ROS1 Alterations as a Potential Driver of Gliomas in Infant, Pediatric, and Adult Patients.

Gliomas harboring oncogenic ROS1 alterations are uncommon and primarily described in infants. Our goal was to characterize the clinicopathological features and molecular signatures of the full spectrum of ROS1 fusion-positive gliomas across all age groups. Through a retrospective multi-institutional collaboration, we report a collection of unpublished ROS1 fusion gliomas along with the characterization and meta-analysis of new and published cases. A cohort of 32 new and 58 published cases was divided into the following 3 age groups: 19 infants, 40 pediatric patients, and 31 adults with gliomas. Tumors in infants and adults showed uniformly high-grade morphology; however, tumors in pediatric patients exhibited diverse histologic features. The GOPC::ROS1 fusion was prevalent (61/79, 77%) across all age groups, and 10 other partner genes were identified. Adult tumors showed recurrent genomic alterations characteristic of IDH wild-type glioblastoma, including the +7/-10/CDKN2A deletion; amplification of CDK4, MDM2, and PDGFRA genes; and mutations involving TERTp, TP53, PIK3R1, PIK3CA, PTEN, and NF1 genes. Infant tumors showed few genomic alterations, whereas pediatric tumors showed moderate genomic complexity. The outcomes were significantly poorer in adult patients. Although not statistically significant, tumors in infant and pediatric patients with high-grade histology and in hemispheric locations appeared more aggressive than tumors with lower grade histology or those in nonhemispheric locations. In conclusion, this study is the largest to date to characterize the clinicopathological and molecular signatures of ROS1 fusion-positive gliomas from infant, pediatric, and adult patients. We conclude that ROS1 likely acts as a driver in infant and pediatric gliomas and as a driver or codriver in adult gliomas. Integrated comprehensive clinical testing might be helpful in identifying such patients for possible targeted therapy.

Surgical management of symptomatic hemangioma of the geniculate ganglion: fascicular-sparing resection or grafting?

Geniculate ganglion hemangioma (GGH) is rarely presented in the neurosurgical literature. It extends extradurally on the middle fossa floor and displaces the intratemporal part of the facial nerve. Surgical treatment is advisable at early symptoms. Proposed techniques include fascicular-sparing resection or nerve interruption with grafting. No definitive conclusions exist about the superiority of a certain technique in preserving facial nerve integrity and function. Through the description of a surgically managed symptomatic GGH, we herein discuss literature data about the surgical results of fascicular-sparing resection versus grafting. A PRISMA-based literature search was performed on the PubMed database. Only articles in English and published since 1990 were selected and furtherly filtered based on the best relevance. Statistical comparisons were performed with ANOVA. One hundred sixteen GGHs were collected, 56 were treated by fascicular-sparing resection, and 60 were treated by grafting. The facial function was improved, or unchanged, in 53 patients of the fascicular-sparing group and 30 patients of the grafting one. Sixty-five patients achieved a good (House-Brackmann (HB) grade III) postoperative facial outcome, of which 47 and 18 belonged to the fascicular-sparing and grafting group, respectively. Greater efficacy of the fascicular-sparing technique in the achievement of a better facial outcome was found (p = 0.0014; p = 0.0022). A surgical resection at the earliest symptoms is critical to preserve the facial nerve function in GGHs. Fascicular-sparing resection should be pursued in symptomatic cases with residual facial function (I-III HB). Conversely, grafting has a rationale for higher HB grades (V-VI). Broader studies are required to confirm these findings and turn them into new therapeutic perspectives.

Supporting farmer wellbeing: exploring a potential role for farm advisory staff.

