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1.
Cell ; 180(5): 878-894.e19, 2020 03 05.
Article in English | MEDLINE | ID: mdl-32059783

ABSTRACT

Pathogenic autoantibodies arise in many autoimmune diseases, but it is not understood how the cells making them evade immune checkpoints. Here, single-cell multi-omics analysis demonstrates a shared mechanism with lymphoid malignancy in the formation of public rheumatoid factor autoantibodies responsible for mixed cryoglobulinemic vasculitis. By combining single-cell DNA and RNA sequencing with serum antibody peptide sequencing and antibody synthesis, rare circulating B lymphocytes making pathogenic autoantibodies were found to comprise clonal trees accumulating mutations. Lymphoma driver mutations in genes regulating B cell proliferation and V(D)J mutation (CARD11, TNFAIP3, CCND3, ID3, BTG2, and KLHL6) were present in rogue B cells producing the pathogenic autoantibody. Antibody V(D)J mutations conferred pathogenicity by causing the antigen-bound autoantibodies to undergo phase transition to insoluble aggregates at lower temperatures. These results reveal a pre-neoplastic stage in human lymphomagenesis and a cascade of somatic mutations leading to an iconic pathogenic autoantibody.


Subject(s)
Autoantibodies/genetics , Autoimmune Diseases/genetics , B-Lymphocytes/immunology , Lymphoma/genetics , Animals , Autoantibodies/immunology , Autoimmune Diseases/immunology , Autoimmune Diseases/pathology , B-Lymphocytes/pathology , CARD Signaling Adaptor Proteins/genetics , Carrier Proteins/genetics , Clonal Evolution/genetics , Clonal Evolution/immunology , Cyclin D3/genetics , Guanylate Cyclase/genetics , Humans , Immediate-Early Proteins/genetics , Immunoglobulin Variable Region/genetics , Immunoglobulin Variable Region/immunology , Inhibitor of Differentiation Proteins/genetics , Lymphoma/immunology , Lymphoma/pathology , Mice , Mutation/genetics , Mutation/immunology , Neoplasm Proteins/genetics , Sequence Analysis, DNA/methods , Sequence Analysis, RNA/methods , Single-Cell Analysis/methods , Tumor Necrosis Factor alpha-Induced Protein 3/genetics , Tumor Suppressor Proteins/genetics , V(D)J Recombination/genetics
2.
Nature ; 608(7924): 757-765, 2022 08.
Article in English | MEDLINE | ID: mdl-35948641

ABSTRACT

The notion that mobile units of nucleic acid known as transposable elements can operate as genomic controlling elements was put forward over six decades ago1,2. However, it was not until the advancement of genomic sequencing technologies that the abundance and repertoire of transposable elements were revealed, and they are now known to constitute up to two-thirds of mammalian genomes3,4. The presence of DNA regulatory regions including promoters, enhancers and transcription-factor-binding sites within transposable elements5-8 has led to the hypothesis that transposable elements have been co-opted to regulate mammalian gene expression and cell phenotype8-14. Mammalian transposable elements include recent acquisitions and ancient transposable elements that have been maintained in the genome over evolutionary time. The presence of ancient conserved transposable elements correlates positively with the likelihood of a regulatory function, but functional validation remains an essential step to identify transposable element insertions that have a positive effect on fitness. Here we show that CRISPR-Cas9-mediated deletion of a transposable element-namely the LINE-1 retrotransposon Lx9c11-in mice results in an exaggerated and lethal immune response to virus infection. Lx9c11 is critical for the neogenesis of a non-coding RNA (Lx9c11-RegoS) that regulates genes of the Schlafen family, reduces the hyperinflammatory phenotype and rescues lethality in virus-infected Lx9c11-/- mice. These findings provide evidence that a transposable element can control the immune system to favour host survival during virus infection.


