Walid Fakhouri - Academia.edu (original) (raw)

Papers by Walid Fakhouri

Research paper thumbnail of Quantitative Modeling of a Transcriptional Grammar: Short‐Range Repression in Drosophila

The FASEB Journal, Apr 1, 2010

Research paper thumbnail of High incidence and regional distribution of cleft palate in Finns are associated with a functional variant in an IRF6 enhancer

In Finland the frequency of isolated cleft palate (CP) is higher than that of isolated cleft lip ... more In Finland the frequency of isolated cleft palate (CP) is higher than that of isolated cleft lip (CL) or cleft lip with cleft palate (CLP). This trend contrasts to that in other countries but its genetic underpinnings are unknown. We performed a genome-wide association study for orofacial cleft, which includes CL, CLP, and CP in the Finnish population. We identified rs570516915, a single nucleotide polymorphism that is virtually specific to Finns and Estonians, as being strongly associated with orofacial cleft, and predominantly with CP (p = 5.25 x 10-34, OR = 8.65, 95% CI 6.11-12.25). The risk allele frequency for rs570516915 parallels the regional variation of CP prevalence in Finland, and the association was replicated in an independent sample of CP cases from Estonia (p < 1.3 x 10-11). The rs570516915 variant lies in an IRF6 (Interferon Regulatory Factor 6) enhancer active in ectodermal and oral epithelial cells. Other variants in the IRF6 locus, including those in the same e...

Research paper thumbnail of Systematic review of hormonal and genetic factors involved in the nonsyndromic disorders of the lower jaw

Developmental Dynamics, 2018

Main Points: 1. Zebrafish embryos at the end of pronuclear fusion and before initiation of zygoti... more Main Points: 1. Zebrafish embryos at the end of pronuclear fusion and before initiation of zygotic mitosis are resistant to teratogenic effects of heat. 2. The teratogenic heat resilient window exists transiently during the maternally controlled phase of development. 3. Heat shock during the teratogenic heat resilient window enables generation of morphologically normal zebrafish tetraploids. 4. Diploidization of haploids by transient heat shocks during the teratogenic heat resilient windows aids in effective generation of gynogenic diploids.

Research paper thumbnail of Can Genetic Factors Compromise the Success of Dental Implants? A Systematic Review and Meta-Analysis

Dental implants provide a predictable treatment option for partial and complete edentulism via th... more Dental implants provide a predictable treatment option for partial and complete edentulism via the placement of fixed permanent artificial root to support prosthetic dental crowns. Despite the high survival rates, long-term implant failures are still reported leading to implant removal and additional financial and health burdens. While extrinsic factors that improve survival rate of implants have been well explored, the impact of genetic factors on this matter is poorly understood. A systematic review and meta-analysis study was conducted to determine whether genetic factors contribute to increase the risk of dental implant failure. A comprehensive search for peer-reviewed articles on dental implants and genetics was performed using various literature database libraries. The study design was conducted according to PRISMA guidelines, and the obtained records were registered in PROSPERO database. According to the exclusion/inclusion criteria, 11 studies were eligible for this study ou...

Research paper thumbnail of Allele-specific epigenome maps reveal sequence-dependent stochastic switching at regulatory loci

Science (New York, N.Y.), Sep 23, 2018

To assess the impact of genetic variation in regulatory loci on human health, we construct a high... more To assess the impact of genetic variation in regulatory loci on human health, we construct a high-resolution map of allelic imbalances in DNA methylation, histone marks, and gene transcription in 71 epigenomes from 36 distinct cell and tissue types from 13 donors. Deep whole-genome bisulfite sequencing of 49 methylomes reveals sequence-dependent CpG methylation imbalances at thousands of heterozygous regulatory loci. Such loci are enriched for stochastic switching, defined as random transitions between fully methylated and unmethylated states of DNA. The methylation imbalances at thousands of loci are explainable by different relative frequencies of the methylated and unmethylated states for the two alleles. Further analyses provide a unifying model that links sequence-dependent allelic imbalances of the epigenome, stochastic switching at gene regulatory loci, and disease-associated genetic variation.

Research paper thumbnail of Colorectal Cancer-Associated Genes Are Associated with Tooth Agenesis and May Have a Role in Tooth Development

Scientific reports, Jan 14, 2018

Previously reported co-occurrence of colorectal cancer (CRC) and tooth agenesis (TA) and the over... more Previously reported co-occurrence of colorectal cancer (CRC) and tooth agenesis (TA) and the overlap in disease-associated gene variants suggest involvement of similar molecular pathways. Here, we took an unbiased approach and tested genome-wide significant CRC-associated variants for association with isolated TA. Thirty single nucleotide variants (SNVs) in CRC-predisposing genes/loci were genotyped in a discovery dataset composed of 440 individuals with and without isolated TA. Genome-wide significant associations were found between TA and ATF1 rs11169552 (P = 4.36 × 10) and DUSP10 rs6687758 (P = 1.25 × 10), and positive association found with CASC8 rs10505477 (P = 8.2 × 10). Additional CRC marker haplotypes were also significantly associated with TA. Genotyping an independent dataset consisting of 52 cases with TA and 427 controls confirmed the association with CASC8. Atf1 and Dusp10 expression was detected in the mouse developing teeth from early bud stages to the formation of th...