INTRODUCTION: Farmers in Ireland experience poor health outcomes and are considered 'hard to reach'. Agricultural advisors ('advisors') are uniquely positioned to support and signpost farmers on health issues. This paper explores the acceptability and terms of reference of a potential health role for advisors, and offers key recommendations for developing a bespoke farmers' health training programme. METHODS: Following ethical approval, eleven focus groups (n=26 female, n=35 male, age-range 20s-70s) were conducted with farmers (n=4), advisors (n=4), farming organisations (n=2) and farmers' 'significant others' (n=1). Utilizing Thematic Content Analysis, transcripts were coded iteratively and emerging themes were grouped into primary and subthemes. RESULTS: Our analysis identified three themes. 'Scope and acceptability of a potential health role for advisors' examines how participants envision and are receptive to such a role. 'Roles, responsibilities and boundaries' considers both a health promotion and 'health connector' advisory role - normalising health conversations and signposting farmers to services/supports. Finally, 'trouble-shooting potential obstacles to advisors assuming a health role' reflects on the barriers that may impede advisors capacity or potential to have a broader health role. DISCUSSION: Within the context of the stress process theory, findings provide unique insights into how advisory can mediate stress and contribute to farmers' health and wellbeing. Finally, findings have important implications for potentially extending the reach of training to other aspects of farming support services (eg agri-banking, agri-business, veterinary services etc.), as well as serving as a springboard for the development of similar initiatives in other jurisdictions.

Does farming experience matter? A comparison of farm health and safety attitudes, perceptions, and intentions of agricultural science students with and without farming experience.

INTRODUCTION: This study addresses two main questions: 'How does having the experience of farming influence college students' intrinsic motivations towards farm health and safety (FHS)?' and 'Are there any differences between the motivations reported by students with and without having such experience?'. This study seeks to investigate the role of farming experience in students' cognitive factors and intentions to evaluate whether sharing experiences and stories positively shape students' cognitive factors to perform FHS behaviours. METHODS: A cross-sectional online survey using a semi-structured questionnaire was assigned to a nationally representative sample of agricultural science students in Ireland (n= 430). Applying independent sample t-test and ANOVA test, multiple comparisons were made to examine if having the experience of farming affects FHS intrinsic motivations. RESULTS: This study illustrated students without farming experience are less likely to perceive farming as a dangerous occupation while they reported a slightly positive attitude and intention compared with their counterparts with experience of farming. Our study illustrated students with experience of farming gave a lower priority to FHS and control over safety behaviour (pessimistic approach) and they reported a slightly higher level of risk perception (optimistic perception). DISCUSSION: Having experience of farming (destructive experience - the experience of farming without having a near miss or injury or having heard of accidents, ie negative factors affecting students' motivations) may not be necessarily a positive factor as risk-taking is admitted as a norm and a part of the nature of the work. Conversely, having experience of FHS issues (constructive experience - any kind of farming experience that positively shapes students' motivations towards FHS) can positively shape attitude, perceptions, and intention. Therefore, we recommend that constructive experiences (positive affecting intrinsic motivations) should be incorporated into the FHS training of students through peer-to-peer sharing as this enhances attitudes, perceptions, and willingness of the majority of students.

Quantification of aneuploidy in targeted sequencing data using ASCETS.

SUMMARY: The expansion of targeted panel sequencing efforts has created opportunities for large-scale genomic analysis, but tools for copy-number quantification on panel data are lacking. We introduce ASCETS, a method for the efficient quantitation of arm and chromosome-level copy-number changes from targeted sequencing data. AVAILABILITY AND IMPLEMENTATION: ASCETS is implemented in R and is freely available to non-commercial users on GitHub: https://github.com/beroukhim-lab/ascets, along with detailed documentation. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

DICER1 mutations in primary central nervous system tumors: new insights into histologies, mutations, and prognosis.