Subject(s)
DNA Transposable Elements , Host Microbial Interactions , Immunity , Retroelements , Virus Diseases , Animals , CRISPR-Cas Systems/genetics , DNA Transposable Elements/genetics , DNA Transposable Elements/immunology , Evolution, Molecular , Host Microbial Interactions/genetics , Host Microbial Interactions/immunology , Immunity/genetics , Mice , RNA, Untranslated/genetics , Regulatory Sequences, Nucleic Acid/genetics , Retroelements/genetics , Retroelements/immunology , Virus Diseases/genetics , Virus Diseases/immunology
3.
PLoS Genet ; 17(4): e1009465, 2021 04.
Article in English | MEDLINE | ID: mdl-33857129

ABSTRACT

How temperature determines sex remains unknown. A recent hypothesis proposes that conserved cellular mechanisms (calcium and redox; 'CaRe' status) sense temperature and identify genes and regulatory pathways likely to be involved in driving sexual development. We take advantage of the unique sex determining system of the model organism, Pogona vitticeps, to assess predictions of this hypothesis. P. vitticeps has ZZ male: ZW female sex chromosomes whose influence can be overridden in genetic males by high temperatures, causing male-to-female sex reversal. We compare a developmental transcriptome series of ZWf females and temperature sex reversed ZZf females. We demonstrate that early developmental cascades differ dramatically between genetically driven and thermally driven females, later converging to produce a common outcome (ovaries). We show that genes proposed as regulators of thermosensitive sex determination play a role in temperature sex reversal. Our study greatly advances the search for the mechanisms by which temperature determines sex.


Subject(s)
Lizards/genetics , Sex Chromosomes/genetics , Sex Determination Processes/genetics , Transcriptome/genetics , Animals , Female , Lizards/growth & development , Male , Sex Determination Analysis/methods , Temperature , Transcription, Genetic/genetics
4.
BMC Genomics ; 24(1): 243, 2023 May 05.
Article in English | MEDLINE | ID: mdl-37147622

ABSTRACT

BACKGROUND: Sex determination is the process whereby the bipotential embryonic gonads become committed to differentiate into testes or ovaries. In genetic sex determination (GSD), the sex determining trigger is encoded by a gene on the sex chromosomes, which activates a network of downstream genes; in mammals these include SOX9, AMH and DMRT1 in the male pathway, and FOXL2 in the female pathway. Although mammalian and avian GSD systems have been well studied, few data are available for reptilian GSD systems. RESULTS: We conducted an unbiased transcriptome-wide analysis of gonad development throughout differentiation in central bearded dragon (Pogona vitticeps) embryos with GSD. We found that sex differentiation of transcriptomic profiles occurs at a very early stage, before the gonad consolidates as a body distinct from the gonad-kidney complex. The male pathway genes dmrt1 and amh and the female pathway gene foxl2 play a key role in early sex differentiation in P. vitticeps, but the central player of the mammalian male trajectory, sox9, is not differentially expressed in P. vitticeps at the bipotential stage. The most striking difference from GSD systems of other amniotes is the high expression of the male pathway genes amh and sox9 in female gonads during development. We propose that a default male trajectory progresses if not repressed by a W-linked dominant gene that tips the balance of gene expression towards the female trajectory. Further, weighted gene expression correlation network analysis revealed novel candidates for male and female sex differentiation. CONCLUSION: Our data reveal that interpretation of putative mechanisms of GSD in reptiles cannot solely depend on lessons drawn from mammals.


Subject(s)
Reptiles , Sex Determination Processes , Sex Differentiation , Animals , Female , Male , Gene Expression , Gene Expression Regulation, Developmental , Gonads/metabolism , Reptiles/genetics , Sex Determination Processes/genetics , Sex Differentiation/genetics , SOX9 Transcription Factor/genetics
5.
Clin Endocrinol (Oxf) ; 96(3): 288-301, 2022 03.
Article in English | MEDLINE | ID: mdl-34750858

ABSTRACT

Obesity is becoming increasingly prevalent in paediatric populations worldwide. In addition to increasing prevalence, the severity of obesity is also continuing to rise. Taken together, these findings demonstrate a worrying trend and highlight one of the most significant challenges to public health. Childhood obesity affects multiple organs in the body and is associated with both significant morbidity and ultimately premature mortality. The prevalence of complications associated with obesity, including dyslipidaemia, hypertension, fatty liver disease and psychosocial complications are becoming increasingly prevalent within the paediatric populations. Treatment guidelines currently focus on intervention with lifestyle and behavioural modifications, with pharmacotherapy and surgery reserved for patients who are refractory to such treatment. Research into adult obesity has established pharmacological novel therapies, which have been approved and established in clinical practice; however, the research and implementation of such therapies in paediatric populations have been lagging behind. Despite the relative lack of widespread research in comparison to the adult population, newer therapies are being trialled, which should allow a greater availability of treatment options for childhood obesity in the future. This review summarizes the current evidence for the management of obesity in terms of medical and surgical options. Both future therapeutic agents and those which cause weight loss but have an alternative indication are also included and discussed as part of the review. The review summarizes the most recent research for each intervention and demonstrates the potential efficacy and limitations of each treatment option.