Research paper thumbnail of Intercellular Genetic Interaction Between Irf6 and Twist1 during Craniofacial Development

Scientific Reports, 2017

Interferon Regulatory Factor 6 (IRF6) and TWIST1 are transcription factors necessary for craniofa... more Interferon Regulatory Factor 6 (IRF6) and TWIST1 are transcription factors necessary for craniofacial development. Human genetic studies showed that mutations in IRF6 lead to cleft lip and palate and mandibular abnormalities. In the mouse, we found that loss of Irf6 causes craniosynostosis and mandibular hypoplasia. Similarly, mutations in TWIST1 cause craniosynostosis, mandibular hypoplasia and cleft palate. Based on this phenotypic overlap, we asked if Irf6 and Twist1 interact genetically during craniofacial formation. While single heterozygous mice are normal, double heterozygous embryos (Irf6 +/− ; Twist1 +/−) can have severe mandibular hypoplasia that leads to agnathia and cleft palate at birth. Analysis of spatiotemporal expression showed that Irf6 and Twist1 are found in different cell types. Consistent with the intercellular interaction, we found reduced expression of Endothelin1 (EDN1) in mandible and transcription factors that are critical for mandibular patterning including DLX5, DLX6 and HAND2, were also reduced in mesenchymal cells. Treatment of mandibular explants with exogenous EDN1 peptides partially rescued abnormalities in Meckel's cartilage. In addition, partial rescue was observed when double heterozygous embryos also carried a null allele of p53. Considering that variants in IRF6 and TWIST1 contribute to human craniofacial defects, this gene-gene interaction may have implications on craniofacial disorders. Development of the face is a highly coordinated process that starts after gastrulation with the formation of the frontonasal and pharyngeal arches. The arches are lined by ectoderm superficially and endoderm internally. Cranial neural crest (CNC) cells that may be considered a fourth germ-layer, migrate from the mid-and hindbrain regions into the frontonasal and pharyngeal arches. CNC cells than give rise to many tissues, including bone, cartilage, neuron, ganglia, smooth muscle and odontoblasts 1, 2. In the mandible, CNC and cranial paraxial mesodermal cells contribute to the formation of Meckel's cartilage and the tongue 3-6. Meckel's cartilage provides structural support and biochemical cues for CNC-derived mesenchyme during mandibular development 4, 7. Also, signaling from oral epithelium is critical in regulating proliferation and differentiation of CNC 6, 8. Hence, the development of craniofacial tissues is highly coordinated and interconnected. For example, micrognathia (undersized mandible) can lead to glossoptosis and cleft palate, as seen in patients with Pierre Robin sequence 9, 10. Mandibular disorders are common congenital malformations that can occur as part of genetic syndromes or as an isolated form that can lead to a sequence of anomalies associated with tongue, palate and pharynx 11, 12. The phenotypic expression of mandibular abnormalities ranges from hyperplasia (macrognathia) to hypoplasia (micrognathia) and to a more severe form characterized by total loss of the mandible (agnathia) 10-12. Micrognathia is the most common mandibular birth defect with a frequency of 1 in 1600 live births 12. Although

Research paper thumbnail of The effect of non-coding DNA variations on P53 and cMYC competitive inhibition at cis-overlapping motifs

Human molecular genetics, Jan 7, 2016

Non-coding DNA variations play a critical role in increasing the risk for development of common c... more Non-coding DNA variations play a critical role in increasing the risk for development of common complex diseases, and account for the majority of SNPs highly associated with cancer. However, it remains a challenge to identify etiologic variants and to predict their pathological effects on target gene expression for clinical purposes. Cis-overlapping motifs (COMs) are elements of enhancer regions that impact gene expression by enabling competitive binding and switching between transcription factors. Mutations within COMs are especially important when the involved transcription factors have opposing effects on gene regulation, like P53 tumor suppressor and cMYC proto-oncogene. In this study, genome-wide analysis of ChIP-seq data from human cancer and mouse embryonic cells identified a significant number of putative regulatory elements with signals for both P53 and cMYC. Each co-occupied element contains, on average, two COMs, and one common SNP every two COMs. Gene ontology of predict...

Research paper thumbnail of Skeletal malocclusion: a developmental disorder with a life-long morbidity

Journal of clinical medicine research, 2014

The likelihood of birth defects in orofacial tissues is high due to the structural and developmen... more The likelihood of birth defects in orofacial tissues is high due to the structural and developmental complexity of the face and the susceptibility to intrinsic and extrinsic perturbations. Skeletal malocclusion is caused by the distortion of the proper mandibular and/or maxillary growth during fetal development. Patients with skeletal malocclusion may suffer from dental deformities, bruxism, teeth crowding, trismus, mastication difficulties, breathing obstruction and digestion disturbance if the problem is left untreated. In this review, we focused on skeletal malocclusion that affects 27.9% of the US population with different severity levels. We summarized the prevalence of class I, II and III of malocclusion in different ethnic groups and discussed the most frequent medical disorders associated with skeletal malocclusion. Dental anomalies that lead to malocclusion such as tooth agenesis, crowding, missing teeth and abnormal tooth size are not addressed in this review. We propose a...

Research paper thumbnail of Medication-related osteonecrosis of the jaws after tooth extraction in senescent female mice treated with zoledronic acid: Microtomographic, histological and immunohistochemical characterization

PLOS ONE

Treatment with cumulative dosages of zoledronic acid (ZA) in elderly patients is a risk factor fo... more Treatment with cumulative dosages of zoledronic acid (ZA) in elderly patients is a risk factor for the development of medication-related osteonecrosis of the jaws (MRONJ), mainly related to surgical triggers such as tooth extraction. However, animal models for the investigation and understanding of MRONJ pathophysiology in senescent and postmenopausal stages remains to be developed and characterized. The aim of this study was to analyze MRONJ development in senescent female mice treated with cumulative dosages of ZA. For this purpose, twenty 129/Sv female mice, 64 weeks old, were treated with 0.9% saline solution as control group (n = 10), and with ZA at 250μg/Kg (n = 10), once a week, starting 4 weeks before the upper right incisor extraction and until the end of the experimental time points (7 days and 21 days). At 7 and 21 days post-surgery, specimens were harvested for microCT, histological, birefringence and immunohistochemical analysis. Clinically, an incomplete epithelialization was observed in ZA group at 7 days and a delayed bone matrix mineralization and collagen maturation at 7 and 21 days compared to the controls. Controls revealed sockets filled with mature bone at 21 days as observed by microCT and birefringence, while ZA group presented delayed bone deposition at 7 and 21 days, as well increased leukocyte infiltration and blood clot at 7 days, and increased bone sequestrum and empty osteocyte lacunae at 21 days (p<0.05). Also, ZA group presented decreased quantity of TGFb+ and Runx-2+ cells at 7 days, and decreased quantity of TRAP+ osteoclasts compared to the control at 21 days (p<0.05).

