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Liang K, Feliciano JL, Marrone KA, Murray JC, Hann CL, Anagnostou V, Tackett SA, Shin EJ, Hales RK, Voong KR, Battafarano RJ, Yang SC, Broderick SR, Ha JS, Forde PM, Brahmer JR, Lam VK. Clinical features and outcomes of advanced HER2+ esophageal/GEJ cancer with brain metastasis. ESMO Open 2024; 9:102199. [PMID: 38071928 PMCID: PMC10837776 DOI: 10.1016/j.esmoop.2023.102199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 10/30/2023] [Accepted: 11/15/2023] [Indexed: 01/26/2024] Open
Abstract
BACKGROUND Brain metastasis (BRM) is uncommon in gastroesophageal cancer. As such, clinicopathologic and molecular determinants of BRM and impact on clinical outcome remain incompletely understood. METHODS We retrospectively analyzed clinicopathologic data from advanced esophageal/gastroesophageal junction (E/GEJ) patients at Johns Hopkins from 2003 to 2021. We investigated the association between several clinical and molecular features and the occurrence of BRM, with particular focus on human epidermal growth factor receptor 2 (HER2) overexpression. Survival outcomes and time to BRM onset were also evaluated. RESULTS We included 515 patients with advanced E/GEJ cancer. Tumors were 78.3% esophageal primary, 82.9% adenocarcinoma, 31.0% HER2 positive. Cumulative incidence of BRM in the overall cohort and within HER2+ subgroup was 13.8% and 24.3%, respectively. HER2 overexpression was associated with increased risk of BRM [odds ratio 2.45; 95% confidence interval (CI) 1.10-5.46]. On initial presentation with BRM, 50.7% had a solitary brain lesion and 11.3% were asymptomatic. HER2+ status was associated with longer median time to onset of BRM (14.0 versus 6.3 months, P < 0.01), improved median progression free survival on first-line systemic therapy (hazard ratio 0.35, 95% CI 0.16-0.80), and improved median overall survival (hazard ratio 0.20, 95% CI 0.08-0.54) in patients with BRM. CONCLUSION HER2 overexpression identifies a gastroesophageal cancer molecular subtype that is significantly associated with increased risk of BRM, though with later onset of BRM and improved survival likely reflecting the impact of central nervous system-penetrant HER2-directed therapy. The prevalence of asymptomatic and solitary brain lesions suggests that brain surveillance for HER2+ patients warrants prospective investigation.
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Affiliation(s)
- K Liang
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, USA
| | - J L Feliciano
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, USA
| | - K A Marrone
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, USA
| | - J C Murray
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, USA
| | - C L Hann
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, USA
| | - V Anagnostou
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, USA
| | - S A Tackett
- Department of Medicine, Biostatistics, Epidemiology and Data Management (BEAD) Core, Johns Hopkins University School of Medicine, Baltimore, USA
| | - E J Shin
- Department of Gastroenterology & Hepatology, Johns Hopkins University School of Medicine, Baltimore, USA
| | - R K Hales
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, USA; Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, USA
| | - K R Voong
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, USA; Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, USA
| | - R J Battafarano
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, USA
| | - S C Yang
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, USA
| | - S R Broderick
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, USA
| | - J S Ha
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, USA
| | - P M Forde
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, USA
| | - J R Brahmer
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, USA
| | - V K Lam
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, USA.
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Petrin AL, Zeng E, Thomas MA, Moretti-Ferreira D, Marazita ML, Xie XJ, Murray JC, Moreno-Uribe LM. DNA methylation differences in monozygotic twins with Van der Woude syndrome. Front Dent Med 2023; 4:1120948. [PMID: 36936396 PMCID: PMC10019782 DOI: 10.3389/fdmed.2023.1120948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023] Open
Abstract
Introduction Van der Woude Syndrome (VWS) is an autosomal dominant disorder responsible for 2% of all syndromic orofacial clefts (OFCs) with IRF6 being the primary causal gene (70%). Cases may present with lip pits and either cleft lip, cleft lip with cleft palate, or cleft palate, with marked phenotypic discordance even among individuals carrying the same mutation. This suggests that genetic or epigenetic modifiers may play additional roles in the syndrome's etiology and variability in expression. We report the first DNA methylation profiling of 2 pairs of monozygotic twins with VWS. Our goal is to explore epigenetic contributions to VWS etiology and variable phenotypic expressivity by comparing DNAm profiles in both twin pairs. While the mutations that cause VWS in these twins are known, the additional mechanism behind their phenotypic risk and variability in expression remains unclear. Methods We generated whole genome DNAm data for both twin pairs. Differentially methylated positions (DMPs) were selected based on: (1) a coefficient of variation in DNAm levels in unaffected individuals < 20%, and (2) intra-twin pair absolute difference in DNAm levels >5% (delta beta > | 0.05|). We then divided the DMPs in two subgroups for each twin pair for further analysis: (1) higher methylation levels in twin A (Twin A > Twin B); and (2) higher methylation levels in twin B (Twin B >Twin A). Results and Discussion Gene ontology analysis revealed a list of enriched genes that showed significant differential DNAm, including clef-associated genes. Among the cleft-associated genes, TP63 was the most significant hit (p=7.82E-12). Both twin pairs presented differential DNAm levels in CpG sites in/near TP63 (Twin 1A > Twin 1B and Twin 2A < Twin 2B). The genes TP63 and IRF6 function in a biological regulatory loop to coordinate epithelial proliferation and differentiation in a process that is critical for palatal fusion. The effects of the causal mutations in IRF6 can be further impacted by epigenetic dysregulation of IRF6 itself, or genes in its pathway. Our data shows evidence that changes in DNAm is a plausible mechanism that can lead to markedly distinct phenotypes, even among individuals carrying the same mutation.
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Affiliation(s)
- A. L. Petrin
- College of Dentistry and Dental Clinics, University of Iowa, Iowa, IA, United States
- CORRESPONDENCE A. L. Petrin
| | - E. Zeng
- College of Dentistry and Dental Clinics, University of Iowa, Iowa, IA, United States
| | - M. A. Thomas
- Departments of Medical Genetics and Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - D. Moretti-Ferreira
- Department of Chemical and Biological Sciences, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - M. L. Marazita
- Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA, United States
| | - X. J. Xie
- College of Dentistry and Dental Clinics, University of Iowa, Iowa, IA, United States
| | - J. C. Murray
- Carver College of Medicine, University of Iowa, Iowa, IA, United States
| | - L. M. Moreno-Uribe
- College of Dentistry and Dental Clinics, University of Iowa, Iowa, IA, United States
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Gowans LJJ, Comnick CL, Mossey PA, Eshete MA, Adeyemo WL, Naicker T, Awotoye WA, Petrin A, Adeleke C, Donkor P, Busch TD, James O, Ogunlewe MO, Li M, Olotu J, Hassan M, Adeniyan OA, Obiri-Yeboah S, Arthur FKN, Agbenorku P, Oti AA, Olatosi O, Adamson OO, Fashina AA, Zeng E, Marazita ML, Adeyemo AA, Murray JC, Butali A. Genome-Wide Scan for Parent-of-Origin Effects in a sub-Saharan African Cohort With Nonsyndromic Cleft Lip and/or Cleft Palate (CL/P). Cleft Palate Craniofac J 2022; 59:841-851. [PMID: 34382870 PMCID: PMC9884465 DOI: 10.1177/10556656211036316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
OBJECTIVE Nonsyndromic cleft lip and/or cleft palate (NSCL/P) have multifactorial etiology where genetic factors, gene-environment interactions, stochastic factors, gene-gene interactions, and parent-of-origin effects (POEs) play cardinal roles. POEs arise when the parental origin of alleles differentially impacts the phenotype of the offspring. The aim of this study was to identify POEs that can increase risk for NSCL/P in humans using a genome-wide dataset. METHODS The samples (174 case-parent trios from Ghana, Ethiopia, and Nigeria) included in this study were from the African only genome wide association studies (GWAS) that was published in 2019. Genotyping of individual DNA using over 2 million multiethnic and African ancestry-specific single-nucleotide polymorphisms from the Illumina Multi-Ethnic Genotyping Array v2 15070954 A2 (genome build GRCh37/hg19) was done at the Center for Inherited Diseases Research. After quality control checks, PLINK was employed to carry out POE analysis employing the pooled subphenotypes of NSCL/P. RESULTS We observed possible hints of POEs at a cluster of genes at a 1 mega base pair window at the major histocompatibility complex class 1 locus on chromosome 6, as well as at other loci encompassing candidate genes such as ASB18, ANKEF1, AGAP1, GABRD, HHAT, CCT7, DNMT3A, EPHA7, FOXO3, lncRNAs, microRNA, antisense RNAs, ZNRD1, ZFAT, and ZBTB16. CONCLUSION Findings from our study suggest that some loci may increase the risk for NSCL/P through POEs. Additional studies are required to confirm these suggestive loci in NSCL/P etiology.
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Affiliation(s)
- LJJ Gowans
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana,School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana,Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa, IA, USA
| | - CL Comnick
- Division of Biostatistics and Computational Biology, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - PA Mossey
- Department of Orthodontics, University of Dundee, Dundee, UK
| | - MA Eshete
- Department of Surgery, School of Medicine, Addis Ababa University, Addis Ababa, Ethiopia
| | - WL Adeyemo
- Department of Oral and Maxillofacial Surgery, University of Lagos, Akoka, Lagos, Nigeria
| | - T Naicker
- Department of Pediatrics, University of KwaZulu-Natal and Inkosi Albert Luthuli Central Hospital, South Africa
| | - WA Awotoye
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa, IA, USA
| | - A Petrin
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa, IA, USA
| | - C Adeleke
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa, IA, USA
| | - P Donkor
- School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - TD Busch
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa, IA, USA
| | - O James
- Department of Oral and Maxillofacial Surgery, University of Lagos, Akoka, Lagos, Nigeria
| | - MO Ogunlewe
- Department of Oral and Maxillofacial Surgery, University of Lagos, Akoka, Lagos, Nigeria
| | - M Li
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa, IA, USA
| | - J Olotu
- Department of Anatomy, University of Port Harcourt, Nigeria
| | - M Hassan
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa, IA, USA
| | - OA Adeniyan
- NHS Foundation Trust (Queens Hospital, Belvedere Road, Burton-On-Trent), Staffordshire, UK
| | - S Obiri-Yeboah
- School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - FKN Arthur
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - P Agbenorku
- School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - AA Oti
- School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - O Olatosi
- Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - OO Adamson
- Department of Oral and Maxillofacial Surgery, University of Lagos, Akoka, Lagos, Nigeria
| | - AA Fashina
- Department of Oral and Maxillofacial Surgery, University of Lagos, Akoka, Lagos, Nigeria
| | - E Zeng
- Division of Biostatistics and Computational Biology, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - ML Marazita
- Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA,Clinical and Translational Science Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - AA Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, MD, USA
| | - JC Murray
- Department of Pediatrics, University of Iowa, Iowa, IA, USA
| | - A Butali
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa, IA, USA
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Hurst C, Murray JC, Granic A, Hillman SJ, Cooper R, Sayer AA, Robinson SM, Dodds RM. 684 LONG-TERM CONDITIONS, MULTIMORBIDITY, LIFESTYLE FACTORS AND GRIP STRENGTH CHANGE OVER 9 YEARS IN 44,315 UK BIOBANK PARTICIPANTS. Age Ageing 2022. [DOI: 10.1093/ageing/afac036.684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Introduction
Weak grip strength is associated with a range of adverse health outcomes, and an accelerated decline in grip strength confers an even greater risk. To date there has been limited research into the factors associated with change in grip strength in mid-life. Using data from UK Biobank our aim was to investigate the associations of long-term conditions (LTCs), multimorbidity and lifestyle factors with patterns of change in grip strength.
Methods
We used data from 44,315 UK Biobank participants with grip strength measured at baseline (2006–10) and a subsequent study visit around nine years later. At baseline, participants’ LTCs were self-reported and categorised against a hierarchy. Multimorbidity was characterised by the number of LTC categories present (0, 1, 2 and 3+). Lifestyle factors (body mass index (BMI), smoking, diet and physical activity) were also assessed. Change in grip strength was grouped into four patterns: decline, stable low, stable high or reference (no change or increase) and used as the outcome in multinomial logistic regression models.
Results
Most LTC categories were associated with adverse patterns of change in grip strength (stable low and/or decline): for example, musculoskeletal/trauma conditions were associated with an increased risk of the stable low pattern (Relative Risk Ratio [RRR] = 1.63; 95% Confidence Interval [CI] 1.49–1.79). Multimorbidity and lifestyle factors had independent associations with grip strength change: those with 3+ categories of LTCs were more likely to experience decline in grip strength (RRR = 1.18;95% CI 1.08–1.28) compared to those with no LTCs. Low physical activity was associated with adverse patterns of grip strength, while raised BMI had divergent associations (both the decline and stable high patterns of grip strength change).
Conclusion
Individuals living with multimorbidity and those with lifestyle risk factors such as low physical activity are at increased risk of loss of strength over time.
