Divergent patterns of healthy aging across human brain regions at single-cell resolution reveal links to neurodegenerative disease.

Age is a major common risk factor underlying neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. Previous studies reported that chronological age correlates with differential gene expression across different brain regions. However, prior datasets have not disambiguated whether expression associations with age are due to changes in cell numbers and/or gene expression per cell. In this study, we leveraged single nucleus RNA-sequencing (snRNAseq) to examine changes in cell proportions and transcriptomes in four different brain regions, each from 12 donors aged 20-30 years (young) or 60-85 years (old). We sampled 155,192 nuclei from two cortical regions (entorhinal cortex and middle temporal gyrus) and two subcortical regions (putamen and subventricular zone) relevant to neurodegenerative diseases or the proliferative niche. We found no changes in cellular composition of different brain regions with healthy aging. Surprisingly, we did find that each brain region has a distinct aging signature, with only minor overlap in differentially associated genes across regions. Moreover, each cell type shows distinct age-associated expression changes, including loss of protein synthesis genes in cortical inhibitory neurons, axonogenesis genes in excitatory neurons and oligodendrocyte precursor cells, enhanced gliosis markers in astrocytes and disease-associated markers in microglia, and genes critical for neuron-glia communication. Importantly, we find cell type-specific enrichments of age associations with genes nominated by Alzheimer's disease and Parkinson's disease genome-wide association studies (GWAS), such as apolipoprotein E (APOE), and leucine-rich repeat kinase 2 (LRRK2) in microglia that are independent of overall expression levels across cell types. We present this data as a new resource which highlights, first, region- and cell type-specific transcriptomic changes in healthy aging that may contribute to selective vulnerability and, second, provide context for testing GWAS-nominated disease risk genes in relevant subtypes and developing more targeted therapeutic strategies. The data is readily accessible without requirement for extensive computational support in a public website, https://brainexp-hykyffa56a-uc.a.run.app/.

Natural and human-driven selection of a single non-coding body size variant in ancient and modern canids.

Domestic dogs (Canis lupus familiaris) are the most variable-sized mammalian species on Earth, displaying a 40-fold size difference between breeds.1 Although dogs of variable size are found in the archeological record,2-4 the most dramatic shifts in body size are the result of selection over the last two centuries, as dog breeders selected and propagated phenotypic extremes within closed breeding populations.5 Analyses of over 200 domestic breeds have identified approximately 20 body size genes regulating insulin processing, fatty acid metabolism, TGFß signaling, and skeletal formation.6-10 Of these, insulin-like growth factor 1 (IGF1) predominates, controlling approximately 15% of body size variation between breeds.8 The identification of a functional mutation associated with IGF1 has thus far proven elusive.6,10,11 Here, to identify and elucidate the role of an ancestral IGF1 allele in the propagation of modern canids, we analyzed 1,431 genome sequences from 13 species, including both ancient and modern canids, thus allowing us to define the evolutionary history of both ancestral and derived alleles at this locus. We identified a single variant in an antisense long non-coding RNA (IGF1-AS) that interacts with the IGF1 gene, creating a duplex. While the derived mutation predominates in both modern gray wolves and large domestic breeds, the ancestral allele, which predisposes to small size, was common in small-sized breeds and smaller wild canids. Our analyses demonstrate that this major regulator of canid body size nearly vanished in Pleistocene wolves, before its recent resurgence resulting from human-imposed selection for small-sized breed dogs.

Best practices for analyzing imputed genotypes from low-pass sequencing in dogs.

Although DNA array-based approaches for genome-wide association studies (GWAS) permit the collection of thousands of low-cost genotypes, it is often at the expense of resolution and completeness, as SNP chip technologies are ultimately limited by SNPs chosen during array development. An alternative low-cost approach is low-pass whole genome sequencing (WGS) followed by imputation. Rather than relying on high levels of genotype confidence at a set of select loci, low-pass WGS and imputation rely on the combined information from millions of randomly sampled low-confidence genotypes. To investigate low-pass WGS and imputation in the dog, we assessed accuracy and performance by downsampling 97 high-coverage (> 15×) WGS datasets from 51 different breeds to approximately 1× coverage, simulating low-pass WGS. Using a reference panel of 676 dogs from 91 breeds, genotypes were imputed from the downsampled data and compared to a truth set of genotypes generated from high-coverage WGS. Using our truth set, we optimized a variant quality filtering strategy that retained approximately 80% of 14 M imputed sites and lowered the imputation error rate from 3.0% to 1.5%. Seven million sites remained with a MAF > 5% and an average imputation quality score of 0.95. Finally, we simulated the impact of imputation errors on outcomes for case-control GWAS, where small effect sizes were most impacted and medium-to-large effect sizes were minorly impacted. These analyses provide best practice guidelines for study design and data post-processing of low-pass WGS-imputed genotypes in dogs.