Research paper thumbnail of An Insight into Acute Pericoronitis and the Need for an Evidence-Based Standard of Care

Dentistry Journal

Background: Pericoronitis is inflammation of the operculum associated with a partially erupted th... more Background: Pericoronitis is inflammation of the operculum associated with a partially erupted third molar. It is a highly prevalent infection of the oral cavity and presents as a painful sensation of the soft tissue encompassing the crown of the involved tooth. Though pericoronitis is common, there is no evidence-based standard-of-care for treatment of emergency patients with acute pericoronitis. Study Design: In this study, anonymous clinicians were asked to participate in an online survey with questions formulated to identify professional clinical background, emergency treatment preferred for acute pericoronitis, number of associated complications, frequency of third molar extraction, and patient satisfaction. Results and Conclusion: A statistical analysis of the collected data regarding the variance among different treatment plans and associated complications revealed little consensus in the treatment of pericoronitis. The lack of consistency of the responses focusing on the pre...

Research paper thumbnail of Identification of Disease Risk DNA Variations is Shaping the Future of Precision Health

Genes

In recent years, the knowledge generated by decoding the human genome has allowed groundbreaking ... more In recent years, the knowledge generated by decoding the human genome has allowed groundbreaking genetic research to better understand genomic architecture and heritability in healthy and disease states. The vast amount of data generated over time and yet to be generated provides the basis for translational research towards the development of preventive and therapeutic strategies for many conditions. In this special issue, we highlight the discoveries of disease-associated and protective DNA variations in common human diseases and developmental disorders.

Research paper thumbnail of A Cleft Lip and Palate Gene, Irf6 , is Involved in Osteoblast Differentiation of Craniofacial Bone

Developmental Dynamics

Background: Interferon regulatory factor 6 (IRF6) plays a critical role in embryonic tissue devel... more Background: Interferon regulatory factor 6 (IRF6) plays a critical role in embryonic tissue development, including differentiation of epithelial cells. Besides orofacial clefting due to haploinsufficiency of IRF6, recent human genetic studies indicated that mutations in IRF6 are linked to small mandible and digit abnormalities. The function of IRF6 has been well studied in oral epithelium; however, its role in craniofacial skeletal formation remains unknown. In this study, we investigated the role of Irf6 in craniofacial bone development using comparative analyses between wild-type (WT) and Irf6-null littermate mice. Results: Immunostaining revealed the expression of IRF6 in hypertrophic chondrocytes, osteocytes, and bone matrix of craniofacial tissues. Histological analysis of Irf6-null mice showed a remarkable reduction in the number of lacunae, embedded osteocytes in matrices, and a reduction in mineralization during bone formation. These abnormalities may explain the decreased craniofacial bone density detected by micro-CT, loss of incisors, and mandibular bone abnormality of Irf6-null mice. To validate the autonomous role of IRF6 in bone, extracted primary osteoblasts from calvarial bone of WT and Irf6-null pups showed no effect on osteoblastic viability and proliferation. However, a reduction in mineralization was detected in Irf6-null cells. Conclusions: Altogether, these findings suggest an autonomous role of Irf6 in regulating bone differentiation and mineralization. Developmental

Research paper thumbnail of Mandibular Explant Assay for Investigating Extrinsic Stimuli on Bone and Cartilage Development

Bio-protocol, Jan 5, 2017

A major issue in developmental biology is to determine how embryonic tissues respond to molecular... more A major issue in developmental biology is to determine how embryonic tissues respond to molecular signals in a timely manner and given the position-restricted instructions during morphogenesis, of which Meckel's cartilage is a classical example. Theexplant model is a practical and convenient system that allows investigation of bone and cartilage responses to specific stimuli under a controlled manner that closely mimics theconditions. In this protocol, the explant model was applied to test whether Meckel's cartilage and surrounding tissues are responsive to the Endothelin1 (Edn1) signaling molecule and whether it would rescue the phenotype of genetic mutations. The system allows a high degree of manipulation in terms of the concentrations of exogenous compounds added to the explant, time points with regards to measuring mandibular development, and the method of application of exogenous molecules and teratogens.

Research paper thumbnail of Ultrastructural studies on the mode of action of fluorescent pseudomonads alone and in combination with acibenzolar-s-methyl effective against Fusarium oxysporum f. sp. lycopersici in tomato plants

Zeitschrift Fur Pflanzenkrankheiten Und Pflanzenschutz, 2001

Research paper thumbnail of Health-related quality of life outcomes with prasugrel among medically managed non–ST-segment elevation acute coronary syndrome patients: Insights from the Targeted Platelet Inhibition to Clarify the Optimal Strategy to Medically Manage Acute Coronary Syndromes (TRILOGY ACS) trial

American Heart Journal, 2016

Few studies have assessed treatment effects on health-related quality of life (HRQoL) in patients... more Few studies have assessed treatment effects on health-related quality of life (HRQoL) in patients with acute coronary syndrome (ACS) treated without revascularization. The TRILOGY ACS trial randomized patients with ACS to either prasugrel or clopidogrel therapy plus aspirin. Outcomes showed a complex pattern suggestive of late benefits with respect to repeat clinical events and benefits confined to patients who underwent angiography. Here, we examine the HRQoL correlates of these patterns. HRQoL was measured at baseline and 3, 12, and 24 months or end of study (EOS) in 7243 patients aged &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt;75 years using the EuroQol 3-level, group 5-dimension index (EQ-5D). Linear mixed effects models for repeated measures were used to examine treatment differences in HRQoL overall, stratified by angiography status, and among patients who did and did not have non-fatal events. No baseline differences in HRQoL were seen between patients randomized to prasugrel (n=3620) or clopidogrel (n=3623). At 24 months, remaining patients assigned to prasugrel (n=1450) vs. clopidogrel (n=1443) had higher EQ-5D index scores (86.4 vs. 84.9, P=.01). Mixed effects models found no difference in EQ-5D scores among prasugrel and clopidogrel patients overall across subgroups stratified by angiography status. However, among patients with non-fatal clinical events, patients on clopidogrel reported a larger decrement in HRQoL than patients on prasugrel (79.5±18.1 vs. 80.6±18.0; P=.02). Overall, there was no difference in HRQoL outcomes among patients receiving prasugrel vs. clopidogrel. However, the differential effects of the treatments among patients with non-fatal events require further investigation.