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Affiliation(s)
- C Hurst
- AGE Research Group, Newcastle University, UK
- NIHR Newcastle Biomedical Research Centre, Newcastle University and Newcastle upon Tyne NHS Foundation Trust, UK
| | - J C Murray
- AGE Research Group, Newcastle University, UK
- NIHR Newcastle Biomedical Research Centre, Newcastle University and Newcastle upon Tyne NHS Foundation Trust, UK
| | - A Granic
- AGE Research Group, Newcastle University, UK
- NIHR Newcastle Biomedical Research Centre, Newcastle University and Newcastle upon Tyne NHS Foundation Trust, UK
| | - S J Hillman
- AGE Research Group, Newcastle University, UK
- NIHR Newcastle Biomedical Research Centre, Newcastle University and Newcastle upon Tyne NHS Foundation Trust, UK
| | - R Cooper
- Department of Sport and Exercise Sciences, Manchester Metropolitan University, UK
| | - A A Sayer
- AGE Research Group, Newcastle University, UK
- NIHR Newcastle Biomedical Research Centre, Newcastle University and Newcastle upon Tyne NHS Foundation Trust, UK
| | - S M Robinson
- AGE Research Group, Newcastle University, UK
- NIHR Newcastle Biomedical Research Centre, Newcastle University and Newcastle upon Tyne NHS Foundation Trust, UK
| | - R M Dodds
- AGE Research Group, Newcastle University, UK
- NIHR Newcastle Biomedical Research Centre, Newcastle University and Newcastle upon Tyne NHS Foundation Trust, UK
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Awotoye W, Comnick C, Pendleton C, Zeng E, Alade A, Mossey PA, Gowans LJJ, Eshete MA, Adeyemo WL, Naicker T, Adeleke C, Busch T, Li M, Petrin A, Olotu J, Hassan M, Pape J, Miller SE, Donkor P, Anand D, Lachke SA, Marazita ML, Adeyemo AA, Murray JC, Albokhari D, Sobreira N, Butali A. Genome-wide Gene-by-Sex Interaction Studies Identify Novel Nonsyndromic Orofacial Clefts Risk Locus. J Dent Res 2021; 101:465-472. [PMID: 34689653 DOI: 10.1177/00220345211046614] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Risk loci identified through genome-wide association studies have explained about 25% of the phenotypic variations in nonsyndromic orofacial clefts (nsOFCs) on the liability scale. Despite the notable sex differences in the incidences of the different cleft types, investigation of loci for sex-specific effects has been understudied. To explore the sex-specific effects in genetic etiology of nsOFCs, we conducted a genome-wide gene × sex (GxSex) interaction study in a sub-Saharan African orofacial cleft cohort. The sample included 1,019 nonsyndromic orofacial cleft cases (814 cleft lip with or without cleft palate and 205 cleft palate only) and 2,159 controls recruited from 3 sites (Ethiopia, Ghana, and Nigeria). An additive logistic model was used to examine the joint effects of the genotype and GxSex interaction. Furthermore, we examined loci with suggestive significance (P < 1E-5) in the additive model for the effect of the GxSex interaction only. We identified a novel risk locus on chromosome 8p22 with genome-wide significant joint and GxSex interaction effects (rs2720555, p2df = 1.16E-08, pGxSex = 1.49E-09, odds ratio [OR] = 0.44, 95% CI = 0.34 to 0.57). For males, the risk of cleft lip with or without cleft palate at this locus decreases with additional copies of the minor allele (p < 0.0001, OR = 0.60, 95% CI = 0.48 to 0.74), but the effect is reversed for females (p = 0.0004, OR = 1.36, 95% CI = 1.15 to 1.60). We replicated the female-specific effect of this locus in an independent cohort (p = 0.037, OR = 1.30, 95% CI = 1.02 to 1.65), but no significant effect was found for the males (p = 0.29, OR = 0.86, 95% CI = 0.65 to 1.14). This locus is in topologically associating domain with craniofacially expressed and enriched genes during embryonic development. Rare coding mutations of some of these genes were identified in nsOFC cohorts through whole exome sequencing analysis. Our study is additional proof that genome-wide GxSex interaction analysis provides an opportunity for novel findings of loci and genes that contribute to the risk of nsOFCs.
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Affiliation(s)
- W Awotoye
- Iowa Institute for Oral Health Research, University of Iowa, Iowa City, IA, USA
| | - C Comnick
- Division of Biostatistics and Computational Biology, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - C Pendleton
- Division of Biostatistics and Computational Biology, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - E Zeng
- Division of Biostatistics and Computational Biology, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - A Alade
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA.,Department of Epidemiology, College of Public Health, University of Iowa, Iowa City, IA, USA
| | - P A Mossey
- Department of Orthodontics, University of Dundee, Dundee, UK
| | - L J J Gowans
- Komfo Anokye Teaching Hospital and Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - M A Eshete
- Department of Surgery, School of Medicine, Addis Ababa University, Addis Ababa, Ethiopia
| | - W L Adeyemo
- Department of Oral and Maxillofacial Surgery, University of Lagos, Lagos, Nigeria
| | - T Naicker
- Department of Pediatrics, University of KwaZulu-Natal, Durban, South Africa
| | - C Adeleke
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - T Busch
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - M Li
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - A Petrin
- Iowa Institute for Oral Health Research, University of Iowa, Iowa City, IA, USA
| | - J Olotu
- Department of Anatomy, University of Port Harcourt, Choba, Nigeria
| | - M Hassan
- Department of Orthodontics, University of Dundee, Dundee, UK
| | - J Pape
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - S E Miller
- Iowa Institute for Oral Health Research, University of Iowa, Iowa City, IA, USA
| | - P Donkor
- Department of Orthodontics, University of Dundee, Dundee, UK
| | - D Anand
- Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - S A Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE, USA.,Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA
| | - M L Marazita
- Center for Craniofacial and Dental Genetics, Departments of Oral Biology and Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - A A Adeyemo
- National Human Genomic Research Institute, Bethesda, MD, USA
| | - J C Murray
- Department of Pediatrics, University of Iowa, Iowa City, IA, USA
| | - D Albokhari
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - N Sobreira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - A Butali
- Iowa Institute for Oral Health Research, University of Iowa, Iowa City, IA, USA.,Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
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Bowden-Brown KJ, Murray JC, Hurst C, Granic A, Sayer AA, Dodds RM. 31 Physical Activity, Muscle Strength and Quantity: Preliminary Findings From the Mass_Lifecourse Cohort. Age Ageing 2021. [DOI: 10.1093/ageing/afab029.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Introduction
We established the MASS_Lifecourse study to investigate changes in skeletal muscle between ages 45–85. Reduced physical activity (PA) is a key factor linked to the development of sarcopenia. Our aim was the describe the amount and patterns of PA and sedentary behaviour (SB), and relationships with muscle strength and quantity, among MASS_Lifecourse participants.
Method
Participants wore a triaxial accelerometer on their dominant wrist for seven days. Recordings were analysed to calculate time in moderate-vigorous PA (MVPA) with time not in MVPA classified as SB based on wrist position. Muscle strength was measured with a Jamar grip dynamometer and the 5 chair-stand test. Muscle quantity was assessed using appendicular lean muscle mass from dual-energy X-ray absorptiometry. Physical performance was assessed by gait speed.
Results
68 participants (31 male) aged 47–84 (mean 65) participated in the present study. Median daily MVPA was 19.1 (IQR 7.1, 36.6) minutes and was lower with age. The mean sedentary time per day was 767.1 minutes per day and increased with age. The pattern of MVPA across the day changed with age: the oldest group (75–84 years) achieved a lower morning activity peak followed by an earlier decline whilst the younger groups were more consistently active throughout the day. Participants were more active than population reference data from the Active Lives Survey. Time spent in MVPA was positively associated with muscle strength and physical performance, whereas SB was negatively associated. Muscle quantity was not associated with PA or SB.
Conclusions
Participants in the MASS_Lifecourse study are more active than the general population but still show age-related declines in physical activity and strength. Future work in the cohort aims to elucidate mechanisms underlying the age-related loss of muscle strength and quantity.
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Affiliation(s)
- K J Bowden-Brown
- AGE Research Group, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
| | - J C Murray
- AGE Research Group, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
| | - C Hurst
- AGE Research Group, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
| | - A Granic
- AGE Research Group, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
| | - A A Sayer
- AGE Research Group, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
| | - R M Dodds
- AGE Research Group, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
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7
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Gray KJ, Kovacheva VP, Mirzakhani H, Bjonnes AC, Almoguera B, Wilson ML, Ingles SA, Lockwood CJ, Hakonarson H, McElrath TF, Murray JC, Norwitz ER, Karumanchi SA, Bateman BT, Keating BJ, Saxena R. Risk of pre-eclampsia in patients with a maternal genetic predisposition to common medical conditions: a case-control study. BJOG 2020; 128:55-65. [PMID: 32741103 DOI: 10.1111/1471-0528.16441] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/19/2020] [Indexed: 12/17/2022]
Abstract
OBJECTIVE To assess whether women with a genetic predisposition to medical conditions known to increase pre-eclampsia risk have an increased risk of pre-eclampsia in pregnancy. DESIGN Case-control study. SETTING AND POPULATION Pre-eclampsia cases (n = 498) and controls (n = 1864) in women of European ancestry from five US sites genotyped on a cardiovascular gene-centric array. METHODS Significant single-nucleotide polymorphisms (SNPs) from 21 traits in seven disease categories (cardiovascular, inflammatory/autoimmune, insulin resistance, liver, obesity, renal and thrombophilia) with published genome-wide association studies (GWAS) were used to create a genetic instrument for each trait. Multivariable logistic regression was used to test the association of each continuous scaled genetic instrument with pre-eclampsia. Odds of pre-eclampsia were compared across quartiles of the genetic instrument and evaluated for significance. MAIN OUTCOME MEASURES Genetic predisposition to medical conditions and relationship with pre-eclampsia. RESULTS An increasing burden of risk alleles for elevated diastolic blood pressure (DBP) and increased body mass index (BMI) were associated with an increased risk of pre-eclampsia (DBP, overall OR 1.11, 95% CI 1.01-1.21, P = 0.025; BMI, OR 1.10, 95% CI 1.00-1.20, P = 0.042), whereas alleles associated with elevated alkaline phosphatase (ALP) were protective (OR 0.89, 95% CI 0.82-0.97, P = 0.008), driven primarily by pleiotropic effects of variants in the FADS gene region. The effect of DBP genetic loci was even greater in early-onset pre-eclampsia cases (at <34 weeks of gestation, OR 1.30, 95% CI 1.08-1.56, P = 0.005). For other traits, there was no evidence of an association. CONCLUSIONS These results suggest that the underlying genetic architecture of pre-eclampsia may be shared with other disorders, specifically hypertension and obesity. TWEETABLE ABSTRACT A genetic predisposition to increased diastolic blood pressure and obesity increases the risk of pre-eclampsia.
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Affiliation(s)
- K J Gray
- Division of Maternal-Fetal Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - V P Kovacheva
- Department of Anesthesiology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - H Mirzakhani
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - A C Bjonnes
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - B Almoguera
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - M L Wilson
- Department of Preventative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - S A Ingles
- Department of Preventative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - C J Lockwood
- Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - H Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, Divisions of Human Genetics and Pulmonary Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - T F McElrath
- Division of Maternal-Fetal Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - J C Murray
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - E R Norwitz
- Department of Obstetrics & Gynecology, Tufts Medical Center, Boston, Massachusetts, USA
| | - S A Karumanchi
- Center for Vascular Biology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA.,Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - B T Bateman
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - B J Keating
- Department of Surgery and Pediatrics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - R Saxena
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
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8
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Eshete MA, Liu H, Li M, Adeyemo WL, Gowans LJJ, Mossey PA, Busch T, Deressa W, Donkor P, Olaitan PB, Aregbesola BS, Braimah RO, Oseni GO, Oginni F, Audu R, Onwuamah C, James O, Augustine-Akpan E, Rahman LA, Ogunlewe MO, Arthur FKN, Bello SA, Agbenorku P, Twumasi P, Abate F, Hailu T, Demissie Y, Hailu A, Plange-Rhule G, Obiri-Yeboah S, Dunnwald MM, Gravem PE, Marazita ML, Adeyemo AA, Murray JC, Cornell RA, Butali A. Loss-of-Function GRHL3 Variants Detected in African Patients with Isolated Cleft Palate. J Dent Res 2017; 97:41-48. [PMID: 28886269 DOI: 10.1177/0022034517729819] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
In contrast to the progress that has been made toward understanding the genetic etiology of cleft lip with or without cleft palate, relatively little is known about the genetic etiology for cleft palate only (CPO). A common coding variant of grainyhead like transcription factor 3 ( GRHL3) was recently shown to be associated with risk for CPO in Europeans. Mutations in this gene were also reported in families with Van der Woude syndrome. To identify rare mutations in GRHL3 that might explain the missing heritability for CPO, we sequenced GRHL3 in cases of CPO from Africa. We recruited participants from Ghana, Ethiopia, and Nigeria. This cohort included case-parent trios, cases and other family members, as well as controls. We sequenced exons of this gene in DNA from a total of 134 nonsyndromic cases. When possible, we sequenced them in parents to identify de novo mutations. Five novel mutations were identified: 2 missense (c.497C>A; p.Pro166His and c.1229A>G; p.Asp410Gly), 1 splice site (c.1282A>C p.Ser428Arg), 1 frameshift (c.470delC; p.Gly158Alafster55), and 1 nonsense (c.1677C>A; p.Tyr559Ter). These mutations were absent from 270 sequenced controls and from all public exome and whole genome databases, including the 1000 Genomes database (which includes data from Africa). However, 4 of the 5 mutations were present in unaffected mothers, indicating that their penetrance is incomplete. Interestingly, 1 mutation damaged a predicted sumoylation site, and another disrupted a predicted CK1 phosphorylation site. Overexpression assays in zebrafish and reporter assays in vitro indicated that 4 variants were functionally null or hypomorphic, while 1 was dominant negative. This study provides evidence that, as in Caucasian populations, mutations in GRHL3 contribute to the risk of nonsyndromic CPO in the African population.
