Dup15q Alliance, Lawrence T Reiter. Originally published in JMIR Research Protocols (http://www.researchprotocols.org), 18.10.2017.)
- Published
- 2017
- Full Text
- View/download PDF
10. Identification of novel candidate disease genes from de novo exonic copy number variants.
- Author
-
Gambin T, Yuan B, Bi W, Liu P, Rosenfeld JA, Coban-Akdemir Z, Pursley AN, Nagamani SCS, Marom R, Golla S, Dengle L, Petrie HG, Matalon R, Emrick L, Proud MB, Treadwell-Deering D, Chao HT, Koillinen H, Brown C, Urraca N, Mostafavi R, Bernes S, Roeder ER, Nugent KM, Bader PI, Bellus G, Cummings M, Northrup H, Ashfaq M, Westman R, Wildin R, Beck AE, Immken L, Elton L, Varghese S, Buchanan E, Faivre L, Lefebvre M, Schaaf CP, Walkiewicz M, Yang Y, Kang SL, Lalani SR, Bacino CA, Beaudet AL, Breman AM, Smith JL, Cheung SW, Lupski JR, Patel A, Shaw CA, and Stankiewicz P
- Subjects
- Cohort Studies, Genome, Human, Homeodomain Proteins genetics, Humans, Intracellular Signaling Peptides and Proteins genetics, Membrane Proteins genetics, Neurodevelopmental Disorders genetics, Protein Serine-Threonine Kinases genetics, Retrospective Studies, Serine-Threonine Kinase 3, Transcription Factors genetics, Whole Genome Sequencing, DNA Copy Number Variations, Exons, Genetic Diseases, Inborn
- Abstract
Background: Exon-targeted microarrays can detect small (<1000 bp) intragenic copy number variants (CNVs), including those that affect only a single exon. This genome-wide high-sensitivity approach increases the molecular diagnosis for conditions with known disease-associated genes, enables better genotype-phenotype correlations, and facilitates variant allele detection allowing novel disease gene discovery., Methods: We retrospectively analyzed data from 63,127 patients referred for clinical chromosomal microarray analysis (CMA) at Baylor Genetics laboratories, including 46,755 individuals tested using exon-targeted arrays, from 2007 to 2017. Small CNVs harboring a single gene or two to five non-disease-associated genes were identified; the genes involved were evaluated for a potential disease association., Results: In this clinical population, among rare CNVs involving any single gene reported in 7200 patients (11%), we identified 145 de novo autosomal CNVs (117 losses and 28 intragenic gains), 257 X-linked deletion CNVs in males, and 1049 inherited autosomal CNVs (878 losses and 171 intragenic gains); 111 known disease genes were potentially disrupted by de novo autosomal or X-linked (in males) single-gene CNVs. Ninety-one genes, either recently proposed as candidate disease genes or not yet associated with diseases, were disrupted by 147 single-gene CNVs, including 37 de novo deletions and ten de novo intragenic duplications on autosomes and 100 X-linked CNVs in males. Clinical features in individuals with de novo or X-linked CNVs encompassing at most five genes (224 bp to 1.6 Mb in size) were compared to those in individuals with larger-sized deletions (up to 5 Mb in size) in the internal CMA database or loss-of-function single nucleotide variants (SNVs) detected by clinical or research whole-exome sequencing (WES). This enabled the identification of recently published genes (BPTF, NONO, PSMD12, TANGO2, and TRIP12), novel candidate disease genes (ARGLU1 and STK3), and further confirmation of disease association for two recently proposed disease genes (MEIS2 and PTCHD1). Notably, exon-targeted CMA detected several pathogenic single-exon CNVs missed by clinical WES analyses., Conclusions: Together, these data document the efficacy of exon-targeted CMA for detection of genic and exonic CNVs, complementing and extending WES in clinical diagnostics, and the potential for discovery of novel disease genes by genome-wide assay.