Subject(s)
Pediatric Obesity , Adult , Child , Humans , Life Style , Medical History Taking , Pediatric Obesity/therapy , Weight Loss
6.
Bioessays ; 42(7): e2000016, 2020 07.
Article in English | MEDLINE | ID: mdl-32307742

ABSTRACT

Fusion genes formed by chromosomal rearrangements are common drivers of cancer. Recent innovations in the field of next-generation sequencing (NGS) have seen a dynamic shift from traditional fusion detection approaches, such as visual characterization by fluorescence, to more precise multiplexed methods. There are many different NGS-based approaches to fusion gene detection and deciding on the most appropriate method can be difficult. Beyond the experimental approach, consideration needs to be given to factors such as the ease of implementation, processing time, associated costs, and the level of expertise required for data analysis. Here, the different NGS-based methods for fusion gene detection, the basic principles underlying the techniques, and the benefits and limitations of each approach are reviewed. This article concludes with a discussion of how NGS will impact fusion gene detection in a clinical context and from where the next innovations are evolving.


Subject(s)
High-Throughput Nucleotide Sequencing , Neoplasms , Humans , Neoplasms/genetics
7.
Mod Pathol ; 33(10): 1896-1909, 2020 10.
Article in English | MEDLINE | ID: mdl-32457410

ABSTRACT

Salivary duct carcinoma (SDCa) is a rare cancer with high rate of metastases and poor survival despite aggressive multimodality treatment. This study analyzes the genetic changes in SDCa, their impact on cancer pathways, and evaluates whether molecular patterns can identify subgroups with distinct clinical characteristics and outcome. Clinicopathologic details and tissue samples from 66 patients (48 males, 18 females) treated between 1995 and 2018 were obtained from multiple institutions. Androgen receptor (AR) was assessed by immunohistochemistry, and the Illumina TruSight 170 gene panel was used for DNA sequencing. Male gender, lympho-vascular invasion, lymph node metastasis, and smoking were significant predictors of disease-free survival. AR was present in 79%. Frequently encountered alterations were mutations in TP53 (51%), PIK3CA (32%) and HRAS (22%), as well as amplifications of CDK4/6 (22%), ERBB2 (21%), MYC (16%), and deletions of CDKN2A (13%). TP53 mutation and MYC amplifications were associated with decreased disease-free survival. Analysis of cancer pathways revealed that the PI3K pathway was most commonly affected. Alterations in the cell cycle pathway were associated with impaired disease-free survival (HR 2.6, P = 0.038). Three subgroups based on AR and ERBB2 status were identified, which featured distinct molecular patterns and outcome. Among AR positive SDCa, HRAS mutations were restricted to AR positive tumors without ERBB2 amplification and HRAS mutations featured high co-occurrence with PIK3CA alterations, which seems specific to SDCa. AR negative SDCa were associated with poor disease-free survival in multivariate analysis (HR 4.5, P = 0.010) and none of these tumors exhibited ERBB2 amplification or HRAS mutations. AR and ERBB2 status in SDCa thus classifies tumors with distinct molecular profiles relevant to future targeted therapy. Furthermore, clinical factors such as smoking and molecular features such as MYC amplification may serve as markers of poor prognosis of SDCa.


Subject(s)
Biomarkers, Tumor/genetics , Carcinoma, Ductal/genetics , Salivary Gland Neoplasms/genetics , Adult , Aged , Aged, 80 and over , Female , Humans , Male , Middle Aged , Prognosis
8.
Oral Dis ; 26(7): 1513-1522, 2020 Oct.
Article in English | MEDLINE | ID: mdl-32369672