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Affiliation(s)
- M A Eshete
- 1 School of Public Health, Addis Ababa University, Addis Ababa, Ethiopia.,2 Yekatit 12 Hospital Medical College, Addis Ababa, Ethiopia.,3 Department of Surgery, School of Medicine, Addis Ababa University, Addis Ababa, Ethiopia
| | - H Liu
- 4 Department of Anatomy and Cell Biology, University of Iowa, Iowa City, IA, USA.,5 State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory for Oral Biomedicine of Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - M Li
- 6 Department of Oral Pathology, Radiology and Medicine, University of Iowa, Iowa City, IA, USA
| | - W L Adeyemo
- 7 Department of Oral and Maxillofacial Surgery, University of Lagos, Lagos, Nigeria
| | - L J J Gowans
- 8 Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - P A Mossey
- 9 Department of Orthodontics, University of Dundee, Dundee, UK
| | - T Busch
- 6 Department of Oral Pathology, Radiology and Medicine, University of Iowa, Iowa City, IA, USA
| | - W Deressa
- 1 School of Public Health, Addis Ababa University, Addis Ababa, Ethiopia
| | - P Donkor
- 8 Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - P B Olaitan
- 10 Department of Plastic Surgery, Ladoke Akintola University of Science and Technology, Osogbo, Nigeria
| | - B S Aregbesola
- 11 Department of Oral and Maxillofacial Surgery, Obafemi Awolowo University, Ile Ife, Nigeria
| | - R O Braimah
- 12 Department of Oral and Maxillofacial Surgery, Usmanu Danfodiyo University, Sokoto, Nigeria
| | - G O Oseni
- 10 Department of Plastic Surgery, Ladoke Akintola University of Science and Technology, Osogbo, Nigeria
| | - F Oginni
- 11 Department of Oral and Maxillofacial Surgery, Obafemi Awolowo University, Ile Ife, Nigeria
| | - R Audu
- 13 Department of Virology, Nigerian Institute of Medical Research, Lagos, Nigeria
| | - C Onwuamah
- 13 Department of Virology, Nigerian Institute of Medical Research, Lagos, Nigeria
| | - O James
- 7 Department of Oral and Maxillofacial Surgery, University of Lagos, Lagos, Nigeria
| | - E Augustine-Akpan
- 6 Department of Oral Pathology, Radiology and Medicine, University of Iowa, Iowa City, IA, USA
| | - L A Rahman
- 14 Division of Pediatric Surgery, Department of Surgery, University of Ilorin, Ilorin, Nigeria
| | - M O Ogunlewe
- 7 Department of Oral and Maxillofacial Surgery, University of Lagos, Lagos, Nigeria
| | - F K N Arthur
- 8 Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - S A Bello
- 15 State House Clinic, Abuja, Nigeria
| | - P Agbenorku
- 8 Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - P Twumasi
- 8 Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - F Abate
- 2 Yekatit 12 Hospital Medical College, Addis Ababa, Ethiopia
| | - T Hailu
- 2 Yekatit 12 Hospital Medical College, Addis Ababa, Ethiopia
| | - Y Demissie
- 2 Yekatit 12 Hospital Medical College, Addis Ababa, Ethiopia.,3 Department of Surgery, School of Medicine, Addis Ababa University, Addis Ababa, Ethiopia
| | - A Hailu
- 2 Yekatit 12 Hospital Medical College, Addis Ababa, Ethiopia.,3 Department of Surgery, School of Medicine, Addis Ababa University, Addis Ababa, Ethiopia
| | - G Plange-Rhule
- 8 Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - S Obiri-Yeboah
- 8 Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - M M Dunnwald
- 4 Department of Anatomy and Cell Biology, University of Iowa, Iowa City, IA, USA
| | - P E Gravem
- 16 Plastic and Reconstructive Surgery Department, Haukeland University Hospital, Bergen, Norway
| | - M L Marazita
- 17 Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - A A Adeyemo
- 18 National Human Genomic Research Institute, Bethesda, MD, USA
| | - J C Murray
- 19 Department of Pediatrics University of Iowa, Iowa City, IA, USA
| | - R A Cornell
- 4 Department of Anatomy and Cell Biology, University of Iowa, Iowa City, IA, USA
| | - A Butali
- 6 Department of Oral Pathology, Radiology and Medicine, University of Iowa, Iowa City, IA, USA
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9
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Lansdon LA, Bernabe HV, Nidey N, Standley J, Schnieders MJ, Murray JC. The Use of Variant Maps to Explore Domain-Specific Mutations of FGFR1. J Dent Res 2017; 96:1339-1345. [PMID: 28825856 DOI: 10.1177/0022034517726496] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Here we describe the genotype-phenotype correlations of diseases caused by variants in Fibroblast Growth Factor Receptor 1 ( FGFR1) and report a novel, de novo variant in FGFR1 in an individual with multiple congenital anomalies. The proband presented with bilateral cleft lip and palate, malformed auricles, and bilateral ectrodactyly of his hands and feet at birth. He was later diagnosed with diabetes insipidus, spastic quadriplegia, developmental delay, agenesis of the corpus callosum, and enlargement of the third cerebral ventricle. We noted the substantial phenotypic overlap with individuals with Hartsfield syndrome, the rare combination of holoprosencephaly and ectrodactyly. Sequencing of FGFR1 identified a previously unreported de novo variant in exon 11 (p.Gly487Cys), which we modeled to determine its predicted effect on the protein structure. Although it was not predicted to significantly alter protein folding stability, it is possible this variant leads to the formation of nonnative intra- or intermolecular disulfide bonds. We then mapped this and other disease-associated variants to a 3-dimensional model of FGFR1 to assess which protein domains harbored the highest number of pathogenic changes. We observed the greatest number of variants within the domains involved in FGF binding and FGFR activation. To further explore the contribution of each variant to disease, we recorded the phenotype resulting from each FGFR1 variant to generate a series of phenotype-specific protein maps and compared our results to benign variants appearing in control databases. It is our hope that the use of phenotypic maps such as these will further the understanding of genetic disease in general and diseases caused by variation in FGFR1 specifically.
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Affiliation(s)
- L A Lansdon
- 1 Department of Pediatrics, University of Iowa, Iowa City, IA, USA.,2 Department of Biology, University of Iowa, Iowa City, IA, USA.,3 Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA, USA
| | - H V Bernabe
- 4 Department of Biomedical Engineering, University of Iowa, Iowa City, IA, USA
| | - N Nidey
- 1 Department of Pediatrics, University of Iowa, Iowa City, IA, USA
| | - J Standley
- 1 Department of Pediatrics, University of Iowa, Iowa City, IA, USA
| | - M J Schnieders
- 4 Department of Biomedical Engineering, University of Iowa, Iowa City, IA, USA
| | - J C Murray
- 1 Department of Pediatrics, University of Iowa, Iowa City, IA, USA.,3 Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA, USA
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10
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Parada-Sanchez MT, Chu EY, Cox LL, Undurty SS, Standley JM, Murray JC, Cox TC. Disrupted IRF6-NME1/2 Complexes as a Cause of Cleft Lip/Palate. J Dent Res 2017; 96:1330-1338. [PMID: 28767310 DOI: 10.1177/0022034517723615] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Mutations and common polymorphisms in interferon regulatory factor 6 ( IRF6) are associated with both syndromic and nonsyndromic forms of cleft lip/palate (CLP). To date, much of the focus on this transcription factor has been on identifying its direct targets and the gene regulatory network in which it operates. Notably, however, IRF6 is found predominantly in the cytoplasm, with its import into the nucleus tightly regulated like other members of the IRF family. To provide further insight into the role of IRF6 in the pathogenesis of CLP, we sought to identify direct IRF6 protein interactors using a combination of yeast 2-hybrid screens and co-immunoprecipitation assays. Using this approach, we identified NME1 and NME2, well-known regulators of Rho-type GTPases, E-cadherin endocytosis, and epithelial junctional remodeling, as bona fide IRF6 partner proteins. The NME proteins co-localize with IRF6 in the cytoplasm of primary palatal epithelial cells in vivo, and their interaction with IRF6 is significantly enhanced by phosphorylation of key serine residues in the IRF6 C-terminus. Furthermore, CLP associated IRF6 missense mutations disrupt the ability of IRF6 to bind the NME proteins and result in elevated activation of Rac1 and RhoA, compared to wild-type IRF6, when ectopically expressed in 293T epithelial cells. Significantly, we also report the identification of 2 unique missense mutations in the NME proteins in patients with CLP (NME1 R18Q in an IRF6 and GRHL3 mutation-negative patient with van der Woude syndrome and NME2 G71V in a patient with nonsyndromic CLP). Both variants disrupted the ability of the respective proteins to interact with IRF6. The data presented suggest an important role for cytoplasmic IRF6 in regulating the availability or localization of the NME1/2 complex and thus the dynamic behavior of epithelia during lip/palate development.
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Affiliation(s)
- M T Parada-Sanchez
- 1 School of Dentistry, Universidad de Antioquia, Medellín, Colombia.,2 Departments of Oral Health Sciences, University of Washington, Seattle, WA, USA
| | - E Y Chu
- 2 Departments of Oral Health Sciences, University of Washington, Seattle, WA, USA
| | - L L Cox
- 3 Departments of Pediatrics (Craniofacial Medicine), University of Washington, Seattle, WA, USA.,4 Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA, USA
| | - S S Undurty
- 5 Division of Neonatology, Department of Pediatrics, University of Iowa, Iowa City, IA, USA
| | - J M Standley
- 5 Division of Neonatology, Department of Pediatrics, University of Iowa, Iowa City, IA, USA
| | - J C Murray
- 5 Division of Neonatology, Department of Pediatrics, University of Iowa, Iowa City, IA, USA
| | - T C Cox
- 3 Departments of Pediatrics (Craniofacial Medicine), University of Washington, Seattle, WA, USA.,4 Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA, USA.,6 Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia
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11
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Moreno Uribe LM, Fomina T, Munger RG, Romitti PA, Jenkins MM, Gjessing HK, Gjerdevik M, Christensen K, Wilcox AJ, Murray JC, Lie RT, Wehby GL. A Population-Based Study of Effects of Genetic Loci on Orofacial Clefts. J Dent Res 2017; 96:1322-1329. [PMID: 28662356 DOI: 10.1177/0022034517716914] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Prior genome-wide association studies for oral clefts have focused on clinic-based samples with unclear generalizability. Prior samples were also small for investigating effects by cleft type and exclusively studied isolated clefts (those occurring without other birth defects). We estimated the effects of 17 top loci on cleft types in both isolated and nonisolated cases in the largest consortium to date of European-descent population-based studies. Our analytic approach focused on a mother-child dyad case-control design, but it also allowed analyzing mother-only or child-only genotypes to maximize power. Our total sample included 1,875 cases with isolated clefts, 459 cases with nonisolated clefts, and 3,749 controls. After correcting for multiple testing, we observed significant associations between fetal single-nucleotide polymorphisms (SNPs) at IRF6, PAX7, 8q21.3, 8q24, KIAA1598-VAX1, and MAFB and isolated cleft lip only (CLO) and cleft lip and palate (CLP). Significant associations were observed between isolated CLO and fetal SNPs near TPM1 and NOG1 and between CLP and fetal SNPs at ABCA4-ARHGAP29, THADA, FOXE1, and SPRY2. Overall, effects were similar for isolated CLO and CLP, except for ABCA4-ARHGAP29. A protective effect was observed for the fetal NOG1 SNP on cleft palate only, opposite in direction to the effect on CLO. For most fetal SNPs, a dose-response allelic effect was observed. No evidence of parent-of-origin or maternal genome effects was observed. Overall, effect direction and magnitude were similar between isolated and nonisolated clefts, suggesting that several loci are modifiers of cleft risk in both isolated and nonisolated forms. Our results provide reliable estimates of the effects of top loci on risks of oral clefts in a population of European descent.