- Published
- 2017
- Full Text
- View/download PDF
11. Dental Pulp Stem Cells Model Early Life and Imprinted DNA Methylation Patterns.
- Author
-
Dunaway K, Goorha S, Matelski L, Urraca N, Lein PJ, Korf I, Reiter LT, and LaSalle JM
- Subjects
- Cell Line, Chromosome Duplication, Female, Genome, Human, Humans, Induced Pluripotent Stem Cells metabolism, Placenta metabolism, Pregnancy, Syndrome, DNA Methylation genetics, Dental Pulp cytology, Genomic Imprinting, Stem Cells cytology, Stem Cells metabolism
- Abstract
Early embryonic stages of pluripotency are modeled for epigenomic studies primarily with human embryonic stem cells (ESC) or induced pluripotent stem cells (iPSCs). For analysis of DNA methylation however, ESCs and iPSCs do not accurately reflect the DNA methylation levels found in preimplantation embryos. Whole genome bisulfite sequencing (WGBS) approaches have revealed the presence of large partially methylated domains (PMDs) covering 30%-40% of the genome in oocytes, preimplantation embryos, and placenta. In contrast, ESCs and iPSCs show abnormally high levels of DNA methylation compared to inner cell mass (ICM) or placenta. Here we show that dental pulp stem cells (DPSCs), derived from baby teeth and cultured in serum-containing media, have PMDs and mimic the ICM and placental methylome more closely than iPSCs and ESCs. By principal component analysis, DPSC methylation patterns were more similar to two other neural stem cell types of human derivation (EPI-NCSC and LUHMES) and placenta than were iPSCs, ESCs or other human cell lines (SH-SY5Y, B lymphoblast, IMR90). To test the suitability of DPSCs in modeling epigenetic differences associated with disease, we compared methylation patterns of DPSCs derived from children with chromosome 15q11.2-q13.3 maternal duplication (Dup15q) to controls. Differential methylation region (DMR) analyses revealed the expected Dup15q hypermethylation at the imprinting control region, as well as hypomethylation over SNORD116, and novel DMRs over 147 genes, including several autism candidate genes. Together these data suggest that DPSCs are a useful model for epigenomic and functional studies of human neurodevelopmental disorders. Stem Cells 2017;35:981-988., (© 2016 AlphaMed Press.)
- Published
- 2017
- Full Text
- View/download PDF
12. A Rare Inherited 15q11.2-q13.1 Interstitial Duplication with Maternal Somatic Mosaicism, Renal Carcinoma, and Autism.
- Author
-
Urraca N, Potter B, Hundley R, Pivnick EK, McVicar K, Thibert RL, Ledbetter C, Chamberlain R, Miravalle L, Sirois CL, Chamberlain S, and Reiter LT
- Abstract
Chromosome 15q11-q13.1 duplication is a common copy number variant associated with autism spectrum disorder (ASD). Most cases are de novo , maternal in origin and fully penetrant for ASD. Here, we describe a unique family with an interstitial 15q11.2-q13.1 maternal duplication and the presence of somatic mosaicism in the mother. She is typically functioning, but formal autism testing showed mild ASD. She had several congenital anomalies, and she is the first 15q Duplication case reported in the literature to develop unilateral renal carcinoma. Her two affected children share some of these clinical characteristics, and have severe ASD. Several tissues in the mother, including blood, skin, a kidney tumor, and normal kidney margin tissues were studied for the presence of the 15q11-q13.1 duplication. We show the mother has somatic mosaicism for the duplication in several tissues to varying degrees. A growth competition assay in two types of stem cells from duplication 15q individuals was also performed. Our results suggest that the presence of this interstitial duplication 15q chromosome may confer a previously unknown growth advantage in this particular individual, but not in the general interstitial duplication 15q population.
- Published
- 2016
- Full Text
- View/download PDF
13. Characterization of neurons from immortalized dental pulp stem cells for the study of neurogenetic disorders.
- Author
-
Urraca N, Memon R, El-Iyachi I, Goorha S, Valdez C, Tran QT, Scroggs R, Miranda-Carboni GA, Donaldson M, Bridges D, and Reiter LT
- Subjects
- Cell Differentiation, Cell Proliferation, Cells, Cultured, Dental Pulp cytology, Humans, Stem Cells, Dental Pulp metabolism, Nervous System Diseases genetics, Neurons metabolism
- Abstract
A major challenge to the study and treatment of neurogenetic syndromes is accessing live neurons for study from affected individuals. Although several sources of stem cells are currently available, acquiring these involve invasive procedures, may be difficult or expensive to generate and are limited in number. Dental pulp stem cells (DPSCs) are multipotent stem cells that reside deep the pulp of shed teeth. To investigate the characteristics of DPSCs that make them a valuable resource for translational research, we performed a set of viability, senescence, immortalization and gene expression studies on control DPSC and derived neurons. We investigated the basic transport conditions and maximum passage number for primary DPSCs. We immortalized control DPSCs using human telomerase reverse transcriptase (hTERT) and evaluated neuronal differentiation potential and global gene expression changes by RNA-seq. We show that neurons from immortalized DPSCs share morphological and electrophysiological properties with non-immortalized DPSCs. We also show that differentiation of DPSCs into neurons significantly alters gene expression for 1305 transcripts. Here we show that these changes in gene expression are concurrent with changes in protein levels of the transcriptional repressor REST/NRSF, which is known to be involved in neuronal differentiation. Immortalization significantly altered the expression of 183 genes after neuronal differentiation, 94 of which also changed during differentiation. Our studies indicate that viable DPSCs can be obtained from teeth stored for ≥72 h, these can then be immortalized and still produce functional neurons for in vitro studies, but that constitutive hTERT immortalization is not be the best approach for long term use of patient derived DPSCs for the study of disease., (Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.)