ABSTRACT

OBJECTIVE: Hypohidrotic ectodermal dysplasia (HED) is a hereditary disorder characterized by abnormal structures and functions of the ectoderm-derived organs, including teeth. HED patients exhibit a variety of dental symptoms, such as hypodontia. Although disruption of the EDA/EDAR/EDARADD/NF-κB pathway is known to be responsible for HED, it remains unclear whether this pathway is involved in the process of enamel formation. EXPERIMENTAL SUBJECTS AND METHODS: To address this question, we examined the mice overexpressing Ikkß (an essential component required for the activation of NF-κB pathway) under the keratin 5 promoter (K5-Ikkß). RESULTS: Upregulation of the NF-κB pathway was confirmed in the ameloblasts of K5-Ikkß mice. Premature abrasion was observed in the molars of K5-Ikkß mice, which was accompanied by less mineralized enamel. However, no significant changes were observed in the enamel thickness and the pattern of enamel rods in K5-Ikkß mice. Klk4 expression was significantly upregulated in the ameloblasts of K5-Ikkß mice at the maturation stage, and the expression of its substrate, amelogenin, was remarkably reduced. This suggests that abnormal enamel observed in K5-Ikkß mice was likely due to the compromised degradation of enamel protein at the maturation stage. CONCLUSION: Therefore, we could conclude that the overactivation of the NF-κB pathway impairs the process of amelogenesis.


Subject(s)
Ameloblasts , NF-kappa B , Amelogenesis/genetics , Animals , Dental Enamel , Humans , Mice , Molar
9.
Dev Dyn ; 248(3): 201-210, 2019 03.
Article in English | MEDLINE | ID: mdl-30653268

ABSTRACT

BACKGROUND: The timing, location, and level of gene expression are crucial for normal organ development, because morphogenesis requires strict genetic control. MicroRNAs (miRNAs) are noncoding small single-stranded RNAs that play a critical role in regulating gene expression level. Although miRNAs are known to be involved in many biological events, the role of miRNAs in organogenesis is not fully understood. Mammalian eyelids fuse and separate during development and growth. In mice, failure of this process results in the eye-open at birth (EOB) phenotype. RESULTS: It has been shown that conditional deletion of mesenchymal Dicer (an essential protein for miRNA processing; Dicer fl/fl ;Wnt1Cre) leads to the EOB phenotype with full penetrance. Here, we identified that the up-regulation of Wnt signaling resulted in the EOB phenotype in Dicer mutants. Down-regulation of Fgf signaling observed in Dicer mutants was caused by an inverse relationship between Fgf and Wnt signaling. Shh and Bmp signaling were down-regulated as the secondary effects in Dicer fl/fl ;Wnt1Cre mice. Wnt, Shh, and Fgf signaling were also found to mediate the epithelial-mesenchymal interactions in eyelid development. CONCLUSIONS: miRNAs control eyelid development through Wnt. Developmental Dynamics 248:201-210, 2019. © 2019 Wiley Periodicals, Inc.


Subject(s)
Eyelids/growth & development , MicroRNAs/physiology , Wnt Signaling Pathway , Animals , DEAD-box RNA Helicases/deficiency , Gene Expression Regulation, Developmental , Mice , Organogenesis , Phenotype , Ribonuclease III/deficiency
10.
Prostate ; 79(10): 1191-1196, 2019 07.
Article in English | MEDLINE | ID: mdl-31090091

ABSTRACT

BACKGROUND: The androgen-regulated gene TMPRSS2 to the ETS transcription factor gene ERG fusion is the most common genomic alteration acquired during prostate tumorigenesis and biased toward men of European ancestry. In contrast, African American men present with more advanced disease, yet their tumors are less likely to acquire TMPRSS2-ERG. Data for Africa is scarce. METHODS: RNA was made available for genomic analyses from 181 prostate tissue biopsy cores from Black South African men, 94 with and 87 without pathological evidence for prostate cancer. Reverse transcription polymerase chain reaction was used to screen for the TMPRSS2-ERG fusion, while transcript junction coordinates and isoform frequencies, including novel gene fusions, were determined using targeted RNA sequencing. RESULTS: Here we report a frequency of 13% for TMPRSS2-ERG in tumors from Black South Africans. Present in 12/94 positive versus 1/87 cancer negative prostate tissue cores, this suggests a 92.62% predictivity for a positive cancer diagnosis (P = 0.0031). At a frequency of almost half that reported for African Americans and roughly a quarter of that reported for men of European ancestry, acquisition of TMPRSS2-ERG appears to be inversely associated with aggressive prostate cancer. Further support was provided by linking the presence of TMPRSS2-ERG to low-grade disease in younger patients (P = 0.0466), with higher expressing distal ERG fusion junction coordinates. CONCLUSIONS: Only the second study of its kind for the African continent, we support a link between TMPRSS2-ERG status and prostate cancer racial health disparity beyond the borders of the United States. We call for urgent evaluation of androgen deprivation therapy within Africa.