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Affiliation(s)
- L M Moreno Uribe
- 1 Department of Orthodontics and Dows Institute, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - T Fomina
- 2 Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - R G Munger
- 3 Department of Nutrition and Food Sciences, Utah State University, Logan, UT, USA
| | - P A Romitti
- 4 Department of Epidemiology, College of Public Health, University of Iowa, Iowa City, IA, USA
| | - M M Jenkins
- 5 National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - H K Gjessing
- 2 Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,6 Norwegian Institute of Public Health, Bergen and Oslo, Norway
| | - M Gjerdevik
- 2 Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,6 Norwegian Institute of Public Health, Bergen and Oslo, Norway
| | - K Christensen
- 7 Department of Public Health, University of Southern Denmark; Department of Clinical Genetics and Department of Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark
| | - A J Wilcox
- 8 Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, USA
| | - J C Murray
- 9 Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - R T Lie
- 2 Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,6 Norwegian Institute of Public Health, Bergen and Oslo, Norway
| | - G L Wehby
- 10 Departments of Health Management and Policy, Economics, and Preventive and Community Dentistry, and Public Policy Center, University of Iowa, Iowa City, IA, USA
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12
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Gowans LJJ, Adeyemo WL, Eshete M, Mossey PA, Busch T, Aregbesola B, Donkor P, Arthur FKN, Bello SA, Martinez A, Li M, Augustine-Akpan EA, Deressa W, Twumasi P, Olutayo J, Deribew M, Agbenorku P, Oti AA, Braimah R, Plange-Rhule G, Gesses M, Obiri-Yeboah S, Oseni GO, Olaitan PB, Abdur-Rahman L, Abate F, Hailu T, Gravem P, Ogunlewe MO, Buxó CJ, Marazita ML, Adeyemo AA, Murray JC, Butali A. Association Studies and Direct DNA Sequencing Implicate Genetic Susceptibility Loci in the Etiology of Nonsyndromic Orofacial Clefts in Sub-Saharan African Populations. J Dent Res 2016; 95:1245-56. [PMID: 27369588 DOI: 10.1177/0022034516657003] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Orofacial clefts (OFCs) are congenital dysmorphologies of the human face and oral cavity, with a global incidence of 1 per 700 live births. These anomalies exhibit a multifactorial pattern of inheritance, with genetic and environmental factors both playing crucial roles. Many loci have been implicated in the etiology of nonsyndromic cleft lip with or without cleft palate (NSCL/P) in populations of Asian and European ancestries, through genome-wide association studies and candidate gene studies. However, few populations of African descent have been studied to date. Here, the authors show evidence of an association of some loci with NSCL/P and nonsyndromic cleft palate only (NSCPO) in cohorts from Africa (Ghana, Ethiopia, and Nigeria). The authors genotyped 48 single-nucleotide polymorphisms that were selected from previous genome-wide association studies and candidate gene studies. These markers were successfully genotyped on 701 NSCL/P and 163 NSCPO cases, 1,070 unaffected relatives, and 1,078 unrelated controls. The authors also directly sequenced 7 genes in 184 nonsyndromic OFC (NSOFC) cases and 96 controls from Ghana. Population-specific associations were observed in the case-control analyses of the subpopulations, with West African subpopulations (Ghana and Nigeria) showing a similar pattern of associations. In meta-analyses of the case-control cohort, PAX7 (rs742071, P = 5.10 × 10(-3)), 8q24 (rs987525, P = 1.22 × 10(-3)), and VAX1 (rs7078160, P = 0.04) were nominally associated with NSCL/P, and MSX1 (rs115200552, P = 0.01), TULP4 (rs651333, P = 0.04), CRISPLD2 (rs4783099, P = 0.02), and NOG1 (rs17760296, P = 0.04) were nominally associated with NSCPO. Moreover, 7 loci exhibited evidence of threshold overtransmission in NSOFC cases through the transmission disequilibrium test and through analyses of the family-based association for disease traits. Through DNA sequencing, the authors also identified 2 novel, rare, potentially pathogenic variants (p.Asn323Asp and p.Lys426IlefsTer6) in ARHGAP29 In conclusion, the authors have shown evidence for the association of many loci with NSCL/P and NSCPO. To the best of this knowledge, this study is the first to demonstrate any of these association signals in any African population.
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Affiliation(s)
- L J J Gowans
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana Cleft Clinic, Komfo Anokye Teaching Hospital, Kumasi, Ghana Department of Pediatrics, University of Iowa, Iowa City, IA, USA Department of Oral Pathology, Radiology and Medicine, University of Iowa, Iowa City, IA, USA
| | - W L Adeyemo
- College of Medicine, University of Lagos, Lagos, Nigeria
| | - M Eshete
- Addis Ababa University, Addis Ababa, Ethiopia
| | - P A Mossey
- Department of Orthodontics, University of Dundee, Dundee, Scotland
| | - T Busch
- Department of Oral Pathology, Radiology and Medicine, University of Iowa, Iowa City, IA, USA
| | - B Aregbesola
- Obafemi Awolowo University Teaching Hospital, Ile-Ife, Nigeria
| | - P Donkor
- Cleft Clinic, Komfo Anokye Teaching Hospital, Kumasi, Ghana Department of Surgery, School of Medical Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - F K N Arthur
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - S A Bello
- Department of Oral and Maxillofacial Surgery, State House Hospital, Abuja, Nigeria
| | - A Martinez
- Department of Oral Pathology, Radiology and Medicine, University of Iowa, Iowa City, IA, USA
| | - M Li
- Department of Oral Pathology, Radiology and Medicine, University of Iowa, Iowa City, IA, USA
| | - E A Augustine-Akpan
- Department of Oral Pathology, Radiology and Medicine, University of Iowa, Iowa City, IA, USA
| | - W Deressa
- Addis Ababa University, Addis Ababa, Ethiopia
| | - P Twumasi
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - J Olutayo
- College of Medicine, University of Lagos, Lagos, Nigeria
| | - M Deribew
- Addis Ababa University, Addis Ababa, Ethiopia
| | - P Agbenorku
- Cleft Clinic, Komfo Anokye Teaching Hospital, Kumasi, Ghana Department of Surgery, School of Medical Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - A A Oti
- Cleft Clinic, Komfo Anokye Teaching Hospital, Kumasi, Ghana Department of Surgery, School of Medical Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - R Braimah
- Obafemi Awolowo University Teaching Hospital, Ile-Ife, Nigeria
| | - G Plange-Rhule
- Cleft Clinic, Komfo Anokye Teaching Hospital, Kumasi, Ghana
| | - M Gesses
- Yekatit 12 Hospital Medical College, Addis Ababa, Ethiopia
| | - S Obiri-Yeboah
- Cleft Clinic, Komfo Anokye Teaching Hospital, Kumasi, Ghana Department of Surgery, School of Medical Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - G O Oseni
- Department of Burns and Plastic Surgery, Ladoke Akintola University of Technology Teaching Hospital, Osogbo, Nigeria
| | - P B Olaitan
- Department of Burns and Plastic Surgery, Ladoke Akintola University of Technology Teaching Hospital, Osogbo, Nigeria
| | - L Abdur-Rahman
- Division of Pediatric Surgery, Department of Surgery, University of Ilorin, Ilorin, Nigeria
| | - F Abate
- Yekatit 12 Hospital Medical College, Addis Ababa, Ethiopia
| | - T Hailu
- Yekatit 12 Hospital Medical College, Addis Ababa, Ethiopia
| | - P Gravem
- Haukeland University Hospital Bergen, Bergen, Norway
| | - M O Ogunlewe
- Department of Burns and Plastic Surgery, Ladoke Akintola University of Technology Teaching Hospital, Osogbo, Nigeria
| | - C J Buxó
- School of Dental Medicine, University of Puerto Rico Medical Science Campus, San Juan, Puerto Rico
| | - M L Marazita
- Department of Oral Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - A A Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - J C Murray
- Department of Pediatrics, University of Iowa, Iowa City, IA, USA
| | - A Butali
- Department of Oral Pathology, Radiology and Medicine, University of Iowa, Iowa City, IA, USA
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13
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Abstract
We report the case of a 53-year-old female, treated by bisphosphonate for 12 years, who presented atraumatic fractures of both fibulas. Her X-rays showed bilateral distal fibula fractures with radiological features similar to atypical femur fractures. The distal fibula should be considered as a potential site for stress fractures in bisphosphonate users. Bisphosphonates are the most widely used drugs in the treatment of osteoporosis. During the last decade, the occurrence of atypical fractures, mostly subtrochanteric and diaphyseal femoral fractures, has been acknowledged in patients with long-term use of bisphosphonates. We report the case of a 53-year-old female on alendronate therapy for the past 12 years who presented with a few months history of atraumatic right, and subsequently left, lateral ankle pain. Her X-rays showed bilateral distal fibula fractures with radiological features similar to atypical femur fractures. She had been treated conservatively with walking boots and her treatment with bisphosphonate had been stopped 5 months prior to the fractures. Callus was progressively seen on serial follow-up X-rays, and both fractures healed completely within a reasonable period of 1 year. Investigations did not reveal any secondary causes of osteoporosis or metabolic bone disorders. To our knowledge, this is the first reported case of bilateral distal fibula fractures in a patient on long-term bisphosphonate therapy.
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Affiliation(s)
- J C Murray
- Division of Orthopaedic Surgery, Department of Surgery, CHU de Québec and Université Laval, Québec, QC, Canada
| | - M C Audet
- Division of Rheumatology, Department of Medicine, Université Laval, Québec, QC, Canada
- Department of Rheumatology, CHU de Québec, Québec, QC, Canada
| | - M Bédard
- Division of Orthopaedic Surgery, Department of Surgery, CHU de Québec and Université Laval, Québec, QC, Canada
| | - L Michou
- Division of Rheumatology, Department of Medicine, Université Laval, Québec, QC, Canada.
- Department of Rheumatology, CHU de Québec, Québec, QC, Canada.
- CHU de Québec Research Centre, Québec, QC, G1V 4G2, Canada.
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14
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Leslie EJ, Koboldt DC, Kang CJ, Ma L, Hecht JT, Wehby GL, Christensen K, Czeizel AE, Deleyiannis FWB, Fulton RS, Wilson RK, Beaty TH, Schutte BC, Murray JC, Marazita ML. IRF6 mutation screening in non-syndromic orofacial clefting: analysis of 1521 families. Clin Genet 2015; 90:28-34. [PMID: 26346622 DOI: 10.1111/cge.12675] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 09/03/2015] [Accepted: 09/04/2015] [Indexed: 01/12/2023]
Abstract
Van der Woude syndrome (VWS) is an autosomal dominant malformation syndrome characterized by orofacial clefting (OFC) and lower lip pits. The clinical presentation of VWS is variable and can present as an isolated OFC, making it difficult to distinguish VWS cases from individuals with non-syndromic OFCs. About 70% of causal VWS mutations occur in IRF6, a gene that is also associated with non-syndromic OFCs. Screening for IRF6 mutations in apparently non-syndromic cases has been performed in several modestly sized cohorts with mixed results. In this study, we screened 1521 trios with presumed non-syndromic OFCs to determine the frequency of causal IRF6 mutations. We identified seven likely causal IRF6 mutations, although a posteriori review identified two misdiagnosed VWS families based on the presence of lip pits. We found no evidence for association between rare IRF6 polymorphisms and non-syndromic OFCs. We combined our results with other similar studies (totaling 2472 families) and conclude that causal IRF6 mutations are found in 0.24-0.44% of apparently non-syndromic OFC families. We suggest that clinical mutation screening for IRF6 be considered for certain family patterns such as families with mixed types of OFCs and/or autosomal dominant transmission.
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Affiliation(s)
- E J Leslie
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - D C Koboldt
- The Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - C J Kang
- The Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - L Ma
- Department of Oral Maxillofacial Surgery, Peking University School of Stomatology, Beijing, China
| | - J T Hecht
- Department of Pediatrics, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - G L Wehby
- Department of Health Management and Policy, College of Public Health, University of Iowa, Iowa City, IA, USA
| | - K Christensen
- Department of Epidemiology, Institute of Public Health, University of Southern Denmark, Odense, Denmark
| | - A E Czeizel
- Foundation for the Community Control of Hereditary Diseases, Budapest, Hungary
| | - F W-B Deleyiannis
- Department of Surgery, Plastic and Reconstructive Surgery, University of Colorado School of Medicine, Denver, CO, USA
| | - R S Fulton
- The Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - R K Wilson
- The Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - T H Beaty
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - B C Schutte
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - J C Murray
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - M L Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
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15
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Hewett PW, Murray JC. Human omental mesothelial cells: a simple method for isolation and discrimination from endothelial cells. In Vitro Cell Dev Biol Anim 2015; 30A:145-7. [PMID: 25939161 DOI: 10.1007/bf02631436] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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16
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Kim B, Wang S, Lee JM, Jeong Y, Ahn T, Son DS, Park HW, Yoo HS, Song YJ, Lee E, Oh YM, Lee SB, Choi J, Murray JC, Zhou Y, Song PH, Kim KA, Weiner LM. Synthetic lethal screening reveals FGFR as one of the combinatorial targets to overcome resistance to Met-targeted therapy. Oncogene 2014; 34:1083-93. [PMID: 24662823 DOI: 10.1038/onc.2014.51] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 12/30/2013] [Accepted: 01/14/2014] [Indexed: 12/28/2022]
Abstract
Met is a receptor tyrosine kinase that promotes cancer progression. In addition, Met has been implicated in resistance of tumors to various targeted therapies such as epidermal growth factor receptor inhibitors in lung cancers, and has been prioritized as a key molecular target for cancer therapy. However, the underlying mechanism of resistance to Met-targeting drugs is poorly understood. Here, we describe screening of 1310 genes to search for key regulators related to drug resistance to an anti-Met therapeutic antibody (SAIT301) by using a small interfering RNA-based synthetic lethal screening method. We found that knockdown of 69 genes in Met-amplified MKN45 cells sensitized the antitumor activity of SAIT301. Pathway analysis of these 69 genes implicated fibroblast growth factor receptor (FGFR) as a key regulator for antiproliferative effects of Met-targeting drugs. Inhibition of FGFR3 increased target cell apoptosis through the suppression of Bcl-xL expression, followed by reduced cancer cell growth in the presence of Met-targeting drugs. Treatment of cells with the FGFR inhibitors substantially restored the efficacy of SAIT301 in SAIT301-resistant cells and enhanced the efficacy in SAIT301-sensitive cells. In addition to FGFR3, integrin β3 is another potential target for combination treatment with SAIT301. Suppression of integrin β3 decreased AKT phosphorylation in SAIT301-resistant cells and restored SAIT301 responsiveness in HCC1954 cells, which are resistant to SAIT301. Gene expression analysis using CCLE database shows that cancer cells with high levels of FGFR and integrin β3 are resistant to crizotinib treatment, suggesting that FGFR and integrin β3 could be used as predictive markers for Met-targeted therapy and provide a potential therapeutic option to overcome acquired and innate resistance for the Met-targeting drugs.
