Identification and functional analysis of glycemic trait loci in the China Health and Nutrition Survey.

To identify genetic contributions to type 2 diabetes (T2D) and related glycemic traits (fasting glucose, fasting insulin, and HbA1c), we conducted genome-wide association analyses (GWAS) in up to 7,178 Chinese subjects from nine provinces in the China Health and Nutrition Survey (CHNS). We examined patterns of population structure within CHNS and found that allele frequencies differed across provinces, consistent with genetic drift and population substructure. We further validated 32 previously described T2D- and glycemic trait-loci, including G6PC2 and SIX3-SIX2 associated with fasting glucose. At G6PC2, we replicated a known fasting glucose-associated variant (rs34177044) and identified a second signal (rs2232326), a low-frequency (4%), probably damaging missense variant (S324P). A variant within the lead fasting glucose-associated signal at SIX3-SIX2 co-localized with pancreatic islet expression quantitative trait loci (eQTL) for SIX3, SIX2, and three noncoding transcripts. To identify variants functionally responsible for the fasting glucose association at SIX3-SIX2, we tested five candidate variants for allelic differences in regulatory function. The rs12712928-C allele, associated with higher fasting glucose and lower transcript expression level, showed lower transcriptional activity in reporter assays and increased binding to GABP compared to the rs12712928-G, suggesting that rs12712928-C contributes to elevated fasting glucose levels by disrupting an islet enhancer, resulting in reduced gene expression. Taken together, these analyses identified multiple loci associated with glycemic traits across China, and suggest a regulatory mechanism at the SIX3-SIX2 fasting glucose GWAS locus.

Genetic model of MS severity predicts future accumulation of disability.

No genetic modifiers of multiple sclerosis (MS) severity have been independently validated, leading to a lack of insight into genetic determinants of the rate of disability progression. We investigated genetic modifiers of MS severity in prospectively acquired training (N = 205) and validation (N = 94) cohorts, using the following advances: (1) We focused on 113 genetic variants previously identified as related to MS severity; (2) We used a novel, sensitive outcome: MS Disease Severity Scale (MS-DSS); (3) Instead of validating individual alleles, we used a machine learning technique (random forest) that captures linear and complex nonlinear effects between alleles to derive a single Genetic Model of MS Severity (GeM-MSS). The GeM-MSS consists of 19 variants located in vicinity of 12 genes implicated in regulating cytotoxicity of immune cells, complement activation, neuronal functions, and fibrosis. GeM-MSS correlates with MS-DSS (r = 0.214; p = 0.043) in a validation cohort that was not used in the modeling steps. The recognized biology identifies novel therapeutic targets for inhibiting MS disability progression.

Minimal adverse events occur when inducing emesis with apomorphine in brachycephalic, mesocephalic, and dolichocephalic dogs.

OBJECTIVE: To determine risks of complications with emesis induction and whether facial conformation is associated with the frequency of complications. ANIMALS: 1,788 client-owned dogs that presented immediately or by referral from a primary care veterinarian following ingestion of toxic or foreign materials. METHODS: Patients with emesis induced with apomorphine for removal of toxic or foreign materials were retrospectively identified. Collected data included patient factors, routes of apomorphine administration, other therapies, adverse events, and patient outcomes. RESULTS: 2 types of complications were identified in a very small number of patients (11 [0.6%]), with 3 (0.17%) having regurgitation postemesis and 8 (0.44%) having prolonged vomiting. No significant difference was found in the rates of repeated vomiting or regurgitation between brachycephalic dogs and nonbrachycephalic dogs (P = .375 and P = 1.00, respectively). Brachycephalic dogs had 1.6 times greater odds of having emesis induction due to toxin ingestion compared to foreign material ingestion. The presence of clinical signs of toxicity at the time of emesis induction was associated with regurgitation (P < .001), and the development of regurgitation was associated with admission to hospital (P = .001). CLINICAL RELEVANCE: This study found no increased risk of complications when emesis was induced using apomorphine in brachycephalic breeds compared to nonbrachycephalic breeds, regardless of indication for emesis induction. Facial conformation is not a reason to withhold emesis induction.