Subject(s)
Oncogene Fusion/genetics , Prostatic Neoplasms/genetics , Serine Endopeptidases/genetics , Adult , Aged , Aged, 80 and over , Black People , Genomic Instability , Health Status Disparities , Humans , Male , Middle Aged , Prostate/pathology , Prostatic Neoplasms/pathology , South Africa , Transcriptional Regulator ERG/genetics , White People
11.
Nat Methods ; 13(9): 792-8, 2016 09.
Article in English | MEDLINE | ID: mdl-27502218

ABSTRACT

RNA sequencing (RNA-seq) can be used to assemble spliced isoforms, quantify expressed genes and provide a global profile of the transcriptome. However, the size and diversity of the transcriptome, the wide dynamic range in gene expression and inherent technical biases confound RNA-seq analysis. We have developed a set of spike-in RNA standards, termed 'sequins' (sequencing spike-ins), that represent full-length spliced mRNA isoforms. Sequins have an entirely artificial sequence with no homology to natural reference genomes, but they align to gene loci encoded on an artificial in silico chromosome. The combination of multiple sequins across a range of concentrations emulates alternative splicing and differential gene expression, and it provides scaling factors for normalization between samples. We demonstrate the use of sequins in RNA-seq experiments to measure sample-specific biases and determine the limits of reliable transcript assembly and quantification in accompanying human RNA samples. In addition, we have designed a complementary set of sequins that represent fusion genes arising from rearrangements of the in silico chromosome to aid in cancer diagnosis. RNA sequins provide a qualitative and quantitative reference with which to navigate the complexity of the human transcriptome.


Subject(s)
Gene Expression Profiling/standards , Genes, Synthetic , RNA Splicing , RNA, Messenger/genetics , Sequence Analysis, RNA/standards , Chromosomes, Artificial , Humans , Quality Control , RNA Splicing/genetics , RNA, Messenger/chemical synthesis , RNA, Messenger/chemistry , Reference Standards , Sequence Analysis, RNA/methods
12.
Dev Dyn ; 245(9): 937-46, 2016 09.
Article in English | MEDLINE | ID: mdl-27302476

ABSTRACT

BACKGROUND: Non-gustatory filiform papillae play critical roles in helping to grip food, drawing food to the esophagus, cleaning the mouth, and spreading saliva. The molecular mechanisms of filiform tongue papillae development however are not fully understood. RESULTS: We found Ikkα and Irf6 expression in developing tongue epithelium, and describe here specific tongue abnormalities in mice with mutation of these genes, indicating a role for Ikkα and Irf6 in filiform papillae development. Ikkα and Irf6 mutant tongues showed ectopic vertical epithelium at the midline, while lateral sides of mutant tongues adhered to the oral mucosa. Both the ectopic median vertical epithelium and adhered epithelium exhibited the presence of filiform tongue papillae, whereas epithelium between the median vertical epithelium and adhered tongue showed a loss of filiform tongue papillae. Timing of filiform papillae development was found to be slightly different between the midline and lateral regions of the wild-type tongue. CONCLUSIONS: Filiform papillae thus develop through distinct molecular mechanisms between the regions of tongue dorsum in the medio-lateral axis, with some filiform papillae developing under the control of Ikkα and Irf6. Developmental Dynamics 245:937-946, 2016. © 2016 Wiley Periodicals, Inc.


Subject(s)
Epithelium/metabolism , I-kappa B Kinase/metabolism , Interferon Regulatory Factors/metabolism , Tongue/embryology , Tongue/metabolism , Animals , Epithelium/embryology , Epithelium/ultrastructure , I-kappa B Kinase/genetics , Immunohistochemistry , In Situ Hybridization , Interferon Regulatory Factors/genetics , Mice , Mice, Transgenic , Microscopy, Electron, Scanning , Tongue/ultrastructure
13.
Mol Carcinog ; 55(12): 1940-1951, 2016 12.
Article in English | MEDLINE | ID: mdl-26676339

