1
|
Rebhun RB, York D, De Graaf FMD, Yoon P, Batcher KL, Luker ME, Ryan S, Peyton J, Kent MS, Stern JA, Bannasch DL. A variant in the 5'UTR of ERBB4 is associated with lifespan in Golden Retrievers. GeroScience 2024; 46:2849-2862. [PMID: 37855863 PMCID: PMC11009206 DOI: 10.1007/s11357-023-00968-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 09/29/2023] [Indexed: 10/20/2023] Open
Abstract
Genome-wide association studies (GWAS) in long-lived human populations have led to identification of variants associated with Alzheimer's disease and cardiovascular disease, the latter being the most common cause of mortality in people worldwide. In contrast, naturally occurring cancer represents the leading cause of death in pet dogs, and specific breeds like the Golden Retriever (GR) carry up to a 65% cancer-related death rate. We hypothesized that GWAS of long-lived GRs might lead to the identification of genetic variants capable of modifying longevity within this cancer-predisposed breed. A GWAS was performed comparing GR dogs ≥ 14 years to dogs dying prior to age 12 which revealed a significant association to ERBB4, the only member of the epidermal growth factor receptor family capable of serving as both a tumor suppressor gene and an oncogene. No coding variants were identified, however, distinct haplotypes in the 5'UTR were associated with reduced lifespan in two separate populations of GR dogs. When all GR dogs were analyzed together (n = 304), the presence of haplotype 3 was associated with shorter survival (11.8 years vs. 12.8 years, p = 0.024). GRs homozygous for haplotype 3 had the shortest survival, and GRs homozygous for haplotype 1 had the longest survival (11.6 years vs. 13.5 years, p = 0.0008). Sub-analyses revealed that the difference in lifespan for GRs carrying at least 1 copy of haplotype 3 was specific to female dogs (p = 0.009), whereas survival remained significantly different in both male and female GRs homozygous for haplotype 1 or haplotype 3 (p = 0.026 and p = 0.009, respectively). Taken together, these findings implicate a potential role for ERBB4 in GR longevity and provide evidence that within-breed canine lifespan studies could serve as a mechanism to identify favorable or disease-modifying variants important to the axis of aging and cancer.
Collapse
Affiliation(s)
- Robert B Rebhun
- Department of Surgical and Radiological Sciences, University of California, Davis, CA, USA.
| | - Daniel York
- Department of Surgical and Radiological Sciences, University of California, Davis, CA, USA
| | - Flora M D De Graaf
- Department of Population Health and Reproduction, University of California, Davis, CA, USA
| | - Paula Yoon
- Veterinary Medical Teaching Hospital, University of California, Davis, CA, USA
| | - Kevin L Batcher
- Department of Population Health and Reproduction, University of California, Davis, CA, USA
| | - Madison E Luker
- Department of Surgical and Radiological Sciences, University of California, Davis, CA, USA
| | - Stephanie Ryan
- Department of Population Health and Reproduction, University of California, Davis, CA, USA
| | - Jamie Peyton
- Veterinary Medical Teaching Hospital, University of California, Davis, CA, USA
| | - Michael S Kent
- Department of Surgical and Radiological Sciences, University of California, Davis, CA, USA
| | - Joshua A Stern
- Department of Medicine and Epidemiology, University of California, Davis, CA, USA
| | - Danika L Bannasch
- Department of Population Health and Reproduction, University of California, Davis, CA, USA.
| |
Collapse
|
2
|
Estevam MV, Toniollo GH, Apparicio M. The most common congenital malformations in dogs: Literature review and practical guide. Res Vet Sci 2024; 171:105230. [PMID: 38492280 DOI: 10.1016/j.rvsc.2024.105230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 03/04/2024] [Accepted: 03/12/2024] [Indexed: 03/18/2024]
Abstract
Congenital malformations can affect almost 7% of canine newborns. The increase of commercial dog breeding and inbreeding used to maintain the striking characteristics of each breed, the appearance of malformations has become increasingly common, especially in brachycephalic dogs. The causes are diverse, and include genetic, nutritional, iatrogenic, and infectious factors, often making it difficult to establish a cause-consequence relationship. The high mortality associated with malformations comes not only from the fact that some are incompatible with life, but also because even if many undergo surgical treatment or correction, they require specific management, monitoring, and clinical treatment for an indefinite period of time. The most common malformations such as cleft lip and palate, hydrocephalus and anasarca have been studied for a long time, and it is currently known that brachycephalic dogs have a greater predisposition, however, for other less common conditions as gastroschisis and hypospadias, there is only a few case reports. The appearance of congenital defects in a litter leads to financial losses for the breeder, emotional losses for the owner and the veterinarian and harms the well-being of that individual. For this reason, the aim of this review article is to gather relevant information on the characteristics, diagnosis, and management of the main malformations in puppies. It is essential that the veterinarian is prepared to diagnose and treat these conditions, reducing negative impacts on animals and owners.
Collapse
Affiliation(s)
- Marina Vilela Estevam
- Department of Pathology, Reproduction and One Health, São Paulo State University - FCAV Unesp, Jaboticabal, SP, Brazil
| | - Gilson Helio Toniollo
- Department of Pathology, Reproduction and One Health, São Paulo State University - FCAV Unesp, Jaboticabal, SP, Brazil
| | - Maricy Apparicio
- Department of Veterinary Surgery and Animal Reproduction, São Paulo State University - FMVZ Unesp, Botucatu, SP, Brazil.
| |
Collapse
|
3
|
Purbantoro SD, Taephatthanasagon T, Purwaningrum M, Hirankanokchot T, Peralta S, Fiani N, Sawangmake C, Rattanapuchpong S. Trends of regenerative tissue engineering for oral and maxillofacial reconstruction in veterinary medicine. Front Vet Sci 2024; 11:1325559. [PMID: 38450027 PMCID: PMC10915013 DOI: 10.3389/fvets.2024.1325559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 02/05/2024] [Indexed: 03/08/2024] Open
Abstract
Oral and maxillofacial (OMF) defects are not limited to humans and are often encountered in other species. Reconstructing significant tissue defects requires an excellent strategy for efficient and cost-effective treatment. In this regard, tissue engineering comprising stem cells, scaffolds, and signaling molecules is emerging as an innovative approach to treating OMF defects in veterinary patients. This review presents a comprehensive overview of OMF defects and tissue engineering principles to establish proper treatment and achieve both hard and soft tissue regeneration in veterinary practice. Moreover, bench-to-bedside future opportunities and challenges of tissue engineering usage are also addressed in this literature review.
Collapse
Affiliation(s)
- Steven Dwi Purbantoro
- Veterinary Stem Cell and Bioengineering Innovation Center (VSCBIC), Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- Veterinary Stem Cell and Bioengineering Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Teeanutree Taephatthanasagon
- Veterinary Stem Cell and Bioengineering Innovation Center (VSCBIC), Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- Veterinary Stem Cell and Bioengineering Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Medania Purwaningrum
- Veterinary Stem Cell and Bioengineering Innovation Center (VSCBIC), Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- Veterinary Stem Cell and Bioengineering Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- Department of Biochemistry, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Thanyathorn Hirankanokchot
- Veterinary Stem Cell and Bioengineering Innovation Center (VSCBIC), Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Santiago Peralta
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States
| | - Nadine Fiani
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States
| | - Chenphop Sawangmake
- Veterinary Stem Cell and Bioengineering Innovation Center (VSCBIC), Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- Veterinary Stem Cell and Bioengineering Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- Department of Pharmacology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence in Regenerative Dentistry, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand
| | - Sirirat Rattanapuchpong
- Veterinary Stem Cell and Bioengineering Innovation Center (VSCBIC), Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- Veterinary Stem Cell and Bioengineering Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- Academic Affairs, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| |
Collapse
|
4
|
Marc S, Savici J, Sicoe B, Boldura OM, Paul C, Otavă G. Exencephaly-Anencephaly Sequence Associated with Maxillary Brachygnathia, Spinal Defects, and Palatoschisis in a Male Domestic Cat. Animals (Basel) 2023; 13:3882. [PMID: 38136919 PMCID: PMC10741185 DOI: 10.3390/ani13243882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 12/08/2023] [Accepted: 12/15/2023] [Indexed: 12/24/2023] Open
Abstract
Anencephaly, a severe neural tube defect characterized by the absence of major parts of the brain and skull, is a rare congenital disorder that has been observed in various species, including cats. Considering the uncommon appearance of anencephaly, this paper aims to present anencephaly in a stillborn male kitten from an accidental inbreeding using various paraclinical methods. Histological examination of tissue samples from the cranial region, where parts of the skull were absent, revealed the presence of atypical nerve tissue with neurons and glial cells organized in clusters, surrounded by an extracellular matrix and with an abundance of blood vessels, which are large, dilated, and filled with blood, not characteristic of nerve tissue structure. In CT scans, the caudal part of the frontal bone, the fronto-temporal limits, and the parietal bone were observed to be missing. CT also revealed that the dorsal tubercle of the atlas, the dorsal neural arch, and the spinal process of the C2-C7 bones were missing. In conclusion, the kitten was affected by multiple congenital malformations, a combination of exencephaly-anencephaly, maxillary brachygnathism, closed cranial spina bifida at the level of cervical vertebrae, kyphoscoliosis, palatoschisis, and partial intestinal atresia. The importance of employing imaging techniques cannot be overstated when it comes to the accurate diagnosis of neural tube defects.
Collapse
Affiliation(s)
- Simona Marc
- Faculty of Veterinary Medicine, University of Life Sciences “King Mihai I” from Timisoara, Calea Aradului 119, 300645 Timisoara, Romania; (S.M.); (J.S.); (B.S.); (O.M.B.); (G.O.)
| | - Jelena Savici
- Faculty of Veterinary Medicine, University of Life Sciences “King Mihai I” from Timisoara, Calea Aradului 119, 300645 Timisoara, Romania; (S.M.); (J.S.); (B.S.); (O.M.B.); (G.O.)
| | - Bogdan Sicoe
- Faculty of Veterinary Medicine, University of Life Sciences “King Mihai I” from Timisoara, Calea Aradului 119, 300645 Timisoara, Romania; (S.M.); (J.S.); (B.S.); (O.M.B.); (G.O.)
| | - Oana Maria Boldura
- Faculty of Veterinary Medicine, University of Life Sciences “King Mihai I” from Timisoara, Calea Aradului 119, 300645 Timisoara, Romania; (S.M.); (J.S.); (B.S.); (O.M.B.); (G.O.)
| | - Cristina Paul
- Department of Applied Chemistry and Engineering of Organic and Natural Compounds, Faculty of Industrial Chemistry and Environmental Engineering, Politehnica University Timisoara, Carol Telbisz 6, 300001 Timisoara, Romania
| | - Gabriel Otavă
- Faculty of Veterinary Medicine, University of Life Sciences “King Mihai I” from Timisoara, Calea Aradului 119, 300645 Timisoara, Romania; (S.M.); (J.S.); (B.S.); (O.M.B.); (G.O.)
| |
Collapse
|
5
|
Lin Y, Shi J, Shi B, Jia Z. MMP16 as NSCL ± P Susceptible Gene in Western Han Chinese. Cleft Palate Craniofac J 2023; 60:1625-1631. [PMID: 36120833 DOI: 10.1177/10556656221125392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
OBJECTIVE The role of MMP16 in lip development is unclear. This study aimed to identify nonsyndromic cleft lip with or without palate (NSCL ± P) susceptible loci of MMP16 in western Han Chinese. DESIGN We performed targeted sequencing around MMP16 combined with a 2-phase association analysis on common variants. Phase 2 association analysis was performed with NSCL ± P specific subphenotypes (NSCL and NSCLP). Then we used rare variants burden analysis and genotyping, accompanied by motif analysis. SETTING This study was completed in a tertiary medical center. PATIENTS, PARTICIPANTS Phase 1 targeted sequencing included 159 patients with NSCL ± P and 542 normal controls; phase 2 included 1626 patients with NSCL ± P (1047 NSCL and 579 NSCLP) and 2255 normal controls. INTERVENTIONS Venous blood samples were collected from patients and used to extract DNA. MAIN OUTCOME MEASURES After Bonferroni correction, phase 1 significant threshold of p-value was 4.28 × 10-5 (0.05/1167 single nucleotide polymorphisms [SNPs]), and phase 2 was .00025 (0.05/200 SNPs). Burden analysis significant threshold p-value was .05. RESULTS Common variants phase 1 association analysis identified 11 statistically significant SNPs (lowest p = 1.90 × 10-9, odds ratio (OR) = 0.27, 95% CI: 0.17-0.44), phase 2 replication identified 16 SNPs in NSCL ± P (lowest p = 6.26 × 10-6, OR = 0.77, 95% CI: 0.69-0.86) and 9 in NSCL (lowest p = 8.44 × 10-5, OR = 0.76, 95% CI: 0.66-0.87). Rare variants burden analysis showed no significant results, genotyping results showed they were maternally inherited. CONCLUSIONS Our study identified MMP16 susceptible SNPs in NSCL ± P and NSCL, emphasizing its potential role in lip development. Our study also highlighted the importance to perform association analysis with subphenotypes divided.
Collapse
Affiliation(s)
- Yansong Lin
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, Department of Cleft Lip and Palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jiayu Shi
- Division of Growth and Development and Section of Orthodontics, School of Dentistry, University of California, Los Angeles, CA, USA
| | - Bing Shi
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, Department of Cleft Lip and Palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Zhonglin Jia
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, Department of Cleft Lip and Palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| |
Collapse
|
6
|
Yu Y, Zhen Q, Chen W, Yu Y, Li Z, Wang Y, Fan W, Luo S, Wang D, Bai Y, Bian Z, He M, Sun L. Genome-wide meta-analyses identify five new risk loci for nonsyndromic orofacial clefts in the Chinese Han population. Mol Genet Genomic Med 2023; 11:e2226. [PMID: 37326468 PMCID: PMC10568389 DOI: 10.1002/mgg3.2226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 05/12/2023] [Accepted: 05/31/2023] [Indexed: 06/17/2023] Open
Abstract
BACKGROUND Nonsyndromic orofacial clefts (NSOFCs) are the most common craniofacial birth malformations in humans and are generally classified as nonsyndromic cleft lip with or without cleft palate (NSCL/P) and nonsyndromic cleft palate only (NSCPO). Genome-wide association studies (GWASs) of NSOFCs have demonstrated multiple risk loci and candidate genes; however, published risk factors are able to explain only a small fraction of the observed NSOFCs heritability. METHODS Here, we performed GWASs of 1615 NSCPO cases and 2340 controls, and then conducted genome-wide meta-analyses of NSOFCs, totaling 6812 NSCL/P cases, 2614 NSCPO cases, and 19,165 controls from the Chinese Han population. RESULTS We identify 47 risk loci with genome-wide pmeta -value <5.0 × 10-8 , 5 risk loci (1p32.1, 3p14.1, 3p14.3, 3p21.31, and 13q22.1) of which are new. All of the 47 susceptibility loci conjointly account for 44.12% of the NSOFCs' heritability in the Chinese Han population. CONCLUSION Our results improve the comprehending of genetic susceptibility to NSOFCs and provide new views into the genetic etiology of craniofacial anomalies.