Research paper thumbnail of Characteristics of fluorescent pseudomonad isolates towards controlling of tomato wilt caused by Fusarium oxysporum f. sp. lycopersici

Zeitschrift Fur Pflanzenkrankheiten Und Pflanzenschutz, 2003

Out of a screening of 80 fluorescent pseudomonad (fl. Ps.) strains, nine isolates (W21, W34, WB15... more Out of a screening of 80 fluorescent pseudomonad (fl. Ps.) strains, nine isolates (W21, W34, WB15, WB52, G54, G307, G308, G309 and CW2) were capable of reducing the fusarium wilt disease on tomato plants. On King&#39;s B agar medium, isolates W34, WB52, G308 and CW2 effectively inhibited the mycelial growth of Fusarium oxysporum f. sp. lycopersici (Fol) 7 days after incubation, while isolates WB15, W21 and G307 caused slight inhibition of the mycelium growth. Interestingly, the two isolates G54 and G309 did not cause any inhibition to the fungal growth. The biochemical and physiological characteristics of the nine effective isolates of fluorescent pseudomonads exhibited a wide variation in production of several substances considered as biocontrol factors such as: siderophores, cyanide, chitinase, gelatinase, proteinase, arginine dihydrolase, salicylic acid and antimicrobial metabolites. Application of fl. Ps. isolates by dipping tomato roots in the bacterial suspension proved to be superior to soil drenching in controlling tomato wilt disease. Furthermore, reisolation studies revealed that the population densities of G309 on tomato roots was always higher after root dipping than after soil drenching. Compatibility tests in vitro showed that the nine different fluorescent pseudomonad isolates could be combined. Compared to single application of isolates, control of fusarium wilt was more effective when the tomato plants were treated with combinations of G54 and CW2 or G54, WB52 and W34.

Research paper thumbnail of Enhancement of population densities of fluorescent pseudomonads in the rhizosphere of tomato plants by addition of acibenzolar- S -methyl

Canadian Journal of Microbiology, 2002

Fluorescent pseudomonad isolates G309 and CW2, in combination with the resistance inducer acibenz... more Fluorescent pseudomonad isolates G309 and CW2, in combination with the resistance inducer acibenzolar-S-methyl (ASM), improved control of fungal and bacterial diseases on tomato plants. The interactions of the bacteria in the presence of ASM showed that in vitro growth of Pseudomonas fluorescens G309 and Pseudomonas sp. strain CW2 was not affected in King's B broth supplemented with 10 and 20 μM ASM. Also, the bacterial cells were not able to utilize ASM as a nutrient source. In vitro production of the two antimicrobial secondary metabolites phenazine-1-carboxylic acid and 2-OH-phenazine by the isolate CW2 was not affected within 3 days from incubation. In contrary, addition of ASM at a concentration of 20 μM to King's B liquid medium significantly increased production of salicylic acid by isolate G309. When roots of tomato plants were treated with G309 or CW2 cell suspensions containing 20 μM ASM, the number of bacterial cells recovered from the rhizosphere was significantl...

Research paper thumbnail of A Cleft Lip and Palate Gene, Irf6 , is Involved in Osteoblast Differentiation of Craniofacial Bone

Developmental Dynamics

Background: Interferon regulatory factor 6 (IRF6) plays a critical role in embryonic tissue devel... more Background: Interferon regulatory factor 6 (IRF6) plays a critical role in embryonic tissue development, including differentiation of epithelial cells. Besides orofacial clefting due to haploinsufficiency of IRF6, recent human genetic studies indicated that mutations in IRF6 are linked to small mandible and digit abnormalities. The function of IRF6 has been well studied in oral epithelium; however, its role in craniofacial skeletal formation remains unknown. In this study, we investigated the role of Irf6 in craniofacial bone development using comparative analyses between wild-type (WT) and Irf6-null littermate mice. Results: Immunostaining revealed the expression of IRF6 in hypertrophic chondrocytes, osteocytes, and bone matrix of craniofacial tissues. Histological analysis of Irf6-null mice showed a remarkable reduction in the number of lacunae, embedded osteocytes in matrices, and a reduction in mineralization during bone formation. These abnormalities may explain the decreased craniofacial bone density detected by micro-CT, loss of incisors, and mandibular bone abnormality of Irf6-null mice. To validate the autonomous role of IRF6 in bone, extracted primary osteoblasts from calvarial bone of WT and Irf6-null pups showed no effect on osteoblastic viability and proliferation. However, a reduction in mineralization was detected in Irf6-null cells. Conclusions: Altogether, these findings suggest an autonomous role of Irf6 in regulating bone differentiation and mineralization. Developmental

Research paper thumbnail of A Cleft Lip and Palate Gene, Irf6 , is Involved in Osteoblast Differentiation of Craniofacial Bone

Developmental Dynamics

Background: Interferon regulatory factor 6 (IRF6) plays a critical role in embryonic tissue devel... more Background: Interferon regulatory factor 6 (IRF6) plays a critical role in embryonic tissue development, including differentiation of epithelial cells. Besides orofacial clefting due to haploinsufficiency of IRF6, recent human genetic studies indicated that mutations in IRF6 are linked to small mandible and digit abnormalities. The function of IRF6 has been well studied in oral epithelium; however, its role in craniofacial skeletal formation remains unknown. In this study, we investigated the role of Irf6 in craniofacial bone development using comparative analyses between wild-type (WT) and Irf6-null littermate mice. Results: Immunostaining revealed the expression of IRF6 in hypertrophic chondrocytes, osteocytes, and bone matrix of craniofacial tissues. Histological analysis of Irf6-null mice showed a remarkable reduction in the number of lacunae, embedded osteocytes in matrices, and a reduction in mineralization during bone formation. These abnormalities may explain the decreased craniofacial bone density detected by micro-CT, loss of incisors, and mandibular bone abnormality of Irf6-null mice. To validate the autonomous role of IRF6 in bone, extracted primary osteoblasts from calvarial bone of WT and Irf6-null pups showed no effect on osteoblastic viability and proliferation. However, a reduction in mineralization was detected in Irf6-null cells. Conclusions: Altogether, these findings suggest an autonomous role of Irf6 in regulating bone differentiation and mineralization. Developmental

