The annotation of GBA1 has been concealed by its protein-coding pseudogene GBAP1.

Mutations in GBA1 cause Gaucher disease and are the most important genetic risk factor for Parkinson's disease. However, analysis of transcription at this locus is complicated by its highly homologous pseudogene, GBAP1. We show that >50% of short RNA-sequencing reads mapping to GBA1 also map to GBAP1. Thus, we used long-read RNA sequencing in the human brain, which allowed us to accurately quantify expression from both GBA1 and GBAP1. We discovered significant differences in expression compared to short-read data and identify currently unannotated transcripts of both GBA1 and GBAP1. These included protein-coding transcripts from both genes that were translated in human brain, but without the known lysosomal function-yet accounting for almost a third of transcription. Analyzing brain-specific cell types using long-read and single-nucleus RNA sequencing revealed region-specific variations in transcript expression. Overall, these findings suggest nonlysosomal roles for GBA1 and GBAP1 with implications for our understanding of the role of GBA1 in health and disease.

A data-driven single-cell and spatial transcriptomic map of the human prefrontal cortex.

The molecular organization of the human neocortex historically has been studied in the context of its histological layers. However, emerging spatial transcriptomic technologies have enabled unbiased identification of transcriptionally defined spatial domains that move beyond classic cytoarchitecture. We used the Visium spatial gene expression platform to generate a data-driven molecular neuroanatomical atlas across the anterior-posterior axis of the human dorsolateral prefrontal cortex. Integration with paired single-nucleus RNA-sequencing data revealed distinct cell type compositions and cell-cell interactions across spatial domains. Using PsychENCODE and publicly available data, we mapped the enrichment of cell types and genes associated with neuropsychiatric disorders to discrete spatial domains.

hadge: a comprehensive pipeline for donor deconvolution in single-cell studies.

Single-cell multiplexing techniques (cell hashing and genetic multiplexing) combine multiple samples, optimizing sample processing and reducing costs. Cell hashing conjugates antibody-tags or chemical-oligonucleotides to cell membranes, while genetic multiplexing allows to mix genetically diverse samples and relies on aggregation of RNA reads at known genomic coordinates. We develop hadge (hashing deconvolution combined with genotype information), a Nextflow pipeline that combines 12 methods to perform both hashing- and genotype-based deconvolution. We propose a joint deconvolution strategy combining best-performing methods and demonstrate how this approach leads to the recovery of previously discarded cells in a nuclei hashing of fresh-frozen brain tissue.

RAB32 Ser71Arg in autosomal dominant Parkinson's disease: linkage, association, and functional analyses.

