Nucleosome reorganisation in breast cancer tissues.

BACKGROUND: Nucleosome repositioning in cancer is believed to cause many changes in genome organisation and gene expression. Understanding these changes is important to elucidate fundamental aspects of cancer. It is also important for medical diagnostics based on cell-free DNA (cfDNA), which originates from genomic DNA regions protected from digestion by nucleosomes. RESULTS: We have generated high-resolution nucleosome maps in paired tumour and normal tissues from the same breast cancer patients using MNase-assisted histone H3 ChIP-seq and compared them with the corresponding cfDNA from blood plasma. This analysis has detected single-nucleosome repositioning at key regulatory regions in a patient-specific manner and common cancer-specific patterns across patients. The nucleosomes gained in tumour versus normal tissue were particularly informative of cancer pathways, with ~ 20-fold enrichment at CpG islands, a large fraction of which marked promoters of genes encoding DNA-binding proteins. The tumour tissues were characterised by a 5-10 bp decrease in the average distance between nucleosomes (nucleosome repeat length, NRL), which is qualitatively similar to the differences between pluripotent and differentiated cells. This effect was correlated with gene activity, differential DNA methylation and changes in local occupancy of linker histone variants H1.4 and H1X. CONCLUSIONS: Our study offers a novel resource of high-resolution nucleosome maps in breast cancer patients and reports for the first time the effect of systematic decrease of NRL in paired tumour versus normal breast tissues from the same patient. Our findings provide a new mechanistic understanding of nucleosome repositioning in tumour tissues that can be valuable for patient diagnostics, stratification and monitoring.

NucPosDB: a database of nucleosome positioning in vivo and nucleosomics of cell-free DNA.

Nucleosome positioning is involved in many gene regulatory processes happening in the cell, and it may change as cells differentiate or respond to the changing microenvironment in a healthy or diseased organism. One important implication of nucleosome positioning in clinical epigenetics is its use in the "nucleosomics" analysis of cell-free DNA (cfDNA) for the purpose of patient diagnostics in liquid biopsies. The rationale for this is that the apoptotic nucleases that digest chromatin of the dying cells mostly cut DNA between nucleosomes. Thus, the short pieces of DNA in body fluids reflect the positions of nucleosomes in the cells of origin. Here, we report a systematic nucleosomics database - NucPosDB - curating published nucleosome positioning datasets in vivo as well as datasets of sequenced cell-free DNA (cfDNA) that reflect nucleosome positioning in situ in the cells of origin. Users can select subsets of the database by a number of criteria and then obtain raw or processed data. NucPosDB also reports the originally determined regions with stable nucleosome occupancy across several individuals with a given condition. An additional section provides a catalogue of computational tools for the analysis of nucleosome positioning or cfDNA experiments and theoretical algorithms for the prediction of nucleosome positioning preferences from DNA sequence. We provide an overview of the field, describe the structure of the database in this context, and demonstrate data variability using examples of different medical conditions. NucPosDB is useful both for the analysis of fundamental gene regulation processes and the training of computational models for patient diagnostics based on cfDNA. The database currently curates ~ 400 publications on nucleosome positioning in cell lines and in situ as well as cfDNA from > 10,000 patients and healthy volunteers. For open-access cfDNA datasets as well as key MNase-seq datasets in human cells, NucPosDB allows downloading processed mapped data in addition to the regions with stable nucleosome occupancy. NucPosDB is available at https://generegulation.org/nucposdb/ .

Case report of post streptococcal multifocal choroiditis in a young pregnant female: A success story.

BACKGROUND: Multifocal choroiditis (MFC) is described as a chronic bilateral progressive inflammatory outer chorioretinopathy, that usually affects healthy myopic Caucasian women with no associated systemic/ocular diseases. This patient had a severe acute presentation of aggressive multifocal choroiditis that was treated with systemic steroids. CASE PRESENTATION: This is a retrospective case report of a 30-year-old, white, European, female who was 10 weeks pregnant. She had bilateral severe vision loss and rapidly progressive rash and arthritis. The patient was extensively investigated for inflammatory and infectious etiologies by a multidisciplinary team including rheumatology and obstetrics and gynecology. Antistreptolysin levels were moderately raised. Serial retinal optical coherence tomography scans were performed and were critical for assessing disease activity and demonstrating the extent of retinal and choroidal lesions. CONCLUSION: This was a challenging case as the patient was pregnant. Nevertheless, a multidisciplinary team, opted for treatment with systemic steroids which then lead to recovery of her vision.

Toxoplasmosis Related Neuroretinitis: More than Meets the Eye.

BACKGROUND: The intracellular protozoan Toxoplasma (T. gondii) is a parasitic infection, normally asymptomatic in immunocompetent patients. It often manifests ophthalmically, with focal necrotizing retinitis, and is more rarely associated with vitritis and anterior uveitis. Neuroretinitis, which results in severe, painless visual loss, optic disc edema, and a macular star, is an unusual first presentation of toxoplasmosis which despite being rare, when it does occur tends to affect young, immunosuppressed patients. CASE PRESENTATION: This case report describes a 34-year-old, white, European, immunocompetent female, who developed sudden visual loss and was found to have optic disc edema and stellate macular exudates. She was managed in an ophthalmic unit in the UK, a country with a low prevalence of toxoplasmosis Following extensive investigation, confirming Toxoplasma the standard anti-toxoplasmosis treatment was commenced, resulting in visual improvement over the following 6 months. CONCLUSION: Toxoplasmic neuroretinitis should be considered with no background of systemic illness and in the absence of classical risk factors.

Results From a Patient Experience Study in Pediatric Gastrointestinal Endoscopy.

OBJECTIVE: Gastrointestinal endoscopy in children has become a standard diagnostic and therapeutic modality. The aim of our study was to characterize the most memorable elements of the patient experience from the parent's and patient's perspective and determine ways to improve the overall quality of their experience. METHODS: Using a structured questionnaire, we conducted 47 phone interviews with families who had recently undergone gastrointestinal endoscopic procedures. RESULTS: Our study showed clear communication and mutual agreement on care decisions contributed to positive experiences. Inadequate communication of information regarding alternatives to the procedure and risk of complications during the informed consent discussion contributed to negative patient experiences. Standardization of postprocedure follow-up and timely communication of pathology findings also had potential for improvement. CONCLUSION: Our study revealed 2 areas for quality improvement interventions: The need to ensure that alternatives and complications are thoroughly discussed and the need for standardization of postprocedure follow-up.