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1.
Cell ; 178(6): 1421-1436.e24, 2019 09 05.
Article in English | MEDLINE | ID: mdl-31491386

ABSTRACT

The developmental disorder Floating-Harbor syndrome (FHS) is caused by heterozygous truncating mutations in SRCAP, a gene encoding a chromatin remodeler mediating incorporation of histone variant H2A.Z. Here, we demonstrate that FHS-associated mutations result in loss of SRCAP nuclear localization, alter neural crest gene programs in human in vitro models and Xenopus embryos, and cause craniofacial defects. These defects are mediated by one of two H2A.Z subtypes, H2A.Z.2, whose knockdown mimics and whose overexpression rescues the FHS phenotype. Selective rescue by H2A.Z.2 is conferred by one of the three amino acid differences between the H2A.Z subtypes, S38/T38. We further show that H2A.Z.1 and H2A.Z.2 genomic occupancy patterns are qualitatively similar, but quantitatively distinct, and H2A.Z.2 incorporation at AT-rich enhancers and expression of their associated genes are both sensitized to SRCAP truncations. Altogether, our results illuminate the mechanism underlying a human syndrome and uncover selective functions of H2A.Z subtypes during development.


Subject(s)
Abnormalities, Multiple/genetics , Chromatin Assembly and Disassembly , Chromatin/metabolism , Craniofacial Abnormalities/genetics , Growth Disorders/genetics , Heart Septal Defects, Ventricular/genetics , Histones/genetics , Adenosine Triphosphatases/genetics , Amino Acid Substitution , Animals , Embryonic Stem Cells , HEK293 Cells , Humans , Mutation , Xenopus laevis
2.
Cell ; 167(5): 1170-1187, 2016 11 17.
Article in English | MEDLINE | ID: mdl-27863239

ABSTRACT

A class of cis-regulatory elements, called enhancers, play a central role in orchestrating spatiotemporally precise gene-expression programs during development. Consequently, divergence in enhancer sequence and activity is thought to be an important mediator of inter- and intra-species phenotypic variation. Here, we give an overview of emerging principles of enhancer function, current models of enhancer architecture, genomic substrates from which enhancers emerge during evolution, and the influence of three-dimensional genome organization on long-range gene regulation. We discuss intricate relationships between distinct elements within complex regulatory landscapes and consider their potential impact on specificity and robustness of transcriptional regulation.


Subject(s)
Enhancer Elements, Genetic , Evolution, Molecular , Genome-Wide Association Study , Transcription, Genetic , Blood/metabolism , Blood Cells/metabolism , Epigenomics , Hematopoiesis , Humans , Quantitative Trait Loci
3.
Mol Cell ; 83(9): 1446-1461.e6, 2023 05 04.
Article in English | MEDLINE | ID: mdl-36996812

ABSTRACT

Enhancer clusters overlapping disease-associated mutations in Pierre Robin sequence (PRS) patients regulate SOX9 expression at genomic distances over 1.25 Mb. We applied optical reconstruction of chromatin architecture (ORCA) imaging to trace 3D locus topology during PRS-enhancer activation. We observed pronounced changes in locus topology between cell types. Subsequent analysis of single-chromatin fiber traces revealed that these ensemble-average differences arise through changes in the frequency of commonly sampled topologies. We further identified two CTCF-bound elements, internal to the SOX9 topologically associating domain, which promote stripe formation, are positioned near the domain's 3D geometric center, and bridge enhancer-promoter contacts in a series of chromatin loops. Ablation of these elements results in diminished SOX9 expression and altered domain-wide contacts. Polymer models with uniform loading across the domain and frequent cohesin collisions recapitulate this multi-loop, centrally clustered geometry. Together, we provide mechanistic insights into architectural stripe formation and gene regulation over ultra-long genomic ranges.


