An association test of the spatial distribution of rare missense variants within protein structures identifies Alzheimer's disease-related patterns.

More than 90% of genetic variants are rare in most modern sequencing studies, such as the Alzheimer's Disease Sequencing Project (ADSP) whole-exome sequencing (WES) data. Furthermore, 54% of the rare variants in ADSP WES are singletons. However, both single variant and unit-based tests are limited in their statistical power to detect an association between rare variants and phenotypes. To best use missense rare variants and investigate their biological effect, we examine their association with phenotypes in the context of protein structures. We developed a protein structure-based approach, protein optimized kernel evaluation of missense nucleotides (POKEMON), which evaluates rare missense variants based on their spatial distribution within a protein rather than their allele frequency. The hypothesis behind this test is that the three-dimensional spatial distribution of variants within a protein structure provides functional context to power an association test. POKEMON identified three candidate genes (TREM2, SORL1, and EXOC3L4) and another suggestive gene from the ADSP WES data. For TREM2 and SORL1, two known Alzheimer's disease (AD) genes, the signal from the spatial cluster is stable even if we exclude known AD risk variants, indicating the presence of additional low-frequency risk variants within these genes. EXOC3L4 is a novel AD risk gene that has a cluster of variants primarily shared by case subjects around the Sec6 domain. This cluster is also validated in an independent replication data set and a validation data set with a larger sample size.

Analytical and clinical validation of direct detection of antimicrobial resistance markers by plasma microbial cell-free DNA sequencing.

Sequencing of plasma microbial cell-free DNA (mcfDNA) has gained increased acceptance as a valuable adjunct to standard-of-care testing for diagnosis of infections throughout the body. Here, we report the analytical and clinical validation of a novel application of mcfDNA sequencing, the non-invasive detection of seven common antimicrobial resistance (AMR) genetic markers in 18 important pathogens. The AMR markers include SCCmec, mecA, mecC, vanA, vanB, blaCTX-M, and blaKPC. The AMR markers were computationally linked to the pathogens detected. Analytical validation showed high reproducibility (100%), inclusivity (54 to 100%), and exclusivity (100%). Clinical accuracy was assessed with 114 unique plasma samples from patients at seven study sites with concordant culture results for target bacteria from a variety of specimen types and correlated with available phenotypic antimicrobial susceptibility test results and genotypic results. The positive percent agreement (PPA), negative percent agreement (NPA), and diagnostic yield (DY) were estimated for each AMR marker. DY was defined as the percentage of tests that yielded an actionable result of either detected or not detected. The results for the combination of SCCmec and mecA for staphylococci were PPA 19/20 (95.0%), NPA 21/22 (95.4%), DY 42/60 (70.0%); vanA for enterococci were PPA 3/3 (100%), NPA 2/2 (100%), DY 5/6 (83.3%); blaCTX-M for gram-negative bacilli were PPA 5/6 (83.3%), NPA 29/29 (100%), DY 35/49 (71.4%); and blaKPC for gram-negative bacilli were PPA 0/2 (0%), NPA: 23/23 (100%), DY 25/44 (56.8%). The addition of AMR capability to plasma mcfDNA sequencing should provide clinicians with an effective new culture-independent tool for optimization of therapy. IMPORTANCE: This manuscript is ideally suited for the Innovative Diagnostic Methods sections as it reports the analytical and clinical validation of a novel application of plasma microbial cell-free DNA sequencing for direct detection of seven selected antimicrobial resistance markers in 18 target pathogens. Clearly, it has potential clinical utility in optimizing therapy and was incorporated into the Karius test workflow in September 2023. In addition, the workflow could readily be adapted to expand the number of target bacteria and antimicrobial resistance markers as needed.

Relationship between Workload, Psychological State and Recovery in Female Soccer Athletes.

This study assessed the multifaceted relations between measures of workload, psychological state, and recovery throughout an entire soccer season in female collegiate soccer athletes (19.8±1.2 yrs, 132±12.3 lbs, 63±3.2 in). A prospective longitudinal study was utilized to measure workload (GPS training load, Rate of Perceived Exertion (RPE), psychological state (mental stress, mental fatigue, and mood), and recovery (sleep duration, sleep quality, and soreness), during 90 observations (59 training sessions and 21 games). Separate linear-mixed effect models were used to assess outcomes of RPE, soreness, and sleep duration. A linear mixed-effects model explained 59% of the variance in RPE following each session. Specifically, each standard deviation increase in GPS load and mental stress in the morning prior to training increased RPE by 1.46 (SE=0.08) and 0.29 (SE=0.07), respectively, following that day's training. Furthermore, a significant interaction was found between several predictor variables and chronological day in the season while predicting RPE. Specifically, for each standard deviation increase in GPS load, RPE went up by 0.0055 per day during the season suggesting that load had a higher impact on RPE as the season progressed. In contrast, the interaction of day by mental stress, sleep duration, and soreness continued to be stronger as the season progressed. Each linear mixed-effect model predicted a larger amount of variance when accounting for individual variations in the random effects.