Research paper thumbnail of Quantitative Modeling of a Transcriptional Grammar: Short‐Range Repression in Drosophila

The FASEB Journal, Apr 1, 2010

Research paper thumbnail of High incidence and regional distribution of cleft palate in Finns are associated with a functional variant in an IRF6 enhancer

In Finland the frequency of isolated cleft palate (CP) is higher than that of isolated cleft lip ... more In Finland the frequency of isolated cleft palate (CP) is higher than that of isolated cleft lip (CL) or cleft lip with cleft palate (CLP). This trend contrasts to that in other countries but its genetic underpinnings are unknown. We performed a genome-wide association study for orofacial cleft, which includes CL, CLP, and CP in the Finnish population. We identified rs570516915, a single nucleotide polymorphism that is virtually specific to Finns and Estonians, as being strongly associated with orofacial cleft, and predominantly with CP (p = 5.25 x 10-34, OR = 8.65, 95% CI 6.11-12.25). The risk allele frequency for rs570516915 parallels the regional variation of CP prevalence in Finland, and the association was replicated in an independent sample of CP cases from Estonia (p < 1.3 x 10-11). The rs570516915 variant lies in an IRF6 (Interferon Regulatory Factor 6) enhancer active in ectodermal and oral epithelial cells. Other variants in the IRF6 locus, including those in the same e...

Research paper thumbnail of Systematic review of hormonal and genetic factors involved in the nonsyndromic disorders of the lower jaw

Developmental Dynamics, 2018

Main Points: 1. Zebrafish embryos at the end of pronuclear fusion and before initiation of zygoti... more Main Points: 1. Zebrafish embryos at the end of pronuclear fusion and before initiation of zygotic mitosis are resistant to teratogenic effects of heat. 2. The teratogenic heat resilient window exists transiently during the maternally controlled phase of development. 3. Heat shock during the teratogenic heat resilient window enables generation of morphologically normal zebrafish tetraploids. 4. Diploidization of haploids by transient heat shocks during the teratogenic heat resilient windows aids in effective generation of gynogenic diploids.

Research paper thumbnail of Can Genetic Factors Compromise the Success of Dental Implants? A Systematic Review and Meta-Analysis

Dental implants provide a predictable treatment option for partial and complete edentulism via th... more Dental implants provide a predictable treatment option for partial and complete edentulism via the placement of fixed permanent artificial root to support prosthetic dental crowns. Despite the high survival rates, long-term implant failures are still reported leading to implant removal and additional financial and health burdens. While extrinsic factors that improve survival rate of implants have been well explored, the impact of genetic factors on this matter is poorly understood. A systematic review and meta-analysis study was conducted to determine whether genetic factors contribute to increase the risk of dental implant failure. A comprehensive search for peer-reviewed articles on dental implants and genetics was performed using various literature database libraries. The study design was conducted according to PRISMA guidelines, and the obtained records were registered in PROSPERO database. According to the exclusion/inclusion criteria, 11 studies were eligible for this study ou...

Research paper thumbnail of Allele-specific epigenome maps reveal sequence-dependent stochastic switching at regulatory loci

Science (New York, N.Y.), Sep 23, 2018

To assess the impact of genetic variation in regulatory loci on human health, we construct a high... more To assess the impact of genetic variation in regulatory loci on human health, we construct a high-resolution map of allelic imbalances in DNA methylation, histone marks, and gene transcription in 71 epigenomes from 36 distinct cell and tissue types from 13 donors. Deep whole-genome bisulfite sequencing of 49 methylomes reveals sequence-dependent CpG methylation imbalances at thousands of heterozygous regulatory loci. Such loci are enriched for stochastic switching, defined as random transitions between fully methylated and unmethylated states of DNA. The methylation imbalances at thousands of loci are explainable by different relative frequencies of the methylated and unmethylated states for the two alleles. Further analyses provide a unifying model that links sequence-dependent allelic imbalances of the epigenome, stochastic switching at gene regulatory loci, and disease-associated genetic variation.

Research paper thumbnail of Colorectal Cancer-Associated Genes Are Associated with Tooth Agenesis and May Have a Role in Tooth Development

Scientific reports, Jan 14, 2018

Previously reported co-occurrence of colorectal cancer (CRC) and tooth agenesis (TA) and the over... more Previously reported co-occurrence of colorectal cancer (CRC) and tooth agenesis (TA) and the overlap in disease-associated gene variants suggest involvement of similar molecular pathways. Here, we took an unbiased approach and tested genome-wide significant CRC-associated variants for association with isolated TA. Thirty single nucleotide variants (SNVs) in CRC-predisposing genes/loci were genotyped in a discovery dataset composed of 440 individuals with and without isolated TA. Genome-wide significant associations were found between TA and ATF1 rs11169552 (P = 4.36 × 10) and DUSP10 rs6687758 (P = 1.25 × 10), and positive association found with CASC8 rs10505477 (P = 8.2 × 10). Additional CRC marker haplotypes were also significantly associated with TA. Genotyping an independent dataset consisting of 52 cases with TA and 427 controls confirmed the association with CASC8. Atf1 and Dusp10 expression was detected in the mouse developing teeth from early bud stages to the formation of th...

Research paper thumbnail of Intercellular Genetic Interaction Between Irf6 and Twist1 during Craniofacial Development