Guideline on the peri-operative management of patients with sickle cell disease: Guideline from the Association of Anaesthetists.

Sickle cell disease is a multisystem disease characterised by chronic haemolytic anaemia, painful vaso-occlusive crises and acute and chronic end-organ damage. It is one of the most common serious inherited single gene conditions worldwide and has a major impact on the health of affected individuals. Peri-operative complications are higher in patients with sickle cell disease compared with the general population and may be sickle or non-sickle-related. Complications may be reduced by meticulous peri-operative care and transfusion, but unnecessary transfusion should be avoided, particularly to reduce the risk of allo-immunisation. Planned surgery and anaesthesia for patients with sickle cell disease should ideally be undertaken in centres with experience in caring for these patients. In an emergency, advice should be sought from specialists with experience in sickle cell disease through the haemoglobinopathy network arrangements. Emerging data suggest that patients with sickle cell disease are at increased risk of COVID-19 infection but may have a relatively mild clinical course. Outcomes are determined by pre-existing comorbidities, as for the general population.

Genetic analysis of the modern Australian labradoodle dog breed reveals an excess of the poodle genome.

The genomic diversity of the domestic dog is an invaluable resource for advancing understanding of mammalian biology, evolutionary biology, morphologic variation, and behavior. There are approximately 350 recognized breeds in the world today, many established through hybridization and selection followed by intense breeding programs aimed at retaining or enhancing specific traits. As a result, many breeds suffer from an excess of particular diseases, one of many factors leading to the recent trend of "designer breed" development, i.e. crossing purebred dogs from existing breeds in the hope that offspring will be enriched for desired traits and characteristics of the parental breeds. We used a dense panel of 150,106 SNPs to analyze the population structure of the Australian labradoodle (ALBD), to understand how such breeds are developed. Haplotype and admixture analyses show that breeds other than the poodle (POOD) and Labrador retriever (LAB) contributed to ALBD formation, but that the breed is, at the genetic level, predominantly POOD, with all small and large varieties contributing to its construction. Allele frequency analysis reveals that the breed is enhanced for variants associated with a poodle-like coat, which is perceived by breeders to have an association with hypoallergenicity. We observed little enhancement for LAB-specific alleles. This study provides a blueprint for understanding how dog breeds are formed, highlighting the limited scope of desired traits in defining new breeds.

Whole Genome Analysis of a Single Scottish Deerhound Dog Family Provides Independent Corroboration That a SGK3 Coding Variant Leads to Hairlessness.

The breeds of domestic dog, Canis lupus familiaris, display a range of coat types with variation in color, texture, length, curl, and growth pattern. One trait of interest is that of partial or full hairlessness, which is found in a small number of breeds. While the standard for some breeds, such as the Xoloitzcuintli, requires sparse hair on their extremities, others are entirely bald, including the American Hairless Terrier. We identified a small, rare family of Scottish Deerhounds in which coated parents produced a mixed litter of coated and hairless offspring. To identify the underlying variant, we performed whole genome sequencing of the dam and five offspring, comparing single nucleotide polymorphisms and small insertions/deletions against an established catalog of 91 million canine variants. Of 325 homozygous alternative alleles found in both hairless dogs, 56 displayed the expected pattern of segregation and only a single, high impact variant within a coding region was observed: a single base pair insertion in exon two of SGK3 leading to a potential frameshift, thus verifying recently published findings. In addition, we observed that gene expression levels between coated and hairless dogs are similar, suggesting a mechanism other than non-sense mediated decay is responsible for the phenotype.