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Affiliation(s)
- B Kim
- BioTherapeutics Lab, Samsung Advanced Institute of Technology (SAIT), Giheung-gu, Yongin-si, Gyeonggi-do, South Korea
| | - S Wang
- Lombardi Comprehensive Cancer Center, Department of Oncology, Georgetown University Medical Center, Washington, DC, USA
| | - J M Lee
- BioTherapeutics Lab, Samsung Advanced Institute of Technology (SAIT), Giheung-gu, Yongin-si, Gyeonggi-do, South Korea
| | - Y Jeong
- BioTherapeutics Lab, Samsung Advanced Institute of Technology (SAIT), Giheung-gu, Yongin-si, Gyeonggi-do, South Korea
| | - T Ahn
- BioTherapeutics Lab, Samsung Advanced Institute of Technology (SAIT), Giheung-gu, Yongin-si, Gyeonggi-do, South Korea
| | - D-S Son
- BioTherapeutics Lab, Samsung Advanced Institute of Technology (SAIT), Giheung-gu, Yongin-si, Gyeonggi-do, South Korea
| | - H W Park
- BioTherapeutics Lab, Samsung Advanced Institute of Technology (SAIT), Giheung-gu, Yongin-si, Gyeonggi-do, South Korea
| | - H-s Yoo
- BioTherapeutics Lab, Samsung Advanced Institute of Technology (SAIT), Giheung-gu, Yongin-si, Gyeonggi-do, South Korea
| | - Y-J Song
- BioTherapeutics Lab, Samsung Advanced Institute of Technology (SAIT), Giheung-gu, Yongin-si, Gyeonggi-do, South Korea
| | - E Lee
- BioTherapeutics Lab, Samsung Advanced Institute of Technology (SAIT), Giheung-gu, Yongin-si, Gyeonggi-do, South Korea
| | - Y M Oh
- BioTherapeutics Lab, Samsung Advanced Institute of Technology (SAIT), Giheung-gu, Yongin-si, Gyeonggi-do, South Korea
| | - S B Lee
- BioTherapeutics Lab, Samsung Advanced Institute of Technology (SAIT), Giheung-gu, Yongin-si, Gyeonggi-do, South Korea
| | - J Choi
- BioTherapeutics Lab, Samsung Advanced Institute of Technology (SAIT), Giheung-gu, Yongin-si, Gyeonggi-do, South Korea
| | - J C Murray
- Lombardi Comprehensive Cancer Center, Department of Oncology, Georgetown University Medical Center, Washington, DC, USA
| | - Y Zhou
- Biostatistics and Bioinformatics Facility, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - P H Song
- BioTherapeutics Lab, Samsung Advanced Institute of Technology (SAIT), Giheung-gu, Yongin-si, Gyeonggi-do, South Korea
| | - K-A Kim
- BioTherapeutics Lab, Samsung Advanced Institute of Technology (SAIT), Giheung-gu, Yongin-si, Gyeonggi-do, South Korea
| | - L M Weiner
- Lombardi Comprehensive Cancer Center, Department of Oncology, Georgetown University Medical Center, Washington, DC, USA
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17
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Weh E, Reis LM, Tyler RC, Bick D, Rhead WJ, Wallace S, McGregor TL, Dills SK, Chao MC, Murray JC, Semina EV. Novel B3GALTL mutations in classic Peters plus syndrome and lack of mutations in a large cohort of patients with similar phenotypes. Clin Genet 2013; 86:142-8. [PMID: 23889335 DOI: 10.1111/cge.12241] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Revised: 07/17/2013] [Accepted: 07/17/2013] [Indexed: 11/30/2022]
Abstract
Peters plus syndrome (PPS) is a rare autosomal-recessive disorder characterized by Peters anomaly of the eye, short stature, brachydactyly, dysmorphic facial features, developmental delay, and variable other systemic abnormalities. In this report, we describe screening of 64 patients affected with PPS, isolated Peters anomaly and PPS-like phenotypes. Mutations in the coding region of B3GALTL were identified in nine patients; six had a documented phenotype of classic PPS and the remaining three had a clinical diagnosis of PPS with incomplete clinical documentation. A total of nine different pathogenic alleles were identified. Five alleles are novel including one frameshift, c.168dupA, p.(Gly57Argfs*11), one nonsense, c.1234C>T, p.(Arg412*), two missense, c.1045G>A, p.(Asp349Asn) and c.1181G>A, p.(Gly394Glu), and one splicing, c.347+5G>T, mutations. Consistent with previous reports, the c.660+1G>A mutation was the most common mutation identified, seen in eight of the nine patients and accounting for 55% of pathogenic alleles in this study and 69% of all reported pathogenic alleles; while two patients were homozygous for this mutation, the majority had a second rare pathogenic allele. We also report the absence of B3GALTL mutations in 55 cases of PPS-like phenotypes or isolated Peters anomaly, further establishing the strong association of B3GALTL mutations with classic PPS only.
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Affiliation(s)
- E Weh
- Department of Pediatrics, Children's Research Institute, Medical College of Wisconsin, Children's Hospital of Wisconsin, Milwaukee, WI, USA; Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI, USA
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18
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Mann PC, Cooper ME, Ryckman KK, Comas B, Gili J, Crumley S, Bream EN, Byers HM, Piester T, Schaefer A, Christine PJ, Lawrence A, Schaa KL, Kelsey KJ, Berends SK, Gadow E, Cosentino V, Castilla EE, Camelo JL, Saleme C, Day LJ, England SK, Marazita ML, Dagle JM, Murray JC, Murray JC. Polymorphisms in the fetal progesterone receptor and a calcium-activated potassium channel isoform are associated with preterm birth in an Argentinian population. J Perinatol 2013; 33:336-40. [PMID: 23018797 PMCID: PMC3719965 DOI: 10.1038/jp.2012.118] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
OBJECTIVE To investigate genetic etiologies of preterm birth (PTB) in Argentina through evaluation of single-nucleotide polymorphisms (SNPs) in candidate genes and population genetic admixture. STUDY DESIGN Genotyping was performed in 389 families. Maternal, paternal and fetal effects were studied separately. Mitochondrial DNA (mtDNA) was sequenced in 50 males and 50 females. Y-chromosome anthropological markers were evaluated in 50 males. RESULT Fetal association with PTB was found in the progesterone receptor (PGR, rs1942836; P=0.004). Maternal association with PTB was found in small conductance calcium activated potassium channel isoform 3 (KCNN3, rs883319; P=0.01). Gestational age associated with PTB in PGR rs1942836 at 32-36 weeks (P=0.0004). MtDNA sequencing determined 88 individuals had Amerindian consistent haplogroups. Two individuals had Amerindian Y-chromosome consistent haplotypes. CONCLUSION This study replicates single locus fetal associations with PTB in PGR, maternal association in KCNN3, and demonstrates possible effects for divergent racial admixture on PTB.
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Affiliation(s)
- Paul C. Mann
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, 52242
| | - Margaret E. Cooper
- Department of Oral Biology and Center for Craniofacial and Dental Genetics, Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, 15219
| | - Kelli K. Ryckman
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, 52242
| | - Belén Comas
- Centro de Educación Médica e Investigaciones Clínicas, Buenos Aires, Capital Federal, Argentina,Instituto Nacional de Genética Médica Populacional and Estudio Colaborativo Latino Americano de Malformaciones Congénitas at Laboratório de Epidemiologia de Malformações Congênitas Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Juan Gili
- Centro de Educación Médica e Investigaciones Clínicas, Buenos Aires, Capital Federal, Argentina,Instituto Nacional de Genética Médica Populacional and Estudio Colaborativo Latino Americano de Malformaciones Congénitas at Laboratório de Epidemiologia de Malformações Congênitas Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Suzanne Crumley
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, 52242
| | - Elise N.A. Bream
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, 52242
| | - Heather M. Byers
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, 52242
| | - Travis Piester
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, 52242
| | - Amanda Schaefer
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, 52242
| | - Paul J. Christine
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, 52242
| | - Amy Lawrence
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, 52242
| | - Kendra L. Schaa
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, 52242
| | | | - Susan K. Berends
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, 52242
| | - Enrique Gadow
- Centro de Educación Médica e Investigaciones Clínicas, Buenos Aires, Capital Federal, Argentina
| | - Viviana Cosentino
- Centro de Educación Médica e Investigaciones Clínicas, Buenos Aires, Capital Federal, Argentina
| | - Eduardo E. Castilla
- Centro de Educación Médica e Investigaciones Clínicas, Buenos Aires, Capital Federal, Argentina,Instituto Nacional de Genética Médica Populacional and Estudio Colaborativo Latino Americano de Malformaciones Congénitas at Laboratório de Epidemiologia de Malformações Congênitas Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Jorge López Camelo
- Centro de Educación Médica e Investigaciones Clínicas, Buenos Aires, Capital Federal, Argentina,Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Capital Federal, Argentina,Instituto Multidisciplinario de Biología Celular, La Plata, Buenos Aires, Argentina
| | - Cesar Saleme
- Instituto de Maternidad y Ginecología Nuestra Señora de las Mercedes, San Miguel de Tucumán, Tucumán, Argentina
| | - Lori J. Day
- Department of Obstetrics and Gynecology, University of Iowa, Iowa City, Iowa, 52242
| | - Sarah K. England
- Department of Obstetrics and Gynecology, University of Iowa, Iowa City, Iowa, 52242,Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, Iowa, 52242
| | - Mary L. Marazita
- Department of Oral Biology and Center for Craniofacial and Dental Genetics, Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, 15219
| | - John M. Dagle
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, 52242
| | - Jeffrey C. Murray
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, 52242,Corresponding Author: Jeffrey C. Murray, MD Professor, Departments of Pediatrics, Epidemiology, and Biological Sciences University of Iowa Carver College of Medicine 500 Newton Road, 2182 ML, Iowa City, IA 52242-1181 319-335-6897 phone; 319-335-6970 fax
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Beaty TH, Taub MA, Scott AF, Murray JC, Marazita ML, Schwender H, Parker MM, Hetmanski JB, Balakrishnan P, Mansilla MA, Mangold E, Ludwig KU, Noethen MM, Rubini M, Elcioglu N, Ruczinski I. Confirming genes influencing risk to cleft lip with/without cleft palate in a case-parent trio study. Hum Genet 2013; 132:771-81. [PMID: 23512105 DOI: 10.1007/s00439-013-1283-6] [Citation(s) in RCA: 114] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 02/27/2013] [Indexed: 10/27/2022]
Abstract
A collection of 1,108 case-parent trios ascertained through an isolated, nonsyndromic cleft lip with or without cleft palate (CL/P) was used to replicate the findings from a genome-wide association study (GWAS) conducted by Beaty et al. (Nat Genet 42:525-529, 2010), where four different genes/regions were identified as influencing risk to CL/P. Tagging SNPs for 33 different genes were genotyped (1,269 SNPs). All four of the genes originally identified as showing genome-wide significance (IRF6, ABCA4 and MAF, plus the 8q24 region) were confirmed in this independent sample of trios (who were primarily of European and Southeast Asian ancestry). In addition, eight genes classified as 'second tier' hits in the original study (PAX7, THADA, COL8A1/FILIP1L, DCAF4L2, GADD45G, NTN1, RBFOX3 and FOXE1) showed evidence of linkage and association in this replication sample. Meta-analysis between the original GWAS trios and these replication trios showed PAX7, COL8A1/FILIP1L and NTN1 achieved genome-wide significance. Tests for gene-environment interaction between these 33 genes and maternal smoking found evidence for interaction with two additional genes: GRID2 and ELAVL2 among European mothers (who had a higher rate of smoking than Asian mothers). Formal tests for gene-gene interaction (epistasis) failed to show evidence of statistical interaction in any simple fashion. This study confirms that many different genes influence risk to CL/P.
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Affiliation(s)
- T H Beaty
- Department of Epidemiology, School of Public Health, Johns Hopkins University, 615N Wolfe St., Baltimore, MD 21205, USA.
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Leslie EJ, Murray JC. Evaluating rare coding variants as contributing causes to non-syndromic cleft lip and palate. Clin Genet 2012; 84:496-500. [PMID: 22978696 DOI: 10.1111/cge.12018] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Revised: 09/11/2012] [Accepted: 09/11/2012] [Indexed: 02/02/2023]
Abstract
Rare coding variants are a current focus in studies of complex disease. Previously, at least 68 rare coding variants were reported from candidate gene sequencing studies in non-syndromic cleft lip and palate (NSCL/P), a common birth defect. Advances in sequencing technology have now resulted in thousands of sequenced exomes, providing a large resource for comparative genetic studies. We collated rare coding variants reported to contribute to NSCL/P and compared them to variants identified from control exome databases to determine if some might be rare but benign variants. Seventy-one percentage of the variants described as etiologic for NSCL/P were not present in the exome data, suggesting that many likely contribute to disease. Our results strongly support a role for rare variants previously reported in the majority of NSCL/P candidate genes but diminish support for variants in others. However, because clefting is a complex trait it is not possible to be definitive about the role of any particular variant for its risk for NSCL/P.