Subject(s)
Chromatin , Regulatory Sequences, Nucleic Acid , Humans , Chromatin/genetics , Promoter Regions, Genetic , Gene Expression Regulation , Genome , Cell Cycle Proteins/metabolism , Enhancer Elements, Genetic , CCCTC-Binding Factor/genetics , CCCTC-Binding Factor/metabolism
4.
Cell ; 157(6): 1445-1459, 2014 Jun 05.
Article in English | MEDLINE | ID: mdl-24856970

ABSTRACT

Chromatin modifying activities inherent to polycomb repressive complexes PRC1 and PRC2 play an essential role in gene regulation, cellular differentiation, and development. However, the mechanisms by which these complexes recognize their target sites and function together to form repressive chromatin domains remain poorly understood. Recruitment of PRC1 to target sites has been proposed to occur through a hierarchical process, dependent on prior nucleation of PRC2 and placement of H3K27me3. Here, using a de novo targeting assay in mouse embryonic stem cells we unexpectedly discover that PRC1-dependent H2AK119ub1 leads to recruitment of PRC2 and H3K27me3 to effectively initiate a polycomb domain. This activity is restricted to variant PRC1 complexes, and genetic ablation experiments reveal that targeting of the variant PCGF1/PRC1 complex by KDM2B to CpG islands is required for normal polycomb domain formation and mouse development. These observations provide a surprising PRC1-dependent logic for PRC2 occupancy at target sites in vivo.


Subject(s)
Embryonic Stem Cells/metabolism , F-Box Proteins/metabolism , Histones/metabolism , Jumonji Domain-Containing Histone Demethylases/metabolism , Polycomb Repressive Complex 1/metabolism , Polycomb Repressive Complex 2/metabolism , Animals , Bone Development , CpG Islands , F-Box Proteins/chemistry , F-Box Proteins/genetics , Genes, Lethal , Genome-Wide Association Study , Jumonji Domain-Containing Histone Demethylases/chemistry , Jumonji Domain-Containing Histone Demethylases/genetics , Mice , Protein Structure, Tertiary
5.
Psychooncology ; 33(4): e6334, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38549216

ABSTRACT

OBJECTIVE: (i) To systematically identify constructs and outcome measures used to assess the emotional and mood impact of false positive breast screening test results; (ii) to appraise the reporting clarity and rationale for selecting constructs and outcome measures. METHODS: Databases (MEDLINE, CINAHL, PsycINFO) were systematically searched from 1970. Studies using standardised and non-standardised outcome measures to evaluate the emotion or mood impact of false positive breast screening test results were eligible. A 15-item coding scheme was devised to appraise articles on clarity and rationale for selected constructs and measures. RESULTS: Forty-seven articles were identified. The most investigated constructs were general anxiety and depression and disease-specific anxiety and worry. Twenty-two standardised general outcome questionnaire measures and three standardised disease-specific outcome questionnaire measures were identified. Twenty articles used non-standardised scales/items. Reporting of constructs and outcome measures was generally clear, but rationales for their selection were lacking. Anxiety was typically justified, but justification for depression was almost always absent. Practical and psychometric justification for selecting outcome measures was lacking, and theoretical rationale was absent. CONCLUSIONS: Heterogeneity in constructs and measures, coupled with unclear rationale for these, impedes a thorough understanding of why there are emotional effects of false positive screening test results. This may explain the repeated practice of investigating less relevant outcomes such as depression. There is need to develop a consensual conceptual model of and standardised approach to measuring emotional impact from cancer screening test results, to address heterogeneity and other known issues of interpreting an inconsistent evidence base.


Subject(s)
Anxiety , Emotions , Humans , Anxiety/diagnosis , Affect , Anxiety Disorders , Surveys and Questionnaires
6.
Health Expect ; 27(2): e14023, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38509776

ABSTRACT

BACKGROUND: Understanding healthcare professionals' (HCPs) experiences of caring for women with false-positive screening test results in the National Health Service Breast Screening Programme (NHSBSP) is important for reducing the impact of such results. METHODS: Interviews were undertaken with 12 HCPs from a single NHSBSP unit, including advanced radiographer practitioners, breast radiographers, breast radiologists, clinical nurse specialists (CNSs), and a radiology healthcare assistant. Data were analysed thematically using Template Analysis. RESULTS: Two themes were produced: (1) Gauging and navigating women's anxiety during screening assessment was an inevitable and necessary task for all participants. CNSs were perceived as particularly adept at this, while breast radiographers reported a lack of adequate formal training. (2) Controlling the delivery of information to women (including amount, type and timing of information). HCPs reported various communication strategies to facilitate women's information processing and retention during a distressing time. CONCLUSIONS: Women's anxiety could be reduced through dedicated CNS support, but this should not replace support from other HCPs. Breast radiographers may benefit from more training to emotionally support recalled women. While HCPs emphasised taking a patient-centred communication approach, the use of other strategies (e.g., standardised scripts) and the constraints of the 'one-stop shop' model pose challenges to such an approach. PATIENT AND PUBLIC CONTRIBUTION: During the study design, two Patient and Public Involvement members (women with false-positive-breast screening test results) were consulted to gain an understanding of patient perspectives and experiences of being recalled specifically in the NHSBSP. Their feedback informed the formulations of the research aim, objectives and the direction of the interview guide.


