The NF1 somatic mutational landscape in sporadic human cancers

Abstract Background Neurofibromatosis type 1 (NF1: Online Mendelian Inheritance in Man (OMIM) #162200) is an autosomal dominantly inherited tumour predisposition syndrome. Heritable constitutional mutations in the NF1 gene result in dysregulation of the RAS/MAPK pathway and are causative of NF1. The major known function of the NF1 gene product neurofibromin is to downregulate RAS. NF1 exhibits variable clinical expression and is characterized by benign cutaneous lesions including neurofibromas and café-au-lait macules, as well as a predisposition to various types of malignancy, such as breast cancer and leukaemia. However, acquired somatic mutations in NF1 are also found in a wide variety of malignant neoplasms that are not associated with NF1. Main body Capitalizing upon the availability of next-generation sequencing data from cancer genomes and exomes, we review current knowledge of somatic NF1 mutations in a wide variety of tumours occurring at a number of different sites: breast, colorectum, urothelium, lung, ovary, skin, brain and neuroendocrine tissues, as well as leukaemias, in an attempt to understand their broader role and significance, and with a view ultimately to exploiting this in a diagnostic and therapeutic context. Conclusion As neurofibromin activity is a key to regulating the RAS/MAPK pathway, NF1 mutations are important in the acquisition of drug resistance, to BRAF, EGFR inhibitors, tamoxifen and retinoic acid in melanoma, lung and breast cancers and neuroblastoma. Other curiosities are observed, such as a high rate of somatic NF1 mutation in cutaneous melanoma, lung cancer, ovarian carcinoma and glioblastoma which are not usually associated with neurofibromatosis type 1. Somatic NF1 mutations may be critical drivers in multiple cancers. The mutational landscape of somatic NF1 mutations should provide novel insights into our understanding of the pathophysiology of cancer. The identification of high frequency of somatic NF1 mutations in sporadic tumours indicates that neurofibromin is likely to play a critical role in development, far beyond that evident in the tumour predisposition syndrome NF1

Extending the Planetary Mass Function to Earth Mass by Microlensing at Moderately High Magnification

A measurement by microlensing of the planetary mass function of planets with masses ranging from 5M_E to 10M_J and orbital radii from 0.5 to 10 AU was reported recently. A strategy for extending the mass range down to (1-3)M_E is proposed here. This entails monitoring the peaks of a few tens of microlensing events with moderately high magnifications with 1-2m class telescopes. Planets of a few Earth masses are found to produce deviations of ~ 5% to the peaks of microlensing light curves with durations ~ (0.7-3)hr in events with magnification ~ 100 if the projected separation of the planet lies in the annular region (0.85-1.2)r_E. Similar deviations are produced by Earth mass planets in the annular region (0.95-1.05)r_E. It is possible that sub-Earths could be detected very close to the Einstein ring if they are sufficiently abundant, and also planetary systems with more than one low mass planet.Comment: 12 pages, 20 figures (in press) MNRAS (2013

Effects of fluid and drinking on pneumonia mortality in older adults: A systematic review and meta-analysis.

BACKGROUND AND AIMS: Advice to drink plenty of fluid is common in respiratory infections. We assessed whether low fluid intake (dehydration) altered outcomes in adults with pneumonia. METHODS: We systematically reviewed trials increasing fluid intake and well-adjusted, well-powered observational studies assessing associations between markers of low-intake dehydration (fluid intake, serum osmolality, urea or blood urea nitrogen, urinary output, signs of dehydration) and mortality in adult pneumonia patients (with any type of pneumonia, including community acquired, health-care acquired, aspiration, COVID-19 and mixed types). Medline, Embase, CENTRAL, references of reviews and included studies were searched to 30/10/2020. Studies were assessed for inclusion, risk of bias and data extracted independently in duplicate. We employed random-effects meta-analysis, sensitivity analyses, subgrouping and GRADE assessment. Prospero registration: CRD42020182599. RESULTS: We identified one trial, 20 well-adjusted cohort studies and one case-control study. None suggested that more fluid (hydration) was associated with harm. Ten of 13 well-powered observational studies found statistically significant positive associations in adjusted analyses between dehydration and medium-term mortality. The other three studies found no significant effect. Meta-analysis suggested doubled odds of medium-term mortality in dehydrated (compared to hydrated) pneumonia patients (GRADE moderate-quality evidence, OR 2.3, 95% CI 1.8 to 2.8, 8619 deaths in 128,319 participants). Heterogeneity was explained by a dose effect (greater dehydration increased risk of mortality further), and the effect was consistent across types of pneumonia (including community-acquired, hospital-acquired, aspiration, nursing and health-care associated, and mixed pneumonia), age and setting (community or hospital). The single trial found that educating pneumonia patients to drink ≥1.5 L fluid/d alongside lifestyle advice increased fluid intake and reduced subsequent healthcare use. No studies in COVID-19 pneumonia met the inclusion criteria, but 70% of those hospitalised with COVID-19 have pneumonia. Smaller COVID-19 studies suggested that hydration is as important in COVID-19 pneumonia mortality as in other pneumonias. CONCLUSIONS: We found consistent moderate-quality evidence mainly from observational studies that improving hydration reduces the risk of medium-term mortality in all types of pneumonia. It is remarkable that while many studies included dehydration as a potential confounder, and major pneumonia risk scores include measures of hydration, optimal fluid volume and the effect of supporting hydration have not been assessed in randomised controlled trials of people with pneumonia. Such trials, are needed as potential benefits may be large, rapid and implemented at low cost. Supporting hydration and reversing dehydration has the potential to have rapid positive impacts on pneumonia outcomes, and perhaps also COVID-19 pneumonia outcomes, in older adults