BACKGROUND: Parkinson's disease is a progressive neurodegenerative disorder with multifactorial causes, among which genetic risk factors play a part. The RAB GTPases are regulators and substrates of LRRK2, and variants in the LRRK2 gene are important risk factors for Parkinson's disease. We aimed to explore genetic variability in RAB GTPases within cases of familial Parkinson's disease. METHODS: We did whole-exome sequencing in probands from families in Canada and Tunisia with Parkinson's disease without a genetic cause, who were recruited from the Centre for Applied Neurogenetics (Vancouver, BC, Canada), an international consortium that includes people with Parkinson's disease from 36 sites in 24 countries. 61 RAB GTPases were genetically screened, and candidate variants were genotyped in relatives of the probands to assess disease segregation by linkage analysis. Genotyping was also done to assess variant frequencies in individuals with idiopathic Parkinson's disease and controls, matched for age and sex, who were also from the Centre for Applied Neurogenetics but unrelated to the probands or each other. All participants were aged 18 years or older. The sequencing and genotyping findings were validated by case-control association analyses using bioinformatic data obtained from publicly available clinicogenomic databases (AMP-PD, GP2, and 100 000 Genomes Project) and a private German clinical diagnostic database (University of Tübingen). Clinical and pathological findings were summarised and haplotypes were determined. In-vitro studies were done to investigate protein interactions and enzyme activities. FINDINGS: Between June 1, 2010, and May 31, 2017, 130 probands from Canada and Tunisia (47 [36%] female and 83 [64%] male; mean age 72·7 years [SD 11·7; range 38-96]; 109 White European ancestry, 18 north African, two east Asian, and one Hispanic] underwent whole-exome sequencing. 15 variants in RAB GTPase genes were identified, of which the RAB32 variant c.213C>G (Ser71Arg) cosegregated with autosomal dominant Parkinson's disease in three families (nine affected individuals; non-parametric linkage Z score=1·95; p=0·03). 2604 unrelated individuals with Parkinson's disease and 344 matched controls were additionally genotyped, and five more people originating from five countries (Canada, Italy, Poland, Turkey, and Tunisia) were identified with the RAB32 variant. From the database searches, in which 6043 individuals with Parkinson's disease and 62 549 controls were included, another eight individuals were identified with the RAB32 variant from four countries (Canada, Germany, UK, and USA). Overall, the association of RAB32 c.213C>G (Ser71Arg) with Parkinson's disease was significant (odds ratio [OR] 13·17, 95% CI 2·15-87·23; p=0·0055; I2=99·96%). In the people who had the variant, Parkinson's disease presented at age 54·6 years (SD 12·75, range 31-81, n=16), and two-thirds had a family history of parkinsonism. RAB32 Ser71Arg heterozygotes shared a common haplotype, although penetrance was incomplete. Findings in one individual at autopsy showed sparse neurofibrillary tangle pathology in the midbrain and thalamus, without Lewy body pathology. In functional studies, RAB32 Arg71 activated LRRK2 kinase to a level greater than RAB32 Ser71. INTERPRETATION: RAB32 Ser71Arg is a novel genetic risk factor for Parkinson's disease, with reduced penetrance. The variant was found in individuals with Parkinson's disease from multiple ethnic groups, with the same haplotype. In-vitro assays show that RAB32 Arg71 activates LRRK2 kinase, which indicates that genetically distinct causes of familial parkinsonism share the same mechanism. The discovery of RAB32 Ser71Arg also suggests several genetically inherited causes of Parkinson's disease originated to control intracellular immunity. This shared aetiology should be considered in future translational research, while the global epidemiology of RAB32 Ser71Arg needs to be assessed to inform genetic counselling. FUNDING: National Institutes of Health, the Canada Excellence Research Chairs program, Aligning Science Across Parkinson's, the Michael J Fox Foundation for Parkinson's Research, and the UK Medical Research Council.

A pathogenic variant in RAB32 causes autosomal dominant Parkinson's disease and activates LRRK2 kinase.

Background: Parkinson's disease (PD) is a progressive neurodegenerative disorder. Mendelian forms have revealed multiple genes, with a notable emphasis on membrane trafficking; RAB GTPases play an important role in PD as a subset are both regulators and substrates of LRRK2 protein kinase. To explore the role of RAB GTPases in PD, we undertook a comprehensive examination of their genetic variability in familial PD. Methods: Affected probands from 130 multi-incident PD families underwent whole-exome sequencing and genotyping, Potential pathogenic variants in 61 RAB GTPases were genotyped in relatives to assess disease segregation. These variants were also genotyped in a larger case-control series, totaling 3,078 individuals (2,734 with PD). The single most significant finding was subsequently validated within genetic data (6,043 with PD). Clinical and pathologic findings were summarized for gene-identified patients, and haplotypes were constructed. In parallel, wild-type and mutant RAB GTPase structural variation, protein interactions, and resultant enzyme activities were assessed. Findings: We found RAB32 c.213C>G (Ser71Arg) to co-segregate with autosomal dominant parkinsonism in three multi-incident families. RAB32 Ser71Arg was also significantly associated with PD in case-control samples: genotyping and database searches identified thirteen more patients with the same variant that was absent in unaffected controls. Notably, RAB32 Ser71Arg heterozygotes share a common haplotype. At autopsy, one patient had sparse neurofibrillary tangle pathology in the midbrain and thalamus, without Lewy body pathology. In transfected cells the RAB32 Arg71 was twice as potent as Ser71 wild type to activate LRRK2 kinase. Interpretation: Our study provides unequivocal evidence to implicate RAB32 Ser71Arg in PD. Functional analysis demonstrates LRRK2 kinase activation. We provide a mechanistic explanation to expand and unify the etiopathogenesis of monogenic PD. Funding: National Institutes of Health, the Canada Excellence Research Chairs program, Aligning Science Across Parkinson's, the Michael J. Fox Foundation for Parkinson's Research, and the UK Medical Research Council.

escheR: unified multi-dimensional visualizations with Gestalt principles.