- Published
- 2015
- Full Text
- View/download PDF
14. Assessment of the Tumorigenic Potential of Spontaneously Immortalized and hTERT-Immortalized Cultured Dental Pulp Stem Cells.
- Author
-
Wilson R, Urraca N, Skobowiat C, Hope KA, Miravalle L, Chamberlin R, Donaldson M, Seagroves TN, and Reiter LT
- Subjects
- Animals, Cell Differentiation genetics, Cell Transformation, Neoplastic, Dental Pulp cytology, Humans, Mice, Telomerase pharmacology, Dental Pulp transplantation, Neural Crest transplantation, Neurons cytology, Stem Cell Transplantation adverse effects
- Abstract
Dental pulp stem cells (DPSCs) provide an exciting new avenue to study neurogenetic disorders. DPSCs are neural crest-derived cells with the ability to differentiate into numerous tissues including neurons. The therapeutic potential of stem cell-derived lines exposed to culturing ex vivo before reintroduction into patients could be limited if the cultured cells acquired tumorigenic potential. We tested whether DPSCs that spontaneously immortalized in culture acquired features of transformed cells. We analyzed immortalized DPSCs for anchorage-independent growth, genomic instability, and ability to differentiate into neurons. Finally, we tested both spontaneously immortalized and human telomerase reverse transcriptase (hTERT)-immortalized DPSC lines for the ability to form tumors in immunocompromised animals. Although we observed increased colony-forming potential in soft agar for the spontaneously immortalized and hTERT-immortalized DPSC lines relative to low-passage DPSC, no tumors were detected from any of the DPSC lines tested. We noticed some genomic instability in hTERT-immortalized DPSCs but not in the spontaneously immortalized lines tested. We determined that immortalized DPSC lines generated in our laboratory, whether spontaneously or induced, have not acquired the potential to form tumors in mice. These data suggest cultured DPSC lines that can be differentiated into neurons may be safe for future in vivo therapy for neurobiological diseases., (©AlphaMed Press.)
- Published
- 2015
- Full Text
- View/download PDF
15. The interstitial duplication 15q11.2-q13 syndrome includes autism, mild facial anomalies and a characteristic EEG signature.
- Author
-
Urraca N, Cleary J, Brewer V, Pivnick EK, McVicar K, Thibert RL, Schanen NC, Esmer C, Lamport D, and Reiter LT
- Subjects
- Adolescent, Child, Child, Preschool, Chromosome Aberrations, Chromosomes, Human, Pair 15 genetics, Cohort Studies, DNA Copy Number Variations genetics, Female, Gene Duplication genetics, Genotype, Humans, In Situ Hybridization, Fluorescence methods, Male, Phenotype, Risk Factors, Sleep Wake Disorders genetics, Autistic Disorder genetics, Electroencephalography methods, Facies, Intellectual Disability genetics
- Abstract
Chromosomal copy number variants (CNV) are the most common genetic lesion found in autism. Many autism-associated CNVs are duplications of chromosome 15q. Although most cases of interstitial (int) dup(15) that present clinically are de novo and maternally derived or inherited, both pathogenic and unaffected paternal duplications of 15q have been identified. We performed a phenotype/genotype analysis of individuals with interstitial 15q duplications to broaden our understanding of the 15q syndrome and investigate the contribution of 15q duplication to increased autism risk. All subjects were recruited solely on the basis of interstitial duplication 15q11.2-q13 status. Comparative array genome hybridization was used to determine the duplication size and boundaries while the methylation status of the maternally methylated small nuclear ribonucleoprotein polypeptide N gene was used to determine the parent of origin of the duplication. We determined the duplication size and parental origin for 14 int dup(15) subjects: 10 maternal and 4 paternal cases. The majority of int dup(15) cases recruited were maternal in origin, most likely due to our finding that maternal duplication was coincident with autism spectrum disorder. The size of the duplication did not correlate with the severity of the phenotype as established by Autism Diagnostic Observation Scale calibrated severity score. We identified phenotypes not comprehensively described before in this cohort including mild facial dysmorphism, sleep problems and an unusual electroencephalogram variant. Our results are consistent with the hypothesis that the maternally expressed ubiquitin protein ligase E3A gene is primarily responsible for the autism phenotype in int dup(15) since all maternal cases tested presented on the autism spectrum., (© 2013 International Society for Autism Research, Wiley Periodicals, Inc.)