Scientific Reports, 2017

Interferon Regulatory Factor 6 (IRF6) and TWIST1 are transcription factors necessary for craniofa... more Interferon Regulatory Factor 6 (IRF6) and TWIST1 are transcription factors necessary for craniofacial development. Human genetic studies showed that mutations in IRF6 lead to cleft lip and palate and mandibular abnormalities. In the mouse, we found that loss of Irf6 causes craniosynostosis and mandibular hypoplasia. Similarly, mutations in TWIST1 cause craniosynostosis, mandibular hypoplasia and cleft palate. Based on this phenotypic overlap, we asked if Irf6 and Twist1 interact genetically during craniofacial formation. While single heterozygous mice are normal, double heterozygous embryos (Irf6 +/− ; Twist1 +/−) can have severe mandibular hypoplasia that leads to agnathia and cleft palate at birth. Analysis of spatiotemporal expression showed that Irf6 and Twist1 are found in different cell types. Consistent with the intercellular interaction, we found reduced expression of Endothelin1 (EDN1) in mandible and transcription factors that are critical for mandibular patterning including DLX5, DLX6 and HAND2, were also reduced in mesenchymal cells. Treatment of mandibular explants with exogenous EDN1 peptides partially rescued abnormalities in Meckel's cartilage. In addition, partial rescue was observed when double heterozygous embryos also carried a null allele of p53. Considering that variants in IRF6 and TWIST1 contribute to human craniofacial defects, this gene-gene interaction may have implications on craniofacial disorders. Development of the face is a highly coordinated process that starts after gastrulation with the formation of the frontonasal and pharyngeal arches. The arches are lined by ectoderm superficially and endoderm internally. Cranial neural crest (CNC) cells that may be considered a fourth germ-layer, migrate from the mid-and hindbrain regions into the frontonasal and pharyngeal arches. CNC cells than give rise to many tissues, including bone, cartilage, neuron, ganglia, smooth muscle and odontoblasts 1, 2. In the mandible, CNC and cranial paraxial mesodermal cells contribute to the formation of Meckel's cartilage and the tongue 3-6. Meckel's cartilage provides structural support and biochemical cues for CNC-derived mesenchyme during mandibular development 4, 7. Also, signaling from oral epithelium is critical in regulating proliferation and differentiation of CNC 6, 8. Hence, the development of craniofacial tissues is highly coordinated and interconnected. For example, micrognathia (undersized mandible) can lead to glossoptosis and cleft palate, as seen in patients with Pierre Robin sequence 9, 10. Mandibular disorders are common congenital malformations that can occur as part of genetic syndromes or as an isolated form that can lead to a sequence of anomalies associated with tongue, palate and pharynx 11, 12. The phenotypic expression of mandibular abnormalities ranges from hyperplasia (macrognathia) to hypoplasia (micrognathia) and to a more severe form characterized by total loss of the mandible (agnathia) 10-12. Micrognathia is the most common mandibular birth defect with a frequency of 1 in 1600 live births 12. Although

Research paper thumbnail of The effect of non-coding DNA variations on P53 and cMYC competitive inhibition at cis-overlapping motifs

Human molecular genetics, Jan 7, 2016

Non-coding DNA variations play a critical role in increasing the risk for development of common c... more Non-coding DNA variations play a critical role in increasing the risk for development of common complex diseases, and account for the majority of SNPs highly associated with cancer. However, it remains a challenge to identify etiologic variants and to predict their pathological effects on target gene expression for clinical purposes. Cis-overlapping motifs (COMs) are elements of enhancer regions that impact gene expression by enabling competitive binding and switching between transcription factors. Mutations within COMs are especially important when the involved transcription factors have opposing effects on gene regulation, like P53 tumor suppressor and cMYC proto-oncogene. In this study, genome-wide analysis of ChIP-seq data from human cancer and mouse embryonic cells identified a significant number of putative regulatory elements with signals for both P53 and cMYC. Each co-occupied element contains, on average, two COMs, and one common SNP every two COMs. Gene ontology of predict...

Research paper thumbnail of Skeletal malocclusion: a developmental disorder with a life-long morbidity

Journal of clinical medicine research, 2014

The likelihood of birth defects in orofacial tissues is high due to the structural and developmen... more The likelihood of birth defects in orofacial tissues is high due to the structural and developmental complexity of the face and the susceptibility to intrinsic and extrinsic perturbations. Skeletal malocclusion is caused by the distortion of the proper mandibular and/or maxillary growth during fetal development. Patients with skeletal malocclusion may suffer from dental deformities, bruxism, teeth crowding, trismus, mastication difficulties, breathing obstruction and digestion disturbance if the problem is left untreated. In this review, we focused on skeletal malocclusion that affects 27.9% of the US population with different severity levels. We summarized the prevalence of class I, II and III of malocclusion in different ethnic groups and discussed the most frequent medical disorders associated with skeletal malocclusion. Dental anomalies that lead to malocclusion such as tooth agenesis, crowding, missing teeth and abnormal tooth size are not addressed in this review. We propose a...

Research paper thumbnail of Medication-related osteonecrosis of the jaws after tooth extraction in senescent female mice treated with zoledronic acid: Microtomographic, histological and immunohistochemical characterization

PLOS ONE

Treatment with cumulative dosages of zoledronic acid (ZA) in elderly patients is a risk factor fo... more Treatment with cumulative dosages of zoledronic acid (ZA) in elderly patients is a risk factor for the development of medication-related osteonecrosis of the jaws (MRONJ), mainly related to surgical triggers such as tooth extraction. However, animal models for the investigation and understanding of MRONJ pathophysiology in senescent and postmenopausal stages remains to be developed and characterized. The aim of this study was to analyze MRONJ development in senescent female mice treated with cumulative dosages of ZA. For this purpose, twenty 129/Sv female mice, 64 weeks old, were treated with 0.9% saline solution as control group (n = 10), and with ZA at 250μg/Kg (n = 10), once a week, starting 4 weeks before the upper right incisor extraction and until the end of the experimental time points (7 days and 21 days). At 7 and 21 days post-surgery, specimens were harvested for microCT, histological, birefringence and immunohistochemical analysis. Clinically, an incomplete epithelialization was observed in ZA group at 7 days and a delayed bone matrix mineralization and collagen maturation at 7 and 21 days compared to the controls. Controls revealed sockets filled with mature bone at 21 days as observed by microCT and birefringence, while ZA group presented delayed bone deposition at 7 and 21 days, as well increased leukocyte infiltration and blood clot at 7 days, and increased bone sequestrum and empty osteocyte lacunae at 21 days (p<0.05). Also, ZA group presented decreased quantity of TGFb+ and Runx-2+ cells at 7 days, and decreased quantity of TRAP+ osteoclasts compared to the control at 21 days (p<0.05).