Subject(s)
Breast Neoplasms , State Medicine , Female , Humans , Mammography/psychology , Health Personnel , Allied Health Personnel , Delivery of Health Care , Breast Neoplasms/diagnosis , Qualitative Research
7.
Development ; 147(18)2020 09 21.
Article in English | MEDLINE | ID: mdl-32958507

ABSTRACT

The FaceBase Consortium was established by the National Institute of Dental and Craniofacial Research in 2009 as a 'big data' resource for the craniofacial research community. Over the past decade, researchers have deposited hundreds of annotated and curated datasets on both normal and disordered craniofacial development in FaceBase, all freely available to the research community on the FaceBase Hub website. The Hub has developed numerous visualization and analysis tools designed to promote integration of multidisciplinary data while remaining dedicated to the FAIR principles of data management (findability, accessibility, interoperability and reusability) and providing a faceted search infrastructure for locating desired data efficiently. Summaries of the datasets generated by the FaceBase projects from 2014 to 2019 are provided here. FaceBase 3 now welcomes contributions of data on craniofacial and dental development in humans, model organisms and cell lines. Collectively, the FaceBase Consortium, along with other NIH-supported data resources, provide a continuously growing, dynamic and current resource for the scientific community while improving data reproducibility and fulfilling data sharing requirements.


Subject(s)
Dental Research/methods , Facial Bones/physiology , Skull/physiology , Animals , Databases, Factual , Humans , Reproducibility of Results , Research Personnel
8.
Exp Brain Res ; 239(4): 1165-1178, 2021 Apr.
Article in English | MEDLINE | ID: mdl-33560448

ABSTRACT

Traditional non-invasive imaging methods describe statistical associations of functional co-activation over time. They cannot easily establish hierarchies in communication as done in non-human animals using invasive methods. Here, we interleaved functional MRI (fMRI) recordings with non-invasive transcranial magnetic stimulation (TMS) to map causal communication between the frontal cortex and subcortical target structures including the subgenual anterior cingulate cortex (sgACC) and the amygdala. Seed-based correlation maps from each participant's resting fMRI scan determined individual stimulation sites with high temporal correlation to targets for the subsequent TMS/fMRI session(s). The resulting TMS/fMRI images were transformed to quantile responses, so that regions of high-/low-quantile response corresponded to the areas of the brain with the most positive/negative evoked response relative to the global brain response. We then modeled the average quantile response for a given region (e.g., structure or network) to determine whether TMS was effective in the relative engagement of the downstream targets. Both the sgACC and amygdala were differentially influenced by TMS. Furthermore, we found that the sgACC distributed brain network was modulated in response to fMRI-guided TMS. The amygdala, but not its distributed network, also responded to TMS. Our findings suggest that individual targeting and brain response measurements reflect causal circuit mapping to the sgACC and amygdala in humans. These results set the stage to further map circuits in the brain and link circuit pathway integrity to clinical intervention outcomes, especially when the intervention targets specific pathways and networks as is possible with TMS.


