Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Exploring a Link Between Alzheimer’s and Glioma by Investigating SORL1 Network

Abstract AIMS Use bioinformatics methods to identify and validate associated proteins and genes in the SORL1 network. Generate a bank of patient derived cells in association with the Royal Preston Hospital BTNW tissue bank. Explore identified targets from the bioinformatics in patient derived cells. METHOD Proteins and genes associated with SORL1 and SORLA were identified on GeneCards. Connectivity mapping of known and predicted interactions linked to SORL1 was explored in STRING. For clinical validation differential expression was investigated by comparing genomic data from GTEX and TCGA, available at Xenabrowser. For survival analysis Kaplan-Meier curves were generated on cBioPortal. The five most differently expressed novel targets are taken forward for laboratory experiments using western blots for protein quantification and immunocytochemistry to identify and visualise target proteins. RESULTS A total of 73 genes (30 from GeneCards and 43 from STRING) were obtained. 63 genes from the generated SORL1-related network were shown to be differentially expressed whilst 40 were significantly different between low-surviving patients and high-surviving patients. The top five associated proteins are CKAP4, CTNND1, FN1, HSPA12A and SORCS3. CKAP4, CTNND1 and FN1 are highly expressed in both glioma and glioblastoma, but low expressed in healthy tissue. HSPA12A is low expressed in cancerous brain tissue and highly expressed in healthy samples. SORCS3 is differentially expressed in healthy samples and glioma, but significantly low expressed glioblastoma. CONCLUSION This project provides insight into SORL1 molecular relationships and function in tissue, cultured cells and serum from a patient cohort including demographics, disease progression and site

Circulating miRNA expression in glioblastoma patients & its effect on cell migration

Glioblastoma Multiforme (GB) is the most common malignant human glioma and is currently incurable. Further understanding of the epigenetic mechanisms underpinning GB progression could facilitate earlier diagnosis and improve prognosis. MicroRNAs (miRNAs) are regions of RNA that reduce translation of proteins. Identifying dysregulated circulating miRNA(s) in sera could provide a potential biomarker for diagnosis, accessible through a blood test. GB and control sera supplied by Brain Tumour North West tissue bank was used to profile the circulating expression of miRNAs -20a, -34a, and -92a using quantitative PCR technology. The results were analysed according to age and sex, as well as overall comparison. MiRNA20a was reduced in GB samples as well as in 20–39 year-old (yo), 40–59 yo and male GB patients, but increased expression in GB patients aged 60 and over. MiRNA92a expression was reduced in 40-60yo GB patients however GB patients over the age of 60 showed an increased expression. MiRNA34a was reduced in GB patients overall, in both sexes and two out of three age groups (40–59, and 20–39 yo) when compared to age and sex matched control samples. The effect of miRNA 34a on cellular migration was analysed in human glioma and control human astrocyte cell lines by overexpression and knockdown. The cell lines were cultured in media containing pooled sera from GB patients, healthy individuals, standard fetal bovine serum and exosome depleted serum. Wound healing assays were performed to ascertain cell migration. Inhibition of miRNA 34a-5p significantly increased rate of migration in glioma cells cultured in human control sera. Acknowledgement should be made to Brain Tumour North West for providing the serum samples used in this study

Weight loss interventions for improving fertility: a synthesis of current evidence

Infertility is a widespread issue which is estimated to affect up to 17.5% of the global population. Evidence suggests that the most common causes of female infertility are ovulation disorders (e.g., polycystic ovary syndrome). That said, lifestyle factors such as dietary patterns, stress, alcohol consumption, smoking, and obesity are key determinants which have been shown to impact female physiology and significantly decrease the chances of conception. Obesity has been widely recognized as a significant factor that negatively impacts ovarian stimulation in women and is associated with several reproductive disorders, including anovulation, subfertility, and infertility. Despite improvements in fertility treatments, obesity remains a challenge particularly for fertility clinics because of the poorer pregnancy outcomes observed within the population. In this article, we will explore the effects of weight loss on female fertility and review the various strategies that have been shown to be effective in reducing obesity and improving reproductive outcomes

Evaluating the association of female obesity with the risk of live birth following IVF: Implications for clinical practice

Obesity is a well-established risk factor for infertility. Consequentially, women living with obesity may require fertility treatment to support them to conceive. Due to evidence suggesting obesity is also linked with poorer outcomes following in vitro fertilisation (IVF), local commissioning guidelines on assisted conception recommend a BMI of <30kg/m² before IVF can commence. However, it is currently unclear if these guidelines are evidence based. This commentary aims to critically appraise a recent systematic review by Sermondade et al, 2019 and expand upon the implications of the findings for clinical practice

Brain Tumour Lessons From Alzheimer’s Disease: Beta-Amyloid and SorLA Expression in Glioblastoma

AIMS Exploring how two proteins strongly associated with Alzheimer’s disease are expressed in glioma. Amyloid beta (Aβ) is a peptide cleaved from amyloid precursor protein (APP) that is shuttled around the cell by sorting-related receptor with A-type repeats (SorLA). Low expression of SorLA has been linked to increased risk of Alzheimer’s disease as APP processing shifts towards production of the plaque-forming Aβ42 rather than the more benign Aβ40. METHOD Expression of Aβ40, Aβ42 and SorLA was determined in immortalised cell lines (grade 4 glioblastoma U87MG, grade 2 astrocytoma 1321N1, foetal astrocytes SVGp12), glioblastoma patient-derived cells (PD301, PD304) and normal human astrocytes through western blotting or immunocytochemistry. RESULTS SorLA was present in all cells. Relative optical density was more than 60-fold higher for U87MG glioblastoma cells and approximately 10-fold higher for 1321N1 astrocytoma cells than SVGp12 cells. Similarly, SorLA had a significantly higher expression (p<0.01) in patient derived cells than normal human astrocytes. High expression of SorLA was accompanied by lower Aβ42 in patient derived cells compared to normal human astrocytes. Expression of Aβ40 was similar across patient derived cells and normal human astrocytes. CONCLUSION These data suggest that SorLA is retained in glioblastoma and remains functional to drive APP processing away from Aβ42 production. Future work will determine how high SorLA expression contributes to the increased motility and invasiveness seen in glioblastoma cells by transfecting siRNA to knock down SorLA