Summary: The creation of effective visualizations is a fundamental component of data analysis. In biomedical research, new challenges are emerging to visualize multi-dimensional data in a 2D space, but current data visualization tools have limited capabilities. To address this problem, we leverage Gestalt principles to improve the design and interpretability of multi-dimensional data in 2D data visualizations, layering aesthetics to display multiple variables. The proposed visualization can be applied to spatially-resolved transcriptomics data, but also broadly to data visualized in 2D space, such as embedding visualizations. We provide an open source R package escheR, which is built off of the state-of-the-art ggplot2 visualization framework and can be seamlessly integrated into genomics toolboxes and workflows. Availability and implementation: The open source R package escheR is freely available on Bioconductor (https://bioconductor.org/packages/escheR).

aws-s3-integrity-check: an open-source bash tool to verify the integrity of a dataset stored on Amazon S3.

Amazon Simple Storage Service (Amazon S3) is a widely used platform for storing large biomedical datasets. Unintended data alterations can occur during data writing and transmission, altering the original content and generating unexpected results. However, no open-source and easy-to-use tool exists to verify end-to-end data integrity. Here, we present aws-s3-integrity-check, a user-friendly, lightweight, and reliable bash tool to verify the integrity of a dataset stored in an Amazon S3 bucket. Using this tool, we only needed ∼114 min to verify the integrity of 1,045 records ranging between 5 bytes and 10 gigabytes and occupying ∼935 gigabytes of the Amazon S3 cloud. Our aws-s3-integrity-check tool also provides file-by-file on-screen and log-file-based information about the status of each integrity check. To our knowledge, this tool is the only open-source one that allows verifying the integrity of a dataset uploaded to the Amazon S3 Storage quickly, reliably, and efficiently. The tool is freely available for download and use at https://github.com/SoniaRuiz/aws-s3-integrity-check and https://hub.docker.com/r/soniaruiz/aws-s3-integrity-check.

Pneumomediastinum after Third Molar Extraction: Case Report, Physiopathology, and Literature Review.

Wisdom tooth extraction is a common procedure in dentistry and stomatology. Subcutaneous emphysema is a rare postoperative complication and commonly remains localized. However, it may spread to the mediastinum, endangering the life of the patient. This present paper presents a case study of pneumomediastinum after wisdom tooth extraction without the use of a compressed air turbine and reviews the cases of subcutaneous emphysema after third molar extraction published in the literature since 2010. The aim of this work is to inform preventive measures, pathophysiological processes, and management related to this complication.

Age-related telomere attrition in the human putamen.

Age is a major risk factor for neurodegenerative diseases. Shortening of leucocyte telomeres with advancing age, arguably a measure of "biological" age, is a known phenomenon and epidemiologically correlated with age-related disease. The main mechanism of telomere shortening is cell division, rendering telomere length in post-mitotic cells presumably stable. Longitudinal measurement of human brain telomere length is not feasible, and cross-sectional cortical brain samples so far indicated no attrition with age. Hence, age-related changes in telomere length in the brain and the association between telomere length and neurodegenerative diseases remain unknown. Here, we demonstrate that mean telomere length in the putamen, a part of the basal ganglia, physiologically shortens with age, like leukocyte telomeres. This was achieved by using matched brain and leukocyte-rich spleen samples from 98 post-mortem healthy human donors. Using spleen telomeres as a reference, we further found that mean telomere length was brain region-specific, as telomeres in the putamen were significantly shorter than in the cerebellum. Expression analyses of genes involved in telomere length regulation and oxidative phosphorylation revealed that both region- and age-dependent expression pattern corresponded with region-dependent telomere length dynamics. Collectively, our results indicate that mean telomere length in the human putamen physiologically shortens with advancing age and that both local and temporal gene expression dynamics correlate with this, pointing at a potential mechanism for the selective, age-related vulnerability of the nigro-striatal network.

escheR: Unified multi-dimensional visualizations with Gestalt principles.