- Published
- 2013
- Full Text
- View/download PDF
16. Association study of DRD3 gene in schizophrenia in Mexican sib-pairs.
- Author
-
Urraca N, Camarena B, Aguilar A, Fresán A, Apiquián R, Orozco L, Carnevale A, and Nicolini H
- Subjects
- Adult, Female, Genetic Association Studies, Genotype, Glycine genetics, Humans, Male, Mexico, Serine genetics, Young Adult, Genetic Predisposition to Disease, Polymorphism, Single Nucleotide genetics, Receptors, Dopamine D3 genetics, Schizophrenia genetics, Siblings
- Abstract
Schizophrenia is a heritable, complex mental disorder. We analysed the DRD3 gene as a candidate to be related to schizophrenia and clinical features in affected sib-pairs. A positive association with the -250A/Ser9 haplotype and a trend toward an association with formal thought disorder were observed. A synergic effect of DRD3 polymorphisms on schizophrenia susceptibility is suggested., (Copyright © 2011 Elsevier Ltd. All rights reserved.)
- Published
- 2011
- Full Text
- View/download PDF
17. A single-tube quantitative high-resolution melting curve method for parent-of-origin determination of 15q duplications.
- Author
-
Urraca N, Davis L, Cook EH Jr, Schanen NC, and Reiter LT
- Subjects
- Adult, Child, DNA Mutational Analysis instrumentation, DNA Mutational Analysis standards, Female, Humans, Male, Molecular Diagnostic Techniques methods, Molecular Diagnostic Techniques standards, Mosaicism, Parents, Reference Standards, Trisomy diagnosis, Trisomy genetics, Uniparental Disomy diagnosis, Uniparental Disomy genetics, Chromosome Duplication, Chromosomes, Human, Pair 15 genetics, DNA Mutational Analysis methods, Inheritance Patterns genetics, Nucleic Acid Denaturation
- Abstract
The most common chromosomal abnormalities associated with autism are 15q11-q13 duplications. Maternally derived or inherited duplications of 15q pose a substantial risk for an autism phenotype, while paternally derived duplications may be incompletely penetrant or result in other neurodevelopmental problems. Therefore, the determination of maternal versus paternal origin of this duplication is important for early intervention therapies and for appropriate genetic counseling to the families. We adapted a previous single-reaction tube assay (high-resolution melting curve analysis) to determine the parent of origin of 15q duplications in 28 interstitial duplication 15q samples, one family and two isodicentric subjects. Our method distinguished parent origin in 92% of the independent samples as well as in the familial inherited duplication and in the two isodicentric samples. This method accurately determines parental origin of the duplicated segment and measures the dosage of these alleles in the sample. In addition, it can be performed on samples where parental DNA is not available for microsatellite analysis. The development of this single-tube assay will make it easier for genetic testing laboratories to provide parent-of-origin information and will provide important information to clinical geneticists about autism risk in these individuals.