Collapse
Affiliation(s)
- Yafen Yu
- Department of Dermatologythe First Affiliated Hospital of Anhui Medical UniversityHefeiChina
- Institute of DermatologyAnhui Medical UniversityHefeiChina
- Key Laboratory of Dermatology, Ministry of EducationAnhui Medical UniversityHefeiChina
- Inflammation and Immune Mediated Diseases Laboratory of Anhui ProvinceHefeiChina
- Anhui Provincial Institute of Translational MedicineHefeiChina
| | - Qi Zhen
- Department of Dermatologythe First Affiliated Hospital of Anhui Medical UniversityHefeiChina
- Institute of DermatologyAnhui Medical UniversityHefeiChina
- Key Laboratory of Dermatology, Ministry of EducationAnhui Medical UniversityHefeiChina
- Inflammation and Immune Mediated Diseases Laboratory of Anhui ProvinceHefeiChina
- Anhui Provincial Institute of Translational MedicineHefeiChina
| | - Weiwei Chen
- Department of Dermatologythe First Affiliated Hospital of Anhui Medical UniversityHefeiChina
- Institute of DermatologyAnhui Medical UniversityHefeiChina
- Key Laboratory of Dermatology, Ministry of EducationAnhui Medical UniversityHefeiChina
- Inflammation and Immune Mediated Diseases Laboratory of Anhui ProvinceHefeiChina
- Anhui Provincial Institute of Translational MedicineHefeiChina
| | - Yanqin Yu
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei‐MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of StomatologyWuhan UniversityWuhanChina
| | - Zhuo Li
- Department of Dermatologythe First Affiliated Hospital of Anhui Medical UniversityHefeiChina
- Institute of DermatologyAnhui Medical UniversityHefeiChina
- Key Laboratory of Dermatology, Ministry of EducationAnhui Medical UniversityHefeiChina
- Inflammation and Immune Mediated Diseases Laboratory of Anhui ProvinceHefeiChina
- Anhui Provincial Institute of Translational MedicineHefeiChina
| | - Yirui Wang
- Department of Dermatologythe First Affiliated Hospital of Anhui Medical UniversityHefeiChina
- Institute of DermatologyAnhui Medical UniversityHefeiChina
- Key Laboratory of Dermatology, Ministry of EducationAnhui Medical UniversityHefeiChina
- Inflammation and Immune Mediated Diseases Laboratory of Anhui ProvinceHefeiChina
- Anhui Provincial Institute of Translational MedicineHefeiChina
| | - Wencheng Fan
- Department of Dermatologythe First Affiliated Hospital of Anhui Medical UniversityHefeiChina
- Institute of DermatologyAnhui Medical UniversityHefeiChina
- Key Laboratory of Dermatology, Ministry of EducationAnhui Medical UniversityHefeiChina
- Inflammation and Immune Mediated Diseases Laboratory of Anhui ProvinceHefeiChina
- Anhui Provincial Institute of Translational MedicineHefeiChina
| | - Sihan Luo
- Department of Dermatologythe First Affiliated Hospital of Anhui Medical UniversityHefeiChina
- Institute of DermatologyAnhui Medical UniversityHefeiChina
- Key Laboratory of Dermatology, Ministry of EducationAnhui Medical UniversityHefeiChina
- Inflammation and Immune Mediated Diseases Laboratory of Anhui ProvinceHefeiChina
- Anhui Provincial Institute of Translational MedicineHefeiChina
| | - Daiyue Wang
- Department of Dermatologythe First Affiliated Hospital of Anhui Medical UniversityHefeiChina
- Institute of DermatologyAnhui Medical UniversityHefeiChina
- Key Laboratory of Dermatology, Ministry of EducationAnhui Medical UniversityHefeiChina
- Inflammation and Immune Mediated Diseases Laboratory of Anhui ProvinceHefeiChina
- Anhui Provincial Institute of Translational MedicineHefeiChina
| | - Yuanming Bai
- Department of Dermatologythe First Affiliated Hospital of Anhui Medical UniversityHefeiChina
- Institute of DermatologyAnhui Medical UniversityHefeiChina
- Key Laboratory of Dermatology, Ministry of EducationAnhui Medical UniversityHefeiChina
- Inflammation and Immune Mediated Diseases Laboratory of Anhui ProvinceHefeiChina
- Anhui Provincial Institute of Translational MedicineHefeiChina
| | - Zhuan Bian
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei‐MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of StomatologyWuhan UniversityWuhanChina
| | - Miao He
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei‐MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of StomatologyWuhan UniversityWuhanChina
| | - Liangdan Sun
- Department of Dermatologythe First Affiliated Hospital of Anhui Medical UniversityHefeiChina
- Institute of DermatologyAnhui Medical UniversityHefeiChina
- Key Laboratory of Dermatology, Ministry of EducationAnhui Medical UniversityHefeiChina
- Inflammation and Immune Mediated Diseases Laboratory of Anhui ProvinceHefeiChina
- Anhui Provincial Institute of Translational MedicineHefeiChina
| |
Collapse
|
7
|
Card EB, Morales CE, Kimia R, Ramirez JM, Billingslea M, Marroquín A, Masaya I, Arteaga V, Marazita ML, Friedland LR, Low DW, Schwartz AJ, Scott M, Jackson OA. A Retrospective and Prospective Cohort Study Comparing Pediatric Patients With Cleft Lip and Palate From the United States and Guatemala. J Craniofac Surg 2023; 34:1978-1984. [PMID: 37449578 DOI: 10.1097/scs.0000000000009539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 05/19/2023] [Indexed: 07/18/2023] Open
Abstract
Orofacial clefts (OFC) remain among the most prevalent congenital abnormalities worldwide. In the United States in 2010 to 2014, 16.2 of 10,000 live births are born with OFC compared with 23.6 of 10,000 in Alta Verapaz, Guatemala in 2012. Demographics and cleft severity scores were retrospectively gathered from 514 patients with isolated OFC at the Children's Hospital of Philadelphia scheduled for surgery from 2012 to 2019 and from 115 patients seen during surgical mission trips to Guatemala City from 2017 to 2020. Risk factors were also gathered prospectively from Guatemalan families. The Guatemalan cohort had a significantly lower prevalence of cleft palate only compared with the US cohort, which may be a result of greater cleft severity in the population or poor screening and subsequent increased mortality of untreated cleft palate. Of those with lip involvement, Guatemalan patients were significantly more likely to have complete cleft lip, associated cleft palate, and right-sided and bilateral clefts, demonstrating an increased severity of Guatemalan cleft phenotype. Primary palate and lip repair for the Guatemalan cohort occurred at a significantly older age than that of the US cohort, placing Guatemalan patients at increased risk for long-term complications such as communication difficulties. Potential OFC risk factors identified in the Guatemalan cohort included maternal cooking-fire and agricultural chemical exposure, poor prenatal vitamin intake, poverty, and risk factors related to primarily corn-based diets. OFC patients who primarily rely on surgical missions for cleft care would likely benefit from more comprehensive screening and investigation into risk factors for more severe OFC phenotypes.
Collapse
Affiliation(s)
- Elizabeth B Card
- Division of Plastic Surgery, University of Pennsylvania Health System, Philadelphia, PA
| | - Carrie E Morales
- Division of Plastic Surgery, University of Pennsylvania Health System, Philadelphia, PA
| | - Rotem Kimia
- Division of Plastic and Reconstructive Surgery, Renaissance School of Medicine at Stony Brook University, Stony Brook, NY
| | | | | | | | - Irina Masaya
- Facultad de Ciencias de la Salud, Departamento de Medicina, Universidad Rafael Landívar
| | - Vilma Arteaga
- Guatemalan Functional Occlusion Association, Functional Maxillary Orthopedics and Craniofacial Orthodontics Specialist, Juan Pablo II Children's Hospital, Operation Smile Guatemala, Guatemala
| | - Mary L Marazita
- Center for Craniofacial and Dental Genetics
- Department of Oral and Craniofacial Sciences, School of Dental Medicine
- Department of Human Genetics, Graduate School of Public Health
- Clinical and Translation Sciences
- Department of Psychiatry, School of Medicine, University of Pittsburgh, Pittsburgh, PA
| | - Leonard R Friedland
- Scientific Affairs and Public Health GSK Vaccines, Research and Development Department, GlaxoSmithKline
| | - David W Low
- Division of Plastic and Reconstructive Surgery, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania
| | - Alan Jay Schwartz
- Department of Anesthesiology and Critical Care Medicine, The Children's Hospital of Philadelphia
- Perelman School of Medicine, University of Pennsylvania
| | - Michelle Scott
- Division of Plastic and Reconstructive Surgery, Children's Hospital of Philadelphia
| | - Oksana A Jackson
- Division of Plastic Surgery, Department of Surgery, University of Pennsylvania Health System
| |
Collapse
|
8
|
Ruszkowski JJ, Nowacka-Woszuk J, Nowak T, Rozynek J, Serwanska-Leja K, Gogulski M, Kolodziejski P, Switonski M, Zdun M, Szczerbal I. Cleft Lip and Palate in Four Full-Sib Puppies from a Single Litter of Staffordshire Bull Terrier Dogs: An Anatomical and Genetic Study. Animals (Basel) 2023; 13:2749. [PMID: 37685013 PMCID: PMC10486559 DOI: 10.3390/ani13172749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/12/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023] Open
Abstract
Cleft lip and palate (CLP) is a well-known congenital defect in dogs, characterized by abnormal communication between the oral and nasal cavities. Its incidence rate is high and affects all dog breeds. The etiology of CLP is thought to be multifactorial, caused by both genetic and environmental factors. In this study, four puppies out of seven from a single litter of Staffordshire Bull Terrier dogs with craniofacial abnormalities were anatomically and genetically examined. Classical anatomical preparation, dyed-latex-injection of the arterial vessels, and cone-beam computed tomography were used. The puppies showed variations in their observable abnormalities: three of them had a complete cleft of the palate on both sides, while one puppy had a cleft on the right side only. Cytogenetic analysis showed a normal diploid chromosome number (2n = 78,XX or 78,XY) in the studied animals. Known genomic variants of CLP were examined in the ADAMTS20, DLX6, and MYH3 genes, but no mutations were identified. Further studies are needed to identify the breed-specific genetic variants associated with canine CLP.
Collapse
Affiliation(s)
- Jakub J. Ruszkowski
- Department of Animal Anatomy, Poznan University of Life Sciences, Wojska Polskiego 71C, 60-625 Poznan, Poland; (J.J.R.); (K.S.-L.)
| | - Joanna Nowacka-Woszuk
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637 Poznan, Poland; (J.N.-W.); (T.N.); (J.R.); (M.S.)
| | - Tomasz Nowak
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637 Poznan, Poland; (J.N.-W.); (T.N.); (J.R.); (M.S.)
| | - Jedrzej Rozynek
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637 Poznan, Poland; (J.N.-W.); (T.N.); (J.R.); (M.S.)
| | - Katarzyna Serwanska-Leja
- Department of Animal Anatomy, Poznan University of Life Sciences, Wojska Polskiego 71C, 60-625 Poznan, Poland; (J.J.R.); (K.S.-L.)
| | - Maciej Gogulski
- Department of Preclinical Sciences and Infectious Diseases, Poznan University of Life Sciences, Wolynska 35, 60-637 Poznan, Poland;
- University Centre for Veterinary Medicine, Poznan University of Life Sciences, Szydłowska 43, 60-637 Poznan, Poland
| | - Pawel Kolodziejski
- Department of Animal Physiology, Biochemistry and Biostructure, Poznan University of Life Sciences, Wolynska 35, 60-637 Poznan, Poland;
| | - Marek Switonski
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637 Poznan, Poland; (J.N.-W.); (T.N.); (J.R.); (M.S.)
| | - Maciej Zdun
- Department of Animal Anatomy, Poznan University of Life Sciences, Wojska Polskiego 71C, 60-625 Poznan, Poland; (J.J.R.); (K.S.-L.)
| | - Izabela Szczerbal
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637 Poznan, Poland; (J.N.-W.); (T.N.); (J.R.); (M.S.)
| |
Collapse
|
9
|
Nandadasa S, Martin D, Deshpande G, Robert KL, Stack MS, Itoh Y, Apte SS. Degradomic Identification of Membrane Type 1-Matrix Metalloproteinase as an ADAMTS9 and ADAMTS20 Substrate. Mol Cell Proteomics 2023; 22:100566. [PMID: 37169079 PMCID: PMC10267602 DOI: 10.1016/j.mcpro.2023.100566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 05/05/2023] [Accepted: 05/07/2023] [Indexed: 05/13/2023] Open
Abstract
The secreted metalloproteases ADAMTS9 and ADAMTS20 are implicated in extracellular matrix proteolysis and primary cilium biogenesis. Here, we show that clonal gene-edited RPE-1 cells in which ADAMTS9 was inactivated, and which constitutively lack ADAMTS20 expression, have morphologic characteristics distinct from parental RPE-1 cells. To investigate underlying proteolytic mechanisms, a quantitative terminomics method, terminal amine isotopic labeling of substrates was used to compare the parental and gene-edited RPE-1 cells and their medium to identify ADAMTS9 substrates. Among differentially abundant neo-amino (N) terminal peptides arising from secreted and transmembrane proteins, a peptide with lower abundance in the medium of gene-edited cells suggested cleavage at the Tyr314-Gly315 bond in the ectodomain of the transmembrane metalloprotease membrane type 1-matrix metalloproteinase (MT1-MMP), whose mRNA was also reduced in gene-edited cells. This cleavage, occurring in the MT1-MMP hinge, that is, between the catalytic and hemopexin domains, was orthogonally validated both by lack of an MT1-MMP catalytic domain fragment in the medium of gene-edited cells and restoration of its release from the cell surface by reexpression of ADAMTS9 and ADAMTS20 and was dependent on hinge O-glycosylation. A C-terminally semitryptic MT1-MMP peptide with greater abundance in WT RPE-1 medium identified a second ADAMTS9 cleavage site in the MT1-MMP hemopexin domain. Consistent with greater retention of MT1-MMP on the surface of gene-edited cells, pro-MMP2 activation, which requires cell surface MT1-MMP, was increased. MT1-MMP knockdown in gene-edited ADAMTS9/20-deficient cells restored focal adhesions but not ciliogenesis. The findings expand the web of interacting proteases at the cell surface, suggest a role for ADAMTS9 and ADAMTS20 in regulating cell surface activity of MT1-MMP, and indicate that MT1-MMP shedding does not underlie their observed requirement in ciliogenesis.
Collapse
Affiliation(s)
- Sumeda Nandadasa
- Department of Biomedical Engineering, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio, USA; Department of Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts, USA.
| | - Daniel Martin
- Department of Biomedical Engineering, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio, USA
| | - Gauravi Deshpande
- Imaging Core Facility, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio, USA
| | - Karyn L Robert
- Department of Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - M Sharon Stack
- Department of Chemistry and Biochemistry and Harper Cancer Center, University of Notre Dame, Notre Dame, Indiana, USA
| | - Yoshifumi Itoh
- Kennedy Institute for Rheumatology, University of Oxford, Oxford, UK
| | - Suneel S Apte
- Department of Biomedical Engineering, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio, USA.
| |
Collapse
|
10
|
Zhang Y, Li J, Ji Y, Cheng Y, Fu X. Mutations in the TBX15-ADAMTS2 pathway associate with a novel soft palate dysplasia. Hum Mutat 2022; 43:2102-2115. [PMID: 36124393 DOI: 10.1002/humu.24473] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 08/29/2022] [Accepted: 09/15/2022] [Indexed: 01/25/2023]
Abstract
We reported de novo variants in specific exons of the TBX15 and ADAMTS2 genes in a hitherto undescribed class of patients with unique craniofacial developmental defects. The nine unrelated patients represent unilateral soft palate hypoplasia, lost part of the sphenoid bone in the pterygoid process, but the uvula developed completely. Interestingly, these clinical features are contrary to the palate's anterior-posterior (A-P) developmental direction. Based on developmental characteristics, we suggested that these cases correspond to a novel craniofacial birth defect different from cleft palate, and we named it soft palate dysplasia (SPD). However, little is known about the molecular mechanism of the ADAMTS2 and TBX15 genes in the regulation of soft palate development. Phylogenetic analysis showed that the sequences around these de novo mutation sites are conserved between species. Through cellular co-transfections and chromatin immunoprecipitation assays, we demonstrate that TBX15 binds to the promoter regions of the ADAMTS2 gene and activates the promoter activity. Furthermore, we show that TBX15 and ADAMTS2 are colocalization in the posterior palatal mesenchymal cells during soft palate development in E13.5 mice embryos. Based on these data, we propose that the disruption of the TBX15-ADAMTS2 signaling pathway during embryogenesis leads to a novel SPD.