PURPOSE: We sought to characterize clinical outcomes for adult and pediatric patients with primary CNS tumors harboring DICER1 mutations or loss of DICER1. METHODS: We conducted a retrospective cohort study of 98 patients who were treated between 1995 and 2020 for primary CNS tumors containing DICER1 mutations or loss of DICER1 on chromosome 14q, identified by targeted next generation sequencing. Kaplan-Meier plots and log rank tests were used to analyze survival. Cox proportional-hazards model was used for univariate and multivariable analyses for all-cause mortality (ACM). RESULTS: Within our cohort, the most common malignancies were grade 3/4 glioma (61%), grade 1/2 glioma (17%), and CNS sarcoma (6%). Sarcoma and non-glioma histologies, and tumors with biallelic DICER1 mutations or deletions were common in the pediatric population. Mutations occurred throughout DICER1, including missense mutations in the DexD/H-box helicase, DUF283, RNaseIIIa, and RNaseIIIb domains. For patients with grade 3/4 glioma, MGMT methylation (Hazard ratio [HR] 0.35, 95% Confidence Interval [CI] 0.16-0.73, p = 0.005), IDH1 R132 mutation (HR 0.11, 95% CI 0.03-0.41, p = 0.001), and missense mutation in the DexD/H-box helicase domain (HR 0.06, 95% CI 0.01-0.38, p = 0.003) were independently associated with longer time to ACM on multivariable analyses. CONCLUSION: DICER1 mutations or loss of DICER1 occur in diverse primary CNS tumors, including previously unrecognized grade 3/4 gliomas as the most common histology. While prior studies have described RNaseIIIb hotspot mutations, we document novel mutations in additional DICER1 functional domains. Within the grade 3/4 glioma cohort, missense mutation in the DexD/H-box helicase domain was associated with prolonged survival.

IDH-mutant gliomas with additional class-defining molecular events.

The 2016 WHO classifies IDH-mutant gliomas into oligodendroglioma or diffuse astrocytoma based on co-occurring genetic events. Recent literature addresses the concept of stratifying IDH-mutant gliomas based on prognostically significant molecular events. However, the presence of a second class-defining driver alteration in IDH-mutant gliomas has not been systematically described. We searched the sequencing database at our institutions as well as The Cancer Genome Atlas (TCGA) and cBioPortal for IDH-mutant gliomas with other potentially significant alterations. For each case, we reviewed the clinical information, histology and genetic profile. Of 1702 gliomas tested on our targeted exome sequencing panel, we identified 364 IDH-mutated gliomas, four of which had pathogenic FGFR alterations and one with BRAF V600E mutation. Five additional IDH-mutant gliomas with NTRK fusions were identified through collaboration with an outside institution. Also, a search in the glioma database in cBioPortal (5379 total glioma samples, 1515 cases [28.1%] with IDH1/2 mutation) revealed eight IDH-mutated gliomas with FGFR, NTRK or BRAF pathogenic alterations. All IDH-mutant gliomas with dual mutations identified were hemispheric and had a mean age at diagnosis of 36.2 years (range 16-55 years old). Co-occurring genetic events involved MYCN, RB and PTEN. Notable outcomes included a patient with an IDH1/FGFR1-mutated anaplastic oligodendroglioma who has survived 20 years after diagnosis. We describe a series of 18 IDH-mutant gliomas with co-occurring genetic events that have been described as independent class-defining drivers in other gliomas. While these tumors are rare and the significance of these alterations needs further exploration, alterations in FGFR, NTRK, and BRAF could have potential therapeutic implications and affect clinical trial design and results in IDH-mutant studies. Our data highlights that single gene testing for IDH1 in diffuse gliomas may be insufficient for detection of targets with potential important prognostic and treatment value.

Subependymal giant cell astrocytomas are characterized by mTORC1 hyperactivation, a very low somatic mutation rate, and a unique gene expression profile.

Subependymal giant-cell astrocytomas (SEGAs) are slow-growing brain tumors that are a hallmark feature seen in 5-10% of patients with Tuberous Sclerosis Complex (TSC). Though histologically benign, they can cause serious neurologic symptoms, leading to death if untreated. SEGAs consistently show biallelic loss of TSC1 or TSC2. Herein, we aimed to define other somatic events beyond TSC1/TSC2 loss and identify potential transcriptional drivers that contribute to SEGA formation. Paired tumor-normal whole-exome sequencing was performed on 21 resected SEGAs from 20 TSC patients. Pathogenic variants in TSC1/TSC2 were identified in 19/21 (90%) SEGAs. Copy neutral loss of heterozygosity (size range: 2.2-46 Mb) was seen in 76% (16/21) of SEGAs (44% chr9q and 56% chr16p). An average of 1.4 other somatic variants (range 0-7) per tumor were identified, unlikely of pathogenic significance. Whole transcriptome RNA-sequencing analyses revealed 190 common differentially expressed genes in SEGA (n = 16, 13 from a prior study) in pairwise comparison to each of: low grade diffuse gliomas (n = 530) and glioblastoma (n = 171) from The Cancer Genome Atlas (TCGA) consortium, ganglioglioma (n = 10), TSC cortical tubers (n = 15), and multiple normal tissues. Among these, homeobox transcription factors (TFs) HMX3, HMX2, VAX1, SIX3; and TFs IRF6 and EOMES were all expressed >12-fold higher in SEGAs (FDR/q-value < 0.05). Immunohistochemistry supported the specificity of IRF6, VAX1, SIX3 for SEGAs in comparison to other tumor entities and normal brain. We conclude that SEGAs have an extremely low somatic mutation rate, suggesting that TSC1/TSC2 loss is sufficient to drive tumor growth. The unique and highly expressed SEGA-specific TFs likely reflect the neuroepithelial cell of origin, and may also contribute to the transcriptional and epigenetic state that enables SEGA growth following two-hit loss of TSC1 or TSC2 and mTORC1 activation.