Subject(s)
Magnetic Resonance Imaging , Transcranial Magnetic Stimulation , Animals , Brain/diagnostic imaging , Brain Mapping , Gyrus Cinguli , Humans , Rest
9.
Environ Sci Technol ; 55(14): 10056-10066, 2021 07 20.
Article in English | MEDLINE | ID: mdl-34236189

ABSTRACT

Tailings dam failures can cause devastation to the environment, loss of human life, and require expensive remediation. A promising approach for de-risking brucite-bearing ultramafic tailings is in situ cementation via carbon dioxide (CO2) mineralization, which also sequesters this greenhouse gas within carbonate minerals. In cylindrical test experiments, brucite [Mg(OH)2] carbonation was accelerated by coupling organic and inorganic carbon cycling. Waste organics generated CO2 concentrations similar to that of flue gas (up to 19%). The abundance of brucite (2-10 wt %) had the greatest influence on tailings cementation as evidenced by the increase in total inorganic carbon (TIC; +0.17-0.84%). Brucite consumption ranged from 64-84% of its initial abundance and was mainly influenced by water availability. Higher moisture contents (e.g., 80% saturation) and finer grain sizes (e.g., clay-silt) that allowed for a better distribution of water resulted in greater brucite carbonation. Furthermore, pore clogging and surface passivation by Mg-carbonates may have slowed brucite carbonation over the 10 weeks. Unconfined compressive strengths ranged from 0.4-6.9 MPa and would be sufficient in most scenarios to adequately stabilize tailings. Our study demonstrates the potential for stabilizing brucite-bearing mine tailings through in situ cementation while sequestering CO2.


Subject(s)
Carbon Sequestration , Cementation , Carbon Dioxide , Carbonates , Humans , Magnesium Hydroxide
10.
Qual Life Res ; 29(6): 1609-1619, 2020 Jun.
Article in English | MEDLINE | ID: mdl-32219705

ABSTRACT

PURPOSE: Diagnosing cancer early is an imperative, as help-seeking delays affect survival. Quality of life (QoL) deteriorates after diagnosis, but decline may start when cancer is suspected at the earliest stage of the pathway to treatment. This study examined whether offering guided feedback about personal QoL to adults with potential cancer symptoms, living in deprived communities, changes QoL and promotes help-seeking in primary care. METHODS: Visitors to a CRUK mobile cancer roadshow were recruited in 43 sites. A prospective longitudinal (2 × 2) repeated-measures design was applied. Where they presented a potential cancer symptom, and were 'signposted' to a GP, they were allocated to a symptom condition, or a lifestyle condition, if seeking cancer risk advice. Randomisation was to an Intervention group, who received feedback about personal QoL results (WHOQOL-BREF and WHOQOL importance measures), or a Control group who assessed QoL without feedback. Depression was screened. RESULTS: Of 107 participants, the mean age was 53; 50% were women, 57% were without tertiary education, 66% were unemployed and 45% were currently ill. Over 10 weeks, 54% of all those with symptoms sought help from a medical source and 42% specifically from a GP. Thirty-one completed all three assessments. With symptoms present, psychological, social and environmental QoL were poor, becoming poorer over time. When the symptoms group received feedback, psychological QoL increased, but GP visits were unaffected. However, feedback increased help-seeking from informal social contacts. Lifestyle groups reported consistently good psychological and social QoL. CONCLUSION: This early cancer research offers practical and theoretical implications for QoL interventions in deprived communities.


Subject(s)
Neoplasms/diagnosis , Neoplasms/psychology , Quality of Life/psychology , Adult , Depression/diagnosis , Depression/psychology , Female , Health Status , Humans , Life Style , Longitudinal Studies , Male , Middle Aged , Primary Health Care , Prospective Studies , Risk , Surveys and Questionnaires
11.
Br J Cancer ; 121(4): 351-358, 2019 08.
Article in English | MEDLINE | ID: mdl-31332283

ABSTRACT

BACKGROUND: This is the first review to identify, appraise and synthesise women's experiences of having a false-positive breast screening test result. METHODS: We systematically searched eight databases for qualitative research reporting women's experiences of receiving a false-positive screening test result. Two reviewers independently screened articles. Eight papers reporting seven studies were included. Study quality was appraised. Data were thematically synthesised. RESULTS: Women passively attended screening in order to prove their perceived good health. Consequently, being recalled was unexpected, shocking and disempowering: women felt without options. They endured great uncertainty and stress and sought clarity about their health (e.g. by scrutinising the wording of recall letters and conversations with healthcare professionals). Their result was accompanied by relief and welcome feelings of certainty about their health, but some received unclear explanations of their result, contributing to lasting breast cancer-related worry and an ongoing need for further reassurance. CONCLUSION: The organisation of breast screening programmes may constrain choice for women: they became passive recipients. The way healthcare professionals verbally communicate results to women may contribute to lasting breast cancer-related worry. Women need more reassurance, emotional support and answers to their questions before and during screening assessment, and after receiving their result.