Collapse
Affiliation(s)
- Yuying Zhang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, China.,The Department of Oral and Maxillofacial Surgery, School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Jian Li
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, China.,The Department of Oral and Maxillofacial Surgery, School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Yaoting Ji
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Yibin Cheng
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Xiazhou Fu
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, China
| |
Collapse
|
11
|
Xiao Y, Jiao S, He M, Lin D, Zuo H, Han J, Sun Y, Cao G, Chen Z, Liu H. Chromatin conformation of human oral epithelium can identify orofacial cleft missing functional variants. Int J Oral Sci 2022; 14:43. [PMID: 36008388 PMCID: PMC9411193 DOI: 10.1038/s41368-022-00194-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 07/19/2022] [Accepted: 07/29/2022] [Indexed: 11/09/2022] Open
Abstract
Genome-wide association studies (GWASs) are the most widely used method to identify genetic risk loci associated with orofacial clefts (OFC). However, despite the increasing size of cohort, GWASs are still insufficient to detect all the heritability, suggesting there are more associations under the current stringent statistical threshold. In this study, we obtained an integrated epigenomic dataset based on the chromatin conformation of a human oral epithelial cell line (HIOEC) using RNA-seq, ATAC-seq, H3K27ac ChIP-seq, and DLO Hi-C. Presumably, this epigenomic dataset could reveal the missing functional variants located in the oral epithelial cell active enhancers/promoters along with their risk target genes, despite relatively less-stringent statistical association with OFC. Taken a non-syndromic cleft palate only (NSCPO) GWAS data of the Chinese Han population as an example, 3664 SNPs that cannot reach the strict significance threshold were subjected to this functional identification pipeline. In total, 254 potential risk SNPs residing in active cis-regulatory elements interacting with 1 718 promoters of oral epithelium-expressed genes were screened. Gapped k-mer machine learning based on enhancers interacting with epithelium-expressed genes along with in vivo and in vitro reporter assays were employed as functional validation. Among all the potential SNPs, we chose and confirmed that the risk alleles of rs560789 and rs174570 reduced the epithelial-specific enhancer activity by preventing the binding of transcription factors related to epithelial development. In summary, we established chromatin conformation datasets of human oral epithelial cells and provided a framework for testing and understanding how regulatory variants impart risk for clefts.
Collapse
Affiliation(s)
- Yao Xiao
- The State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory for Oral Biomedicine of Ministry of Education, School and Hospital of Stomatology, Wuhan University, 237 Luoyu Road, Wuhan, China.,Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Shengbo Jiao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Institute of Hydrobiology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Wuhan, China.,College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Miao He
- The State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory for Oral Biomedicine of Ministry of Education, School and Hospital of Stomatology, Wuhan University, 237 Luoyu Road, Wuhan, China
| | - Da Lin
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Huanyan Zuo
- The State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory for Oral Biomedicine of Ministry of Education, School and Hospital of Stomatology, Wuhan University, 237 Luoyu Road, Wuhan, China
| | - Jiahao Han
- The State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory for Oral Biomedicine of Ministry of Education, School and Hospital of Stomatology, Wuhan University, 237 Luoyu Road, Wuhan, China
| | - Yonghua Sun
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Institute of Hydrobiology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Wuhan, China.,College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Gang Cao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Zhi Chen
- The State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory for Oral Biomedicine of Ministry of Education, School and Hospital of Stomatology, Wuhan University, 237 Luoyu Road, Wuhan, China.
| | - Huan Liu
- The State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory for Oral Biomedicine of Ministry of Education, School and Hospital of Stomatology, Wuhan University, 237 Luoyu Road, Wuhan, China. .,Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, China.
| |
Collapse
|
12
|
Belanger JM, Heinonen T, Famula TR, Mandigers PJJ, Leegwater PA, Hytönen MK, Lohi H, Oberbauer AM. Validation of a Chromosome 14 Risk Haplotype for Idiopathic Epilepsy in the Belgian Shepherd Dog Found to Be Associated with an Insertion in the RAPGEF5 Gene. Genes (Basel) 2022; 13:genes13071124. [PMID: 35885906 PMCID: PMC9323784 DOI: 10.3390/genes13071124] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/19/2022] [Accepted: 06/21/2022] [Indexed: 12/04/2022] Open
Abstract
An idiopathic epilepsy (IE) risk haplotype on canine chromosome (CFA) 14 has been reported to interact with the CFA37 common risk haplotype in the Belgian shepherd (BS). Additional IE cases and control dogs were genotyped for the risk haplotypes to validate these previous findings. In the new cohort, the interaction between the two regions significantly elevated IE risk. When the haplotypes were analyzed individually, particular haplotypes on both CFA14 (ACTG) and 37 (GG) were associated with elevated IE risk, though only the CFA37 AA was significantly associated (p < 0.003) with reduced risk in the new cohort. However, the CFA14 ACTG risk was statistically significant when the new and previous cohort data were combined. The frequency of the ACTG haplotype was four-fold higher in BS dogs than in other breeds. Whole genome sequence analysis revealed that a 3-base pair predicted disruptive insertion in the RAPGEF5 gene, which is adjacent to the CFA14 risk haplotype. RAPGEF5 is involved in the Wnt-β-catenin signaling pathway that is crucial for normal brain function. Although this risk variant does not fully predict the likelihood of a BS developing IE, the association with a variant in a candidate gene may provide insight into the genetic control of canine IE.
Collapse
Affiliation(s)
- Janelle M. Belanger
- Department of Animal Science, University of California, Davis, CA 95616, USA; (J.M.B.); (T.R.F.)
| | - Tiina Heinonen
- Department of Medical and Clinical Genetics, University of Helsinki, 00014 Helsinki, Finland; (T.H.); (M.K.H.); (H.L.)
- Department of Veterinary Biosciences, University of Helsinki, 00014 Helsinki, Finland
- Folkhälsan Research Center, 00290 Helsinki, Finland
| | - Thomas R. Famula
- Department of Animal Science, University of California, Davis, CA 95616, USA; (J.M.B.); (T.R.F.)
| | - Paul J. J. Mandigers
- Department of Clinical Sciences, Utrecht University, Yalelaan 108, 3584 CM Utrecht, The Netherlands; (P.J.J.M.); (P.A.L.)
| | - Peter A. Leegwater
- Department of Clinical Sciences, Utrecht University, Yalelaan 108, 3584 CM Utrecht, The Netherlands; (P.J.J.M.); (P.A.L.)
| | - Marjo K. Hytönen
- Department of Medical and Clinical Genetics, University of Helsinki, 00014 Helsinki, Finland; (T.H.); (M.K.H.); (H.L.)
- Department of Veterinary Biosciences, University of Helsinki, 00014 Helsinki, Finland
- Folkhälsan Research Center, 00290 Helsinki, Finland
| | - Hannes Lohi
- Department of Medical and Clinical Genetics, University of Helsinki, 00014 Helsinki, Finland; (T.H.); (M.K.H.); (H.L.)
- Department of Veterinary Biosciences, University of Helsinki, 00014 Helsinki, Finland
- Folkhälsan Research Center, 00290 Helsinki, Finland
| | - Anita M. Oberbauer
- Department of Animal Science, University of California, Davis, CA 95616, USA; (J.M.B.); (T.R.F.)
- Correspondence: ; Tel.: +1-530-752-5484
| |
Collapse
|
13
|
Rs9891446 in NTN1 is associated with right-side cleft lip in Han Chinese Population. Arch Oral Biol 2022; 141:105485. [DOI: 10.1016/j.archoralbio.2022.105485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 05/31/2022] [Accepted: 06/13/2022] [Indexed: 11/18/2022]
|
14
|
ADAM and ADAMTS disintegrin and metalloproteinases as major factors and molecular targets in vascular malfunction and disease. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2022; 94:255-363. [PMID: 35659374 PMCID: PMC9231755 DOI: 10.1016/bs.apha.2021.11.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A Disintegrin and Metalloproteinase (ADAM) and A Disintegrin and Metalloproteinase with Thrombospondin Motifs (ADAMTS) are two closely related families of proteolytic enzymes. ADAMs are largely membrane-bound enzymes that act as molecular scissors or sheddases of membrane-bound proteins, growth factors, cytokines, receptors and ligands, whereas ADAMTS are mainly secreted enzymes. ADAMs have a pro-domain, and a metalloproteinase, disintegrin, cysteine-rich and transmembrane domain. Similarly, ADAMTS family members have a pro-domain, and a metalloproteinase, disintegrin, and cysteine-rich domain, but instead of a transmembrane domain they have thrombospondin motifs. Most ADAMs and ADAMTS are activated by pro-protein convertases, and can be regulated by G-protein coupled receptor agonists, Ca2+ ionophores and protein kinase C. Activated ADAMs and ADAMTS participate in numerous vascular processes including angiogenesis, vascular smooth muscle cell proliferation and migration, vascular cell apoptosis, cell survival, tissue repair, and wound healing. ADAMs and ADAMTS also play a role in vascular malfunction and cardiovascular diseases such as hypertension, atherosclerosis, coronary artery disease, myocardial infarction, heart failure, peripheral artery disease, and vascular aneurysm. Decreased ADAMTS13 is involved in thrombotic thrombocytopenic purpura and microangiopathies. The activity of ADAMs and ADAMTS can be regulated by endogenous tissue inhibitors of metalloproteinases and other synthetic small molecule inhibitors. ADAMs and ADAMTS can be used as diagnostic biomarkers and molecular targets in cardiovascular disease, and modulators of ADAMs and ADAMTS activity may provide potential new approaches for the management of cardiovascular disorders.
Collapse
|
15
|
Goldschmidt S, Hoyer N. Management of Dental and Oral Developmental Conditions in Dogs and Cats. Vet Clin North Am Small Anim Pract 2021; 52:139-158. [PMID: 34838248 DOI: 10.1016/j.cvsm.2021.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Developmental dental and oral disorders are present in juvenile patients less than 12 months of age. The conditions are diverse ranging from cosmetic only to requiring advanced surgical intervention to alleviate pain and secondary complications. Clinical presentation, diagnosis, and appropriate treatment of dental abnormalities including abnormalities in the number, structure, size, and shape of teeth, as well as oral abnormalities including malocclusions, congenital cleft lip and palate, developmental abnormalities resulting in bony proliferation, and soft-tissue abnormalities of the lip and tongue are discussed throughout the article.
Collapse
Affiliation(s)
- Stephanie Goldschmidt
- Dentistry & Oral Surgery, University of Minnesota, 1352 Boyd Avenue, C309 Veterinary Medical Center South, St Paul, MN 55108, USA.
| | - Naomi Hoyer
- Dentistry & Oral Surgery, Colorado State University, 300 W Drake, Fort Collins, CO 80523, USA
| |
Collapse
|
16
|
Yin B, Shi JY, Shi B, Zheng Q, Jia ZL. Association Between SNPs in 1q32.2 and NSCL ± P in Han Chinese Population. Cleft Palate Craniofac J 2021; 59:1520-1526. [PMID: 34730443 DOI: 10.1177/10556656211052837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
OBJECTIVES Non-syndromic cleft lip with or without cleft palate (NSCL ± P) is one of the most common birth malformations. Currently, numerous susceptibility SNPs have been reported by GWA studies, however, the replications of them among NSCL ± P from Han Chinese were very limited. DESIGN In this study, we selected 16 SNPs around 1q32.2 based on the published GWA studies and replicated them among 302 trios with NSCL ± P from Han Chinese Population. The genotypic data was analyzed with FBAT, PLINK and R package. SETTING The study was conducted in a tertiary medical center. PATIENTS, PARTICIPANTS 302 patients with CL ± P and their parents. MAIN OUTCOME MEASURES To ascertain the genetic variants in 1q32.2 in patients with CL ± P in Han Chinese Population. INTERVENTIONS Blood samples were collected. RESULTS We found T allele (Z = 4.26, p = 0.00002) and T/T homozygotes (Z = 4.4, p = 0.000011) at rs12063989 was significantly over-transmitted among non-syndromic cleft lip with or without cleft palate (NSCL ± P). CONCLUSIONS We found rs12063989 exhibited significant association with the occurrence of NSCL ± P, which would provide new evidence for the future study in the etiology of NSCL ± P.
Collapse
Affiliation(s)
- Bin Yin
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of cleft lip and palate, West China Hospital of Stomatology, 12530Sichuan University, Chengdu, China
| | - Jia-Yu Shi
- Division of Growth and Development and Section of Orthodontics, School of Dentistry, University of California, Los Angeles, USA
| | - Bing Shi
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of cleft lip and palate, West China Hospital of Stomatology, 12530Sichuan University, Chengdu, China
| | - Qian Zheng
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of cleft lip and palate, West China Hospital of Stomatology, 12530Sichuan University, Chengdu, China
| | - Zhong-Lin Jia
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of cleft lip and palate, West China Hospital of Stomatology, 12530Sichuan University, Chengdu, China
| |
Collapse
|
17
|
Leonard BC, Kermanian CS, Michalak SR, Kass PH, Hollingsworth SR, Good KL, Maggs DJ, Thomasy SM. A Retrospective Study of Corneal Endothelial Dystrophy in Dogs (1991-2014). Cornea 2021; 40:578-583. [PMID: 32947393 PMCID: PMC7960559 DOI: 10.1097/ico.0000000000002488] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 06/25/2020] [Indexed: 11/25/2022]
Abstract
PURPOSE To retrospectively evaluate the clinical data, diagnostic tests, treatments, and outcomes for dogs with corneal endothelial dystrophy (CED) and determine risk factors for CED when compared with a canine reference population. METHODS Medical records of 99 dogs (1991-2014) diagnosed with CED at the University of California Davis Veterinary Medical Teaching Hospital were reviewed and compared with 458,680 dogs comprising the general hospital population during the study period. Retrieved data included signalment, examination findings, diagnoses, treatments, and outcomes associated with CED. The exact Pearson χ2 test or exact Kruskal-Wallis test was used to compare parameters between the groups. Progression of corneal edema was assessed using 3 independent Kaplan-Meier curves, identifying clinically significant changes in corneal opacity. RESULTS Boston terriers, German wirehaired pointers, and Dachshunds were overrepresented in the CED-affected group, whereas Labradors were underrepresented. Dogs older than 11 years were overrepresented in the CED-affected group, whereas intact dogs were underrepresented. Surgical intervention was performed (n = 11) based on the severity of disease and secondary complications from CED. Median time to progression of corneal edema was 1) 368 days when an at-risk eye initially without edema developed edema at a subsequent visit, 2) 701 days when there was progression from mild to marked corneal edema, and 3) 340 days when there was progression from focal to diffuse corneal edema. CONCLUSIONS Many CED-affected dogs progress over months to years without surgical intervention, making dogs with CED a useful model for studying genetic predispositions and development of novel therapeutics for Fuchs endothelial corneal dystrophy.