Loss of histone H3 trimethylation on lysine 27 and nuclear expression of transducin-like enhancer 1 in primary intracranial sarcoma, DICER1-mutant.

AIMS: Primary intracranial sarcoma, DICER1-mutant is a recently described central nervous system tumour with specific genomic and DNA-methylation profiles. Although some of its histological features (focal spindle-cell morphology, intracytoplasmic eosinophilic granules, and focal heterologous differentiation) are common across most reported cases, the presence of significant histological variability and the lack of differentiation pose diagnostic challenges. We aim to further define the immunoprofile of this tumor. METHODS AND RESULTS: We reviewed the clinical history and performed immunohistochemistry for glial fibrillary acidic protein, oligodendrocyte transcription factor 2, SOX2, SOX10, S100, histone H3 trimethylated on lysine 27 (H3K27me3), desmin, myogenin, CD99, epithelial membrane antigen (EMA) and transducin-like enhancer of split 1 (TLE1) on six primary intracranial sarcomas, DICER1-mutant, with appropriate controls. Targeted exome sequencing was performed on all cases. The sarcomas showed diffuse (n = 4), mosaic (n = 1) or minimal (≤5%, n = 1) loss of H3K27 trimethylation and nuclear TLE1 expression (n = 6). Four had immunohistochemical evidence of myogenic differentiation. SOX2, SOX10, S100 and EMA were negative; CD99 expression ranged from focal cytoplasmic (n = 4) to crisp diffuse membranous (n = 2). One tumour had focal cartilaginous differentiation. Similar immunohistochemical findings were observed in a pleuropulmonary blastoma (albeit with focal TLE1 expression), a DICER1-related pineoblastoma, and an embryonal tumour with a multilayered rosette-like DICER1-related cerebellar tumour. Targeted exome sequencing confirmed the presence of pathogenic biallelic DICER1 mutations in all tumours included in this study. CONCLUSION: We conclude that H3K27me3 and TLE1 immunostains, when utilised in combination, can be helpful diagnostic markers for primary intracranial sarcoma, DICER1-mutant.

Immune profiling of pituitary tumors reveals variations in immune infiltration and checkpoint molecule expression.

PURPOSE: Pituitary tumors are the second most common primary brain tumors. Functional tumors demonstrate increased PD-L1 expression, but expression of other checkpoint regulators has not been characterized. We sought to characterize the immune microenvironment of human pituitary tumors to identify new treatment opportunities. METHODS: 72 pituitary tumors were evaluated for expression of the immune regulatory markers programmed death ligand 1 (PD-L1), programmed death ligand 2 (PD-L2), V-domain Ig suppressor of T cell activation (VISTA), lymphocyte activation gene 3 (LAG3) and tumor necrosis factor receptor superfamily member 4 (OX40) by immunohistochemistry (IHC). Lymphocyte infiltration, macrophage infiltration, and angiogenesis were analyzed using IHC. Expression of pituitary tumor initiating cell marker CD15 and mismatch repair proteins MutS protein homolog 2 (MSH2) and MutS protein homolog 6 (MSH6) was also assessed. RESULTS: Pituitary tumors were infiltrated by macrophages and T cells, and they expressed varying levels of PD-L1, PD-L2, VISTA, LAG3, and OX40. Functional tumors and tumors with high expression of tumor stem cell markers had higher immune cell infiltration and greater expression of immunosuppressive checkpoint regulators. Increased PD-L1 and LAG3 and reduced VISTA were observed in primary tumors compared to recurrent tumors. CONCLUSION: Immune cell infiltration and checkpoint regulator expression vary depending on functional status and presence of pituitary tumor initiating cells. Functional tumors may have a particularly immunosuppressive microenvironment. Further studies of immune checkpoint blockade of pituitary tumors, particularly functional tumors, are warranted, though combination therapy may be required.