The creation of effective visualizations is a fundamental component of data analysis. In biomedical research, new challenges are emerging to visualize multi-dimensional data in a 2D space, but current data visualization tools have limited capabilities. To address this problem, we leverage Gestalt principles to improve the design and interpretability of multi-dimensional data in 2D data visualizations, layering aesthetics to display multiple variables. The proposed visualization can be applied to spatially-resolved transcriptomics data, but also broadly to data visualized in 2D space, such as embedding visualizations. We provide an open source R package escheR, which is built off of the state-of-the-art ggplot2 visualization framework and can be seamlessly integrated into genomics toolboxes and workflows.

Epigenomic Blood-Based Early Detection of Pancreatic Cancer Employing Cell-Free DNA.

BACKGROUND & AIMS: Early detection of pancreatic cancer (PaC) can drastically improve survival rates. Approximately 25% of subjects with PaC have type 2 diabetes diagnosed within 3 years prior to the PaC diagnosis, suggesting that subjects with type 2 diabetes are at high risk of occult PaC. We have developed an early-detection PaC test, based on changes in 5-hydroxymethylcytosine (5hmC) signals in cell-free DNA from plasma. METHODS: Blood was collected from 132 subjects with PaC and 528 noncancer subjects to generate epigenomic and genomic feature sets yielding a predictive PaC signal algorithm. The algorithm was validated in a blinded cohort composed of 102 subjects with PaC, 2048 noncancer subjects, and 1524 subjects with non-PaCs. RESULTS: 5hmC differential profiling and additional genomic features enabled the development of a machine learning algorithm capable of distinguishing subjects with PaC from noncancer subjects with high specificity and sensitivity. The algorithm was validated with a sensitivity for early-stage (stage I/II) PaC of 68.3% (95% confidence interval [CI], 51.9%-81.9%) and an overall specificity of 96.9% (95% CI, 96.1%-97.7%). CONCLUSIONS: The PaC detection test showed robust early-stage detection of PaC signal in the studied cohorts with varying type 2 diabetes status. This assay merits further clinical validation for the early detection of PaC in high-risk individuals.

Integrated single cell and unsupervised spatial transcriptomic analysis defines molecular anatomy of the human dorsolateral prefrontal cortex.

Generation of a molecular neuroanatomical map of the human prefrontal cortex reveals novel spatial domains and cell-cell interactions relevant for psychiatric disease. The molecular organization of the human neocortex has been historically studied in the context of its histological layers. However, emerging spatial transcriptomic technologies have enabled unbiased identification of transcriptionally-defined spatial domains that move beyond classic cytoarchitecture. Here we used the Visium spatial gene expression platform to generate a data-driven molecular neuroanatomical atlas across the anterior-posterior axis of the human dorsolateral prefrontal cortex (DLPFC). Integration with paired single nucleus RNA-sequencing data revealed distinct cell type compositions and cell-cell interactions across spatial domains. Using PsychENCODE and publicly available data, we map the enrichment of cell types and genes associated with neuropsychiatric disorders to discrete spatial domains. Finally, we provide resources for the scientific community to explore these integrated spatial and single cell datasets at research.libd.org/spatialDLPFC/.

Photizo: an open-source library for cross-sample analysis of FTIR spectroscopy data.

MOTIVATION: With continually improved instrumentation, Fourier transform infrared (FTIR) microspectroscopy can now be used to capture thousands of high-resolution spectra for chemical characterization of a sample. The spatially resolved nature of this method lends itself well to histological profiling of complex biological specimens. However, current software can make joint analysis of multiple samples challenging and, for large datasets, computationally infeasible. RESULTS: To overcome these limitations, we have developed Photizo-an open-source Python library enabling high-throughput spectral data pre-processing, visualization and downstream analysis, including principal component analysis, clustering, macromolecular quantification and mapping. Photizo can be used for analysis of data without a spatial component, as well as spatially resolved data, obtained e.g. by scanning mode IR microspectroscopy and IR imaging by focal plane array detector. AVAILABILITY AND IMPLEMENTATION: The code underlying this article is available at https://github.com/DendrouLab/Photizo with access to example data available at https://zenodo.org/record/6417982#.Yk2O9TfMI6A.

No strong HLA association with MOG antibody disease in the UK population.