ABSTRACT

Wild-type TP53 exons 5-8 contain CpG dinucleotides that are prone to methylation-dependent mutation during carcinogenesis, but the regulatory effects of methylation affecting these CpG sites are unclear. To clarify this, we first assessed site-specific TP53 CpG methylation in normal and transformed cells. Both DNA damage and cell ageing were associated with site-specific CpG demethylation in exon 5 accompanied by induction of a truncated TP53 isoform regulated by an adjacent intronic promoter (P2). We then synthesized novel synonymous TP53 alleles with divergent CpG content but stable encodement of the wild-type polypeptide. Expression of CpG-enriched TP53 constructs selectively reduced production of the full-length transcript (P1), consistent with a causal relationship between intragenic demethylation and transcription. 450K methylation comparison of normal (TP53-wildtype) and cancerous (TP53-mutant) human cells and tissues revealed focal cancer-associated declines in CpG methylation near the P1 transcription start site, accompanied by rises near the alternate exon 5 start site. These data confirm that site-specific changes of intragenic TP53 CpG methylation are extrinsically inducible, and suggest that human cancer progression is mediated in part by dysregulation of damage-inducible intragenic CpG demethylation that alters TP53 P1/P2 isoform expression. © 2015 The Authors. Molecular Carcinogenesis Published by Wiley Periodicals, Inc.


Subject(s)
CpG Islands , DNA Damage , DNA Methylation , Genes, p53 , Neoplasms/genetics , Tumor Suppressor Protein p53/genetics , Animals , Base Sequence , Caco-2 Cells , Cell Line , Cell Line, Tumor , Exons , Gene Expression Regulation, Neoplastic , Humans , Introns , Mice , Promoter Regions, Genetic , Transcriptional Activation
14.
Dev Biol ; 365(1): 61-70, 2012 May 01.
Article in English | MEDLINE | ID: mdl-22366192

ABSTRACT

Thickening and the subsequent invagination of the epithelium are an important initial step in ectodermal organ development. Ikkα has been shown to play a critical role in controlling epithelial growth, since Ikkα mutant mice show protrusions (evaginations) of incisor tooth, whisker and hair follicle epithelium rather than invagination. We show here that mutation of the Interferon regulatory factor (Irf) family, Irf6 also results in evagination of incisor epithelium. In common with Ikkα mutants, Irf6 mutant evagination occurs in a NF-κB-independent manner and shows the same molecular changes as those in Ikkα mutants. Irf6 thus also plays a critical role in regulating epithelial invagination. In addition, we also found that canonical Wnt signaling is upregulated in evaginated incisor epithelium of both Ikkα and Irf6 mutant embryos.


Subject(s)
Epithelium/embryology , Interferon Regulatory Factors/genetics , Tooth/embryology , Animals , Epithelium/physiology , Gene Expression Regulation, Developmental , I-kappa B Kinase/genetics , Mice , Mutation , Organogenesis , Signal Transduction , Tooth/cytology , Tooth/physiology
15.
Proc Natl Acad Sci U S A ; 107(1): 92-7, 2010 Jan 05.
Article in English | MEDLINE | ID: mdl-20018657

ABSTRACT

Changes in tooth shape have played a major role in vertebrate evolution with modification of dentition allowing an organism to adapt to new feeding strategies. The current view is that molar teeth evolved from simple conical teeth, similar to canines, by progressive addition of extra "cones" to form progressively complex multicuspid crowns. Mammalian incisors, however, are neither conical nor multicuspid, and their evolution is unclear. We show that hypomorphic mutation of a cell surface receptor, Lrp4, which modulates multiple signaling pathways, produces incisors with grooved enamel surfaces that exhibit the same molecular characteristics as the tips of molar cusps. Mice with a null mutation of Lrp4 develop extra cusps on molars and have incisors that exhibit clear molar-like cusp and root morphologies. Molecular analysis identifies misregulation of Shh and Bmp signaling in the mutant incisors and suggests an uncoupling of the processes of tooth shape determination and morphogenesis. Incisors thus possess a developmentally suppressed, cuspid crown-like morphogenesis program similar to that in molars that is revealed by loss of Lrp4 activity. Several mammalian species naturally possess multicuspid incisors, suggesting that mammals have the capacity to form multicuspid teeth regardless of location in the oral jaw. Localized loss of enamel may thus have been an intermediary step in the evolution of cusps, both of which use Lrp4-mediated signaling.