Collapse
Affiliation(s)
- Brian C. Leonard
- Departments of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California, Davis, Davis, CA
| | - Celine S. Kermanian
- Departments of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California, Davis, Davis, CA
| | - Sarah R. Michalak
- Departments of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California, Davis, Davis, CA
| | - Philip H. Kass
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA
| | - Steven R. Hollingsworth
- Departments of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California, Davis, Davis, CA
| | - Kathryn L. Good
- Departments of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California, Davis, Davis, CA
| | - David J. Maggs
- Departments of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California, Davis, Davis, CA
| | - Sara M. Thomasy
- Departments of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California, Davis, Davis, CA
- Department of Ophthalmology & Vision Science, School of Medicine, University of California, Davis, Davis, CA
| |
Collapse
|
18
|
Zhang W, Venkataraghavan S, Hetmanski JB, Leslie EJ, Marazita ML, Feingold E, Weinberg SM, Ruczinski I, Taub MA, Scott AF, Ray D, Beaty TH. Detecting Gene-Environment Interaction for Maternal Exposures Using Case-Parent Trios Ascertained Through a Case With Non-Syndromic Orofacial Cleft. Front Cell Dev Biol 2021; 9:621018. [PMID: 33937227 PMCID: PMC8085423 DOI: 10.3389/fcell.2021.621018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 03/15/2021] [Indexed: 12/13/2022] Open
Abstract
Two large studies of case-parent trios ascertained through a proband with a non-syndromic orofacial cleft (OFC, which includes cleft lip and palate, cleft lip alone, or cleft palate alone) were used to test for possible gene-environment (G × E) interaction between genome-wide markers (both observed and imputed) and self-reported maternal exposure to smoking, alcohol consumption, and multivitamin supplementation during pregnancy. The parent studies were as follows: GENEVA, which included 1,939 case-parent trios recruited largely through treatment centers in Europe, the United States, and Asia, and 1,443 case-parent trios from the Pittsburgh Orofacial Cleft Study (POFC) also ascertained through a proband with an OFC including three major racial/ethnic groups (European, Asian, and Latin American). Exposure rates to these environmental risk factors (maternal smoking, alcohol consumption, and multivitamin supplementation) varied across studies and among racial/ethnic groups, creating substantial differences in power to detect G × E interaction, but the trio design should minimize spurious results due to population stratification. The GENEVA and POFC studies were analyzed separately, and a meta-analysis was conducted across both studies to test for G × E interaction using the 2 df test of gene and G × E interaction and the 1 df test for G × E interaction alone. The 2 df test confirmed effects for several recognized risk genes, suggesting modest G × E effects. This analysis did reveal suggestive evidence for G × Vitamin interaction for CASP9 on 1p36 located about 3 Mb from PAX7, a recognized risk gene. Several regions gave suggestive evidence of G × E interaction in the 1 df test. For example, for G × Smoking interaction, the 1 df test suggested markers in MUSK on 9q31.3 from meta-analysis. Markers near SLCO3A1 also showed suggestive evidence in the 1 df test for G × Alcohol interaction, and rs41117 near RETREG1 (a.k.a. FAM134B) also gave suggestive significance in the meta-analysis of the 1 df test for G × Vitamin interaction. While it remains quite difficult to obtain definitive evidence for G × E interaction in genome-wide studies, perhaps due to small effect sizes of individual genes combined with low exposure rates, this analysis of two large case-parent trio studies argues for considering possible G × E interaction in any comprehensive study of complex and heterogeneous disorders such as OFC.
Collapse
Affiliation(s)
- Wanying Zhang
- Department of Epidemiology, School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Sowmya Venkataraghavan
- Department of Epidemiology, School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Jacqueline B. Hetmanski
- Department of Epidemiology, School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Elizabeth J. Leslie
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, United States
| | - Mary L. Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, School of Dental Medicine and Clinical and Translational Science, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States
| | - Eleanor Feingold
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States
| | - Seth M. Weinberg
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, School of Dental Medicine and Clinical and Translational Science, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States
| | - Ingo Ruczinski
- Department of Biostatistics, School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Margaret A. Taub
- Department of Biostatistics, School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Alan F. Scott
- Department of Genetic Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, United States
| | - Debashree Ray
- Department of Epidemiology, School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Terri H. Beaty
- Department of Epidemiology, School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| |
Collapse
|
19
|
Gonzales KL, Famula TR, Feng LC, Power HMN, Bullis JM. Folic acid supplementation does not decrease stillbirths and congenital malformations in a guide dog colony. J Small Anim Pract 2021; 62:286-292. [PMID: 33496345 DOI: 10.1111/jsap.13292] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/28/2020] [Accepted: 11/26/2020] [Indexed: 11/29/2022]
Abstract
OBJECTIVES To investigate if maternal folic acid supplementation (5 mg) is associated with a reduction of cleft palates, umbilical hernias, stillbirths and caesarean sections in a guide dog breeding colony. MATERIALS AND METHODS Labrador retrievers, golden retrievers and Labrador/golden Crosses from the breeding colony of a professional guide dog training organisation were eligible for inclusion. Dams in the treatment group (n = 137) received 5 mg oral folic acid supplementation daily from the start of pro-oestrous through day 40 of gestation. A historical control group (n = 134) was selected from the previous calendar year for comparison. A logistic regression model identified the relative risk of disease (cleft palates, umbilical hernias, stillbirths and caesarean sections) for puppies whose dams did or did not receive folic acid supplementation. RESULTS A total of 1917 puppies (890 control, 1027 treatment; from 294 litters) were produced during the entire study period, with 994 puppies (494 control, 500 treatment; from 144 litters) born to the subset of dams (n = 72) who produced litters during both the control and treatment periods. All 95% highest posterior densities of relative risk included 1.0, failing to detect differences between the treatment and control groups on incidence rate of cleft palate (control: 2.25%; treatment: 2.34%), umbilical hernias (control: 1.91%; treatment: 3.12%), stillbirths (control: 3.26%; treatment: 2.92%) and caesarean sections (control: 1.45%; treatment: 1.28%). CLINICAL SIGNIFICANCE There was no observable reduction of cleft palate, umbilical hernia, stillbirth or caesarean section associated with folic acid supplementation during pregnancy in the study colony. For a domestic dog cohort with a low tendency of hereditary malformations, such as this study colony, 5 mg dietary folic acid supplementation should not be expected to drastically improve or eradicate these diseases.
Collapse
Affiliation(s)
- K L Gonzales
- Guide Dogs for the Blind, San Rafael, California, 94903, USA
| | - T R Famula
- Department of Animal Science, University of California Davis, California, 95616, USA
| | - L C Feng
- Guide Dogs for the Blind, San Rafael, California, 94903, USA
| | - H M N Power
- Guide Dogs for the Blind, San Rafael, California, 94903, USA
| | - J M Bullis
- Guide Dogs for the Blind, San Rafael, California, 94903, USA
| |
Collapse
|
20
|
Guan D, Martínez A, Castelló A, Landi V, Luigi-Sierra MG, Fernández-Álvarez J, Cabrera B, Delgado JV, Such X, Jordana J, Amills M. A genome-wide analysis of copy number variation in Murciano-Granadina goats. Genet Sel Evol 2020; 52:44. [PMID: 32770942 PMCID: PMC7414533 DOI: 10.1186/s12711-020-00564-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 07/28/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND In this work, our aim was to generate a map of the copy number variations (CNV) segregating in a population of Murciano-Granadina goats, the most important dairy breed in Spain, and to ascertain the main biological functions of the genes that map to copy number variable regions. RESULTS Using a dataset that comprised 1036 Murciano-Granadina goats genotyped with the Goat SNP50 BeadChip, we were able to detect 4617 and 7750 autosomal CNV with the PennCNV and QuantiSNP software, respectively. By applying the EnsembleCNV algorithm, these CNV were assembled into 1461 CNV regions (CNVR), of which 486 (33.3% of the total CNVR count) were consistently called by PennCNV and QuantiSNP and used in subsequent analyses. In this set of 486 CNVR, we identified 78 gain, 353 loss and 55 gain/loss events. The total length of all the CNVR (95.69 Mb) represented 3.9% of the goat autosomal genome (2466.19 Mb), whereas their size ranged from 2.0 kb to 11.1 Mb, with an average size of 196.89 kb. Functional annotation of the genes that overlapped with the CNVR revealed an enrichment of pathways related with olfactory transduction (fold-enrichment = 2.33, q-value = 1.61 × 10-10), ABC transporters (fold-enrichment = 5.27, q-value = 4.27 × 10-04) and bile secretion (fold-enrichment = 3.90, q-value = 5.70 × 10-03). CONCLUSIONS A previous study reported that the average number of CNVR per goat breed was ~ 20 (978 CNVR/50 breeds), which is much smaller than the number we found here (486 CNVR). We attribute this difference to the fact that the previous study included multiple caprine breeds that were represented by small to moderate numbers of individuals. Given the low frequencies of CNV (in our study, the average frequency of CNV is 1.44%), such a design would probably underestimate the levels of the diversity of CNV at the within-breed level. We also observed that functions related with sensory perception, metabolism and embryo development are overrepresented in the set of genes that overlapped with CNV, and that these loci often belong to large multigene families with tens, hundreds or thousands of paralogous members, a feature that could favor the occurrence of duplications or deletions by non-allelic homologous recombination.
Collapse
Affiliation(s)
- Dailu Guan
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Amparo Martínez
- Departamento de Genética, Universidad de Córdoba, 14071, Córdoba, Spain
| | - Anna Castelló
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.,Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Vincenzo Landi
- Departamento de Genética, Universidad de Córdoba, 14071, Córdoba, Spain.,Department of Veterinary Medicine, University of Bari "Aldo Moro", SP. 62 per Casamassima km. 3, 70010, Valenzano, BA, Italy
| | - María Gracia Luigi-Sierra
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Javier Fernández-Álvarez
- Asociación Nacional de Criadores de Caprino de Raza Murciano-Granadina (CAPRIGRAN), 18340, Granada, Spain
| | - Betlem Cabrera
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.,Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | | | - Xavier Such
- Group of Research in Ruminants (G2R), Department of Animal and Food Science, Universitat Autònoma de Barcelona (UAB), Bellaterra, Barcelona, Spain
| | - Jordi Jordana
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Marcel Amills
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain. .,Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.
| |
Collapse
|
21
|
Yin B, Shi JY, Lin YS, Shi B, Jia ZL. SNPs at TP63 gene was specifically associated with right-side cleft lip in Han Chinese population. Oral Dis 2020; 27:559-566. [PMID: 32687624 DOI: 10.1111/odi.13566] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 07/05/2020] [Accepted: 07/15/2020] [Indexed: 02/05/2023]
Abstract
OBJECTIVES Non-syndromic cleft lip with or without palate is one of the most common birth malformations. TP63 and GREM1 were recently reported to be associated with NSCL/P. However, there were few studies focused on their associations in non-syndromic cleft lip only (NSCLO). DESIGN Initial screening and replication in large cohorts were used to locate the susceptible SNPs of TP63 and GREM1. Firstly, variations were screened among 192 NSCLO cases by the Sanger sequencing. Then, we selected five associated SNPs in initial screening phase and replicated among 1,006 NSCLO cases and 1,823 normal controls. RESULTS Initial chi-square test showed that rs7653848, rs7624324, rs6790167, and rs1345186 in TP63 and rs2280738 in GREM1 achieved statistical significance (p < .05); the subsequent replication analysis showed that rs1345186 was specifically significant in right-side cleft lip (RCL; p = .017, OR = 1.33, and 95% CI: 1.05-1.69). CONCLUSION This study firstly used the subphenotype of cleft lip samples to verify the association between TP63 and GREM1, which indicated that TP63 is a promising susceptible gene for RCL in Chinese population. And further confirmed the different etiology in the right-sided cleft lip, left-sided cleft lip, and bilateral cleft lip of NSCLO. This will give new reference for the future research and genetic counseling.
Collapse
Affiliation(s)
- Bin Yin
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Cleft Lip and Palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jia-Yu Shi
- Division of Growth and Development and Section of Orthodontics, School of Dentistry, University of California, Los Angeles, CA, USA
| | - Yan-Song Lin
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Cleft Lip and Palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Bing Shi
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Cleft Lip and Palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Zhong-Lin Jia
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Cleft Lip and Palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| |
Collapse
|
22
|
Freiberger K, Hemker S, McAnally R, King R, Meyers-Wallen VN, Schutte BC, Fyfe JC. Secondary Palate Development in the Dog ( Canis lupus familiaris). Cleft Palate Craniofac J 2020; 58:230-236. [PMID: 32705901 DOI: 10.1177/1055665620943771] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
OBJECTIVE To investigate the gestational timing of morphologic events in normal canine secondary palate development as a baseline for studies in dog models of isolated cleft palate (CP). METHODS Beagle and beagle/cocker spaniel-hybrid fetal dogs were obtained by cesarean-section on various days of gestation, timed from the initial rise of serum progesterone concentration. Morphology of fetal heads was determined by examining serial coronal sections. RESULTS On gestational day 35 (d35), the palatal shelves pointed ventrally alongside the tongue. On d36, palatal shelves were elongated and elevated to a horizontal position above the tongue but were not touching. On d37, palatine shelves and vomer were touching, but the medial epithelial seam (MES) between the apposed shelves remained. Immunostaining with epithelial protein markers showed that the MES gradually dissolved and was replaced by mesenchyme during d37-d44, and palate fusion was complete by d44. Examination of remnant MES suggested that fusion of palatal shelves began in mid-palate and moved rostrally and caudally. CONCLUSION Palate development occurs in dogs in the steps described in humans and mice, but palate closure occurs at an intermediate time in gestation. These normative data will form the basis of future studies to determine pathophysiologic mechanisms in dog models of CP. Added clinical significance is the enhancement of dogs as a large animal model to test new approaches for palate repair, with the obvious advantage of achieving full maturity within 2 years rather than 2 decades.
Collapse
Affiliation(s)
- Katharina Freiberger
- Microbiology & Molecular Genetics, 3078Michigan State University, East Lansing, MI, USA
| | - Shelby Hemker
- Microbiology & Molecular Genetics, 3078Michigan State University, East Lansing, MI, USA
| | - Ryan McAnally
- Microbiology & Molecular Genetics, 3078Michigan State University, East Lansing, MI, USA
| | - Rachel King
- Microbiology & Molecular Genetics, 3078Michigan State University, East Lansing, MI, USA
| | | | - Brian C Schutte
- Microbiology & Molecular Genetics, 3078Michigan State University, East Lansing, MI, USA.,Pediatrics & Human Development, 3078Michigan State University, East Lansing, MI, USA
| | - John C Fyfe
- Microbiology & Molecular Genetics, 3078Michigan State University, East Lansing, MI, USA
| |
Collapse
|
23
|
Reynolds K, Zhang S, Sun B, Garland MA, Ji Y, Zhou CJ. Genetics and signaling mechanisms of orofacial clefts. Birth Defects Res 2020; 112:1588-1634. [PMID: 32666711 DOI: 10.1002/bdr2.1754] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 06/11/2020] [Accepted: 06/15/2020] [Indexed: 12/31/2022]
Abstract
Craniofacial development involves several complex tissue movements including several fusion processes to form the frontonasal and maxillary structures, including the upper lip and palate. Each of these movements are controlled by many different factors that are tightly regulated by several integral morphogenetic signaling pathways. Subject to both genetic and environmental influences, interruption at nearly any stage can disrupt lip, nasal, or palate fusion and result in a cleft. Here, we discuss many of the genetic risk factors that may contribute to the presentation of orofacial clefts in patients, and several of the key signaling pathways and underlying cellular mechanisms that control lip and palate formation, as identified primarily through investigating equivalent processes in animal models, are examined.