Improvements in assays for detecting serum antibodies against myelin oligodendrocyte glycoprotein (MOG) have led to the appreciation of MOG-antibody-associated disease (MOGAD) as a novel disorder. However, much remains unknown about its etiology. We performed human leukocyte antigen (HLA) analysis in 82 MOGAD patients of European ancestry in the UK population. No HLA class II associations were observed, thus questioning the mechanism of anti-MOG antibody generation. A weak protective association of HLA-C*03:04 was observed (OR = 0.26, 95% CI = 0.10-0.71, pc  = 0.013), suggesting a need for continued efforts to better understand MOGAD genetics and pathophysiology.

Mechanisms of calcification in Fahr disease and exposure of potential therapeutic targets.

PURPOSE OF REVIEW: There is growing interest in disorders involved in ectopic mineralization. Fahr disease or idiopathic basal ganglia calcification can serve as a model for ectopic mineralization in the basal ganglia, which is fairly common in the general population. In this review, we will focus on causative gene mutations and corresponding pathophysiologic pathways in Fahr disease. RECENT FINDINGS: Patients with Fahr disease have a variability of symptoms, such as movement disorders, psychiatric signs, and cognitive impairment, but can also be asymptomatic. Fahr disease is mostly autosomal dominant inherited, and there are mutations found in 4 causative genes. Mutations in SLC20A2 and XPR1 lead to a disrupted phosphate metabolism involving brain-specific inorganic phosphate transporters. Mutations in PDGFB and PDGFRB are associated with disrupted blood-brain barrier integrity and dysfunctional pericyte maintenance. In addition, the MYORG gene has recently been discovered to be involved in the autosomal recessive inheritance of Fahr. SUMMARY: Knowledge about the mutations and corresponding pathways may expose therapeutic opportunities for patients with Fahr disease and vascular calcifications in the brain in general.

Death education for children and young people in public schools.

BACKGROUND: Conversations about death are often associated with fear, anxiety, avoidance and misunderstandings. Many adults feel that these discussions are inappropriate and confusing for young people. In this project, two fourth-year nursing students partnered with a local palliative care team to examine death education for children. The nursing students focused on children's understandings of death and their coping abilities, the lack of appropriate discussions about death with children, and the implementation of death education in public schools. Three online death education resources were identified and evaluated for use in public schools. This project fueled preliminary local discussions and advocacy efforts in the provision of death education for children. In the future, death education will need to be incorporated into education plans at local schools, and could be done in collaboration with the local palliative care team.

Inequity in California's Smokefree Workplace Laws: A Legal Epidemiologic Analysis of Loophole Closures.

INTRODUCTION: California's landmark 1994 Smokefree Workplace Act contained numerous exemptions, or loopholes, believed to contribute to inequities in smokefree air protections among low-income communities and communities of color (e.g., permitting smoking in warehouses, hotel common areas). Cities/counties were not prevented from adopting stronger laws. This study coded municipal laws and state law changes (in 2015-2016) for loophole closures and determined their effects in reducing inequities in smokefree workplace protections. METHODS: Public health attorneys reviewed current laws for 536 of California's 539 cities and counties from January 2017 to May 2018 and coded for 19 loophole closures identified from legislative actions (inter-rater reliability, 87%). The local policy data were linked with population demographics from intercensal estimates (2012-2016) and adult smoking prevalence (2014). The analyses were cross-sectional and conducted in February-June 2019. RESULTS: Between 1994 and 2018, jurisdictions closed 6.09 loopholes on average (SD=5.28). Urban jurisdictions closed more loopholes than rural jurisdictions (mean=6.40 vs 3.94, p<0.001), and loophole closure scores correlated positively with population size, median household income, and percentage white, non-Hispanic residents (p<0.001 for all). Population demographics and the loophole closure score explained 43% of the variance in jurisdictions' adult smoking prevalence. State law changes in 2015-2016 increased loophole closure scores and decreased jurisdiction variation (mean=9.74, SD=3.56); closed more loopholes in rural versus urban jurisdictions (meangain=4.44 vs 3.72, p=0.002); and in less populated, less affluent jurisdictions, with greater racial/ethnic diversity, and higher smoking prevalence (p<0.001 for all). CONCLUSIONS: Although jurisdictions made important progress in closing loopholes in smokefree air law, state law changes achieved greater reductions in inequities in policy coverage.