Pigment epithelium derived factor drives melanocyte proliferation and migration in neurofibromatosis café au lait macules

Background: RASopathies, which include neurofibromatosis type 1 (NF1), are defined by Ras/mitogen‐activated protein kinase (Ras/MAPK) pathway activation. They represent a group of clinically related disorders often characterised by multiple Café au Lait Macules (CALMs). Objectives: To determine, using in depth transcriptomic analysis of NF1 melanocytes from CALM and unaffected skin, (1) the gene(s) responsible for melanocyte proliferation and migration, and (2) the activated signalling pathway(s) in NF1 melanoma. Methods: Classical NF1 (n = 2, who develop tumours) and 3bp deletion NF1 (p. Met992del, who do not develop tumours) (n = 3) patients underwent skin biopsies from CALM and unaffected skin. Melanocytes were isolated and propagated, with five replicates from each tissue sample. DNA and RNA were extracted for mutational analysis and transcriptomic profiling with six replicates per sample. Mechanistic determination was undertaken using melanocyte and melanoma cell lines. Results: All CALMs in NF1 were associated with biallelic NF1 loss, resulting in amplification of Ras/MAPK and Wnt pathway signalling. CALMs were also associated with reduced SERPINF1 gene expression (and pigment epithelium‐derived factor (PEDF) levels, the reciprocal protein), a known downstream target of the master regulator of melanocyte differentiation microphthalmia‐associated transcription factor (MITF), leading to increased melanocyte proliferation, migration and invasion. In classical NF1 and melanoma, but not 3bp deletion NF1, there was also activation of the PI3K/AKT pathway. Pigment epithelium‐derived factor was found to reduce cell proliferation and invasion of NF1 melanoma. Conclusions: Melanocyte proliferation and migration leading to CALMs in NF1 arises from biallelic NF1 loss, resulting in RAS/MAPK pathway activation, and reduced expression of the tumour suppressor PEDF. Activation of the PI3K/AKT pathway in classical NF1 and NF1 melanoma may facilitate tumour growth

Recent smell loss is the best predictor of COVID-19 among individuals with recent respiratory symptoms

In a preregistered, cross-sectional study we investigated whether olfactory loss is a reliable predictor of COVID-19 using a crowdsourced questionnaire in 23 languages to assess symptoms in individuals self-reporting recent respiratory illness. We quantified changes in chemosensory abilities during the course of the respiratory illness using 0-100 visual analog scales (VAS) for participants reporting a positive (C19+; n=4148) or negative (C19-; n=546) COVID-19 laboratory test outcome. Logistic regression models identified univariate and multivariate predictors of COVID-19 status and post-COVID-19 olfactory recovery. Both C19+ and C19- groups exhibited smell loss, but it was significantly larger in C19+ participants (mean±SD, C19+: -82.5±27.2 points; C19-: -59.8±37.7). Smell loss during illness was the best predictor of COVID-19 in both univariate and multivariate models (ROC AUC=0.72). Additional variables provide negligible model improvement. VAS ratings of smell loss were more predictive than binary chemosensory yes/no-questions or other cardinal symptoms (e.g., fever). Olfactory recovery within 40 days of respiratory symptom onset was reported for ~50% of participants and was best predicted by time since respiratory symptom onset. We find that quantified smell loss is the best predictor of COVID-19 amongst those with symptoms of respiratory illness. To aid clinicians and contact tracers in identifying individuals with a high likelihood of having COVID-19, we propose a novel 0-10 scale to screen for recent olfactory loss, the ODoR-19. We find that numeric ratings ≤2 indicate high odds of symptomatic COVID-19 (4<10). Once independently validated, this tool could be deployed when viral lab tests are impractical or unavailable