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Affiliation(s)
- E J Leslie
- Department of Pediatrics, University of Iowa, Iowa City, IA, USA
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Packer RJ, Rood BR, Onar-Thomas A, Goldman S, Fisher MJ, Smith C, Boyett J, Kun L, Nelson MB, Compton P, Macey P, Patel S, Jacob E, O'Neil S, Finlay J, Harper R, Legault G, Chhabra A, Allen JC, Si SJ, Flores N, Haley K, Malvar J, Fangusaro J, Dhall G, Sposto R, Davidson TB, Finlay JL, Krieger M, Finlay JL, Zhou T, Miller DC, Geyer JR, Pollack IF, Gajjar A, Cohen BH, Nellan A, Murray JC, Honeycutt J, Gomez A, Head H, Braly E, Puccetti DM, Patel N, Kennedy T, Bradley K, Howard S, Salamat S, Iskandar B, Slavc I, Peyrl A, Chocholous M, Kieran M, Azizi A, Czech T, Dieckmann K, Haberler C, Sadighi ZS, Ellezam B, Khatua S, Ater J, Biswas A, Kakkar A, Goyal S, Mallick S, Sarkar C, Sharma MC, Julka PK, Rath GK, Glass T, Cochrane DD, Rassekh SR, Goddard K, Hukin J, Deopujari CE, Khakoo Y, Hanmantgad S, Forester K, McDonald SA, De Braganca K, Yohay K, Wolff JE, Kwiecien R, Rutkowski S, Pietsch T, Faldum A, Kortmann RD, Kramm C, Fouladi M, Olson J, Stewart C, Kocak M, Onar-Thomas A, Wagner L, Packer R, Goldman S, Gururangan S, Blaney S, Pollack I, Smith C, Demuth T, Kun L, Boyett J, Gilbertson R, Powell MK, Klement GL, Roffidal T, Fonkem E, Wolff JE. CLIN-PEDIATRICS CLINICAL RESEARCH. Neuro Oncol 2012. [DOI: 10.1093/neuonc/nos234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Murray JC, Rainusso N, Roberts RA, Gomez AM, Egler R, Russell H, Okcu MF, Gururangan S, Fangusaro J, Young-Poussaint T, Lesh S, Onar A, Gilbertson R, Packer R, McLendon R, Friedman HS, Boyett J, Kun LE, Venkatramani R, Haley K, Gilles F, Sposto R, Ji L, Olshefski R, Garvin J, Tekautz T, Kennedy G, Rassekh R, Moore T, Gardner S, Allen J, Shore R, Moertel C, Atlas M, Lasky J, Finlay J, Valera ET, Brassesco MS, Scrideli CA, Oliveira RS, Machado HR, Tone LG, Finlay JL, Kreimer S, Dagri J, Grimm J, Bluml S, Britt B, Dhall G, Gilles F, Finlay JL, Brown RJ, Dhall G, Shah A, Kapoor N, Abdel-Azim H, Rao AAN, Wallace D, Boyett J, Gajjar A, Packer RJ, Pearlman ML, Sadighi Z, Bingham R, Vats T, Khatua S, Ko RH, O'Neil S, Lavey RS, Finlay JL, Dhall G, Davidson TB, Gilles F, Tovar J, Grimm J, Wong K, Olch A, Dhall G, Finlay JL, Murray JC, Honeycutt JH, Donahue DJ, Head HW, Alles AJ, Ray A, Pearlman M, Vats T, Khatua S, Baskin J, Qaddoumi I, Ahchu MS, Alabi SF, Arambu IC, Castellanos M, Gamboa Y, Martinez R, Montero M, Ocampo E, Howard SC, Finlay JL, Broniscer A, Baker SD, Baker JN, Panandiker AP, Onar-Thomas A, Chin TK, Merchant TE, Davidoff A, Kaste SC, Gajjar A, Stewart CF, Espinoza J, Haley K, Patel N, Dhall G, Gardner S, Jeffrey A, Torkildson J, Cornelius A, Rassekh R, Bedros A, Etzl M, Garvin J, Pradhan K, Corbett R, Sullivan M, McGowage G, Puccetti D, Stein D, Jasty R, Ji L, Sposto R, Finlay JL, Antony R, Gardner S, Patel M, Wong KE, Britt B, Dhall G, Grimm J, Krieger M, McComb G, Gilles F, Sposto R, Finlay JL, Davidson TB, Sanchez-Lara PA, Randolph LM, Krieger MD, Wu S, Panigrahy A, Shimada H, Erdreich-Epstein A, Puccetti DM, Patel N, Kennedy T, Salamat S, Bradfield Y, Park HJ, Yoon JH, Ahn HS, Shin HY, Kim SK, Im HJ, Ra YS, Won SC, Baek HJ, Sung KW, Hah JO, Lim YT, Lee GS, Lee YH, Kim HS, Park JK, Kim MK, Park JE, Chung NG, Choi HS, Campen CJ, Fisher PG, Ruge MI, Simon T, Suchorska B, Lehrke R, Hamisch C, Koerber F, Treuer H, Berthold F, Sturm V, Voges J, Davidson TB, Finlay JL, Dhall G, Kirsch M, Lindner C, Schackert G, Brown RJ, Krieger M, Dhall G, Finlay JL. PEDIATRICS CLINICAL RESEARCH. Neuro Oncol 2011. [DOI: 10.1093/neuonc/nor156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Shaffer JR, Wang X, Feingold E, Lee M, Begum F, Weeks DE, Cuenco KT, Barmada MM, Wendell SK, Crosslin DR, Laurie CC, Doheny KF, Pugh EW, Zhang Q, Feenstra B, Geller F, Boyd HA, Zhang H, Melbye M, Murray JC, Weyant RJ, Crout R, McNeil DW, Levy SM, Slayton RL, Willing MC, Broffitt B, Vieira AR, Marazita ML. Genome-wide association scan for childhood caries implicates novel genes. J Dent Res 2011; 90:1457-62. [PMID: 21940522 DOI: 10.1177/0022034511422910] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Dental caries is the most common chronic disease in children and a major public health concern due to its increasing incidence, serious health and social co-morbidities, and socio-demographic disparities in disease burden. We performed the first genome-wide association scan for dental caries to identify associated genetic loci and nominate candidate genes affecting tooth decay in 1305 US children ages 3-12 yrs. Affection status was defined as 1 or more primary teeth with evidence of decay based on intra-oral examination. No associations met strict criteria for genome-wide significance (p < 10E-7); however, several loci (ACTN2, MTR, and EDARADD, MPPED2, and LPO) with plausible biological roles in dental caries exhibited suggestive evidence for association. Analyses stratified by home fluoride level yielded additional suggestive loci, including TFIP11 in the low-fluoride group, and EPHA7 and ZMPSTE24 in the sufficient-fluoride group. Suggestive loci were tested but not significantly replicated in an independent sample (N = 1695, ages 2-7 yrs) after adjustment for multiple comparisons. This study reinforces the complexity of dental caries, suggesting that numerous loci, mostly having small effects, are involved in cariogenesis. Verification/replication of suggestive loci may highlight biological mechanisms and/or pathways leading to a fuller understanding of the genetic risks for dental caries.
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Affiliation(s)
- J R Shaffer
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
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Mossey PA, Shaw WC, Munger RG, Murray JC, Murthy J, Little J. Global oral health inequalities: challenges in the prevention and management of orofacial clefts and potential solutions. Adv Dent Res 2011; 23:247-58. [PMID: 21490237 DOI: 10.1177/0022034511402083] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The birth prevalence of orofacial clefts, one of the most common congenital anomalies, is approximately one in 700 live births, but varies with geography, ethnicity, and socio-economic status. There is a variation in infant mortality and access to care both between and within countries, so some clefts remain unrepaired into adulthood. Quality of care also varies, and even among repaired clefts there is residual deformity and morbidity that significantly affects some children. The two major issues in attempts to address these inequalities are (a) etiology/possibilities for prevention and (b) management and quality of care. For prevention, collaborative research efforts are required in developing countries, in line with the WHO approach to implement the recommendations of the 2008 Millennium Development Goals (www.un.org/millenniumgoals). This includes the "common risk factor" approach, which analyzes biological and social determinants of health alongside other chronic health problems such as diabetes and obesity, as outlined in the Marmot Health inequalities review (2008) (www.ucl.ac.uk/gheg/marmotreview). Simultaneously, orofacial cleft research should involve clinical researchers to identify inequalities in access to treatment and identify the best interventions for minimizing mortality and residual deformity. The future research agenda also requires engagement with implementation science to get research findings into practice.
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Affiliation(s)
- P A Mossey
- University of Dundee Dental Hospital & School, Scotland, UK.
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Butali A, Mossey PA, Adeyemo WL, Jezewski PA, Onwuamah CK, Ogunlewe MO, Ugboko VI, Adejuyigbe O, Adigun AI, Abdur-Rahman LO, Onah II, Audu RA, Idigbe EO, Mansilla MA, Dragan EA, Petrin AL, Bullard SA, Uduezue AO, Akpata O, Osaguona AO, Olasoji HO, Ligali TO, Kejeh BM, Iseh KR, Olaitan PB, Adebola AR, Efunkoya E, Adesina OA, Oluwatosin OM, Murray JC. Genetic studies in the Nigerian population implicate an MSX1 mutation in complex oral facial clefting disorders. Cleft Palate Craniofac J 2011; 48:646-53. [PMID: 21740177 DOI: 10.1597/10-133] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Orofacial clefts are the most common malformations of the head and neck, with a worldwide prevalence of 1 in 700 births. They are commonly divided into CL(P) and CP based on anatomic, genetic, and embryologic findings. A Nigerian craniofacial anomalies study (NigeriaCRAN) was set up in 2006 to investigate the role of gene-environment interaction in the origin of orofacial clefts in Nigeria. SUBJECTS AND METHODS DNA isolated from saliva from Nigerian probands was used for genotype association studies and direct sequencing of cleft candidate genes: MSX1 , IRF6 , FOXE1, FGFR1 , FGFR2 , BMP4 , MAFB, ABCA4 , PAX7, and VAX1 , and the chromosome 8q region. RESULTS A missense mutation A34G in MSX1 was observed in nine cases and four HapMap controls. No other apparent causative variations were identified. Deviation from Hardy Weinberg equilibrium (HWE) was observed in these cases (p = .00002). A significant difference was noted between the affected side for unilateral CL (p = .03) and bilateral clefts and between clefts on either side (p = .02). A significant gender difference was also observed for CP (p = .008). CONCLUSIONS Replication of a mutation previously implicated in other populations suggests a role for the MSX1 A34G variant in the development of CL(P).
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Abstract
Mutations in the human GLI2 gene were first reported in association with defective anterior pituitary formation, panhypopituitarism, and forebrain anomalies represented by typical holoprosencephaly (HPE) and holoprosencephaly-like (HPE-L) phenotypes and postaxial polydactyly. Subsequently, anophthalmia plus orbital anomalies, heminasal aplasia, branchial arch anomalies and polydactyly have also been incorporated into the general phenotype. Here we described six Brazilian patients with phenotypic manifestations that range from isolated cleft lip/palate with polydactyly, branchial arch anomalies to semi-lobar holoprosencephaly. Novel sequence variants were found in the GLI2 gene in patients with marked involvement of the temporomandibular joint (TMJ), a new clinical finding observed with mutations of this gene. Clinical, molecular and genetic aspects are discussed.
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Affiliation(s)
- C D P Bertolacini
- Hospital of Rehabilitation of Craniofacial Anomalies, USP, Bauru, SP, Brazil
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Tasdemiroglu E, Kaya M, Yildirim CH, Lucas KG, Bao L, Bruggeman R, Specht C, Murray JC, Donahue DJ, Galliani CA, Blondin NA, Hui P, Vortmeyer A, Hasbani J, Baehring J, Jensen RL, Lee J, Lake WB, Baskaya MK, Salamat MS, Kennedy T, Abraham S, Jensen RL, Lusis EA, Scheithauer B, Yachnis AT, Chicoine MR, Paulus W, Perry A, Chan DT, Kam MK, Ma BB, Ng SC, Siu DY, Ng HK, Poon WS, Dunbar EM, Dong HJ, Liu C, Chi YY, Keeling C, Yachnis AT, Stephen JH, Sievert AJ, Resnick AC, Storm PB, Judkins AR, Santi M, Kirsch M, Stelling A, Koch E, Salzer R, Schackert G, Steiner G, Pollo B, Maderna E, Valletta L, Guzzetti S, Eoli M, Calatozzolo C, Nunziata R, Salmaggi A, Finocchiaro G, Kastenhuber ER, Campos C, Brennan CW, Mellinghoff IK, Huse JT, Zhang H, Sergey M, Estrada DK, Kay AB, Wagner AS, Khanlou N, Vinters HV, Cloughesy TF, Yong WH. Pathology. Neuro Oncol 2010. [DOI: 10.1093/neuonc/noq116.s10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Abstract
Orofacial clefts are common and burdensome birth defects with a complex genetic and environmental etiology. The contribution of nutritional factors and supplements to the etiology of orofacial clefts has long been theorized and studied. Multiple studies have evaluated the role of folic acid in the occurrence and recurrence of orofacial clefts, using observational and non-randomized interventional designs. While preventive effects of folic acid on orofacial clefts are commonly reported, the evidence remains generally inconsistent. This paper reviews the findings of the main studies of the effects of folic acid on orofacial clefts, summarizes study limitations, and discusses research needs with a focus on studying the effects of high dosage folic acid on the recurrence of oral clefts using a randomized clinical trial design. The role of folic acid in the prevention of neural tube defects is also briefly summarized and discussed as a reference model for orofacial clefts.
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Affiliation(s)
- G L Wehby
- Department of Health Management and Policy, College of Public Health, University of Iowa, Iowa City, IA 52242, USA
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Steffen KM, Cooper ME, Shi M, Caprau D, Simhan HN, Dagle JM, Marazita ML, Murray JC. Maternal and fetal variation in genes of cholesterol metabolism is associated with preterm delivery. J Perinatol 2007; 27:672-80. [PMID: 17855807 PMCID: PMC2706423 DOI: 10.1038/sj.jp.7211806] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
OBJECTIVE To examine the contribution of variants in fetal and maternal cholesterol metabolism genes in preterm delivery (PTD). STUDY DESIGN A total of 40 single-nucleotide polymorphisms (SNPs) in 16 genes related to cholesterol metabolism were examined for 414 preterm infants (gestational ages 22 to 36 weeks; comprising 305 singletons and 109 twins) and at least 1 parent. Fetal effects were assessed using the transmission disequilibrium test (TDT) for each SNP, followed by a log linear model-based approach to utilize families with missing parental genotypes for those SNPs showing significance under TDT. Genetic variant effects were examined for a role in PTD, gestational age and birth weight. Maternal effects were estimated using a log linear model-based approach. RESULT Among singleton gestations, suggestive association (P<0.01 without adjusting for multiple comparisons) was found between birth weight and fetal DHCR7 gene/SNP combinations (rs1630498, P=0.002 and rs2002064, P=0.003). Among all gestations, suggestive associations were found between PTD and fetal HMGCR (rs2303152, P=0.002) and APOA1 (rs 5070, P=0.004). The result for HMGCR was further supported by the log linear model-based test in the single births (P=0.007) and in all births (P=0.006). New associations (APOE and ABCA1) were observed when birth weight was normalized for gestational age suggesting independent effects of variants on birth weight separate from effects on PTD. Testing for maternally mediated genetic effects has identified suggestive association between ABCA1 (rs4149313, P=0.004) and decreased gestational age. CONCLUSION Variants in maternal and fetal genes for cholesterol metabolism were associated with PTD and decreased birth weight or gestational age in this study. Genetic markers may serve as one mechanism to identify high-risk mothers and fetuses for targeted nutritional treatment and/or prevention of low birth weight or PTD.