Characterization of molecular signatures of supratentorial ependymomas.

Ependymomas show poor correlation between World Health Organization grade and clinical outcome. A subgroup of supratentorial ependymomas are characterized by C11orf95-RELA fusions, presumed to be secondary to chromothripsis of chromosome 11, resulting in constitutive activation of the NF-κB signaling pathway and overexpression of cyclin D1, p65, and L1 cell adhesion molecule (L1CAM). These RELA-fused ependymomas are recognized as a separate, molecularly defined World Health Organization entity and might be associated with poor clinical outcome. In this study, we show that immunohistochemistry for NF-κB signaling components, such as L1CAM, p65, and cyclin D1, can help distinguish RELA-fused from non-RELA-fused supratentorial ependymomas. Furthermore, these three markers can reliably differentiate RELA-fused ependymomas from a variety of histologic mimics. Lastly, we report that RELA-fused ependymomas may be associated with different chromosomal copy number changes and molecular alterations compared to their non-RELA-fused counterparts, providing additional insight into the genetic pathogenesis of these tumors and potential targets for directed therapies.

Advances in Diagnostic Immunohistochemistry for Primary Tumors of the Central Nervous System.

As genomic characterization becomes increasingly necessary for accurate diagnosis of tumors of the central nervous system, identification of rapidly assessible biomarkers is equally important to avoid excessive cost and delay in initiation of therapy. This article reviews novel immunohistochemical markers that may be used to determine mutation status, activation of signaling pathways, druggable targets, and cell lineage in many diverse tumor types. In particular, recently added entities to the 2016 WHO classification of central nervous system tumors will be addressed, including IDH-mutant gliomas, diffuse midline glioma, epithelioid glioblastoma, angiocentric glioma, RELA-rearranged ependymoma, embryonal tumors (medulloblastoma, atypical teratoid/rhabdoid tumor, pineoblastoma, embryonal tumor with multilayered rosettes, and other genetically defined high-grade neuroepithelial tumors), and meningiomas associated with germline alterations.

Targetable genetic features of primary testicular and primary central nervous system lymphomas.

Primary central nervous system lymphomas (PCNSLs) and primary testicular lymphomas (PTLs) are extranodal large B-cell lymphomas (LBCLs) with inferior responses to current empiric treatment regimens. To identify targetable genetic features of PCNSL and PTL, we characterized their recurrent somatic mutations, chromosomal rearrangements, copy number alterations (CNAs), and associated driver genes, and compared these comprehensive genetic signatures to those of diffuse LBCL and primary mediastinal large B-cell lymphoma (PMBL). These studies identify unique combinations of genetic alterations in discrete LBCL subtypes and subtype-selective bases for targeted therapy. PCNSLs and PTLs frequently exhibit genomic instability, and near-uniform, often biallelic, CDKN2A loss with rare TP53 mutations. PCNSLs and PTLs also use multiple genetic mechanisms to target key genes and pathways and exhibit near-uniform oncogenic Toll-like receptor signaling as a result of MYD88 mutation and/or NFKBIZ amplification, frequent concurrent B-cell receptor pathway activation, and deregulation of BCL6. Of great interest, PCNSLs and PTLs also have frequent 9p24.1/PD-L1/PD-L2 CNAs and additional translocations of these loci, structural bases of immune evasion that are shared with PMBL.

Regulating the dorsal neural tube expression of Ptf1a through a distal 3' enhancer.