Collapse
Affiliation(s)
- Kurt Reynolds
- Department of Biochemistry and Molecular Medicine, University of California Davis, School of Medicine, Sacramento, California, USA.,Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children-Northern California; University of California Davis, School of Medicine, Sacramento, California, USA.,Biochemistry, Molecular, Cellular, and Developmental Biology (BMCDB) Graduate Group, University of California, Davis, California, USA
| | - Shuwen Zhang
- Department of Biochemistry and Molecular Medicine, University of California Davis, School of Medicine, Sacramento, California, USA.,Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children-Northern California; University of California Davis, School of Medicine, Sacramento, California, USA
| | - Bo Sun
- Department of Biochemistry and Molecular Medicine, University of California Davis, School of Medicine, Sacramento, California, USA.,Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children-Northern California; University of California Davis, School of Medicine, Sacramento, California, USA
| | - Michael A Garland
- Department of Biochemistry and Molecular Medicine, University of California Davis, School of Medicine, Sacramento, California, USA.,Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children-Northern California; University of California Davis, School of Medicine, Sacramento, California, USA
| | - Yu Ji
- Department of Biochemistry and Molecular Medicine, University of California Davis, School of Medicine, Sacramento, California, USA.,Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children-Northern California; University of California Davis, School of Medicine, Sacramento, California, USA.,Biochemistry, Molecular, Cellular, and Developmental Biology (BMCDB) Graduate Group, University of California, Davis, California, USA
| | - Chengji J Zhou
- Department of Biochemistry and Molecular Medicine, University of California Davis, School of Medicine, Sacramento, California, USA.,Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children-Northern California; University of California Davis, School of Medicine, Sacramento, California, USA.,Biochemistry, Molecular, Cellular, and Developmental Biology (BMCDB) Graduate Group, University of California, Davis, California, USA
| |
Collapse
|
24
|
Baker L, Muir P, Sample SJ. Genome-wide association studies and genetic testing: understanding the science, success, and future of a rapidly developing field. J Am Vet Med Assoc 2020; 255:1126-1136. [PMID: 31687891 DOI: 10.2460/javma.255.10.1126] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Dog owners are increasingly interested in using commercially available testing panels to learn about the genetics of their pets, both to identify breed ancestry and to screen for specific genetic diseases. Helping owners interpret and understand results from genetic screening panels is becoming an important issue facing veterinarians. The objective of this review article is to introduce basic concepts behind genetic studies and current genetic screening tests while highlighting their value in veterinary medicine. The potential uses and limitations of commercially available genetic testing panels as screening tests are discussed, including appropriate cautions regarding the interpretation of results. Future directions, particularly with regard to the study of common complex genetic diseases, are also described.
Collapse
|
25
|
Wu P, Zhang X, Zhang G, Chen F, He M, Zhang T, Wang J, Xie K, Dai G. Transcriptome for the breast muscle of Jinghai yellow chicken at early growth stages. PeerJ 2020; 8:e8950. [PMID: 32328350 PMCID: PMC7166044 DOI: 10.7717/peerj.8950] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 03/20/2020] [Indexed: 12/31/2022] Open
Abstract
Background The meat quality of yellow feathered broilers is better than the quality of its production. Growth traits are important in the broiler industry. The exploration of regulation mechanisms for the skeletal muscle would help to increase the growth performance of chickens. At present, some progress has been made by researchers, but the molecular mechanisms of the skeletal muscle still remain unclear and need to be improved. Methods In this study, the breast muscles of fast- and slow-growing female Jinghai yellow chickens (F4F, F8F, F4S, F8S) and slow-growing male Jinghai yellow chickens (M4S, M8S) aged four and eight weeks were selected for transcriptome sequencing (RNA-seq). All analyses of differentially expressed genes (DEGs) and functional enrichment were performed. Finally, we selected nine DEGs to verify the accuracy of the sequencing by qPCR. Results The differential gene expression analysis resulted in 364, 219 and 111 DEGs (adjusted P-value ≤ 0.05) for the three comparison groups, F8FvsF4F, F8SvsF4S, and M8SvsM4S, respectively. Three common DEGs (ADAMTS20, ARHGAP19, and Novel00254) were found, and they were all highly expressed at four weeks of age. In addition, some other genes related to growth and development, such as ANXA1, COL1A1, MYH15, TGFB3 and ACTC1, were obtained. The most common DEGs (n = 58) were found between the two comparison groups F8FvsF4F and F8SvsF4S, and they might play important roles in the growth of female chickens. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway also showed some significant enrichment pathways, for instance, extracellular matrix (ECM)-receptor interaction, focal adhesion, cell cycle, and DNA replication. The two pathways that were significantly enriched in the F8FvsF4F group were all contained in that of F8SvsF4S. The same two pathways were ECM–receptor interaction and focal adhesion, and they had great influence on the growth of chickens. However, many differences existed between male and female chickens in regards to common DEGs and KEGG pathways. The results would help to reveal the regulation mechanism of the growth and development of chickens and serve as a guideline to propose an experimental design on gene function with the DEGs and pathways.
Collapse
Affiliation(s)
- Pengfei Wu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Xinchao Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Genxi Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Fuxiang Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Mingliang He
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Tao Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Jinyu Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Kaizhou Xie
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Guojun Dai
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| |
Collapse
|
26
|
Solis-Lemus CR, Fischer ST, Todor A, Liu C, Leslie EJ, Cutler DJ, Ghosh D, Epstein MP. Leveraging Family History in Case-Control Analyses of Rare Variation. Genetics 2020; 214:295-303. [PMID: 31843756 PMCID: PMC7017020 DOI: 10.1534/genetics.119.302846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Accepted: 12/10/2019] [Indexed: 11/18/2022] Open
Abstract
Standard methods for case-control association studies of rare variation often treat disease outcome as a dichotomous phenotype. However, both theoretical and experimental studies have demonstrated that subjects with a family history of disease can be enriched for risk variation relative to subjects without such history. Assuming family history information is available, this observation motivates the idea of replacing the standard dichotomous outcome variable used in case-control studies with a more informative ordinal outcome variable that distinguishes controls (0), sporadic cases (1), and cases with a family history (2), with the expectation that we should observe increasing number of risk variants with increasing category of the ordinal variable. To leverage this expectation, we propose a novel rare-variant association test that incorporates family history information based on our previous GAMuT framework for rare-variant association testing of multivariate phenotypes. We use simulated data to show that, when family history information is available, our new method outperforms standard rare-variant association methods, like burden and SKAT tests, that ignore family history. We further illustrate our method using a rare-variant study of cleft lip and palate.
Collapse
Affiliation(s)
| | - S Taylor Fischer
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, 30329 Georgia
| | - Andrei Todor
- Department of Human Genetics, Emory University, Atlanta, 30030 Georgia
| | - Cuining Liu
- Department of Biostatistics and Informatics, University of Colorado, Aurora, 80045 Colorado
| | | | - David J Cutler
- Department of Human Genetics, Emory University, Atlanta, 30030 Georgia
| | - Debashis Ghosh
- Department of Biostatistics and Informatics, University of Colorado, Aurora, 80045 Colorado
| | - Michael P Epstein
- Department of Human Genetics, Emory University, Atlanta, 30030 Georgia
| |
Collapse
|
27
|
Craniofacial Analysis May Indicate Co-Occurrence of Skeletal Malocclusions and Associated Risks in Development of Cleft Lip and Palate. J Dev Biol 2020; 8:jdb8010002. [PMID: 32012961 PMCID: PMC7151201 DOI: 10.3390/jdb8010002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 01/21/2020] [Accepted: 01/23/2020] [Indexed: 12/22/2022] Open
Abstract
Non-syndromic orofacial clefts encompass a range of morphological changes affecting the oral cavity and the craniofacial skeleton, of which the genetic and epigenetic etiologic factors remain largely unknown. The objective of this study is to explore the contribution of underlying dentofacial deformities (also known as skeletal malocclusions) in the craniofacial morphology of non-syndromic cleft lip and palate patients (nsCLP). For that purpose, geometric morphometric analysis was performed using full skull cone beam computed tomography (CBCT) images of patients with nsCLP (n = 30), normocephalic controls (n = 60), as well as to sex- and ethnicity- matched patients with an equivalent dentofacial deformity (n = 30). Our outcome measures were shape differences among the groups quantified via principal component analysis and associated principal component loadings, as well as mean shape differences quantified via a Procrustes distance among groups. According to our results, despite the shape differences among all three groups, the nsCLP group shares many morphological similarities in the maxilla and mandible with the dentofacial deformity group. Therefore, the dentoskeletal phenotype in nsCLP could be the result of the cleft and the coexisting dentofacial deformity and not simply the impact of the cleft.
Collapse
|
28
|
Sananmuang T, Mankong K, Jeeratanyasakul P, Chokeshai-Usaha K, Ponglowhapan S. Prenatal diagnosis of foetal hydrocephalus and suspected X-linked recessive inheritance of cleft lip in a Chihuahua. J Vet Med Sci 2019; 82:212-216. [PMID: 31902834 PMCID: PMC7041993 DOI: 10.1292/jvms.18-0516] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
A 3.5-year-old, 2.9 kg, multiparous Chihuahua presented with abdominal distension;
pregnancy was diagnosed. On Day 7 before parturition, prenatal sonograms showed anechoic
bilateral dilated cerebral lateral ventricles, suggesting fluid-filled regions
(ventriculomegaly) in one foetus. A Caesarean section was performed and the male newborn
had an abnormally enlarged dome-shaped head and a cleft lip, and died 6 days after birth.
According to the family pedigree, the X-linked recessive inheritance of an orofacial cleft
from the unaffected mother was suggested. This report clearly demonstrates that canine
foetal ventriculomegaly (hydrocephalus) can be diagnosed in utero. For
dog breeds predisposed to congenital ventriculomegaly, early detection is important for
the prediction of perinatal survival and adequate supportive care can be applied at
delivery.
Collapse
Affiliation(s)
- Thanida Sananmuang
- Faculty of Veterinary Medicine, Rajamangala University of Technology Tawan-Ok, 43 Moo 6 Bangpra, Sriracha, Chonburi 20110, Thailand
| | - Kanchanarat Mankong
- Smile Dog Small Animal Hospital, 9/16 Mhoo 8, Samed, Bang Saen, Chonburi 20130, Thailand
| | | | - Kaj Chokeshai-Usaha
- Faculty of Veterinary Medicine, Rajamangala University of Technology Tawan-Ok, 43 Moo 6 Bangpra, Sriracha, Chonburi 20110, Thailand
| | - Suppawiwat Ponglowhapan
- Department of Obstetrics, Gynaecology and Reproduction, Research Unit of Obstetrics and Reproduction in Animals, Faculty of Veterinary Science, Chulalongkorn University, Henri-Dunant Rd., Pathumwan, Bangkok 10330, Thailand
| |
Collapse
|
29
|
Paiva KBS, Maas CS, dos Santos PM, Granjeiro JM, Letra A. Extracellular Matrix Composition and Remodeling: Current Perspectives on Secondary Palate Formation, Cleft Lip/Palate, and Palatal Reconstruction. Front Cell Dev Biol 2019; 7:340. [PMID: 31921852 PMCID: PMC6923686 DOI: 10.3389/fcell.2019.00340] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 11/29/2019] [Indexed: 12/13/2022] Open
Abstract
Craniofacial development comprises a complex process in humans in which failures or disturbances frequently lead to congenital anomalies. Cleft lip with/without palate (CL/P) is a common congenital anomaly that occurs due to variations in craniofacial development genes, and may occur as part of a syndrome, or more commonly in isolated forms (non-syndromic). The etiology of CL/P is multifactorial with genes, environmental factors, and their potential interactions contributing to the condition. Rehabilitation of CL/P patients requires a multidisciplinary team to perform the multiple surgical, dental, and psychological interventions required throughout the patient's life. Despite progress, lip/palatal reconstruction is still a major treatment challenge. Genetic mutations and polymorphisms in several genes, including extracellular matrix (ECM) genes, soluble factors, and enzymes responsible for ECM remodeling (e.g., metalloproteinases), have been suggested to play a role in the etiology of CL/P; hence, these may be considered likely targets for the development of new preventive and/or therapeutic strategies. In this context, investigations are being conducted on new therapeutic approaches based on tissue bioengineering, associating stem cells with biomaterials, signaling molecules, and innovative technologies. In this review, we discuss the role of genes involved in ECM composition and remodeling during secondary palate formation and pathogenesis and genetic etiology of CL/P. We also discuss potential therapeutic approaches using bioactive molecules and principles of tissue bioengineering for state-of-the-art CL/P repair and palatal reconstruction.
Collapse
Affiliation(s)
- Katiúcia Batista Silva Paiva
- Laboratory of Extracellular Matrix Biology and Cellular Interaction, Department of Anatomy, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Clara Soeiro Maas
- Laboratory of Extracellular Matrix Biology and Cellular Interaction, Department of Anatomy, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Pâmella Monique dos Santos
- Laboratory of Extracellular Matrix Biology and Cellular Interaction, Department of Anatomy, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - José Mauro Granjeiro
- Clinical Research Laboratory in Dentistry, Federal Fluminense University, Niterói, Brazil
- Directory of Life Sciences Applied Metrology, National Institute of Metrology, Quality and Technology, Duque de Caxias, Brazil
| | - Ariadne Letra
- Center for Craniofacial Research, UTHealth School of Dentistry at Houston, Houston, TX, United States
- Pediatric Research Center, UTHealth McGovern Medical School, Houston, TX, United States
- Department of Diagnostic and Biomedical Sciences, UTHealth School of Dentistry at Houston, Houston, TX, United States
| |
Collapse
|
30
|
The functional variant of NTN1 contributes to the risk of nonsyndromic cleft lip with or without cleft palate. Eur J Hum Genet 2019; 28:453-460. [PMID: 31780810 PMCID: PMC7080719 DOI: 10.1038/s41431-019-0549-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 10/22/2019] [Accepted: 10/29/2019] [Indexed: 11/09/2022] Open
Abstract
Previous genome-wide association study of nonsyndromic cleft lip with or without cleft palate (NSCL/P) identified a susceptible variant (rs4791774). We hypothesized that the functional single nucleotide polymorphism (SNP) may be in linkage disequilibrium with this lead SNP. The potential functional SNP (rs4791331) was identified by bioinformatic analysis. A case–control study with 891 orofacial cleft cases and 830 controls was designed to investigate its association with orofacial cleft. The allele-specific DNA-protein binding preference was predicted by JASPAR database. Cell proliferation, cycle and apoptosis, luciferase activity and netrin-1 (NTN1) expression were examined after transfection with the rs4791331 C/T vector in HEK-293 and HEPM cell lines. Forty-six lip tissues of NSCL/P patients were collected to detect NTN1 expression. ntn1a knockout zebrafish models were generated by CRISPR/Cas9 and observed with micro-CT. In the case–control study, the rs4791331-T allele was associated with an increased risk of nonsyndromic orofacial cleft (OR = 1.41, 95% CI = 1.19–1.68), as well as the subgroups cleft lip only (OR = 1.46, 95% CI = 1.14–1.87) and cleft lip and palate (OR = 1.58, 95% CI = 1.27–1.96). The T allele of rs4791331 exhibited anti-apoptotic effects and promoted cell cycle progression at the G1/S transition. Decreased enhancer activity and reduced NTN1 expression following transfection of the T allele were observed. Carriers of the CT/TT genotypes showed significantly lower expression of NTN1 than CC carriers. The ntn1a−/− zebrafish showed relatively wider intermaxillary fissures. These results indicate that rs4791331 (C > T) disrupted motif binding and led to abnormal expression of NTN1, which may be involved in the development of NSCL/P.