The impact of package selection and versioning on single-cell RNA-seq analysis.

Standard single-cell RNA-sequencing analysis (scRNA-seq) workflows consist of converting raw read data into cell-gene count matrices through sequence alignment, followed by analyses including filtering, highly variable gene selection, dimensionality reduction, clustering, and differential expression analysis. Seurat and Scanpy are the most widely-used packages implementing such workflows, and are generally thought to implement individual steps similarly. We investigate in detail the algorithms and methods underlying Seurat and Scanpy and find that there are, in fact, considerable differences in the outputs of Seurat and Scanpy. The extent of differences between the programs is approximately equivalent to the variability that would be introduced in benchmarking scRNA-seq datasets by sequencing less than 5% of the reads or analyzing less than 20% of the cell population. Additionally, distinct versions of Seurat and Scanpy can produce very different results, especially during parts of differential expression analysis. Our analysis highlights the need for users of scRNA-seq to carefully assess the tools on which they rely, and the importance of developers of scientific software to prioritize transparency, consistency, and reproducibility for their tools.

A standard for sharing spatial transcriptomics data.

Spatial transcriptomic technologies have the potential to reveal critical relationships between the function of genes and cells and their spatial organization. Here, we provide a sharing model for spatial transcriptomics data with the aim of establishing a set of primary data and metadata needed to reproduce analyses and facilitate computational methods development.

Incidence of feline idiopathic cystitis and urethral obstruction during COVID-19 human movement restrictions in Queensland, Australia.

OBJECTIVES: Feline idiopathic cystitis (FIC) and urethral obstruction (UO) are commonly linked to increased stress. The influence of human movement restrictions on their incidence remains undetermined. FIC with or without UO is associated with environmental stress factors. The severe acute respiratory syndrome coronavirus 2 (COVID-19) pandemic restricted human movement and working behaviours. It is unknown if these restrictions increased the risk of FIC or UO in cats. METHODS: Total cat emergency accessions and transfers between 8 February 2019 and 8 February 2021 at two private hospitals were retrospectively reviewed. Cats were included in the FIC group if they presented with lower urinary tract signs and supporting urinalysis, and were included in the UO group if they presented with UO. Cats with current urinary tract infection, or previous FIC or UO, were excluded. Groups were considered 'pre-COVID-19' between February 2019 and 2020 and 'COVID-19' between February 2020 and 2021. Cases of FIC and UO were compared between COVID-19 and pre-COVID-19 using Fisher's exact test and relative risk (RR) calculations. RESULTS: The pre-COVID-19 incidence of FIC was 4.3% (63/1477, 95% confidence interval [CI] 0.0332-0.053), non-obstructive FIC was 1.4% (20/1477, 95% CI 0.008-0.020) and UO was 2.9% (43/1477, 95% CI 0.020-0.038). One cat was excluded as obstruction occurred during hospitalisation. The COVID-19 incidence of FIC was 5.4% (113/2081, 95% CI 0.044-0.64), non-obstructive FIC was 2.1% (70/2081, 95% CI 0.014-0.027) and UO was 3.4% (70/2081, 95% CI 0.026-0.042). The risk of non-obstructive FIC (P = 0.122; RR 0.652, 95% CI 0.387-1.096), UO (P = 0.382; RR 0.839, 95% CI 0.577-1.22) or either (P = 0.098; RR 0.773, 95% CI 0.572-1.044) was not significantly higher in the COVID-19 period than the pre-COVID-19 period. CONCLUSIONS AND RELEVANCE: No clear association between COVID-19 movement restrictions and the incidence of UO or non-obstructive FIC was found within this retrospective population.

Voyager: exploratory single-cell genomics data analysis with geospatial statistics.