- Published
- 2010
- Full Text
- View/download PDF
18. Attitudes and anticipated reactions to genetic testing for cancer among patients in Mexico City.
- Author
-
Romero-Hidalgo S, Urraca N, Parra D, Villa AR, Lisker R, and Carnevale A
- Subjects
- Adult, Aged, Female, Humans, Interviews as Topic, Male, Mass Screening, Mexico, Middle Aged, Patient Acceptance of Health Care, Surveys and Questionnaires, Attitude to Health, Breast Neoplasms diagnosis, Breast Neoplasms genetics, Breast Neoplasms prevention & control, Genetic Testing psychology, Prostatic Neoplasms diagnosis, Prostatic Neoplasms genetics, Prostatic Neoplasms prevention & control
- Abstract
The aim of this study was to investigate the attitudes toward cancer predictive genetic testing in a group of non-high-risk women and men and to analyze the factors that may influence their intention to use these tests. We studied a sample of 859 outpatient women and men attending the four tertiary care hospitals of the ISSSTE (Institute of Social Security and Services for Government Employees) in Mexico City. Subjects between the ages of 30 and 74 years with no present or past history of cancer were asked to answer a questionnaire through face-to-face interview. Two different questionnaires were designed, one for women and the other for men, regarding genetic testing of a high-risk gene for breast and prostate cancer, respectively. Descriptive statistics and univariate comparisons were carried out using chi-square test, Wilcoxon's signed rank test, and Friedman test. Multivariate analysis was performed using logistic regression technique. Results showed that the majority of women attended clinics for regular check-ups and for performing screening tests to detect breast cancer, and men did not follow this pattern regarding prostate cancer. Women were more motivated to get genetic testing, more aware about its benefits, and more concerned about having cancer than men.
- Published
- 2009
- Full Text
- View/download PDF
19. Association study of MAO-A and DRD4 genes in schizophrenic patients with aggressive behavior.
- Author
-
Fresan A, Camarena B, Apiquian R, Aguilar A, Urraca N, and Nicolini H
- Subjects
- Adult, Aged, Chi-Square Distribution, Female, Gene Frequency, Genotype, Humans, Male, Middle Aged, Polymorphism, Genetic genetics, Statistics, Nonparametric, Aggression, Genetic Predisposition to Disease, Monoamine Oxidase genetics, Receptors, Dopamine D4 genetics, Schizophrenia genetics, Schizophrenia physiopathology
- Abstract
Genes involved in dopamine neurotransmission are interesting candidates to be analyzed in schizophrenia and aggressive behavior. Therefore, we analyzed the functional polymorphisms of the dopamine receptor D4 (DRD4) and monoamine oxidase A (MAO-A) genes in a sample of 71 schizophrenic patients assessed with the Overt Aggression Scale to measure aggressive behavior. CLUMP analysis of the DRD4 48-bp repeat-exon III polymorphism in schizophrenic patients showed significant differences between the aggressive behavior and the nonaggressive groups (T1 = 18.77, d.f. = 6, p = 0.0046; T3 = 6.54, p = 0.0195). However, analysis of the promoter polymorphism of the MAO-A gene revealed no significant association between aggressive and nonaggressive patients. Finally, analysis of Overt Aggression Scale dimensions exhibited significant differences for the DRD4 and MAO-A genes. Our preliminary findings suggest that the DRD4 and MAO-A genes may be involved in aggressive schizophrenic patients., ((c) 2007 S. Karger AG, Basel.)
- Published
- 2007
- Full Text
- View/download PDF
20. An 8q21 deletion in a patient with comorbid psychosis and mental retardation.
- Author
-
Urraca N, Arenas-Sordo Mde L, Ortiz-Dominguez A, Martinez A, Molina B, Galvez A, and Nicolini H
- Subjects
- Adult, Carpal Bones abnormalities, Chromosome Banding, Chromosome Breakage genetics, Craniofacial Abnormalities diagnosis, Craniofacial Abnormalities genetics, Female, Humans, Karyotyping, Psychotic Disorders diagnosis, Synostosis diagnosis, Synostosis genetics, Chromosome Deletion, Chromosomes, Human, Pair 8, Intellectual Disability genetics, Psychotic Disorders genetics
- Abstract
Systematic investigations indicate that some of the recognized psychiatric disorders can be identified among those with mental retardation due to chromosomal abnormalities. We report a psychotic patient with mild mental retardation (intelligence quotient: 68) and minor anomalies that had a chromosomal aberration not previously described in a psychotic patient. Our patient highlights the importance of the cytogenetic study in psychiatric patients with comorbid mental retardation or minor anomalies. In addition, her psychosis symptoms may be helpful to propose a new candidate gene for psychosis.