Collapse
|
31
|
Six2 regulates Pax9 expression, palatogenesis and craniofacial bone formation. Dev Biol 2019; 458:246-256. [PMID: 31765609 DOI: 10.1016/j.ydbio.2019.11.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 10/30/2019] [Accepted: 11/15/2019] [Indexed: 12/11/2022]
Abstract
In this study, we investigated the role of the transcription factor Six2 in palate development. Six2 was selected using the SysFACE tool to predict genes from the 2p21 locus, a region associated with clefting in humans by GWAS, that are likely to be involved in palatogenesis. We functionally validated the predicted role of Six2 in palatogenesis by showing that 22% of Six2 null embryos develop cleft palate. Six2 contributes to palatogenesis by promoting mesenchymal cell proliferation and regulating bone formation. The clefting phenotype in Six2-/- embryos is similar to Pax9 null embryos, so we examined the functional relationship of these two genes. Mechanistically, SIX2 binds to a PAX9 5' upstream regulatory element and activates PAX9 expression. In addition, we identified a human SIX2 coding variant (p.Gly264Glu) in a proband with cleft palate. We show this missense mutation affects the stability of the SIX2 protein and leads to decreased PAX9 expression. The low penetrance of clefting in the Six2 null mouse combined with the mutation in one patient with cleft palate underscores the potential combinatorial interactions of other genes in clefting. Our study demonstrates that Six2 interacts with the developmental gene regulatory network in the developing palate.
Collapse
|
32
|
Roman N, Carney PC, Fiani N, Peralta S. Incidence patterns of orofacial clefts in purebred dogs. PLoS One 2019; 14:e0224574. [PMID: 31682628 PMCID: PMC6827884 DOI: 10.1371/journal.pone.0224574] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 10/16/2019] [Indexed: 02/08/2023] Open
Abstract
Cleft lip (CL), cleft palate (CP) and cleft lip and palate (CLP) are the most common types of orofacial clefts in dogs. Orofacial clefts in dogs are clinically relevant because of the associated morbidity and high newborn mortality rate and are of interest as comparative models of disease. However, the incidence of CL, CP and CLP has not been investigated in purebred dogs, and the financial impact on breeders is unknown. The aims of this study were to document the incidence patterns of CL, CP and CLP in different breeds of dogs, determine whether defect phenotype is associated with skull type, genetic cluster and geographic location, and estimate the financial impact in breeding programs in the United States by means of an anonymous online survey. A total of 228 orofacial clefts were reported among 7,429 puppies whelped in the 12 preceding months. Breeds in the mastiff/terrier genetic cluster and brachycephalic breeds were predisposed to orofacial clefts. Certain breeds in the ancient genetic cluster were at increased odds of orofacial clefts. Male purebred dogs were at increased odds of CPs. Results confirm that brachycephalic breeds are overrepresented among cases of orofacial clefts. Furthermore, geographic region appeared to be a relevant risk factor and orofacial clefts represented a considerable financial loss to breeders. Improved understanding of the epidemiology of orofacial clefts (frequency, causes, predictors and risk factors) may help in identifying ways to minimize their occurrence. Information gained may potentially help veterinarians and researchers to diagnose, treat and prevent orofacial clefts.
Collapse
Affiliation(s)
- Nicholas Roman
- College of Veterinary Medicine, Cornell University, Ithaca, NY, United States of America
| | - Patrick C. Carney
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States of America
| | - Nadine Fiani
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States of America
| | - Santiago Peralta
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States of America
- * E-mail:
| |
Collapse
|
33
|
Sharma V, Hiller M. Losses of human disease-associated genes in placental mammals. NAR Genom Bioinform 2019; 2:lqz012. [PMID: 33575564 PMCID: PMC7671337 DOI: 10.1093/nargab/lqz012] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 08/24/2019] [Accepted: 10/08/2019] [Indexed: 02/07/2023] Open
Abstract
We systematically investigate whether losses of human disease-associated genes occurred in other mammals during evolution. We first show that genes lost in any of 62 non-human mammals generally have a lower degree of pleiotropy, and are highly depleted in essential and disease-associated genes. Despite this under-representation, we discovered multiple genes implicated in human disease that are truly lost in non-human mammals. In most cases, traits resembling human disease symptoms are present but not deleterious in gene-loss species, exemplified by losses of genes causing human eye or teeth disorders in poor-vision or enamel-less mammals. We also found widespread losses of PCSK9 and CETP genes, where loss-of-function mutations in humans protect from atherosclerosis. Unexpectedly, we discovered losses of disease genes (TYMP, TBX22, ABCG5, ABCG8, MEFV, CTSE) where deleterious phenotypes do not manifest in the respective species. A remarkable example is the uric acid-degrading enzyme UOX, which we found to be inactivated in elephants and manatees. While UOX loss in hominoids led to high serum uric acid levels and a predisposition for gout, elephants and manatees exhibit low uric acid levels, suggesting alternative ways of metabolizing uric acid. Together, our results highlight numerous mammals that are 'natural knockouts' of human disease genes.
Collapse
Affiliation(s)
- Virag Sharma
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany.,Center for Systems Biology Dresden, 01307 Dresden, Germany
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany.,Center for Systems Biology Dresden, 01307 Dresden, Germany
| |
Collapse
|
34
|
Imputation of canine genotype array data using 365 whole-genome sequences improves power of genome-wide association studies. PLoS Genet 2019; 15:e1008003. [PMID: 31525180 PMCID: PMC6762211 DOI: 10.1371/journal.pgen.1008003] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 09/26/2019] [Accepted: 08/19/2019] [Indexed: 12/11/2022] Open
Abstract
Genomic resources for the domestic dog have improved with the widespread adoption of a 173k SNP array platform and updated reference genome. SNP arrays of this density are sufficient for detecting genetic associations within breeds but are underpowered for finding associations across multiple breeds or in mixed-breed dogs, where linkage disequilibrium rapidly decays between markers, even though such studies would hold particular promise for mapping complex diseases and traits. Here we introduce an imputation reference panel, consisting of 365 diverse, whole-genome sequenced dogs and wolves, which increases the number of markers that can be queried in genome-wide association studies approximately 130-fold. Using previously genotyped dogs, we show the utility of this reference panel in identifying potentially novel associations, including a locus on CFA20 significantly associated with cranial cruciate ligament disease, and fine-mapping for canine body size and blood phenotypes, even when causal loci are not in strong linkage disequilibrium with any single array marker. This reference panel resource will improve future genome-wide association studies for canine complex diseases and other phenotypes. Complex traits are controlled by more than one gene and as such are difficult to map. For complex trait mapping in the domestic dog, researchers use the current array of 173,000 variants, with only minimal success. Here, we use a method called imputation to increase the number of variants–from 173,000 to 24 million–that can be queried in canine association studies. We use sequence data from the whole genomes of 365 dogs and wolves to accurately predict variants, in a separate cohort of dogs, that are not present on the array. Using dog body size, blood phenotypes, and a common orthopedic disease that involves rupture of the cranial cruciate ligament, we show that the increase in variants results in an increase in mapping power, through the identification of new associations and the narrowing of regions of interest. This imputation panel is particularly important because of its usefulness in improving complex trait mapping in the dog, which has significant implications for discovery of variants in humans with similar diseases.
Collapse
|
35
|
Yun L, Ma L, Wang M, Yang F, Kan S, Zhang C, Xu M, Li D, Du Y, Zhang W, Pan Y, Wang L. Rs2262251 in lncRNA
RP11‐462G12.2
is associated with nonsyndromic cleft lip with/without cleft palate. Hum Mutat 2019; 40:2057-2067. [DOI: 10.1002/humu.23859] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 06/13/2019] [Accepted: 06/27/2019] [Indexed: 01/13/2023]
Affiliation(s)
- Lu Yun
- Jiangsu Key Laboratory of Oral Diseases Nanjing Medical University Nanjing China
- Department of Orthodontics, College of Stomatology Dalian Medical University Dalian China
| | - Lan Ma
- Jiangsu Key Laboratory of Oral Diseases Nanjing Medical University Nanjing China
- Department of Environmental Genomics, School of Public Health Nanjing Medical University Nanjing China
| | - Meilin Wang
- State Key Laboratory of Reproductive Medicine Nanjing Medical University Nanjing China
- Department of Environmental Genomics, School of Public Health Nanjing Medical University Nanjing China
| | - Fan Yang
- Jiangsu Key Laboratory of Oral Diseases Nanjing Medical University Nanjing China
| | - Shiyi Kan
- Jiangsu Key Laboratory of Oral Diseases Nanjing Medical University Nanjing China
| | - Chi Zhang
- Jiangsu Key Laboratory of Oral Diseases Nanjing Medical University Nanjing China
| | - Min Xu
- Jiangsu Key Laboratory of Oral Diseases Nanjing Medical University Nanjing China
| | - Dandan Li
- Jiangsu Key Laboratory of Oral Diseases Nanjing Medical University Nanjing China
| | - Yifei Du
- Jiangsu Key Laboratory of Oral Diseases Nanjing Medical University Nanjing China
| | - Weibing Zhang
- Jiangsu Key Laboratory of Oral Diseases Nanjing Medical University Nanjing China
| | - Yongchu Pan
- Jiangsu Key Laboratory of Oral Diseases Nanjing Medical University Nanjing China
- State Key Laboratory of Reproductive Medicine Nanjing Medical University Nanjing China
| | - Lin Wang
- Jiangsu Key Laboratory of Oral Diseases Nanjing Medical University Nanjing China
- State Key Laboratory of Reproductive Medicine Nanjing Medical University Nanjing China
| |
Collapse
|
36
|
Ma J, Yin B, Shi JY, Lin YS, Duan SJ, Shi B, Jia ZL. Exon sequencing reveals that missense mutation of PBX1 gene may increase the risk of non-syndromic cleft lip/palate. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2019; 12:2691-2698. [PMID: 31934099 PMCID: PMC6949560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 05/24/2019] [Indexed: 06/10/2023]
Abstract
OBJECTIVE Non-syndromic oral cleft (NSOC) is one of the most common multifactorial birth defects. A previous animal study showed PBX1 gene knockout mice consequently exhibited complete cleft lip/palate (CL/P). However, little is known about the association between PBX1 and NSOC in humans. This study investigated the role of the PBX1 gene in NSOC in the Han Chinese population. METHODS In all, 287 NSOCs were recruited for this study. First, exons in the PBX1 gene were sequenced among 50 non-syndromic cleft lip and palate cases to screen for variations by the Sanger sequencing method. Then, we selected four SNPs to replicate among 237 NSOC trios and analyzed the data by using TDT and parent of origin effect methods. RESULTS Exon sequencing identified six variants of the PBX1 gene. Among them, four variants were common variants. TDT analysis revealed allele G at rs2275558 and allele T at rs3835581 were over-transmitted in NSCL/P (P=0.039 and 0.038, respectively), which could increase the risk for NSCL/P. Parent of origin effect analysis indicated that allele G at rs2275558 was paternally over-transmitted for NSCL/P (P=0.0091). CONCLUSION This is the first report that the PBX1 gene is associated with NSCL/P, which indicates that it is a promising candidate gene for NSCL/P.
Collapse
Affiliation(s)
- Jian Ma
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Development of Cleft Lip and Palate, West China Hospital of Stomatology, Sichuan UniversityP.R. China
- Department of Oral and Maxillofacial Surgery, Hospital of Stomatology, The General Hospital of Ningxia Medical UniversityYinchuan, 750004, Ningxia Province, P.R. China
| | - Bin Yin
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Development of Cleft Lip and Palate, West China Hospital of Stomatology, Sichuan UniversityP.R. China
| | - Jia-Yu Shi
- Division of Growth and Development and Section of Orthodontics, School of Dentistry, University of CaliforniaLos Angeles, USA
| | - Yan-Song Lin
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Development of Cleft Lip and Palate, West China Hospital of Stomatology, Sichuan UniversityP.R. China
| | - Shi-Jun Duan
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Development of Cleft Lip and Palate, West China Hospital of Stomatology, Sichuan UniversityP.R. China
| | - Bing Shi
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Development of Cleft Lip and Palate, West China Hospital of Stomatology, Sichuan UniversityP.R. China
| | - Zhong-Lin Jia
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Development of Cleft Lip and Palate, West China Hospital of Stomatology, Sichuan UniversityP.R. China
| |
Collapse
|
37
|
Zhong S, Khalil RA. A Disintegrin and Metalloproteinase (ADAM) and ADAM with thrombospondin motifs (ADAMTS) family in vascular biology and disease. Biochem Pharmacol 2019; 164:188-204. [PMID: 30905657 DOI: 10.1016/j.bcp.2019.03.033] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 03/20/2019] [Indexed: 12/11/2022]
Abstract
A Disintegrin and Metalloproteinase (ADAM) is a family of proteolytic enzymes that possess sheddase function and regulate shedding of membrane-bound proteins, growth factors, cytokines, ligands and receptors. Typically, ADAMs have a pro-domain, and a metalloproteinase, disintegrin, cysteine-rich and a characteristic transmembrane domain. Most ADAMs are activated by proprotein convertases, but can also be regulated by G-protein coupled receptor agonists, Ca2+ ionophores and protein kinase C activators. A Disintegrin and Metalloproteinase with Thrombospondin Motifs (ADAMTS) is a family of secreted enzymes closely related to ADAMs. Like ADAMs, ADAMTS members have a pro-domain, and a metalloproteinase, disintegrin, and cysteine-rich domain, but they lack a transmembrane domain and instead have characteristic thrombospondin motifs. Activated ADAMs perform several functions and participate in multiple cardiovascular processes including vascular smooth muscle cell proliferation and migration, angiogenesis, vascular cell apoptosis, cell survival, tissue repair, and wound healing. ADAMs may also be involved in pathological conditions and cardiovascular diseases such as atherosclerosis, hypertension, aneurysm, coronary artery disease, myocardial infarction and heart failure. Like ADAMs, ADAMTS have a wide-spectrum role in vascular biology and cardiovascular pathophysiology. ADAMs and ADAMTS activity is naturally controlled by endogenous inhibitors such as tissue inhibitors of metalloproteinases (TIMPs), and their activity can also be suppressed by synthetic small molecule inhibitors. ADAMs and ADAMTS can serve as important diagnostic biomarkers and potential therapeutic targets for cardiovascular disorders. Natural and synthetic inhibitors of ADAMs and ADAMTS could be potential therapeutic tools for the management of cardiovascular diseases.