Subject(s)
Breast Neoplasms/psychology , Qualitative Research , Breast Neoplasms/diagnosis , False Positive Reactions , Female , Humans , Uncertainty , Women's Health
12.
Qual Life Res ; 28(5): 1327-1335, 2019 May.
Article in English | MEDLINE | ID: mdl-30671707

ABSTRACT

PURPOSE: Although a cancer diagnosis is linked with decrements to quality of life (QoL), it is unknown exactly when QoL starts to deteriorate, and whether this occurs during the pre-diagnostic pathway. This study aimed to examine QoL during this phase, and in addition investigate whether QoL levels influence decisions about seeking professional help. This is important, because early diagnosis is linked to lower cancer mortality rates. METHODS: Working alongside a Cancer Research UK Roadshow in socially deprived communities, the recent QoL of adult visitors was assessed, before attending primary care. Using a cross-sectional design, we compared QoL in those presenting a potential cancer symptom/sign, with others seeking lifestyle advice to reduce cancer risk. Self-reported QoL (WHOQOL-BREF), and intention to seek help, were measured. RESULTS: Of 107 recruited, 50% were men. The potential cancer symptom group reported significantly poorer general QoL and psychological QoL, than lifestyle controls. Prior poorer physical QoL predicted stronger intentions to consult a general practitioner (GP) in the next 2 weeks, when controlling for symptom presence. CONCLUSIONS: QoL is poorer for those with potential cancer symptoms, before they first seek advice from primary care. Poorer physical QoL is associated with stronger intentions to make a GP appointment. An implication for longer term health is that if public awareness about the impact of symptoms on QoL was raised, this could provide an impetus to seek help.


Subject(s)
Decision Making , Neoplasms/psychology , Patient Acceptance of Health Care/psychology , Primary Health Care/statistics & numerical data , Quality of Life/psychology , Referral and Consultation/statistics & numerical data , Adult , Aged , Aged, 80 and over , Cross-Sectional Studies , Early Detection of Cancer/psychology , Female , Humans , Life Style , Male , Middle Aged , Neoplasms/diagnosis , Risk , Surveys and Questionnaires , Young Adult
13.
J Med Internet Res ; 21(1): e10421, 2019 01 09.
Article in English | MEDLINE | ID: mdl-30626562

ABSTRACT

BACKGROUND: Current interventions to support medication adherence in people with type 2 diabetes are generally resource-intensive and ineffective. Brief messages, such as those delivered via short message service (SMS) systems, are increasingly used in digital health interventions to support adherence because they can be delivered on a wide scale and at low cost. The content of SMS text messages is a crucial intervention feature for promoting behavior change, but it is often unclear what the rationale is for chosen wording or any underlying mechanisms targeted for behavioral change. There is little guidance for developing and optimizing brief message content for use in mobile device-delivered interventions. OBJECTIVE: This review aimed to (1) identify theoretical constructs (ie, the targets that interventions aim to change) and behavioral strategies (ie, features of intervention content) found to be associated with medication adherence in patients with type 2 diabetes and (2) map these onto a standard taxonomy for behavior change techniques (BCTs, that is, active ingredients of interventions used to promote behavioral change, to produce an evidence-based set of approaches that have shown promise of improving adherence in previous studies and which could be further tested in digital health interventions. METHODS: A rapid systematic review of existing relevant systematic reviews was conducted. MEDLINE and PsycINFO databases were searched from inception to April 10, 2017. Inclusion criteria were (1) systematic reviews of quantitative data if the studies reviewed identified predictors of or correlates with medication adherence or evaluated medication adherence-enhancing interventions and included adult participants taking medication to manage a chronic physical health condition, and (2) systematic reviews of qualitative studies of experiences of medication adherence for adult participants with type 2 diabetes. Data were extracted on review characteristics and BCTs, theoretical constructs, or behavioral strategies associated with improved adherence. Constructs and strategies were mapped onto the BCT version 1 taxonomy. RESULTS: A total of 1701 references were identified; 25 systematic reviews (19 quantitative reviews, 3 qualitative reviews, and 3 mixed-method reviews) were included. Moreover, 20 theoretical constructs (eg, self-efficacy) and 19 behavioral strategies (eg, habit analysis) were identified in the included reviews. In total, 46 BCTs were identified as being related to medication adherence in type 2 diabetes (eg, habit formation, prompts or cues, and information about health consequences). CONCLUSIONS: We identified 46 promising BCTs related to medication adherence in type 2 diabetes on which the content of brief messages delivered through mobile devices to improve adherence could be based. By using explicit systematic review methods and linking our findings to a standardized taxonomy of BCTs, we have described a novel approach for the development of digital message content. Future brief message interventions that aim to support medication adherence could incorporate the identified BCTs.