Studies of genetic variants in monogenic renal tubular disorders

The renal tubules are the functional unit of the kidneys, responsible for: reabsorption of many substances including ions, solutes and water; and the secretion of waste products. The molecular mechanisms underlying these processes are tightly regulated by transporters, channels and receptors, which have different expression profiles within the renal tubular segments and their disruption can lead to disorders, with local and systemic phenotypes. Thus, monogenic renal tubular disorders affecting different segments are excellent tools for the study of specific pathways and mechanisms vital to reabsorption and secretion processes; as well as for gaining an insight into the biological and molecular differences between renal tubular segments. This thesis used next generation DNA sequencing (NGS) and Sanger DNA sequencing methods to identify novel candidate genes, and hence to study the genetic and molecular mechanisms underlying three monogenic renal tubular disorders: Dent’s disease (DD), familial juvenile hyperuricaemic nephropathy (FJHN) and familial hypocalciuric hypercalcaemia (FHH), each affecting different renal segments. For each of these disorders a large proportion of patients (25-55%) lack mutations in any of the known associated genes. However, one of the main issues with NGS remains accurate variant interpretation and therefore, the first aim was to investigate the effectiveness of in silico analysis tools to identify pathogenic variants and to determine the optimum parameters, which were then applied to the ‘gene-discovery’ studies. This thesis identified novel candidate genes for DD (CLCNKA), FJHN (CLDN3 and DENND4C) and FHH (KLOTHO) and revealed an approach for its potential successful application in the clinic for diagnosis.</p

Studies of genetic variants in monogenic renal tubular disorders

The renal tubules are the functional unit of the kidneys, responsible for: reabsorption of many substances including ions, solutes and water; and the secretion of waste products. The molecular mechanisms underlying these processes are tightly regulated by transporters, channels and receptors, which have different expression profiles within the renal tubular segments and their disruption can lead to disorders, with local and systemic phenotypes. Thus, monogenic renal tubular disorders affecting different segments are excellent tools for the study of specific pathways and mechanisms vital to reabsorption and secretion processes; as well as for gaining an insight into the biological and molecular differences between renal tubular segments. This thesis used next generation DNA sequencing (NGS) and Sanger DNA sequencing methods to identify novel candidate genes, and hence to study the genetic and molecular mechanisms underlying three monogenic renal tubular disorders: Dentâs disease (DD), familial juvenile hyperuricaemic nephropathy (FJHN) and familial hypocalciuric hypercalcaemia (FHH), each affecting different renal segments. For each of these disorders a large proportion of patients (25-55%) lack mutations in any of the known associated genes. However, one of the main issues with NGS remains accurate variant interpretation and therefore, the first aim was to investigate the effectiveness of in silico analysis tools to identify pathogenic variants and to determine the optimum parameters, which were then applied to the âgene-discoveryâ studies. This thesis identified novel candidate genes for DD (CLCNKA), FJHN (CLDN3 and DENND4C) and FHH (KLOTHO) and revealed an approach for its potential successful application in the clinic for diagnosis.</p

Does the use of the combined oral contraceptive pill cause changes in the nasal physiology in young women?

The modern COCP has no significant effect on nasal physiology

Whole genome sequence analysis identifies a PAX2 mutation to establish a correct diagnosis for a syndromic form of hyperuricemia

Hereditary hyperuricemia may occur as part of a syndromic disorder or as an isolated nonsyndromic disease, and over 20 causative genes have been identified. Here, we report the use of whole genome sequencing (WGS) to establish a diagnosis in a family in which individuals were affected with gout, hyperuricemia associated with reduced fractional excretion of uric acid, chronic kidney disease (CKD), and secondary hyperparathyroidism, that are consistent with familial juvenile hyperuricemic nephropathy (FJHN). However, single gene testing had not detected mutations in the uromodulin (UMOD) or renin (REN) genes, which cause approximately 30–90% of FJHN. WGS was therefore undertaken, and this identified a heterozygous c.226G>C (p.Gly76Arg) missense variant in the paired box gene 2 (PAX2) gene, which co‐segregated with renal tubulopathy in the family. PAX2 mutations are associated with renal coloboma syndrome (RCS), which is characterized by abnormalities in renal structure and function, and anomalies of the optic nerve. Ophthalmological examination in two adult brothers affected with hyperuricemia, gout, and CKD revealed the presence of optic disc pits, consistent with optic nerve coloboma, thereby revising the diagnosis from FJHN to RCS. Thus, our results demonstrate the utility of WGS analysis in establishing the correct diagnosis in disorders with multiple etiologies