Research paper thumbnail of An Insight into Acute Pericoronitis and the Need for an Evidence-Based Standard of Care

Dentistry Journal

Background: Pericoronitis is inflammation of the operculum associated with a partially erupted th... more Background: Pericoronitis is inflammation of the operculum associated with a partially erupted third molar. It is a highly prevalent infection of the oral cavity and presents as a painful sensation of the soft tissue encompassing the crown of the involved tooth. Though pericoronitis is common, there is no evidence-based standard-of-care for treatment of emergency patients with acute pericoronitis. Study Design: In this study, anonymous clinicians were asked to participate in an online survey with questions formulated to identify professional clinical background, emergency treatment preferred for acute pericoronitis, number of associated complications, frequency of third molar extraction, and patient satisfaction. Results and Conclusion: A statistical analysis of the collected data regarding the variance among different treatment plans and associated complications revealed little consensus in the treatment of pericoronitis. The lack of consistency of the responses focusing on the pre...

Research paper thumbnail of Identification of Disease Risk DNA Variations is Shaping the Future of Precision Health

Genes

In recent years, the knowledge generated by decoding the human genome has allowed groundbreaking ... more In recent years, the knowledge generated by decoding the human genome has allowed groundbreaking genetic research to better understand genomic architecture and heritability in healthy and disease states. The vast amount of data generated over time and yet to be generated provides the basis for translational research towards the development of preventive and therapeutic strategies for many conditions. In this special issue, we highlight the discoveries of disease-associated and protective DNA variations in common human diseases and developmental disorders.

Research paper thumbnail of A Cleft Lip and Palate Gene, Irf6 , is Involved in Osteoblast Differentiation of Craniofacial Bone

Developmental Dynamics

Background: Interferon regulatory factor 6 (IRF6) plays a critical role in embryonic tissue devel... more Background: Interferon regulatory factor 6 (IRF6) plays a critical role in embryonic tissue development, including differentiation of epithelial cells. Besides orofacial clefting due to haploinsufficiency of IRF6, recent human genetic studies indicated that mutations in IRF6 are linked to small mandible and digit abnormalities. The function of IRF6 has been well studied in oral epithelium; however, its role in craniofacial skeletal formation remains unknown. In this study, we investigated the role of Irf6 in craniofacial bone development using comparative analyses between wild-type (WT) and Irf6-null littermate mice. Results: Immunostaining revealed the expression of IRF6 in hypertrophic chondrocytes, osteocytes, and bone matrix of craniofacial tissues. Histological analysis of Irf6-null mice showed a remarkable reduction in the number of lacunae, embedded osteocytes in matrices, and a reduction in mineralization during bone formation. These abnormalities may explain the decreased craniofacial bone density detected by micro-CT, loss of incisors, and mandibular bone abnormality of Irf6-null mice. To validate the autonomous role of IRF6 in bone, extracted primary osteoblasts from calvarial bone of WT and Irf6-null pups showed no effect on osteoblastic viability and proliferation. However, a reduction in mineralization was detected in Irf6-null cells. Conclusions: Altogether, these findings suggest an autonomous role of Irf6 in regulating bone differentiation and mineralization. Developmental

Research paper thumbnail of Mandibular Explant Assay for Investigating Extrinsic Stimuli on Bone and Cartilage Development

Bio-protocol, Jan 5, 2017

A major issue in developmental biology is to determine how embryonic tissues respond to molecular... more A major issue in developmental biology is to determine how embryonic tissues respond to molecular signals in a timely manner and given the position-restricted instructions during morphogenesis, of which Meckel's cartilage is a classical example. Theexplant model is a practical and convenient system that allows investigation of bone and cartilage responses to specific stimuli under a controlled manner that closely mimics theconditions. In this protocol, the explant model was applied to test whether Meckel's cartilage and surrounding tissues are responsive to the Endothelin1 (Edn1) signaling molecule and whether it would rescue the phenotype of genetic mutations. The system allows a high degree of manipulation in terms of the concentrations of exogenous compounds added to the explant, time points with regards to measuring mandibular development, and the method of application of exogenous molecules and teratogens.

Research paper thumbnail of Ultrastructural studies on the mode of action of fluorescent pseudomonads alone and in combination with acibenzolar-s-methyl effective against Fusarium oxysporum f. sp. lycopersici in tomato plants

Zeitschrift Fur Pflanzenkrankheiten Und Pflanzenschutz, 2001

Research paper thumbnail of Health-related quality of life outcomes with prasugrel among medically managed non–ST-segment elevation acute coronary syndrome patients: Insights from the Targeted Platelet Inhibition to Clarify the Optimal Strategy to Medically Manage Acute Coronary Syndromes (TRILOGY ACS) trial

American Heart Journal, 2016

Few studies have assessed treatment effects on health-related quality of life (HRQoL) in patients... more Few studies have assessed treatment effects on health-related quality of life (HRQoL) in patients with acute coronary syndrome (ACS) treated without revascularization. The TRILOGY ACS trial randomized patients with ACS to either prasugrel or clopidogrel therapy plus aspirin. Outcomes showed a complex pattern suggestive of late benefits with respect to repeat clinical events and benefits confined to patients who underwent angiography. Here, we examine the HRQoL correlates of these patterns. HRQoL was measured at baseline and 3, 12, and 24 months or end of study (EOS) in 7243 patients aged &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt;75 years using the EuroQol 3-level, group 5-dimension index (EQ-5D). Linear mixed effects models for repeated measures were used to examine treatment differences in HRQoL overall, stratified by angiography status, and among patients who did and did not have non-fatal events. No baseline differences in HRQoL were seen between patients randomized to prasugrel (n=3620) or clopidogrel (n=3623). At 24 months, remaining patients assigned to prasugrel (n=1450) vs. clopidogrel (n=1443) had higher EQ-5D index scores (86.4 vs. 84.9, P=.01). Mixed effects models found no difference in EQ-5D scores among prasugrel and clopidogrel patients overall across subgroups stratified by angiography status. However, among patients with non-fatal clinical events, patients on clopidogrel reported a larger decrement in HRQoL than patients on prasugrel (79.5±18.1 vs. 80.6±18.0; P=.02). Overall, there was no difference in HRQoL outcomes among patients receiving prasugrel vs. clopidogrel. However, the differential effects of the treatments among patients with non-fatal events require further investigation.