Optimising pain management protocols following cardiac surgery: A protocol for a national quality improvement study.

Pain following cardiac surgery is a multifaceted phenomenon resulting from a number of mechanisms. High-levels of post-operative pain are associated with cardiovascular and respiratory complications and adequate pain management is crucial for enabling fast recovery. However, adequate pain control is complex, a challenge that stems from a combination of poor reporting of pain, significant variation amongst patients and the side-effects of strong, particularly opioid, analgesics. An initial audit at our hospital demonstrated high-levels of post-operative pain following cardiac surgery and a protocol was therefore devised by the anaesthetic department for cardiac surgical pain management. The protocol stratified patients into high- or low-risk of pain based on the presence of risk factors for pain and utilised a combination of pre-operative one-off dose of gabapentin, intra-operative opioid infusion and post-operative multimodal analgesia with paracetamol, weak and strong opioids. Additionally, patients at high-risk of pain also received patient controlled analgesia. Use of this protocol was associated with improved pain scores on the first three post-operative days. We have devised this study to test for reproducibility of the benefit experienced at our hospital at a larger multicentre level. After acquiring pre-existing post-operative pain management strategies through an initial survey, local study leads will undertake a baseline audit. Local study leads will then lead a 4-week period of protocol implementation. Trusts with official pain management protocols will be given the option to re-circulate their pre-existing protocols. Subsequently, pain scores during post-operative days 1-3 will be re-audited.

Hair of the Dog: Identification of a Cis-Regulatory Module Predicted to Influence Canine Coat Composition.

Each domestic dog breed is characterized by a strict set of physical and behavioral characteristics by which breed members are judged and rewarded in conformation shows. One defining feature of particular interest is the coat, which is comprised of either a double- or single-layer of hair. The top coat contains coarse guard hairs and a softer undercoat, similar to that observed in wolves and assumed to be the ancestral state. The undercoat is absent in single-coated breeds which is assumed to be the derived state. We leveraged single nucleotide polymorphism (SNP) array and whole genome sequence (WGS) data to perform genome-wide association studies (GWAS), identifying a locus on chromosome (CFA) 28 which is strongly associated with coat number. Using WGS data, we identified a locus of 18.4 kilobases containing 62 significant variants within the intron of a long noncoding ribonucleic acid (lncRNA) upstream of ADRB1. Multiple lines of evidence highlight the locus as a potential cis-regulatory module. Specifically, two variants are found at high frequency in single-coated dogs and are rare in wolves, and both are predicted to affect transcription factor (TF) binding. This report is among the first to exploit WGS data for both GWAS and variant mapping to identify a breed-defining trait.

Global Capnography Project (GCAP): implementation of capnography in Malawi - an international anaesthesia quality improvement project.

The Lancet Commission on Global Surgery emphasised the importance of access to safe anaesthesia care. Capnography is an essential monitor for safe anaesthesia, but is rarely available in low-income countries. The aim of this study was twofold: to measure the prevalence of capnography in the operating theatres and in intensive care units; and to determine whether its introduction was feasible and could improve the early recognition of critical airway incidents in a low-income country. This is the first project to do this. Forty capnographs were donated to eight hospitals in Malawi. Thirty-two anaesthesia providers received a 1-day capnography training course with pre- and post-course knowledge testing. Providers kept logbooks of capnography use and recorded their responses to abnormal readings. On follow-up at 6 months, providers completed questionnaires on any significant patient safety incidents identified using capnography. In January 2017, at the commencement of the project, only one operating theatre had a capnograph. Overall, 97% and 100% 'capnography gaps' were identified in the theatres and intensive care units, respectively. The mean (SD) scores of our capnography multiple choice questionnaires improved after training from 15.00 (3.16) to 18.70 (0.99), p = < 0.001. The capnography equipment was appropriately robust and performed well. Six months following implementation, 24 (77%) anaesthesia providers reported recognising 44 oesophageal intubations and 28 (90%) believed that capnography had saved lives. This study has shown it is feasible to introduce capnography in a low-income country, resulting in early recognition of critical airway incidents and ultimately helping to save lives. Building on the experience of the first trial of pulse oximetry implementation in low-income countries in 2007, we believe this is one of the most important projects in anaesthesia safety in the last decade.