Subject(s)
Behavior Therapy/methods , Diabetes Mellitus, Type 2/epidemiology , Medication Adherence/statistics & numerical data , Self-Management/methods , Telemedicine/methods , Text Messaging/standards , Adult , Humans , Qualitative Research
14.
Nucleic Acids Res ; 44(14): 6693-706, 2016 08 19.
Article in English | MEDLINE | ID: mdl-27084945

ABSTRACT

DNA methylation is a repressive epigenetic modification that covers vertebrate genomes. Regions known as CpG islands (CGIs), which are refractory to DNA methylation, are often associated with gene promoters and play central roles in gene regulation. Yet how CGIs in their normal genomic context evade the DNA methylation machinery and whether these mechanisms are evolutionarily conserved remains enigmatic. To address these fundamental questions we exploited a transchromosomic animal model and genomic approaches to understand how the hypomethylated state is formed in vivo and to discover whether mechanisms governing CGI formation are evolutionarily conserved. Strikingly, insertion of a human chromosome into mouse revealed that promoter-associated CGIs are refractory to DNA methylation regardless of host species, demonstrating that DNA sequence plays a central role in specifying the hypomethylated state through evolutionarily conserved mechanisms. In contrast, elements distal to gene promoters exhibited more variable methylation between host species, uncovering a widespread dependence on nucleotide frequency and occupancy of DNA-binding transcription factors in shaping the DNA methylation landscape away from gene promoters. This was exemplified by young CpG rich lineage-restricted repeat sequences that evaded DNA methylation in the absence of co-evolved mechanisms targeting methylation to these sequences, and species specific DNA binding events that protected against DNA methylation in CpG poor regions. Finally, transplantation of mouse chromosomal fragments into the evolutionarily distant zebrafish uncovered the existence of a mechanistically conserved and DNA-encoded logic which shapes CGI formation across vertebrate species.


Subject(s)
Conserved Sequence/genetics , CpG Islands/genetics , DNA Methylation/genetics , DNA/genetics , Evolution, Molecular , Animals , Cell Line , Chromosomes, Human, Pair 21/genetics , Female , Gene Expression Regulation , Humans , Male , Mice, Inbred C57BL , Mice, Transgenic , Promoter Regions, Genetic , Protein Binding/genetics , Repetitive Sequences, Nucleic Acid/genetics , Species Specificity , Transcription Factors/metabolism , Vertebrates/genetics
15.
Nature ; 471(7339): 518-22, 2011 Mar 24.
Article in English | MEDLINE | ID: mdl-21430780

ABSTRACT

Melanoma is a tumour of transformed melanocytes, which are originally derived from the embryonic neural crest. It is unknown to what extent the programs that regulate neural crest development interact with mutations in the BRAF oncogene, which is the most commonly mutated gene in human melanoma. We have used zebrafish embryos to identify the initiating transcriptional events that occur on activation of human BRAF(V600E) (which encodes an amino acid substitution mutant of BRAF) in the neural crest lineage. Zebrafish embryos that are transgenic for mitfa:BRAF(V600E) and lack p53 (also known as tp53) have a gene signature that is enriched for markers of multipotent neural crest cells, and neural crest progenitors from these embryos fail to terminally differentiate. To determine whether these early transcriptional events are important for melanoma pathogenesis, we performed a chemical genetic screen to identify small-molecule suppressors of the neural crest lineage, which were then tested for their effects on melanoma. One class of compound, inhibitors of dihydroorotate dehydrogenase (DHODH), for example leflunomide, led to an almost complete abrogation of neural crest development in zebrafish and to a reduction in the self-renewal of mammalian neural crest stem cells. Leflunomide exerts these effects by inhibiting the transcriptional elongation of genes that are required for neural crest development and melanoma growth. When used alone or in combination with a specific inhibitor of the BRAF(V600E) oncogene, DHODH inhibition led to a marked decrease in melanoma growth both in vitro and in mouse xenograft studies. Taken together, these studies highlight developmental pathways in neural crest cells that have a direct bearing on melanoma formation.