Collapse
Affiliation(s)
- Sheng Zhong
- Vascular Surgery Research Laboratories, Division of Vascular and Endovascular Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Raouf A Khalil
- Vascular Surgery Research Laboratories, Division of Vascular and Endovascular Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
38
|
Shaffer JR, LeClair J, Carlson JC, Feingold E, Buxó CJ, Christensen K, Deleyiannis FW, Field LL, Hecht JT, Moreno L, Orioli IM, Padilla C, Vieira AR, Wehby GL, Murray JC, Weinberg SM, Marazita ML, Leslie EJ. Association of low-frequency genetic variants in regulatory regions with nonsyndromic orofacial clefts. Am J Med Genet A 2019; 179:467-474. [PMID: 30582786 PMCID: PMC6374160 DOI: 10.1002/ajmg.a.61002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 08/06/2018] [Accepted: 11/01/2018] [Indexed: 01/24/2023]
Abstract
Genome-wide scans have shown that common risk alleles for orofacial clefts (OFC) tend to be located in noncoding regulatory elements and cumulatively explain only part of the heritability of OFCs. Low-frequency variants may account for some of the "missing" heritability. Therefore, we scanned low-frequency variants located within putative craniofacial enhancers to identify novel OFC risk variants and implicate new regulatory elements in OFC pathogenesis. Analyses were performed in a multiethnic sample of 1,995 cases of cleft lip with or without cleft palate (CL/P), 221 cases with cleft palate (CP) only, and 1,576 unaffected controls. One hundred and nineteen putative craniofacial enhancers identified from ChIP-Seq studies in craniofacial tissues or cell lines contained multiple low-frequency (0.01-1%) variants, which we genotyped in participants using a custom Illumina panel. Two complementary statistical approaches, sequence kernel association test and combined multivariate and collapsing, were used to test association of the aggregated low-frequency variants across each enhancer region with CL/P and CP. We discovered a significant association between CP and a branchial arch enhancer near FOXP1 (mm60; p-value = .0002). Additionally, we observed a suggestive association between CL/P and a forebrain enhancer near FOXE1 (hs1717; p-value = .001). These findings suggest that low-frequency variants in craniofacial enhancer regions contribute to the complex etiology of nonsyndromic OFCs.
Collapse
Affiliation(s)
- John R. Shaffer
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, 15219 USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261 USA
| | - Jessica LeClair
- formerly of Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA 02118, USA
| | - Jenna C. Carlson
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, 15219 USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261 USA
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Eleanor Feingold
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261 USA
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Carmen J. Buxó
- Dental and Craniofacial Genomics Core, School of Dental Medicine, University of Puerto Rico, San Juan, Puerto Rico, 00936, USA
| | - Kaare Christensen
- Department of Epidemiology, Institute of Public Health, University of Southern Denmark, Odense, DK-5000, Denmark
| | - Frederic W.B. Deleyiannis
- Department of Surgery, Plastic and Reconstructive Surgery, University of Colorado School of Medicine, Denver, CO, 80045, USA
| | - L. Leigh Field
- Department of Medical Genetics, University of British Columbia, Vancouver, V6H 3N1, Canada
| | - Jacqueline T. Hecht
- Department of Pediatrics, McGovern Medical School and School of Dentistry UT Health at Houston, Houston, TX, 77030, USA
| | - Lina Moreno
- Department of Orthodontics, College of Dentistry, University of Iowa, Iowa City, IA, 52242, USA
| | - Ieda M. Orioli
- Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-617, Brazil
- ECLAMC (Latin American Collaborative Study of Congenital Malformations) at INAGEMP (National Institute of Population Medical Genetics), Rio de Janeiro, 21941-617, Brazil
| | - Carmencita Padilla
- Department of Pediatrics, College of Medicine; and Institute of Human Genetics, National Institutes of Health; University of the Philippines Manila, Manila, The Philippines, 1000; and Philippine Genome Center, University of the Philippines System, Manila, The Philippines 1101
| | - Alexandre R. Vieira
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, 15219 USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261 USA
| | - George L. Wehby
- Department of Health Management and Policy, College of Public Health, University of Iowa, Iowa City, IA, 52246, USA
| | - Jeffrey C. Murray
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, 52242, USA
| | - Seth M. Weinberg
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, 15219 USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261 USA
- Department of Anthropology, Dietrich School of Arts and Sciences, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Mary L. Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, 15219 USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261 USA
- Clinical and Translational Science, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Elizabeth J. Leslie
- Department of Human Genetics, Emory University School of Medicine, Emory University, Atlanta, GA, 30322
| |
Collapse
|
39
|
Nandadasa S, Kraft CM, Wang LW, O'Donnell A, Patel R, Gee HY, Grobe K, Cox TC, Hildebrandt F, Apte SS. Secreted metalloproteases ADAMTS9 and ADAMTS20 have a non-canonical role in ciliary vesicle growth during ciliogenesis. Nat Commun 2019; 10:953. [PMID: 30814516 PMCID: PMC6393521 DOI: 10.1038/s41467-019-08520-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 01/11/2019] [Indexed: 01/20/2023] Open
Abstract
Although hundreds of cytosolic or transmembrane molecules form the primary cilium, few secreted molecules are known to contribute to ciliogenesis. Here, homologous secreted metalloproteases ADAMTS9 and ADAMTS20 are identified as ciliogenesis regulators that act intracellularly. Secreted and furin-processed ADAMTS9 bound heparan sulfate and was internalized by LRP1, LRP2 and clathrin-mediated endocytosis to be gathered in Rab11 vesicles with a unique periciliary localization defined by super-resolution microscopy. CRISPR-Cas9 inactivation of ADAMTS9 impaired ciliogenesis in RPE-1 cells, which was restored by catalytically active ADAMTS9 or ADAMTS20 acting in trans, but not by their proteolytically inactive mutants. Their mutagenesis in mice impaired neural and yolk sac ciliogenesis, leading to morphogenetic anomalies resulting from impaired hedgehog signaling, which is transduced by primary cilia. In addition to their cognate extracellular proteolytic activity, ADAMTS9 and ADAMTS20 thus have an additional proteolytic role intracellularly, revealing an unexpected regulatory dimension in ciliogenesis. Ciliogenesis is a complex process requiring hundreds of molecules, although few secreted proteins have been implicated. Here, the authors show that the secreted metalloproteases ADAMTS9 and ADAMTS20 intracellularly regulate ciliogenesis from unique periciliary vesicles with proteolytic activity.
Collapse
Affiliation(s)
- Sumeda Nandadasa
- Department of Biomedical Engineering- ND20, Cleveland Clinic Lerner Research Institute, Cleveland, OH, 44195, USA
| | - Caroline M Kraft
- Department of Biomedical Engineering- ND20, Cleveland Clinic Lerner Research Institute, Cleveland, OH, 44195, USA
| | - Lauren W Wang
- Department of Biomedical Engineering- ND20, Cleveland Clinic Lerner Research Institute, Cleveland, OH, 44195, USA
| | - Anna O'Donnell
- Department of Biomedical Engineering- ND20, Cleveland Clinic Lerner Research Institute, Cleveland, OH, 44195, USA
| | - Rushabh Patel
- Department of Biomedical Engineering- ND20, Cleveland Clinic Lerner Research Institute, Cleveland, OH, 44195, USA
| | - Heon Yung Gee
- Department of Pharmacology, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seoul, 03722, South Korea
| | - Kay Grobe
- Institute of Physiological Chemistry and Pathobiochemistry and Cells-in-Motion Cluster of Excellence (EXC1003-CiM), University of Münster, 48149, Münster, Germany
| | - Timothy C Cox
- Division of Craniofacial Medicine, Department of Pediatrics, University of Washington, 1959 NE Pacific St, Seattle, WA, 98195, USA.,Department of Oral and Craniofacial Sciences, UMKC School of Dentistry, 650 E 25th St, Kansas City, MO, 64108, USA
| | - Friedhelm Hildebrandt
- Division of Nephrology, Boston Children's Hospital, Harvard Medical School, 300 Longwood Avenue, Boston, MA, 02115, USA
| | - Suneel S Apte
- Department of Biomedical Engineering- ND20, Cleveland Clinic Lerner Research Institute, Cleveland, OH, 44195, USA.
| |
Collapse
|
40
|
Jiang S, Shi JY, Lin YS, Duan SJ, Chen X, Jiao JJ, Shen W, Jin X, You M, Wang M, Shi B, Jia ZL. NTN1
gene was risk to non-syndromic cleft lip only among Han Chinese population. Oral Dis 2018; 25:535-542. [PMID: 30506619 DOI: 10.1111/odi.13009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 10/30/2018] [Accepted: 11/22/2018] [Indexed: 02/05/2023]
Affiliation(s)
- ShuYuan Jiang
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of cleft lip and palate, West China Hospital of Stomatology; Sichuan University; Chengdu China
| | - Jia-Yu Shi
- Division of Growth and Development and Section of Orthodontics, School of Dentistry; University of California; Los Angeles California
| | - Yan-Song Lin
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of cleft lip and palate, West China Hospital of Stomatology; Sichuan University; Chengdu China
| | - Shi-Jun Duan
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of cleft lip and palate, West China Hospital of Stomatology; Sichuan University; Chengdu China
| | - Xieli Chen
- Beijing Smile Angel Children’s Hospital; Beijing China
| | | | - Wei Shen
- Beijing Smile Angel Children’s Hospital; Beijing China
| | - Xiaoju Jin
- Beijing Smile Angel Children’s Hospital; Beijing China
| | - Miao You
- Beijing Smile Angel Children’s Hospital; Beijing China
| | - Moyao Wang
- Beijing Smile Angel Children’s Hospital; Beijing China
| | - Bing Shi
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of cleft lip and palate, West China Hospital of Stomatology; Sichuan University; Chengdu China
| | - Zhong-Lin Jia
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of cleft lip and palate, West China Hospital of Stomatology; Sichuan University; Chengdu China
| |
Collapse
|
41
|
Diversity of copy number variation in the worldwide goat population. Heredity (Edinb) 2018; 122:636-646. [PMID: 30401973 DOI: 10.1038/s41437-018-0150-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 09/09/2018] [Accepted: 09/18/2018] [Indexed: 11/08/2022] Open
Abstract
Goats (Capra hircus) are an important farm animal species. Copy number variation (CNV) represents a major source of genomic structural variation. We investigated the diversity of CNV distribution in goats using CaprineSNP50 genotyping data generated by the ADAPTmap Project. We identified 6286 putative CNVs in 1023 samples from 50 goat breeds using PennCNV. These CNVs were merged into 978 CNV regions, spanning ~262 Mb of total length and corresponding to ~8.96% of the goat genome. We then divided the samples into six subgroups per geographic distribution and constructed a comparative CNV map. Our results revealed a population differentiation in CNV across different geographical areas, including Western Asia, Eastern Mediterranean, Alpine & Northern Europe, Madagascar, Northwestern Africa, and Southeastern Africa groups. The results of a cluster heatmap analysis based on the CNV count per individual across different groups was generally consistent with the one generated from the SNP data, likely reflecting the population history of different goat breeds. We sought to determine the gene content of these CNV events and found several important CNV-overlapping genes (e.g. EDNRA, ADAMTS20, ASIP, KDM5B, ADAM8, DGAT1, CHRNB1, CLCN7, and EXOSC4), which are involved in local adaptations such as coat color, muscle development, metabolic processes, osteopetrosis, and embryonic development. Therefore, this research generated an extensive CNV map in the worldwide population of goat, which offers novel insight into the goat genome and its functional annotation.
Collapse
|
42
|
Carlson JC, Nidey NL, Butali A, Buxo CJ, Christensen K, Deleyiannis FWD, Hecht JT, Field LL, Moreno-Uribe LM, Orioli IM, Poletta FA, Padilla C, Vieira AR, Weinberg SM, Wehby GL, Feingold E, Murray JC, Marazita ML, Leslie EJ. Genome-wide interaction studies identify sex-specific risk alleles for nonsyndromic orofacial clefts. Genet Epidemiol 2018; 42:664-672. [PMID: 30277614 DOI: 10.1002/gepi.22158] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 07/17/2018] [Accepted: 07/28/2018] [Indexed: 01/11/2023]
Abstract
Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is the most common craniofacial birth defect in humans and is notable for its apparent sexual dimorphism where approximately twice as many males are affected as females. The sources of this disparity are largely unknown, but interactions between genetic and sex effects are likely contributors. We examined gene-by-sex (G × S) interactions in a worldwide sample of 2,142 NSCL/P cases and 1,700 controls recruited from 13 countries. First, we performed genome-wide joint tests of the genetic (G) and G × S effects genome-wide using logistic regression assuming an additive genetic model and adjusting for 18 principal components of ancestry. We further interrogated loci with suggestive results from the joint test ( p < 1.00 × 10 -5 ) by examining the G × S effects from the same model. Out of the 133 loci with suggestive results ( p < 1.00 × 10 -5 ) for the joint test, we observed one genome-wide significant G × S effect in the 10q21 locus (rs72804706; p = 6.69 × 10 -9 ; OR = 2.62 CI [1.89, 3.62]) and 16 suggestive G × S effects. At the intergenic 10q21 locus, the risk of NSCL/P is estimated to increase with additional copies of the minor allele for females, but the opposite effect for males. Our observation that the impact of genetic variants on NSCL/P risk differs for males and females may further our understanding of the genetic architecture of NSCL/P and the sex differences underlying clefts and other birth defects.