Subject(s)
Biological Evolution , Incisor , Morphogenesis/physiology , Odontogenesis/physiology , Ameloblasts/physiology , Animals , Bone Morphogenetic Proteins/genetics , Bone Morphogenetic Proteins/metabolism , Cell Differentiation , Dental Enamel/ultrastructure , Dentin/ultrastructure , Fishes/anatomy & histology , Hedgehog Proteins/genetics , Hedgehog Proteins/metabolism , Incisor/anatomy & histology , Incisor/physiology , LDL-Receptor Related Proteins , Mice , Mice, Knockout , Rabbits , Rats , Receptors, LDL/genetics , Receptors, LDL/metabolism , Signal Transduction/physiology , Tooth Abnormalities/genetics , Tooth Abnormalities/metabolism
16.
J Calif Dent Assoc ; 41(11): 813-7, 2013 Nov.
Article in English | MEDLINE | ID: mdl-24341132

ABSTRACT

A possible avenue to improve the clinical success of bone graft procedures in cleft lip and palate cases is to predetermine the bone donor site and the volume of graft material required for the recipient site. This study utilized cone beam computed tomography to generate three-dimensional reconstructions and volumetrically assess unilateral cleft lip and palate defects. Access to this information can assist in determining an optimal donor site for secondary alveolar bone grafting.


Subject(s)
Alveolar Bone Grafting , Cleft Palate/diagnostic imaging , Cone-Beam Computed Tomography , Adolescent , Child , Cleft Lip/pathology , Cleft Lip/surgery , Cleft Palate/surgery , Cohort Studies , Female , Humans , Imaging, Three-Dimensional/methods , Male , Palatal Expansion Technique , Surgery, Computer-Assisted
17.
PLoS One ; 18(4): e0284327, 2023.
Article in English | MEDLINE | ID: mdl-37053216

ABSTRACT

Intragenic CpG dinucleotides are tightly conserved in evolution yet are also vulnerable to methylation-dependent mutation, raising the question as to why these functionally critical sites have not been deselected by more stable coding sequences. We previously showed in cell lines that altered exonic CpG methylation can modify promoter start sites, and hence protein isoform expression, for the human TP53 tumor suppressor gene. Here we extend this work to the in vivo setting by testing whether synonymous germline modifications of exonic CpG sites affect murine development, fertility, longevity, or cancer incidence. We substituted the DNA-binding exons 5-8 of Trp53, the mouse ortholog of human TP53, with variant-CpG (either CpG-depleted or -enriched) sequences predicted to encode the normal p53 amino acid sequence; a control construct was also created in which all non-CpG sites were synonymously substituted. Homozygous Trp53-null mice were the only genotype to develop tumors. Mice with variant-CpG Trp53 sequences remained tumor-free, but were uniquely prone to dental anomalies causing jaw malocclusion (p < .0001). Since the latter phenotype also characterises murine Rett syndrome due to dysfunction of the trans-repressive MeCP2 methyl-CpG-binding protein, we hypothesise that CpG sites may exert non-coding phenotypic effects via pre-translational cis-interactions of 5-methylcytosine with methyl-binding proteins which regulate mRNA transcript initiation, expression or splicing, although direct effects on mRNA structure or translation are also possible.


Subject(s)
Genes, p53 , Neoplasms , Mice , Humans , Animals , Mutation , Neoplasms/genetics , Methyl-CpG-Binding Protein 2/genetics , RNA, Messenger , CpG Islands , DNA Methylation
18.
Pathology ; 55(4): 478-485, 2023 Jun.
Article in English | MEDLINE | ID: mdl-36906400

ABSTRACT

Our aim was to utilise a 241-gene RNA hybridisation capture sequencing (CaptureSeq) gene panel to identify unexpected fusions in undifferentiated, unclassified or partly classified sarcomas of young individuals (<40 years). The purpose was to determine the utility and yield of a large, targeted fusion panel as a tool for classifying tumours that do not fit typical diagnostic entities at the time of the original diagnosis. RNA hybridisation capture sequencing was performed on 21 archival resection specimens. Successful sequencing was obtained in 12 of 21 samples (57%), two of which (16.6%) harboured translocations. A novel NEAT1::GLI1 fusion, not previously reported in the literature, presented in a young patient with a tumour in the retroperitoneum, which displayed low grade epithelioid cells. The second case, a localised lung metastasis in a young male, demonstrated a EWSR1::NFATC2 translocation. No targeted fusions were identified in the remaining 83.4% (n=10) of cases. Forty-three per cent of the samples failed sequencing as a result of RNA degradation. RNA-based sequencing is an important tool, which helps to redefine the classification of unclassified or partly classified sarcomas of young adults by identifying pathogenic gene fusions in up to 16.6% of the cases. Unfortunately, 43% of the samples underwent significant RNA degradation, falling below the sequencing threshold. As CaptureSeq is not yet available in routine pathology practice, increasing awareness of the yield, failure rate and possible aetiological factors for RNA degradation is fundamental to maximise laboratory procedures to improve RNA integrity, allowing the potential identification of significant gene alterations in solid tumours.