Exploratory spatial data analysis (ESDA) can be a powerful approach to understanding single-cell genomics datasets, but it is not yet part of standard data analysis workflows. In particular, geospatial analyses, which have been developed and refined for decades, have yet to be fully adapted and applied to spatial single-cell analysis. We introduce the Voyager platform, which systematically brings the geospatial ESDA tradition to (spatial) -omics, with local, bivariate, and multivariate spatial methods not yet commonly applied to spatial -omics, united by a uniform user interface. Using Voyager, we showcase biological insights that can be derived with its methods, such as biologically relevant negative spatial autocorrelation. Underlying Voyager is the SpatialFeatureExperiment data structure, which combines Simple Feature with SingleCellExperiment and AnnData to represent and operate on geometries bundled with gene expression data. Voyager has comprehensive tutorials demonstrating ESDA built on GitHub Actions to ensure reproducibility and scalability, using data from popular commercial technologies. Voyager is implemented in both R/Bioconductor and Python/PyPI, and features compatibility tests to ensure that both implementations return consistent results.

Dissemination of a telehealth cardiovascular risk service: The CVRS live protocol.

BACKGROUND: Medical clinics are increasingly hiring clinical pharmacists to improve management of cardiovascular disease (CVD). However, the limited number of clinical pharmacists employed in a clinic may not impact the large number of complex patients needing the services. We have developed a remote telehealth service provided by clinical pharmacists to complement CVD services provided by on-site clinical pharmacists and aid sites without a clinical pharmacist. This cardiovascular risk service (CVRS) has been studied in two NIH-funded trials, however, we identified barriers to optimal intervention implementation. The purpose of this study is to examine how to implement the CVRS into medical offices and see if the intervention will be sustained. METHODS: This is a 5-year, pragmatic, cluster-randomized clinical trial in 13 primary care clinics across the US. We randomized clinics to receive CVRS or usual care and will enroll 325 patient subjects and 288 key stakeholder subjects. We have obtained access to the electronic medical records (EMRs) of all study clinics to recruit subjects and provide the pharmacist intervention. The intervention is staggered so that after 12 months, the usual care sites will receive the intervention for 12 months. Follow-up will be accomplished though medical record abstraction at baseline, 12 months, 24 months, and 36 months. CONCLUSIONS: This study will enroll subjects through 2021 and results will be available in 2024. This study will provide unique information on how the CVRS provided by remote clinical pharmacists can be effectively implemented in medical offices, many of which already employ on-site clinical pharmacists. CLINICAL TRIAL REGISTRATION INFORMATION: NCT03660631: http://clinicaltrials.gov/ct2/show/NCT03660631.

Intrathecal, Not Systemic Inflammation Is Correlated With Multiple Sclerosis Severity, Especially in Progressive Multiple Sclerosis.

Objective: To test the hypothesis that Multiple Sclerosis (MS) patients have increased peripheral inflammation compared to healthy donors and that this systemic activation of the immune system, reflected by acute phase reactants (APRs) measured in the blood, contributes to intrathecal inflammation, which in turn contributes to the development of disability in MS. Methods: Eight serum APRs measured in a prospectively-collected cross-sectional cohort with a total of 51 healthy donors and 291 untreated MS patients were standardized and assembled into related biomarker clusters to derive global measures of systemic inflammation. The resulting APR clusters were compared between diagnostic categories and correlated to equivalently-derived cerebrospinal fluid (CSF) biomarkers of innate and adaptive immunity. Finally, correlations were calculated between biomarkers of systemic and intrathecal inflammation and MS severity measures, which predict future rates of disability progression. Results: While two blood APR clusters were elevated in MS patients, only one exhibited a weak correlation with MS severity. All CSF inflammation clusters, except CSF albumin, correlated with at least one measure of MS severity, with biomarkers of humoral adaptive immunity exhibiting the strongest correlations, especially in Progressive MS. Conclusion: Systemic inflammation does not appear to be strongly associated with intrathecal inflammation in MS. Positive correlations between markers of intrathecal inflammation, especially of humoral immunity, with MS severity measures support a pathogenic role of intrathecal (compartmentalized) inflammation in central nervous system tissue destruction, including in Progressive MS.

Intrathecal B Cells in MS Have Significantly Greater Lymphangiogenic Potential Compared to B Cells Derived From Non-MS Subjects.