Subject(s)
Melanoma/genetics , Melanoma/pathology , Neural Crest/enzymology , Oxidoreductases Acting on CH-CH Group Donors/metabolism , Transcription, Genetic , Amino Acid Substitution , Animals , Animals, Genetically Modified , Cell Differentiation/drug effects , Cell Line, Tumor , Cell Lineage/drug effects , Dihydroorotate Dehydrogenase , Disease Models, Animal , Gene Expression Regulation, Neoplastic , Genes, p53/genetics , Humans , Isoxazoles/pharmacology , Isoxazoles/therapeutic use , Leflunomide , Melanoma/drug therapy , Melanoma/enzymology , Mice , Neural Crest/drug effects , Neural Crest/metabolism , Neural Crest/pathology , Oxidoreductases Acting on CH-CH Group Donors/antagonists & inhibitors , Proto-Oncogene Proteins B-raf/antagonists & inhibitors , Proto-Oncogene Proteins B-raf/chemistry , Proto-Oncogene Proteins B-raf/genetics , Proto-Oncogene Proteins B-raf/metabolism , Rats , Stem Cells/cytology , Stem Cells/drug effects , Stem Cells/pathology , Transcription, Genetic/drug effects , Transcription, Genetic/physiology , Xenograft Model Antitumor Assays , Zebrafish/embryology , Zebrafish/genetics
17.
Nucleic Acids Res ; 40(4): e32, 2012 Feb.
Article in English | MEDLINE | ID: mdl-22156374

ABSTRACT

Across vertebrate genomes methylation of cytosine residues within the context of CpG dinucleotides is a pervasive epigenetic mark that can impact gene expression and has been implicated in various developmental and disease-associated processes. Several biochemical approaches exist to profile DNA methylation, but recently an alternative approach based on profiling non-methylated CpGs was developed. This technique, called CxxC affinity purification (CAP), uses a ZF-CxxC (CxxC) domain to specifically capture DNA containing clusters of non-methylated CpGs. Here we describe a new CAP approach, called biotinylated CAP (Bio-CAP), which eliminates the requirement for specialized equipment while dramatically improving and simplifying the CxxC-based DNA affinity purification. Importantly, this approach isolates non-methylated DNA in a manner that is directly proportional to the density of non-methylated CpGs, and discriminates non-methylated CpGs from both methylated and hydroxymethylated CpGs. Unlike conventional CAP, Bio-CAP can be applied to nanogram quantities of genomic DNA and in a magnetic format is amenable to efficient parallel processing of samples. Furthermore, Bio-CAP can be applied to genome-wide profiling of non-methylated DNA with relatively small amounts of input material. Therefore, Bio-CAP is a simple and streamlined approach for characterizing regions of the non-methylated DNA, whether at specific target regions or genome wide.


Subject(s)
Chromatography, Affinity/methods , CpG Islands , DNA Methylation , Biotinylation , DNA/isolation & purification , High-Throughput Nucleotide Sequencing , Sequence Analysis, DNA , Zinc Fingers
18.
Autism ; : 13623613241251512, 2024 May 10.
Article in English | MEDLINE | ID: mdl-38727194