Subject(s)
Sarcoma , Soft Tissue Neoplasms , Young Adult , Humans , Male , Sarcoma/diagnosis , Sarcoma/genetics , Sarcoma/pathology , Gene Fusion , Transcription Factors/genetics , Soft Tissue Neoplasms/diagnosis , Soft Tissue Neoplasms/genetics , Soft Tissue Neoplasms/pathology , Gene Rearrangement , Oncogene Proteins, Fusion/genetics
19.
JMIR Aging ; 6: e47691, 2023 Sep 19.
Article in English | MEDLINE | ID: mdl-37725423

ABSTRACT

BACKGROUND: Homebound older adults are a high-risk group for depression. However, many of them face barriers to accessing evidence-supported mental health treatments. Digital mental health interventions can potentially improve treatment access, but few web-based interventions are explicitly tailored for depression in older adults. OBJECTIVE: This paper describes the development process of Empower@Home, a web-delivered intervention for depression in homebound older adults that is based on cognitive behavioral therapy, and reports on the outcomes of usability studies. METHODS: Empower@Home was developed in collaboration with community agencies, stakeholders, and older adults, guided by user-centered design principles. User needs were assessed through secondary data analysis, demographic and health profiles from administrative data, and interviews and surveys of community partners. A comparative usability evaluation was conducted with 10 older adults to assess the usability of Empower@Home compared to 2 similar programs. Field testing was conducted with 4 end users to detect additional usability issues. RESULTS: Feedback and recommendations from community partners heavily influenced the content and design of Empower@Home. The intervention consists of 9 sessions, including psychoeducation and an introduction to cognitive behavioral therapy skills and tools through short video clips, in-session exercises, an animated storyline, and weekly out-of-session home practice. A printed workbook accompanies the web-based lessons. In comparative usability testing (N=10), Empower@Home received a System Usability Scale score of 78 (SD 7.4), which was significantly higher than the 2 comparator programs (t9=3.28; P=.005 and t9=2.78; P=.011). Most participants, 80% (n=8), preferred Empower@Home over the comparators. In the longitudinal field test (n=4), all participants reported liking the program procedures and feeling confident in performing program-related tasks. The single-subject line graph showed an overall downward trend in their depression scores over time, offering an encouraging indication of the intervention's potential effects. CONCLUSIONS: Collaboration with community stakeholders and careful consideration of potential implementation issues during the design process can result in more usable, engaging, and effective digital mental health interventions.

20.
J Pediatr Endocrinol Metab ; 35(12): 1547-1551, 2022 Dec 16.
Article in English | MEDLINE | ID: mdl-36177768

ABSTRACT

OBJECTIVES: Primary hyperparathyroidism (PHPT), whilst common in elderly populations, is rare in adolescents. Hereditary cases make up less than 10% of patients with PH. We report two patients with CDC73 mutation presenting in early adolescence. CASE PRESENTATION: Case 1: A 14-year-old patient was referred from an adolescent mental health unit with hypercalcaemia. Imaging revealed a parathyroid adenoma. Genetic testing of the patient showed a heterozygous deletion of CDC73. Case 2: A 10-year-old patient was admitted to the general paediatric ward with symptoms suggestive of hypercalcaemia. The patient was known to carry an autosomal dominant mutation of CDC73. Imaging of the parathyroid gland showed bilateral adenoma. CONCLUSIONS: We present two patients with CDC73 defects, who both presented with symptoms of hypercalcaemia. The cases highlight the difference in paediatric populations with PHPT who are often symptomatic at the time of diagnosis when compared to adult patients.


Subject(s)
Hypercalcemia , Hyperparathyroidism , Parathyroid Neoplasms , Adolescent , Adult , Aged , Child , Humans , Hypercalcemia/genetics , Hyperparathyroidism/complications , Hyperparathyroidism/genetics , Mutation , Parathyroid Neoplasms/genetics , Tumor Suppressor Proteins/genetics
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