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Affiliation(s)
- KM Steffen
- University of Iowa College of Medicine, Iowa City, IA, USA
| | - ME Cooper
- Department of Oral Biology, Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - M Shi
- National Institute of Environmental Health Science, Research Triangle Park, NC, USA
| | - D Caprau
- Department of Pediatrics, University of Iowa, Iowa City, IA, USA
| | - HN Simhan
- Department of Obstetrics and Gynecology, University of Pittsburgh, Pittsburgh, PA, USA
| | - JM Dagle
- Department of Pediatrics, University of Iowa, Iowa City, IA, USA
| | - ML Marazita
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - JC Murray
- Department of Pediatrics, University of Iowa, Iowa City, IA, USA
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Osoegawa K, Vessere GM, Utami KH, Mansilla MA, Johnson MK, Riley BM, L'Heureux J, Pfundt R, Staaf J, van der Vliet WA, Lidral AC, Schoenmakers EFPM, Borg A, Schutte BC, Lammer EJ, Murray JC, de Jong PJ. Identification of novel candidate genes associated with cleft lip and palate using array comparative genomic hybridisation. J Med Genet 2007; 45:81-6. [PMID: 17873121 PMCID: PMC3732463 DOI: 10.1136/jmg.2007.052191] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
AIM AND METHOD We analysed DNA samples isolated from individuals born with cleft lip and cleft palate to identify deletions and duplications of candidate gene loci using array comparative genomic hybridisation (array-CGH). RESULTS Of 83 syndromic cases analysed we identified one subject with a previously unknown 2.7 Mb deletion at 22q11.21 coinciding with the DiGeorge syndrome region. Eighteen of the syndromic cases had clinical features of Van der Woude syndrome and deletions were identified in five of these, all of which encompassed the interferon regulatory factor 6 (IRF6) gene. In a series of 104 non-syndromic cases we found one subject with a 3.2 Mb deletion at chromosome 6q25.1-25.2 and another with a 2.2 Mb deletion at 10q26.11-26.13. Analyses of parental DNA demonstrated that the two deletion cases at 22q11.21 and 6q25.1-25.2 were de novo, while the deletion of 10q26.11-26.13 was inherited from the mother, who also has a cleft lip. These deletions appear likely to be causally associated with the phenotypes of the subjects. Estrogen receptor 1 (ESR1) and fibroblast growth factor receptor 2 (FGFR2) genes from the 6q25.1-25.2 and 10q26.11-26.13, respectively, were identified as likely causative genes using a gene prioritization software. CONCLUSION We have shown that array-CGH analysis of DNA samples derived from cleft lip and palate subjects is an efficient and productive method for identifying candidate chromosomal loci and genes, complementing traditional genetic mapping strategies.
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Affiliation(s)
- K Osoegawa
- Center for Genetics, Children's Hospital Oakland Research Institute (CHORI), 5700 Martin Luther King Jr. Way Oakland, CA 94609, USA.
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Abstract
Van der Woude syndrome (VWS) is an autosomal dominant disorder manifested in cleft lip and/or palate and lip pits. Isolated clefts of the lip and/or palate (ICLP) have both genotype and phenotype overlap with VWS. Subjects with ICLP have abnormalities in brain structure and function. Given the similarities between VWS and ICLP, the current study was designed to evaluate the pattern of brain structure of adults with VWS. Fourteen adults with VWS were compared to age- and gender-matched healthy controls. Brain structure was evaluated using magnetic resonance imaging. All subjects with VWS had enlarged volumes of the anterior regions of the cerebrum. Men with VWS had reduced volumes of the posterior cerebrum. Anterior cerebrum volume was negatively correlated with intelligent quotient in the subjects with VWS indicating that the enlargement of this brain region was 'pathologic.' The pattern of brain structure in VWS is nearly identical to those seen in ICLP. In addition, men are affected more severely. Pathologic enlargement of the tissue and a gender effect with men affected more severely are common features of neurodevelopmental disorders supporting the notion that the brain structure of VWS and ICLP may be because of abnormal brain development.
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Affiliation(s)
- P Nopoulos
- Department of Psychiatry, University of Iowa College of Medicine, IA 52242, USA.
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Abstract
Despite 15 years of evidence, preventable defects still occur
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Abstract
Endothelial-monocyte-activating polypeptide-II (EMAP-II) is a novel multifunctional polypeptide with proinflammatory activity. We have previously shown that the recombinant and native forms of EMAP-II can induce apoptosis in mitogen-stimulated lymphocytes, and that the release of this protein into the extracellular milieu is enhanced by hypoxia. We hypothesised that hypoxia may lead to death of tumour-infiltrating lymphocytes (TILs) via an EMAP-II-dependent mechanism, thereby assisting tumours to evade the immune system. In this study, we used immunohistochemistry to detect EMAP-II, active caspase-3 and cleaved Poly (ADP-ribose) Polymerase (PARP) as indicators of apoptosis in TILs, and carbonic anhydrase IX (CA IX) as a surrogate marker of hypoxia. EMAP-II expression is associated with regions of hypoxia, and furthermore there is a significant association between TILs apoptosis and the presence of hypoxia. Using a coculture model of colorectal cancer cell/lymphocyte interactions, we were also able to demonstrate lymphocyte apoptosis induced by tumour cells, with concomitant caspase-3 activity. Lymphocyte killing was enhanced by direct cell–cell contact, particularly by tumour cells exposed to hypoxic conditions. Our data support the hypothesis that hypoxia plays a role in immune evasion by tumour cells, through EMAP-II-dependent lymphocyte killing.
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Affiliation(s)
- M M S Youssef
- Wolfson Digestive Diseases Centre, University Hospital, Nottingham NG7 2UH, UK.
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Warrington A, Vieira AR, Christensen K, Orioli IM, Castilla EE, Romitti PA, Murray JC. Genetic evidence for the role of loci at 19q13 in cleft lip and palate. J Med Genet 2006; 43:e26. [PMID: 16740910 PMCID: PMC2564544 DOI: 10.1136/jmg.2005.034785] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND Clefts of the lip and palate are common birth defects, affecting approximately 1 in 700 births worldwide. The aetiology of clefting is complex, with multiple genetic and environmental influences. METHODS Genotype based linkage disequilibrium analysis was conducted using the family based association test (FBAT) and the likelihood ratio test (LRT). We also carried out direct sequencing of the PVR and PVRL2 candidate genes based on their homology to PVRL1, a gene shown previously to cause Margarita Island clefting. Participants included 434 patients with cleft lip with or without cleft palate or cleft palate only and their mothers from eight countries in South America, 205 nuclear triads (father-mother-affected child) from Iowa, 541 nuclear triads from Denmark, and 100 patients with cleft lip and palate from the Philippines. RESULTS An allelic variant in the PVR gene showed statistically significant association with both South American and Iowa populations (p = 0.0007 and p = 0.0009, respectively). Direct sequencing of PVR and PVRL2 yielded 26 variants, including two rare amino acid changes, one in each gene, which were not seen in controls. CONCLUSIONS We found an association between a common variant in a gene at 19q and isolated clefting in two heterogeneous populations. However, it is unclear from our data if rare variants in PVR and PVRL2 are sufficient to cause clefting in isolation.
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Mansilla MA, Cooper ME, Goldstein T, Castilla EE, Lopez Camelo JS, Marazita ML, Murray JC. Contributions of PTCH gene variants to isolated cleft lip and palate. Cleft Palate Craniofac J 2006; 43:21-9. [PMID: 16405370 PMCID: PMC2151847 DOI: 10.1597/04-169r.1] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
OBJECTIVE Mutations in patched (PTCH) cause the nevoid basal cell carcinoma syndrome (NBCCS), or Gorlin syndrome. Nevoid basal cell carcinoma syndrome may present with developmental anomalies, including rib and craniofacial abnormalities, and predisposes to several tumor types, including basal cell carcinoma and medulloblastoma. Cleft palate is found in 4% of individuals with nevoid basal cell carcinoma syndrome. Because there might be specific sequence alterations in PTCH that limit expression to orofacial clefting, a genetic study of PTCH was undertaken in cases with cleft lip and/or palate (CL/P) known not to have nevoid basal cell carcinoma syndrome. RESULTS Seven new normal variants spread along the entire gene and three missense mutations were found among cases with cleft lip and/or palate. One of these variants (P295S) was not found in any of 1188 control samples. A second variant was found in a case and also in 1 of 1119 controls. The third missense (S827G) was found in 5 of 1369 cases and in 5 of 1104 controls and is likely a rare normal variant. Linkage and linkage desequilibrium also was assessed using normal variants in and adjacent to the PTCH gene in 220 families (1776 individuals), each with two or more individuals with isolated clefting. Although no statistically significant evidence of linkage (multipoint HLOD peak = 2.36) was uncovered, there was borderline evidence of significant transmission distortion for one haplotype of two single nucleotide polymorphisms located within the PTCH gene (p = .08). CONCLUSION Missense mutations in PTCH may be rare causes of isolated cleft lip and/or palate. An as yet unidentified variant near PTCH may act as a modifier of cleft lip and/or palate.
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Affiliation(s)
- M A Mansilla
- Department of Pediatrics, University of Iowa, Iowa City, Iowa 52242, USA
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Di Paola J, Jugessur A, Goldman T, Reiland J, Tallman D, Sayago C, Murray JC. Platelet glycoprotein I(b)alpha and integrin alpha2 beta1 polymorphisms: gene frequencies and linkage disequilibrium in a population diversity panel. J Thromb Haemost 2005; 3:1511-21. [PMID: 15978109 DOI: 10.1111/j.1538-7836.2005.01273.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Genetic variants in the GP1BA and ITGA2 genes have been proposed as potential modifiers for arterial vascular disease and bleeding disorders. Since ancestry may play an important role in the prevalence of these variants, we sought to determine their allele frequency and linkage disequilibrium in a collection of 1064 DNA samples from 51 ethnic groups. We studied haplotypes of ITGA2 defined by single nucleotide substitutions at positions -52, 807, and 1648, and GP1BA variants defined by sequence changes in positions -5 (Kozak), 1018 (T145M, HPA-2) and 1285 (VNTR A, B, C and D). Frequency of haplotypes of ITGA2 showed considerable variation across the different groups, with a higher prevalence of the haplotype -52C or T/807C/1648A observed in African compared with caucasian and Asian populations. The haplotypes 52C/807T/1648A and -52T/807T/1648A were not observed in caucasians or South Americans. While relative frequencies of the GP1BA Kozak alleles were comparable across groups, the methionine allele (HPA-2b) showed a higher frequency in Africa (0.26) than in the other groups. We also observed a high prevalence of the VNTR B allele in the African and Israeli populations. Haplotype analysis revealed incomplete linkage disequilibrium between the HPA-2 and VNTR alleles. Incorporation of GP1BA variants into the set of SNPs already genotyped by the HapMap project disrupted the pre-existing haplotype block. These data provide a valuable resource for optimal selection of variants best tailored for association studies of vascular disease or bleeding disorders when examining individuals of different ancestral origins.
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Affiliation(s)
- J Di Paola
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA.
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Katz LA, Schultz RE, Semina EV, Torfs CP, Krahn KN, Murray JC. Mutations in PITX2 may contribute to cases of omphalocele and VATER-like syndromes. Am J Med Genet A 2004; 130A:277-83. [PMID: 15378534 DOI: 10.1002/ajmg.a.30329] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Omphalocele is a congenital anomaly with substantial morbidity. Rieger syndrome, an autosomal dominant disorder, is characterized by craniofacial abnormalities and abdominal wall defects. PITX2 mutations are etiologic in >40% of cases of Rieger syndrome. We demonstrate that the birth prevalence of omphalocele is significantly higher in Rieger syndrome than in the general population, with omphaloceles found in 0.03% in the Iowa newborn population and 4.3% of patients with Rieger syndrome. Our objective was to screen coding and conserved non-coding regions of PITX2 for mutations in 209 patients with omphalocele. We identified remarkable evolutionarily conserved regions by comparing the 3'UTR of Pitx2 in 13 vertebrate and 3 invertebrate species. No mutations changing the amino acid sequence were found within the omphalocele population. In one case of omphalocele with VATER-like additional anomalies, a three nucleotide deletion was found in the 3'UTR. This deletion was not seen in 1,186 controls. Also in the 3'UTR, we identified a single nucleotide polymorphism at a highly conserved residue. Our findings suggest additional studies of PITX2 conserved regions will be valuable. We also screened the omphalocele cases for mutations in exon 5 of the gene FLNA. Mutations in FLNA have been shown to cause a broad range of congenital malformations, including otopalatodigital syndrome type 2 in which a missense mutation occurring in exon 5 of FLNA results in omphalocele as part of the phenotype. We did not find any mutations in exon 5 of FLNA in 179 omphalocele cases studied.