Complete Response to Dual Immunotherapy in a Young Adult with Metastatic Alveolar Soft Part Sarcoma Enabled by a Drug Recovery Program in a Community Practice.

Alveolar soft part sarcoma (ASPS) is an extremely rare tumor that frequently occurs in adolescent and young adults (AYA). Survival is poor for patients with metastatic and/or relapsed disease not amenable to local control, and limited therapeutic options are available. A major barrier to cancer care in the United States AYA population is lack of access to coordinated care and appropriate therapies for those who lack insurance or who are underinsured. We report a 25-year-old unemployed, uninsured, single mother who presented with a 12.8 × 21 cm soft tissue thigh mass with heterogeneous avidity, max standardized uptake value of 9, with metastatic disease to the ipsilateral inguinal lymph nodes and to the bilateral lungs. After local control of the primary mass was obtained, a recently developed, comprehensive drug replacement program (DRP) was used to gain access to nivolumab, and after frank progression was noted, ipilimumab was added every 6 weeks. No biomarkers associated with response to immunotherapy were identified. After four cycles, a complete response was observed and patient remains disease free 36 months after beginning dual immunotherapy treatment. We obtained immunotherapy agents through a DRP and describe the development and the utility of this program in the community setting. Our report highlights both first documented sustained complete response to sequenced immunotherapy in an AYA with ASPS as well as a comprehensive DRP, which enabled access to therapy for our patient.

Real-world lung cancer screening decision-making: Barriers and facilitators.

OBJECTIVE: To explore 1) attitudes and priorities among physicians and patients that inform shared decision-making about lung cancer screening in real-world settings and 2) physician and patient perceptions of shared decision-making in real-world lung cancer screening (LCS) practice. MATERIALS AND METHODS: We conducted a qualitative study of 12 physicians and 30 patients meeting LCS screening criteria established by the US Preventative Services Task Force (USPSTF) from two academic primary care practices; one university clinic and one safety net clinic. Interview guides focused on knowledge and attitudes about LCS and experiences with patient-physician communication. RESULTS: Physicians offered LCS inconsistently and were ambivalent about screening because of potential harms, including false positive results, incidental findings, and radiation exposure. Physicians felt that they were incorporating shared decision-making into screening, although they acknowledged that challenges with screening communication posed barriers to shared decision-making. Patients were generally accepting of lung cancer screening. They expressed fewer concerns about screening-related harms but more personal or emotional concerns related to lung cancer. Patients perceived limited shared decision-making in their encounters, but were generally satisfied with the more physician-directed decision-making process. CONCLUSION: Physicians and patients expressed different concerns about LCS and different perceptions about the use of shared decision-making. Findings from this real-world population of screening-eligible patients can be used to inform the design of future interventions to facilitate communication and decision-making tailored to perspectives of both physicians and patients.

Real world usage characteristics of a novel mobile health self-monitoring device: Results from the Scanadu Consumer Health Outcomes (SCOUT) Study.

A wide range of personal wireless health-related sensor devices are being developed with hope of improving health management. Factors related to effective user engagement, however, are not well-known. We sought to identify factors associated with consistent long-term use of the Scanadu Scout multi-parameter vital sign monitor among individuals who invested in the device through a crowd-funding campaign. Email invitations to join the study were sent to 4525 crowd-funding participants from the US. Those completing a baseline survey were sent a device with follow-up surveys at 3, 12, and 18 months. Of 3872 participants receiving a device, 3473 used it during Week 1, decreasing to 1633 (47 percent) in Week 2. Median time from first use of the device to last use was 17 weeks (IQR: 5-51 weeks) and median uses per week was 1.0 (IQR: 0.6-2.0). Consistent long-term use (defined as remaining in the study at least 26 weeks with at least 3 recordings per week during at least 80% of weeks) was associated with older age, not having children in the household, and frequent use of other medical devices. In the subset of participants answering the 12-month survey (n = 1222), consistent long-term users were more likely to consider the device easy to use and to share results with a healthcare provider. Thirty percent of this subset overall reported improved diet or exercise habits and 25 percent considered medication changes in response to device results. The study shows that even among investors in a device, frequency of device usage fell off rapidly. Understanding how to improve the value of information from personal health-related sensors will be critical to their successful implementation in care.