ABSTRACT

LAY ABSTRACT: Repetitive behaviours and interests are a hallmark feature of autism. It is very common for autistic people to experience mental health difficulties, such as obsessive-compulsive disorder. Previous research has investigated similarities and differences between obsessive-compulsive disorder symptoms and repetitive behaviours in autism through questionnaires and observation studies. This is the first study to interview autistic adults about their personal experiences of differentiating between obsessive-compulsive disorder symptoms and repetitive behaviours related to autism. We interviewed 15 autistic adults who experience obsessive-compulsive disorder symptoms. We recorded these interviews and carefully analysed these to find themes. We found some differences between repetitive behaviours and obsessive-compulsive disorder. Participants said repetitive behaviours are part of who they are and what they want to be doing, whereas obsessive-compulsive disorder symptoms conflicted with how they view themselves. Obsessive-compulsive disorder was said to cause negative emotions, while participants said they experience lots of different emotions when doing repetitive behaviours. A similarity participants reported was trying to stop themselves from doing obsessive-compulsive disorder symptoms and repetitive behaviours that other people can see. There was also overlap between obsessive-compulsive disorder and repetitive behaviours. Participants talked about experiences when obsessive-compulsive disorder would take over routines and make them feel more intense and negative. Also, participants' special interests were sometimes connected to the obsessions they experienced. We conclude that clinicians can use these findings to support conversations with autistic clients in differentiating between repetitive behaviours and obsessive-compulsive disorder symptoms. We also think that further research investigating how obsessive-compulsive disorder symptoms might be hidden by autistic and typically developing people is needed.

19.
bioRxiv ; 2024 Jun 22.
Article in English | MEDLINE | ID: mdl-38948693

ABSTRACT

Bridge-like lipid transport proteins (BLTPs) are an evolutionarily conserved family of proteins that localize to membrane contact sites and are thought to mediate the bulk transfer of lipids from a donor membrane, typically the endoplasmic reticulum (ER), to an acceptor membrane, such as a that of the cell or an organelle 1 . Despite the fundamental importance of BLTPs for cellular function, the architecture, composition, and lipid transfer mechanisms remain poorly characterized. Here, we present the subunit composition and the cryo-electron microscopy structure of the native LPD-3 BLTP complex isolated from transgenic C. elegans . LPD-3 folds into an elongated, rod-shaped tunnel whose interior is filled with ordered lipid molecules that are coordinated by a track of ionizable residues that line one side of the tunnel. LPD-3 forms a complex with two previously uncharacterized proteins, here named "Intake" and "Spigot", both of which interact with the N-terminal end of LPD-3 where lipids enter the tunnel. Intake has three transmembrane helices, one of which borders the entrance to the tunnel; Spigot has one transmembrane helix and extends 80 Å along the cytosolic surface of LPD-3. Experiments in multiple model systems indicate that Spigot plays a conserved role in ER-PM contact site formation. Our LPD-3 complex structural data, together with molecular dynamics simulations of the transmembrane region in a lipid bilayer, reveal protein-lipid interactions that suggest a model for how the native LPD-3-complex mediates bulk lipid transport and provide a foundation for mechanistic studies of BLTPs.

20.
Clin Neurophysiol ; 165: 16-25, 2024 Jun 19.
Article in English | MEDLINE | ID: mdl-38945031

ABSTRACT

OBJECTIVE: Transcranial magnetic stimulation (TMS) can efficiently and robustly modulate synaptic plasticity, but little is known about how TMS affects functional connectivity (rs-fMRI). Accordingly, this project characterized TMS-induced rsFC changes in depressed patients who received 3 days of left prefrontal intermittent theta burst stimulation (iTBS). METHODS: rs-fMRI was collected from 16 subjects before and after iTBS. Correlation matrices were constructed from the cleaned rs-fMRI data. Electric-field models were conducted and used to predict pre-post changes in rs-fMRI. Site by orientation heatmaps were created for vectors centered on the stimulation site and a control site (contralateral motor cortex). RESULTS: For the stimulation site, there was a clear relationship between both site and coil orientation, and connectivity changes. As distance from the stimulation site increased, prediction accuracy decreased. Similarly, as eccentricity from the optimal orientation increased, prediction accuracy decreased. The systematic effects described above were not apparent in the heatmap centered on the control site. CONCLUSIONS: These results suggest that rs-fMRI following iTBS changes systematically as a function of the distribution of electrical energy delivered from the TMS pulse, as represented by the e-field model. SIGNIFICANCE: This finding lays the groundwork for future studies to individualize TMS targeting based on how predicted rs-fMRI changes might impact psychiatric symptoms.

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