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Affiliation(s)
- L A Katz
- Department of Pediatrics, University of Iowa, Iowa City, Iowa 52242, USA
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Abstract
In this study, we sought to determine the association between tooth agenesis and DNA sequence variation in the genes MSX1 and PAX9 in an ethnically diverse human population. Since cleft lip/palate is also associated with both tooth agenesis and the gene TGFA, we included TGFA in the analysis as well. Cheek swab samples were obtained for DNA analysis from 116 case/parent trios. Probands had at least one developmentally missing tooth, excluding third molars. Genotyping was performed by single-strand conformational polymorphism or kinetic polymerase chain-reaction assays. Transmission distortion of the marker alleles and DNA sequence analysis was performed. Results showed that tooth agenesis is associated with markers of the genes MSX1 and TGFA. No mutations were found in MSX1 or PAX9 coding regions. There were statistically significant data suggesting that MSX1 interacts with PAX9. These findings suggest that MSX1, PAX9, and TGFA play a role in isolated dental agenesis.
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Affiliation(s)
- A R Vieira
- Department of Pediatrics, University of Iowa, Iowa City 52242-1083, USA.
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Schultz RE, Cooper ME, Daack-Hirsch S, Shi M, Nepomucena B, Graf KA, O'Brien EK, O'Brien SE, Marazita ML, Murray JC. Targeted scan of fifteen regions for nonsyndromic cleft lip and palate in Filipino families. Am J Med Genet A 2004; 125A:17-22. [PMID: 14755461 DOI: 10.1002/ajmg.a.20424] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cleft lip with or without cleft palate (CL/P) is a congenital anomaly with variable birth prevalence based on geographic origins, with the highest rates commonly found in Asian populations. About 70% of cases are nonsyndromic (NS), in which the affected individual has no other abnormalities. NS CL/P is a complex disorder with genetic and environmental effects and no specific genetic loci yet confirmed. Fifteen candidate regions were examined for linkage to NS CL/P. Regions were chosen based on previous suggestive linkage and/or association in human families, or suggestive animal model data. Polymorphic markers in these regions were genotyped for analysis on 36 Filipino families comprised of 126 affected and 218 unaffected individuals. An additional 70 families with 149 affecteds were used for replication of suggestive results. Parametric (LOD score) and nonparametric (SIMIBD) linkage analyses were performed as well as transmission disequilibrium test (TDT) analysis. Five markers yielded suggestive results from the 36 families. The parametric LOD scores for the MSX1-CA and D4S1629 were >1.0 and the SIMIBD P values for D6S1029 and RFC1 are suggestive (<0.06), while the SIMIBD P value of 0.01 for TGFA was significant. Since the Msx1 mouse knockout has cleft palate and MSX1 mutations have been found in rare cases of syndromic CL/P, this locus is especially plausible for linkage. Previous studies have also found linkage of NS CL/P to 4q31 and 6p23. These regions contain several candidate genes, including AP2 at 6p23 and FGF2, BMPR1B, and MADH1 at 4q31. TGFA has both linkage and linkage disequilibrium data supporting it as a candidate gene for NS CL/P. While no region was definitively confirmed for linkage to NS CL/P, the data do support further investigation using larger sample sizes and candidate gene studies at 2p13.2, 4p16.2, 4q31, 6p23, and 16q22-24.
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Affiliation(s)
- R E Schultz
- Department of Pediatrics, University of Iowa, Iowa City, Iowa 52242, USA
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Marçano ACB, Doudney K, Braybrook C, Squires R, Patton MA, Lees MM, Richieri-Costa A, Lidral AC, Murray JC, Moore GE, Stanier P. TBX22 mutations are a frequent cause of cleft palate. J Med Genet 2004; 41:68-74. [PMID: 14729838 PMCID: PMC1757272 DOI: 10.1136/jmg.2003.010868] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Murray JC, Heng YM, Symonds P, Rice K, Ward W, Huggins M, Todd I, Robins RA. Endothelial monocyte-activating polypeptide-II (EMAP-II): a novel inducer of lymphocyte apoptosis. J Leukoc Biol 2004; 75:772-6. [PMID: 14982944 DOI: 10.1189/jlb.1003487] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The novel, proinflammatory cytokine endothelial monocyte-activating polypeptide-II (EMAP-II) was first found in tumor cell supernatants. EMAP-II is closely related or identical to the p43 auxiliary protein of the multisynthase complex, which is involved in protein synthesis. In vitro, EMAP-II induces procoagulant activity, increased expression of E- and P-selectins and tumor necrosis factor receptor-1, and ultimately, programmed cell death (apoptosis) in cultured endothelial cells. EMAP-II is also chemotactic for monocytes and neutrophils. However, the role of the p43/EMAP-II cytokine form in tumors is not understood. We hypothesized an immune-regulatory role within neoplastic tissues and investigated its effects on lymphocytes. EMAP-II causes a dose-dependent inhibition of proliferation and apoptosis in Jurkat T cells and mitogen-activated peripheral blood mononuclear cells. Coculture with DLD-1 colorectal cancer cells or media conditioned by these cells induces apoptosis in Jurkat cells, which is partially reversed by antibodies against EMAP-II. Our data suggest that EMAP-II constitutes a component of a novel, immunosuppressive pathway in solid tumors, which is not normally expressed outside the cell but in tumors, may be subject to abnormal processing and released from tumor cells.
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Affiliation(s)
- J C Murray
- Wolfson Digestive Disease Centre, University Hospital, University of Nottingham, Nottingham, UK.
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Hewett P, Popplewell A, Finney H, Murray JC. Changes in microvessel endothelial cell gene expression in an in vitro human breast tumour endothelial cell model. Angiogenesis 2003; 3:221-9. [PMID: 14517421 DOI: 10.1023/a:1009062519643] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Selective targeting of tumour-endothelium has been proposed as a means of therapy. The successful exploitation of this approach will rely on the identification of suitable targets expressed specifically on the tumour-associated endothelium. In an attempt to identify novel tumour-endothelium associated targets we have used differential mRNA display to identify genes up-regulated in an in vitro breast tumour-endothelial cell culture model. Confluent monolayers of human mammary microvessel endothelial cells (HuMMEC) were incubated for 5 days with MDA-MB-231 breast adenocarcinoma cell-conditioned medium (TCM). mRNAs isolated from TCM-treated and control cells were amplified using 104 combinations of four 3(') anchored T(12)VN primers and 26 'random' 10mers by RT-PCR and the products examined on DNA sequencing gels. Seventy-four sequences were cloned and the differential expression of five genes was confirmed using dot-blots. These were identified as procollagen type-IV, Tie-2/Tek receptor tyrosine kinase, NADH dehydrogenase subunit-6, and ferritin heavy-chain, which were up-regulated, and insulin-like growth factor binding protein-5, which was down-regulated. Increased endothelial expression of basement membrane proteins and tyrosine kinase receptors is known to occur during angiogenesis. Our data support the use of this model for further in vitro investigation of tumour angiogenesis.
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Affiliation(s)
- P Hewett
- University of Nottingham, Laboratory of Molecular Oncology, CRC Academic Department of Clinical Oncology, City Hospital, UK.
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Ferreira de Lima RLL, Moretti-Ferreira D, Richieri-Costa A, Murray JC. Identity by descent and candidate gene mapping of Richieri-Costa and Pereira syndrome. Am J Med Genet A 2003; 122A:56-8. [PMID: 12949973 DOI: 10.1002/ajmg.a.20270] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The Richieri-Costa-Pereira syndrome is a rare autosomal recessive disorder characterized by short stature, Robin sequence, cleft mandible, pre/postaxial anomalies and clubfoot. Of 15 families reported with this disorder 14 are from Brazil suggesting a founder effect. We studied 15 families using identity-by-descent as a hypothesis to attempt gene localization We have examined through linkage analysis 497 polymorphic-markers and also performed direct sequencing of exons for 10 candidate genes selected on the basis of their expression in the developing mandible and limb. No evidence for allele sharing at any locus tested or mutations in candidate genes was found. Additional higher resolution mapping, new families and other candidate genes might improve future chances of gene identification.
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Jezewski PA, Vieira AR, Nishimura C, Ludwig B, Johnson M, O'Brien SE, Daack-Hirsch S, Schultz RE, Weber A, Nepomucena B, Romitti PA, Christensen K, Orioli IM, Castilla EE, Machida J, Natsume N, Murray JC. Complete sequencing shows a role for MSX1 in non-syndromic cleft lip and palate. J Med Genet 2003; 40:399-407. [PMID: 12807959 PMCID: PMC1735501 DOI: 10.1136/jmg.40.6.399] [Citation(s) in RCA: 217] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
MSX1 has been proposed as a gene in which mutations may contribute to non-syndromic forms of cleft lip and/or cleft palate. Support for this comes from human linkage and linkage disequilibrium studies, chromosomal deletions resulting in haploinsufficiency, a large family with a stop codon mutation that includes clefting as a phenotype, and the Msx1 phenotype in a knockout mouse. This report describes a population based scan for mutations encompassing the sense and antisense transcribed sequence of MSX1 (two exons, one intron). We compare the completed genomic sequence of MSX1 to the mouse Msx1 sequence to identify non-coding homology regions, and sequence highly conserved elements. The samples studied were drawn from a panethnic collection including people of European, Asian, and native South American ancestry. The gene was sequenced in 917 people and potentially aetiological mutations were identified in 16. These included missense mutations in conserved amino acids and point mutations in conserved regions not identified in any of 500 controls sequenced. Five different missense mutations in seven unrelated subjects with clefting are described. Evolutionary sequence comparisons of all known Msx1 orthologues placed the amino acid substitutions in context. Four rare mutations were found in non-coding regions that are highly conserved and disrupt probable regulatory regions. In addition, a panel of 18 population specific polymorphic variants were identified that will be useful in future haplotype analyses of MSX1. MSX1 mutations are found in 2% of cases of clefting and should be considered for genetic counselling implications, particularly in those families in which autosomal dominant inheritance patterns or dental anomalies appear to be cosegregating with the clefting phenotype.
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Affiliation(s)
- P A Jezewski
- Department of Periodontics, College of Dentistry, University of Iowa, Iowa City 52242, USA
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Abstract
MSX1 and TGFB3 have been proposed as genes in which mutations may contribute to non-syndromic forms of oral clefts; however, an interaction between these genes has not been described. The present study attempts to detect transmission distortion of MSX1 and TGFB3 in 217 South American children from their respective mothers. With transmission disequilibrium test analysis, cleft lip with/without cleft palate, cleft lip with palate plus cleft palate only, and all datasets combined showed evidence of association with MSX1 (p = 0.004, p = 0.037, and p = 0.001, respectively). With likelihood ratio test analysis, "cleft lip only" showed association with MSX1 (p = 0.04) and "cleft palate only" with TGFB3 (p = 0.02). A joint analysis of MSX1 and TGFB3 suggested that there may be an interaction between these two loci to increase cleft susceptibility. These results suggest that MSX1 and TGFB3 mutations make a contribution to clefts in South American populations.
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Affiliation(s)
- A R Vieira
- Departments of Pediatrics, 2613 JCP, University of Iowa, Iowa City, 52242-1083, USA
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Abstract
The significance of the endothelial cell as a target for antitumor therapy has been recognized for some time, but so far the results of clinical trials exploiting this approach have not been encouraging. The subject is likely to gain new momentum, however, following a number of important recent findings that shed new light on the origins and nature of tumor vasculature. Coupled with rapid developments in the use ofphage-displayed peptide libraries to characterize the human vascular map, as well as highly selective delivery systems, this new understanding of tumor vascular biology should provide many fresh and exciting avenues to explore.
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Affiliation(s)
- J C Murray
- CRUK Tumour Cytokine Biology Group, Wolfson Digestive Diseases Centre, University Hospital, Nottingham, UK.
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Abstract
It has been proposed that susceptibility to clefting in South America is related to Amerindian ancestry, where clefting is present at a higher frequency than in the other admixed populations (Caucasian and African) that make up the diverse racial mix of current South Americans. To clarify the genetic origins and establish a method for genetic mapping, mitochondrial DNA variation and Y-chromosome markers were studied in a South American population affected with clefting. Two-hundred and seventeen subjects and matched controls were selected through the Latin-American Collaborative Study of Congenital Malformations (ECLAMC). The case group showed a higher frequency of Native American haplogroups and a lower frequency of African haplogroups (p < 0.00001). In addition, the case group showed a much higher frequency of the specific native American haplogroup D than the control group (p < 0.00001). For the Y-chromosome markers, the case group showed a lower frequency of the African-specific marker, YAP (p = 0.002), and a higher frequency of the Native American-specific marker, DYS199 (p < 0.00001). Even though differences were found in the frequencies of the markers studied, the contribution of each founder population was similar for both groups. Results suggest a strong Native American maternal contribution and a strong Caucasian (Spanish and Portuguese) paternal contribution to the population studied. The implications of this finding include the possibility of using admixture mapping approaches to this population.
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Affiliation(s)
- A R Vieira
- Department of Pediatrics, University of Iowa, Iowa City 52242-1083, USA
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Watanabe Y, Benson DW, Yano S, Akagi T, Yoshino M, Murray JC. Two novel frameshift mutations in NKX2.5 result in novel features including visceral inversus and sinus venosus type ASD. J Med Genet 2002; 39:807-11. [PMID: 12414819 PMCID: PMC1735007 DOI: 10.1136/jmg.39.11.807] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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