Collapse
Affiliation(s)
- Jenna C Carlson
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania.,Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Nichole L Nidey
- Department of Epidemiology, College of Public Health, University of Iowa, Iowa City, Iowa
| | - Azeez Butali
- Department of Oral Pathology, Radiology and Medicine, Dows Institute for Dental Research, College of Dentistry, University of Iowa, Iowa City, Iowa
| | - Carmen J Buxo
- Dental and Craniofacial Genomics Core, School of Dental Medicine, University of Puerto Rico, San Juan, Puerto Rico
| | - Kaare Christensen
- Department of Epidemiology, Institute of Public Health, University of Southern Denmark, Odense, Denmark
| | - Frederic W-D Deleyiannis
- Department of Surgery, Plastic and Reconstructive Surgery Division, University of Colorado School of Medicine, Denver, Colorado
| | - Jacqueline T Hecht
- Department of Pediatrics, McGovern Medical School and School of Dentistry, UT Health at Houston, Houston, Texas
| | - L Leigh Field
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Lina M Moreno-Uribe
- Department of Orthodontics, College of Dentistry, University of Iowa, Iowa City, Iowa
| | - Ieda M Orioli
- ECLAMC (Latin American Collaborative Study of Congenital Malformations) at INAGEMP (National Institute of Population Medical Genetics), Rio de Janeiro, Brazil.,Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fernando A Poletta
- ECLAMC (Latin American Collaborative Study of Congenital Malformations) at INAGEMP (National Institute of Population Medical Genetics), Rio de Janeiro, Brazil.,CEMIC-CONICET: Center for Medical Education and Clinical Research "Norberto Quirno", Buenos Aires, Argentina
| | - Carmencita Padilla
- Department of Pediatrics, College of Medicine, University of the Philippines, Manila, Philippines.,The Philippine Genome Center, University of the Philippines System, Manilla, Philippines
| | - Alexandre R Vieira
- Department of Oral Biology, Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Seth M Weinberg
- Department of Oral Biology, Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - George L Wehby
- Department of Health Management and Policy, College of Public Health, University of Iowa, Iowa City, Iowa
| | - Eleanor Feingold
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania.,Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Jeffrey C Murray
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Mary L Marazita
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania.,Department of Oral Biology, Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Elizabeth J Leslie
- Department of Human Genetics, Emory University School of Medicine, Emory University, Atlanta, Georgia
| |
Collapse
|
43
|
Affiliation(s)
- Seth M. Weinberg
- Department of Oral Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Anthropology, University of Pittsburgh, Pittsburgh, Pennsylvania, United Staes of America
- * E-mail:
| | - Robert Cornell
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, Iowa, United States America
| | - Elizabeth J. Leslie
- Department of Human Genetics, Emory University, Atlanta, Georgia, United States of America
| |
Collapse
|
44
|
Mead TJ, Apte SS. ADAMTS proteins in human disorders. Matrix Biol 2018; 71-72:225-239. [PMID: 29885460 DOI: 10.1016/j.matbio.2018.06.002] [Citation(s) in RCA: 157] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 06/04/2018] [Accepted: 06/05/2018] [Indexed: 02/07/2023]
Abstract
ADAMTS proteins are a superfamily of 26 secreted molecules comprising two related, but distinct families. ADAMTS proteases are zinc metalloendopeptidases, most of whose substrates are extracellular matrix (ECM) components, whereas ADAMTS-like proteins lack a metalloprotease domain, reside in the ECM and have regulatory roles vis-à-vis ECM assembly and/or ADAMTS activity. Evolutionary conservation and expansion of ADAMTS proteins in mammals is suggestive of crucial embryologic or physiological roles in humans. Indeed, Mendelian disorders or birth defects resulting from naturally occurring ADAMTS2, ADAMTS3, ADAMTS10, ADAMTS13, ADAMTS17, ADAMTS20, ADAMTSL2 and ADAMTSL4 mutations as well as numerous phenotypes identified in genetically engineered mice have revealed ADAMTS participation in major biological pathways. Important roles have been identified in a few acquired conditions. ADAMTS5 is unequivocally implicated in pathogenesis of osteoarthritis via degradation of aggrecan, a major structural proteoglycan in cartilage. ADAMTS7 is strongly associated with coronary artery disease and promotes atherosclerosis. Autoantibodies to ADAMTS13 lead to a platelet coagulopathy, thrombotic thrombocytopenic purpura, which is similar to that resulting from ADAMTS13 mutations. ADAMTS proteins have numerous potential connections to other human disorders that were identified by genome-wide association studies. Here, we review inherited and acquired human disorders in which ADAMTS proteins participate, and discuss progress and prospects in therapeutics.
Collapse
Affiliation(s)
- Timothy J Mead
- Department of Biomedical Engineering, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, United States
| | - Suneel S Apte
- Department of Biomedical Engineering, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, United States.
| |
Collapse
|
45
|
Zhang BH, Huang N, Shi JY, Shi B, Jia ZL. Homozygote C/C at rs12543318 was risk factor for non-syndromic cleft lip only from Western Han Chinese population. J Oral Pathol Med 2018; 47:620-626. [PMID: 29683526 DOI: 10.1111/jop.12719] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2018] [Indexed: 02/05/2023]
Abstract
Non-syndromic cleft lip with or without cleft palate (NSCL/P) is a complex disorder, and it results from both of the genetic modifiers and environmental factors, with genetic modifiers contributes to it more than environmental factors. GWASs made great progress in identifying the candidate genes for NSCL/P, but the findings need to be replicated in other populations. In this study, we selected eleven SNPs from recent GWASs and GWAS meta-analysis to investigate their associations among 308 NSCL/P trios (134 non-syndromic cleft lip only (NSCLO) trios and 174 non-syndromic cleft lip with cleft palate (NSCLP) trios) from Han Chinese population. All SNPs were genotyped using SNPscan method and analyzed the data with FBAT, PLINK, and R package. Allelic TDT analysis showed that allele A at rs12543318 was associated with NSCLO trios (P = .0032, OR = 0.57, 95% CI: 0.39-0.83), and parent-of-origin effect analysis indicated that allele A at rs12543318 was significantly maternally undertransmitted among NSCLO (P = .0046), which implied the potential influence of genomic imprinting; global TDT further confirmed this association. Individual genotypic TDT showed homozygote C/C at rs12543318 was overtransmitted among NSCLO (Z = 3.79, P = .00015) and NSCL/P groups (Z = 3.83, P = .00013), which indicated that it could increase the risk to have cleft babies. Our findings indicated that rs12543318 was associated with NSCLO from Western Han Chinese population, which will give new scientific evidence for later researches in the etiology of NSOCs.
Collapse
Affiliation(s)
- Bi-He Zhang
- State Key Laboratory of Oral Diseases, Department of Cleft Lip and Palate, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Ning Huang
- State Key Laboratory of Oral Diseases, Department of Cleft Lip and Palate, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jia-Yu Shi
- Division of Growth and Development and Section of Orthodontics, School of Dentistry, University of California, Los Angeles, CA, USA
| | - Bing Shi
- State Key Laboratory of Oral Diseases, Department of Cleft Lip and Palate, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Zhong-Lin Jia
- State Key Laboratory of Oral Diseases, Department of Cleft Lip and Palate, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| |
Collapse
|
46
|
Basha M, Demeer B, Revencu N, Helaers R, Theys S, Bou Saba S, Boute O, Devauchelle B, Francois G, Bayet B, Vikkula M. Whole exome sequencing identifies mutations in 10% of patients with familial non-syndromic cleft lip and/or palate in genes mutated in well-known syndromes. J Med Genet 2018; 55:449-458. [DOI: 10.1136/jmedgenet-2017-105110] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 02/02/2018] [Accepted: 02/12/2018] [Indexed: 01/08/2023]
Abstract
BackgroundOral clefts, that is, clefts of the lip and/or cleft palate (CL/P), are the most common craniofacial birth defects with an approximate incidence of ~1/700. To date, physicians stratify patients with oral clefts into either syndromic CL/P (syCL/P) or non-syndromic CL/P (nsCL/P) depending on whether the CL/P is associated with another anomaly or not. In general, patients with syCL/P follow Mendelian inheritance, while those with nsCL/P have a complex aetiology and, as such, do not adhere to Mendelian inheritance. Genome-wide association studies have identified approximately 30 risk loci for nsCL/P, which could explain a small fraction of heritability.MethodsTo identify variants causing nsCL/P, we conducted whole exome sequencing on 84 individuals with nsCL/P, drawn from multiplex families (n=46).ResultsWe identified rare damaging variants in four genes known to be mutated in syCL/P: TP63 (one family), TBX1 (one family), LRP6 (one family) and GRHL3 (two families), and clinical reassessment confirmed the isolated nature of their CL/P.ConclusionThese data demonstrate that patients with CL/P without cardinal signs of a syndrome may still carry a mutation in a gene linked to syCL/P. Rare coding and non-coding variants in syCL/P genes could in part explain the controversial question of ‘missing heritability’ for nsCL/P. Therefore, gene panels designed for diagnostic testing of syCL/P should be used for patients with nsCL/P, especially when there is at least third-degree family history. This would allow a more precise management, follow-up and genetic counselling. Moreover, stratified cohorts would allow hunting for genetic modifiers.
Collapse
|
47
|
Brown EA, Thomasy SM, Murphy CJ, Bannasch DL. Genetic analysis of optic nerve head coloboma in the Nova Scotia Duck Tolling Retriever identifies discordance with the NHEJ1 intronic deletion (collie eye anomaly mutation). Vet Ophthalmol 2018; 21:144-150. [PMID: 28702949 PMCID: PMC5766432 DOI: 10.1111/vop.12488] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Collie eye anomaly (CEA) encompasses a spectrum of different ophthalmic phenotypes from clinically inconsequential choroidal hypoplasia to blindness from coloboma of the optic nerve head (ONH). A previous study found a 7.8-kb deletion in intron 4 of the NHEJ1 gene to be associated with CEA. A genetic test based on this association is recommended for many breeds, including the Nova Scotia Duck Tolling Retriever (NSDTR). Collection of ONH coloboma-affected NSDTR showed lack of concordance of the NHEJ1 intronic deletion with ONH coloboma. Using genomewide single nucleotide polymorphism (SNP) genotyping in 7 ONH coloboma-affected NSDTR cases and 47 unaffected NSDTR controls with no ophthalmic signs, one SNP, located on chromosome 7, demonstrated genomewide significance. However, high genomic inflation may have confounded the results. Therefore, the genomewide association study was repeated using EMMAX to control for population structure in the cohort of 7 cases and 47 controls. However, no regions of the genome were significantly associated with ONH coloboma. These results failed to document significant association with the CEA locus. Due to the complex genetic etiology of ONH coloboma, the NHEJ1 intronic deletion test results should be carefully considered when making breeding decisions. If the goal is to select for visually competent dogs, our data suggest that eye examinations of puppies would be more effective as a guide in selection of breeding pairs than relying solely on currently available genetic tests.
Collapse
Affiliation(s)
- Emily A. Brown
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California—Davis
| | - Sara M. Thomasy
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California—Davis
| | - Christopher J. Murphy
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, Department of Ophthalmology & Vision Science, School of Medicine, University of California—Davis
| | - Danika L. Bannasch
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California—Davis, Davis, CA 95616,
| |
Collapse
|
48
|
Skare Ø, Lie RT, Haaland ØA, Gjerdevik M, Romanowska J, Gjessing HK, Jugessur A. Analysis of Parent-of-Origin Effects on the X Chromosome in Asian and European Orofacial Cleft Triads Identifies Associations with DMD, FGF13, EGFL6, and Additional Loci at Xp22.2. Front Genet 2018. [PMID: 29520293 PMCID: PMC5827165 DOI: 10.3389/fgene.2018.00025] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Background: Although both the mother's and father's alleles are present in the offspring, they may not operate at the same level. These parent-of-origin (PoO) effects have not yet been explored on the X chromosome, which motivated us to develop new methods for detecting such effects. Orofacial clefts (OFCs) exhibit sex-specific differences in prevalence and are examples of traits where a search for various types of effects on the X chromosome might be relevant. Materials and Methods: We upgraded our R-package Haplin to enable genome-wide analyses of PoO effects, as well as power simulations for different statistical models. 14,486 X-chromosome SNPs in 1,291 Asian and 1,118 European case-parent triads of isolated OFCs were available from a previous GWAS. For each ethnicity, cleft lip with or without cleft palate (CL/P) and cleft palate only (CPO) were analyzed separately using two X-inactivation models and a sliding-window approach to haplotype analysis. In addition, we performed analyses restricted to female offspring. Results: Associations were identified in "Dystrophin" (DMD, Xp21.2-p21.1), "Fibroblast growth factor 13" (FGF13, Xq26.3-q27.1) and "EGF-like domain multiple 6" (EGFL6, Xp22.2), with biologically plausible links to OFCs. Unlike EGFL6, the other associations on chromosomal region Xp22.2 had no apparent connections to OFCs. However, the Xp22.2 region itself is of potential interest because it contains genes for clefting syndromes [for example, "Oral-facial-digital syndrome 1" (OFD1) and "Midline 1" (MID1)]. Overall, the identified associations were highly specific for ethnicity, cleft subtype and X-inactivation model, except for DMD in which associations were identified in both CPO and CL/P, in the model with X-inactivation and in Europeans only. Discussion/Conclusion: The specificity of the associations for ethnicity, cleft subtype and X-inactivation model underscores the utility of conducting subanalyses, despite the ensuing need to adjust for additional multiple testing. Further investigations are needed to confirm the associations with DMD, EGF16, and FGF13. Furthermore, chromosomal region Xp22.2 appears to be a hotspot for genes implicated in clefting syndromes and thus constitutes an exciting direction to pursue in future OFCs research. More generally, the new methods presented here are readily adaptable to the study of X-linked PoO effects in other outcomes that use a family-based design.
Collapse
Affiliation(s)
- Øivind Skare
- Department of Occupational Medicine and Epidemiology, National Institute of Occupational Health, Oslo, Norway
| | - Rolv T Lie
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, Oslo, Norway
| | - Øystein A Haaland
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Miriam Gjerdevik
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway
| | - Julia Romanowska
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Computational Biology Unit, University of Bergen, Bergen, Norway
| | - Håkon K Gjessing
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, Oslo, Norway
| | - Astanand Jugessur
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, Oslo, Norway.,Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway
| |
Collapse
|
49
|
Mostowska A, Gaczkowska A, Żukowski K, Ludwig K, Hozyasz K, Wójcicki P, Mangold E, Böhmer A, Heilmann-Heimbach S, Knapp M, Zadurska M, Biedziak B, Budner M, Lasota A, Daktera-Micker A, Jagodziński P. Common variants inDLG1locus are associated with non-syndromic cleft lip with or without cleft palate. Clin Genet 2018; 93:784-793. [DOI: 10.1111/cge.13141] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 09/13/2017] [Accepted: 09/14/2017] [Indexed: 12/31/2022]
Affiliation(s)
- A. Mostowska
- Department of Biochemistry and Molecular Biology; Poznan University of Medical Sciences; Poznan Poland
| | - A. Gaczkowska
- Department of Biochemistry and Molecular Biology; Poznan University of Medical Sciences; Poznan Poland
| | - K. Żukowski
- Department of Animal Genetics and Breeding; National Research Institute of Animal Production; Balice Poland
| | - K.U. Ludwig
- Institute of Human Genetics; University of Bonn; Bonn Germany
- Department of Genomics; Life and Brain Center, University of Bonn; Bonn Germany
| | - K.K. Hozyasz
- Department of Pediatrics; Institute of Mother and Child; Warsaw Poland
| | - P. Wójcicki
- Plastic Surgery Clinic of Medical University in Wroclaw; Wroclaw Poland
- Department of Plastic Surgery in Specialist Medical Center in Polanica Zdroj; Polanica Zdroj Poland
| | - E. Mangold
- Institute of Human Genetics; University of Bonn; Bonn Germany
| | - A.C. Böhmer
- Institute of Human Genetics; University of Bonn; Bonn Germany
- Department of Genomics; Life and Brain Center, University of Bonn; Bonn Germany
| | - S. Heilmann-Heimbach
- Institute of Human Genetics; University of Bonn; Bonn Germany
- Department of Genomics; Life and Brain Center, University of Bonn; Bonn Germany
| | - M. Knapp
- Institute for Medical Biometry, Informatics and Epidemiology; University of Bonn; Bonn Germany
| | - M. Zadurska
- Department of Orthodontics; Medical University of Warsaw; Warsaw Poland
| | - B. Biedziak
- Department of Dental Surgery, Division of Facial Malformation; Poznan University of Medical Sciences; Poznan Poland
| | - M. Budner
- Eastern Poland Burn Treatment and Reconstructive Center; Leczna Poland
| | - A. Lasota
- Department of Jaw Orthopedics; Medical University of Lublin; Lublin Poland
| | - A. Daktera-Micker
- Department of Dental Surgery, Division of Facial Malformation; Poznan University of Medical Sciences; Poznan Poland
| | - P.P. Jagodziński
- Department of Biochemistry and Molecular Biology; Poznan University of Medical Sciences; Poznan Poland
| |
Collapse
|
50
|
Association of CDKAL1 nucleotide variants with the risk of non-syndromic cleft lip with or without cleft palate. J Hum Genet 2018; 63:397-406. [DOI: 10.1038/s10038-017-0397-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 11/01/2017] [Accepted: 11/12/2017] [Indexed: 12/24/2022]
|