Generating the correct balance of inhibitory and excitatory neurons in a neural network is essential for normal functioning of a nervous system. The neural network in the dorsal spinal cord functions in somatosensation where it modulates and relays sensory information from the periphery. PTF1A is a key transcriptional regulator present in a specific subset of neural progenitor cells in the dorsal spinal cord, cerebellum and retina that functions to specify an inhibitory neuronal fate while suppressing excitatory neuronal fates. Thus, the regulation of Ptf1a expression is critical for determining mechanisms controlling neuronal diversity in these regions of the nervous system. Here we identify a sequence conserved, tissue-specific enhancer located 10.8kb 3' of the Ptf1a coding region that is sufficient to direct expression to dorsal neural tube progenitors that give rise to neurons in the dorsal spinal cord in chick and mouse. DNA binding motifs for Paired homeodomain (Pd-HD) and zinc finger (ZF) transcription factors are required for enhancer activity. Mutations in these sequences implicate the Pd-HD motif for activator function and the ZF motif for repressor function. Although no repressor transcription factor was identified, both PAX6 and SOX3 can increase enhancer activity in reporter assays. Thus, Ptf1a is regulated by active and repressive inputs integrated through multiple sequence elements within a highly conserved sequence downstream of the Ptf1a gene.

Hypothyroidism in utero stimulates pancreatic beta cell proliferation and hyperinsulinaemia in the ovine fetus during late gestation.

KEY POINTS: Thyroid hormones are important regulators of growth and maturation before birth, although the extent to which their actions are mediated by insulin and the development of pancreatic beta cell mass is unknown. Hypothyroidism in fetal sheep induced by removal of the thyroid gland caused asymmetric organ growth, increased pancreatic beta cell mass and proliferation, and was associated with increased circulating concentrations of insulin and leptin. In isolated fetal sheep islets studied in vitro, thyroid hormones inhibited beta cell proliferation in a dose-dependent manner, while high concentrations of insulin and leptin stimulated proliferation. The developing pancreatic beta cell is therefore sensitive to thyroid hormone, insulin and leptin before birth, with possible consequences for pancreatic function in fetal and later life. The findings of this study highlight the importance of thyroid hormones during pregnancy for normal development of the fetal pancreas. ABSTRACT: Development of pancreatic beta cell mass before birth is essential for normal growth of the fetus and for long-term control of carbohydrate metabolism in postnatal life. Thyroid hormones are also important regulators of fetal growth, and the present study tested the hypotheses that thyroid hormones promote beta cell proliferation in the fetal ovine pancreatic islets, and that growth retardation in hypothyroid fetal sheep is associated with reductions in pancreatic beta cell mass and circulating insulin concentration in utero. Organ growth and pancreatic islet cell proliferation and mass were examined in sheep fetuses following removal of the thyroid gland in utero. The effects of triiodothyronine (T3 ), insulin and leptin on beta cell proliferation rates were determined in isolated fetal ovine pancreatic islets in vitro. Hypothyroidism in the sheep fetus resulted in an asymmetric pattern of organ growth, pancreatic beta cell hyperplasia, and elevated plasma insulin and leptin concentrations. In pancreatic islets isolated from intact fetal sheep, beta cell proliferation in vitro was reduced by T3 in a dose-dependent manner and increased by insulin at high concentrations only. Leptin induced a bimodal response whereby beta cell proliferation was suppressed at the lowest, and increased at the highest, concentrations. Therefore, proliferation of beta cells isolated from the ovine fetal pancreas is sensitive to physiological concentrations of T3 , insulin and leptin. Alterations in these hormones may be responsible for the increased beta cell proliferation and mass observed in the hypothyroid sheep fetus and may have consequences for pancreatic function in later life.

A transcription factor network specifying inhibitory versus excitatory neurons in the dorsal spinal cord.