- Published
- 2005
- Full Text
- View/download PDF
21. Mu opioid receptor gene as a candidate for the study of obsessive compulsive disorder with and without tics.
- Author
-
Urraca N, Camarena B, Gómez-Caudillo L, Esmer MC, and Nicolini H
- Subjects
- Adult, Alleles, Female, Gene Frequency, Genotype, Humans, Linkage Disequilibrium, Male, Obsessive-Compulsive Disorder complications, Polymorphism, Single Nucleotide, Genetic Predisposition to Disease genetics, Obsessive-Compulsive Disorder genetics, Receptors, Opioid, mu genetics, Tics complications
- Abstract
Obsessive compulsive disorder (OCD) is a complex psychiatric disease characterized by recurring obsessions or compulsions that cause significant distress to the patient. The etiology of this disorder remains largely unknown, although a genetic component has been suggested. Many candidates genes have been evaluated based on a possible serotoninergic and dopaminergic brain dysfunction. We postulate the micro opioid receptor (MOR) gene as a candidate because some observations support a role of the opioid system in OCD. The opioid antagonist, naloxone, rapidly exacerbates OCD symptoms and the opioid agonist, tramadol, was reported to be effective in the treatment of some patients. We studied two single nucleotide polymorphisms (C17T and A118G) in 51 trios with OCD. Genotyping was analyzed with transmission desequilibrium test (TDT). The allelic variant +17T of the C17T polymorphism had a low frequency (1%) in our population that did not allow for statistic analysis. However, for the allelic variant +G of the A118G polymorphism we were able to performed statistical comparisons. Our results showed a trend toward significance (chi(2) McNemar = 3.6, P = 0.065) for TDT in patients with comorbid tics. It is an interesting finding that should be tested in a larger sample of OCD patients with tics., (Copyright 2004 Wiley-Liss, Inc.)
- Published
- 2004
- Full Text
- View/download PDF
22. Patient follow-up is a major problem at genetics clinics.
- Author
-
Esmer C, Urraca N, Carnevale A, and Del Castillo V
- Subjects
- Follow-Up Studies, Genetic Predisposition to Disease prevention & control, Humans, Medical Records, Outpatient Clinics, Hospital, Patient Education as Topic, Genetic Counseling, Genetic Predisposition to Disease genetics, Genetic Testing, Patient Compliance, Patient Dropouts
- Abstract
Children with genetic diseases must be followed for long periods of time to seek new findings. Other patients require further check-ups and studies to be diagnosed. Some patients never return for medical care after the first consultation, which may have serious consequences. We reviewed 400 medical charts of patients with genetic disease to analyze overall attendance to the genetics clinic, investigate some of the causes of failure to seek medical advice, and determine the differences between those first seen as outpatients or as inpatients. The mean follow-up period was 8.3 months (range 0-79), and the average number of visits was 2.8 (range 1-16). Forty eight percent of the cases first seen as inpatients were evaluated only once and 14% twice; while 22 and 21% of the 300 cases first seen as outpatients attended once and twice, respectively (P = 0.0). Appointment keeping was apparently not affected by the presence or absence of diagnosis. Overall, 97 patients were discharged, 7 died, 55 continued on follow-up, 62 attended other hospital services-but not genetics-and 179 were completely lost to follow-up. Diagnosed patients were counseled more frequently than undiagnosed patients (62 vs. 5%); and 71% of the diagnosed patients first seen as outpatients but only 36% of undiagnosed cases first seen as inpatients were counseled, differences between these two groups were significant (P = 0.005). We conclude that keeping the patient with genetic disease on follow-up is a difficult task. New educational strategies must be planned to improve this worrisome situation., (Copyright 2003 Wiley-Liss, Inc.)
- Published
- 2004
- Full Text
- View/download PDF
23. Lack of association of apolipoprotein E polymorphism in obsessive-compulsive disorder.
- Author
-
Nicolini H, Urraca N, Camarena B, Gomez A, Martinez H, Rinetti G, Campillo C, Castelli P, Apiquian R, Fresan A, Garcia-Anaya M, and Cruz C
- Abstract
Obsessive-compulsive disorder (OCD) could be considered a neurodevelopmental disorder, from several lines of evidence. One of the most widely studied genes in these disorders is the apolipoprotein E gene, particularly allele 4. We analyzed for association among patients with OCD versus normal controls and cognitively impaired patients. There were no significant differences between OCD probands compared with population controls. However, the cognitively impaired group showed a higher frequency of allele apolipoprotein E gene compared with normal controls and patients with OCD.
- Published
- 2001
- Full Text
- View/download PDF
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.