Research paper thumbnail of Characteristics of fluorescent pseudomonad isolates towards controlling of tomato wilt caused by Fusarium oxysporum f. sp. lycopersici

Zeitschrift Fur Pflanzenkrankheiten Und Pflanzenschutz, 2003

Out of a screening of 80 fluorescent pseudomonad (fl. Ps.) strains, nine isolates (W21, W34, WB15... more Out of a screening of 80 fluorescent pseudomonad (fl. Ps.) strains, nine isolates (W21, W34, WB15, WB52, G54, G307, G308, G309 and CW2) were capable of reducing the fusarium wilt disease on tomato plants. On King&#39;s B agar medium, isolates W34, WB52, G308 and CW2 effectively inhibited the mycelial growth of Fusarium oxysporum f. sp. lycopersici (Fol) 7 days after incubation, while isolates WB15, W21 and G307 caused slight inhibition of the mycelium growth. Interestingly, the two isolates G54 and G309 did not cause any inhibition to the fungal growth. The biochemical and physiological characteristics of the nine effective isolates of fluorescent pseudomonads exhibited a wide variation in production of several substances considered as biocontrol factors such as: siderophores, cyanide, chitinase, gelatinase, proteinase, arginine dihydrolase, salicylic acid and antimicrobial metabolites. Application of fl. Ps. isolates by dipping tomato roots in the bacterial suspension proved to be superior to soil drenching in controlling tomato wilt disease. Furthermore, reisolation studies revealed that the population densities of G309 on tomato roots was always higher after root dipping than after soil drenching. Compatibility tests in vitro showed that the nine different fluorescent pseudomonad isolates could be combined. Compared to single application of isolates, control of fusarium wilt was more effective when the tomato plants were treated with combinations of G54 and CW2 or G54, WB52 and W34.

Research paper thumbnail of Enhancement of population densities of fluorescent pseudomonads in the rhizosphere of tomato plants by addition of acibenzolar- S -methyl

Canadian Journal of Microbiology, 2002

Fluorescent pseudomonad isolates G309 and CW2, in combination with the resistance inducer acibenz... more Fluorescent pseudomonad isolates G309 and CW2, in combination with the resistance inducer acibenzolar-S-methyl (ASM), improved control of fungal and bacterial diseases on tomato plants. The interactions of the bacteria in the presence of ASM showed that in vitro growth of Pseudomonas fluorescens G309 and Pseudomonas sp. strain CW2 was not affected in King's B broth supplemented with 10 and 20 μM ASM. Also, the bacterial cells were not able to utilize ASM as a nutrient source. In vitro production of the two antimicrobial secondary metabolites phenazine-1-carboxylic acid and 2-OH-phenazine by the isolate CW2 was not affected within 3 days from incubation. In contrary, addition of ASM at a concentration of 20 μM to King's B liquid medium significantly increased production of salicylic acid by isolate G309. When roots of tomato plants were treated with G309 or CW2 cell suspensions containing 20 μM ASM, the number of bacterial cells recovered from the rhizosphere was significantl...

Research paper thumbnail of A Cleft Lip and Palate Gene, Irf6 , is Involved in Osteoblast Differentiation of Craniofacial Bone

Developmental Dynamics

Background: Interferon regulatory factor 6 (IRF6) plays a critical role in embryonic tissue devel... more Background: Interferon regulatory factor 6 (IRF6) plays a critical role in embryonic tissue development, including differentiation of epithelial cells. Besides orofacial clefting due to haploinsufficiency of IRF6, recent human genetic studies indicated that mutations in IRF6 are linked to small mandible and digit abnormalities. The function of IRF6 has been well studied in oral epithelium; however, its role in craniofacial skeletal formation remains unknown. In this study, we investigated the role of Irf6 in craniofacial bone development using comparative analyses between wild-type (WT) and Irf6-null littermate mice. Results: Immunostaining revealed the expression of IRF6 in hypertrophic chondrocytes, osteocytes, and bone matrix of craniofacial tissues. Histological analysis of Irf6-null mice showed a remarkable reduction in the number of lacunae, embedded osteocytes in matrices, and a reduction in mineralization during bone formation. These abnormalities may explain the decreased craniofacial bone density detected by micro-CT, loss of incisors, and mandibular bone abnormality of Irf6-null mice. To validate the autonomous role of IRF6 in bone, extracted primary osteoblasts from calvarial bone of WT and Irf6-null pups showed no effect on osteoblastic viability and proliferation. However, a reduction in mineralization was detected in Irf6-null cells. Conclusions: Altogether, these findings suggest an autonomous role of Irf6 in regulating bone differentiation and mineralization. Developmental

Research paper thumbnail of A Cleft Lip and Palate Gene, Irf6 , is Involved in Osteoblast Differentiation of Craniofacial Bone

Developmental Dynamics

Background: Interferon regulatory factor 6 (IRF6) plays a critical role in embryonic tissue devel... more Background: Interferon regulatory factor 6 (IRF6) plays a critical role in embryonic tissue development, including differentiation of epithelial cells. Besides orofacial clefting due to haploinsufficiency of IRF6, recent human genetic studies indicated that mutations in IRF6 are linked to small mandible and digit abnormalities. The function of IRF6 has been well studied in oral epithelium; however, its role in craniofacial skeletal formation remains unknown. In this study, we investigated the role of Irf6 in craniofacial bone development using comparative analyses between wild-type (WT) and Irf6-null littermate mice. Results: Immunostaining revealed the expression of IRF6 in hypertrophic chondrocytes, osteocytes, and bone matrix of craniofacial tissues. Histological analysis of Irf6-null mice showed a remarkable reduction in the number of lacunae, embedded osteocytes in matrices, and a reduction in mineralization during bone formation. These abnormalities may explain the decreased craniofacial bone density detected by micro-CT, loss of incisors, and mandibular bone abnormality of Irf6-null mice. To validate the autonomous role of IRF6 in bone, extracted primary osteoblasts from calvarial bone of WT and Irf6-null pups showed no effect on osteoblastic viability and proliferation. However, a reduction in mineralization was detected in Irf6-null cells. Conclusions: Altogether, these findings suggest an autonomous role of Irf6 in regulating bone differentiation and mineralization. Developmental