The proper balance of excitatory and inhibitory neurons is crucial for normal processing of somatosensory information in the dorsal spinal cord. Two neural basic helix-loop-helix transcription factors (TFs), Ascl1 and Ptf1a, have contrasting functions in specifying these neurons. To understand how Ascl1 and Ptf1a function in this process, we identified their direct transcriptional targets genome-wide in the embryonic mouse neural tube using ChIP-Seq and RNA-Seq. We show that Ascl1 and Ptf1a directly regulate distinct homeodomain TFs that specify excitatory or inhibitory neuronal fates. In addition, Ascl1 directly regulates genes with roles in several steps of the neurogenic program, including Notch signaling, neuronal differentiation, axon guidance and synapse formation. By contrast, Ptf1a directly regulates genes encoding components of the neurotransmitter machinery in inhibitory neurons, and other later aspects of neural development distinct from those regulated by Ascl1. Moreover, Ptf1a represses the excitatory neuronal fate by directly repressing several targets of Ascl1. Ascl1 and Ptf1a bind sequences primarily enriched for a specific E-Box motif (CAGCTG) and for secondary motifs used by Sox, Rfx, Pou and homeodomain factors. Ptf1a also binds sequences uniquely enriched in the CAGATG E-box and in the binding motif for its co-factor Rbpj, providing two factors that influence the specificity of Ptf1a binding. The direct transcriptional targets identified for Ascl1 and Ptf1a provide a molecular understanding of how these DNA-binding proteins function in neuronal development, particularly as key regulators of homeodomain TFs required for neuronal subtype specification.

Human metabolic individuality in biomedical and pharmaceutical research.

Genome-wide association studies (GWAS) have identified many risk loci for complex diseases, but effect sizes are typically small and information on the underlying biological processes is often lacking. Associations with metabolic traits as functional intermediates can overcome these problems and potentially inform individualized therapy. Here we report a comprehensive analysis of genotype-dependent metabolic phenotypes using a GWAS with non-targeted metabolomics. We identified 37 genetic loci associated with blood metabolite concentrations, of which 25 show effect sizes that are unusually high for GWAS and account for 10-60% differences in metabolite levels per allele copy. Our associations provide new functional insights for many disease-related associations that have been reported in previous studies, including those for cardiovascular and kidney disorders, type 2 diabetes, cancer, gout, venous thromboembolism and Crohn's disease. The study advances our knowledge of the genetic basis of metabolic individuality in humans and generates many new hypotheses for biomedical and pharmaceutical research.

Telling Tales: Using Vignettes to Overcome Optimism Bias in Farm Health and Safety Attitudinal Studies.

OBJECTIVE: Measuring attitudes of farmers to safe farming practices using quantitative causal relationship approaches is central to improving understanding of (un)safe practices. This knowledge is important in the development of effective farm safety interventions. However, the accuracy of quantitative attitudinal studies in explaining farmers' decision-making faces a potential measurement challenge, i.e. a high level of optimism bias. In this paper, we present research that develops and tests farm safety attitudinal questions that are framed around "real-life" farming practices with the objective of reducing optimism bias. METHODS: We apply construal level theory (CLT) to support the design of vignettes that reflect common risk scenarios faced by farmers. Applying qualitative analysis of 274 fatal farm incidents that occurred in Ireland between 2004 and 2018 we identify the occupational behaviors (what farmers do), social (who are farmers), spatial (where farming takes place), and temporal (when farming happens) dimensions of risks resulting in most deaths. The results informed subsequent co-design activities with farm safety experts and farm advisors to develop "real-life" scenarios, attitudinal questions, and response options. The questionnaire was piloted and subsequently implemented to collect data from a sample of 381 farmers with either tractors or livestock. The results of the survey were compared to previous attitudinal research on farmer's attitudes to safety in Ireland to establish if there was as follows: i) increased variance in the responses, and ii) a statistically significant difference in the attitudes of respondents compared to the results reported in previous studies. RESULTS: The findings established that when farmers were provided with real-life scenarios, their responses were less optimistic and more varied, i.e. there was a greater range of responses, compared to previous studies. CONCLUSION: Applying CTL to the development of attitudinal survey instruments anchors attitudinal questions within farming specific occupational, social, spatial, and temporal contexts. The use of vignettes that draw on real-life scenarios offers the potential for improved design of surveys that seek to understand farmer/worker practices. The results suggest that this approach can improve the measurement of attitudes to farm safety.