Although B cell depletion is an effective therapy of multiple sclerosis (MS), the pathogenic functions of B cells in MS remain incompletely understood. We asked whether cerebrospinal fluid (CSF) B cells in MS secrete different cytokines than control-subject B cells and whether cytokine secretion affects MS phenotype. We blindly studied CSF B cells after their immortalization by Epstein-Barr Virus (EBV) in prospectively-collected MS patients and control subjects with other inflammatory-(OIND) or non-inflammatory neurological diseases (NIND) and healthy volunteers (HV). The pilot cohort (n = 80) was analyzed using intracellular cytokine staining (n = 101 B cell lines [BCL] derived from 35 out of 80 subjects). We validated differences in cytokine production in newly-generated CSF BCL (n = 207 BCL derived from subsequent 112 prospectively-recruited subjects representing validation cohort), using ELISA enhanced by objective, flow-cytometry-based B cell counting. After unblinding the pilot cohort, the immortalization efficiency was almost 5 times higher in MS patients compared to controls (p < 0.001). MS subjects' BCLs produced significantly more vascular endothelial growth factor (VEGF) compared to control BCLs. Progressive MS patients BCLs produced significantly more tumor necrosis factor (TNF)-α and lymphotoxin (LT)-α than BCL from relapsing-remitting MS (RRMS) patients. In the validation cohort, we observed lower secretion of IL-1ß in RRMS patients, compared to all other diagnostic categories. The validation cohort validated enhanced VEGF-C production by BCL from RRMS patients and higher TNF-α and LT-α secretion by BCL from progressive MS. No significant differences among diagnostic categories were observed in secretion of IL-6 or GM-CSF. However, B cell secretion of IL-1ß, TNF-α, and GM-CSF correlated significantly with the rate of accumulation of disability measured by MS disease severity scale (MS-DSS). Finally, all three cytokines with increased secretion in different stages of MS (i.e., VEGF-C, TNF-α, and LT-α) enhance lymphangiogenesis, suggesting that intrathecal B cells directly facilitate the formation of tertiary lymphoid follicles, thus compartmentalizing inflammation to the central nervous system.

New Multiple Sclerosis Disease Severity Scale Predicts Future Accumulation of Disability.

The search for the genetic foundation of multiple sclerosis (MS) severity remains elusive. It is, in fact, controversial whether MS severity is a stable feature that predicts future disability progression. If MS severity is not stable, it is unlikely that genotype decisively determines disability progression. An alternative explanation tested here is that the apparent instability of MS severity is caused by inaccuracies of its current measurement. We applied statistical learning techniques to a 902 patient-years longitudinal cohort of MS patients, divided into training (n = 133) and validation (n = 68) sub-cohorts, to test four hypotheses: (1) there is intra-individual stability in the rate of accumulation of MS-related disability, which is also influenced by extrinsic factors. (2) Previous results from observational studies are negatively affected by the insensitive nature of the Expanded Disability Status Scale (EDSS). The EDSS-based MS Severity Score (MSSS) is further disadvantaged by the inability to reliably measure MS onset and, consequently, disease duration (DD). (3) Replacing EDSS with a sensitive scale, i.e., Combinatorial Weight-Adjusted Disability Score (CombiWISE), and substituting age for DD will significantly improve predictions of future accumulation of disability. (4) Adjusting measured disability for the efficacy of administered therapies and other relevant external features will further strengthen predictions of future MS course. The result is a MS disease severity scale (MS-DSS) derived by conceptual advancements of MSSS and a statistical learning method called gradient boosting machines (GBM). MS-DSS greatly outperforms MSSS and the recently developed Age Related MS Severity Score in predicting future disability progression. In an independent validation cohort, MS-DSS measured at the first clinic visit correlated significantly with subsequent therapy-adjusted progression slopes (r = 0.5448, p = 1.56e-06) measured by CombiWISE. To facilitate widespread use of MS-DSS, we developed a free, interactive web application that calculates all aspects of MS-DSS and its contributing scales from user-provided raw data. MS-DSS represents a much-needed tool for genotype-phenotype correlations, for identifying biological processes that underlie MS progression, and for aiding therapeutic decisions.