DNA from multiple viral species is associated with Alzheimer's disease risk.

INTRODUCTION: Multiple infectious agents, including viruses, bacteria, fungi, and protozoa, have been linked to Alzheimer's disease (AD) risk by independent lines of evidence. We explored this association by comparing the frequencies of viral species identified in a large sample of AD cases and controls. METHODS: DNA sequence reads that did not align to the human genome in sequences were mapped to viral reference sequences, quantified, and then were tested for association with AD in whole exome sequences (WES) and whole genome sequences (WGS) datasets. RESULTS: Several viruses were significant predictors of AD according to the machine learning classifiers. Subsequent regression analyses showed that herpes simplex type 1 (HSV-1) (odds ratio [OR] = 3.71, p = 8.03 × 10-4) and human papillomavirus 71 (HPV-71; OR = 3.56, p = 0.02), were significantly associated with AD after Bonferroni correction. The phylogenetic-related cluster of Herpesviridae was significantly associated with AD in several strata of the data (p < 0.01). DISCUSSION: Our results support the hypothesis that viral infection, especially HSV-1, is associated with AD risk.

Whole-genome sequencing study in Koreans identifies novel loci for Alzheimer's disease.

INTRODUCTION: The genetic basis of Alzheimer's disease (AD) in Koreans is poorly understood. METHODS: We performed an AD genome-wide association study using whole-genome sequence data from 3540 Koreans (1583 AD cases, 1957 controls) and single-nucleotide polymorphism array data from 2978 Japanese (1336 AD cases, 1642 controls). Significant findings were evaluated by pathway enrichment and differential gene expression analysis in brain tissue from controls and AD cases with and without dementia prior to death. RESULTS: We identified genome-wide significant associations with APOE in the total sample and ROCK2 (rs76484417, p = 2.71×10-8) among APOE ε4 non-carriers. A study-wide significant association was found with aggregated rare variants in MICALL1 (MICAL like 1) (p = 9.04×10-7). Several novel AD-associated genes, including ROCK2 and MICALL1, were differentially expressed in AD cases compared to controls (p < 3.33×10-3). ROCK2 was also differentially expressed between AD cases with and without dementia (p = 1.34×10-4). DISCUSSION: Our results provide insight into genetic mechanisms leading to AD and cognitive resilience in East Asians. HIGHLIGHTS: Novel genome-wide significant associations for AD identified with ROCK2 and MICALL1. ROCK2 and MICALL1 are differentially expressed between AD cases and controls in the brain. This is the largest whole-genome-sequence study of AD in an East Asian population.

Association of common and rare variants with Alzheimer's disease in more than 13,000 diverse individuals with whole-genome sequencing from the Alzheimer's Disease Sequencing Project.

INTRODUCTION: Alzheimer's disease (AD) is a common disorder of the elderly that is both highly heritable and genetically heterogeneous. METHODS: We investigated the association of AD with both common variants and aggregates of rare coding and non-coding variants in 13,371 individuals of diverse ancestry with whole genome sequencing (WGS) data. RESULTS: Pooled-population analyses of all individuals identified genetic variants at apolipoprotein E (APOE) and BIN1 associated with AD (p < 5 × 10-8). Subgroup-specific analyses identified a haplotype on chromosome 14 including PSEN1 associated with AD in Hispanics, further supported by aggregate testing of rare coding and non-coding variants in the region. Common variants in LINC00320 were observed associated with AD in Black individuals (p = 1.9 × 10-9). Finally, we observed rare non-coding variants in the promoter of TOMM40 distinct of APOE in pooled-population analyses (p = 7.2 × 10-8). DISCUSSION: We observed that complementary pooled-population and subgroup-specific analyses offered unique insights into the genetic architecture of AD. HIGHLIGHTS: We determine the association of genetic variants with Alzheimer's disease (AD) using 13,371 individuals of diverse ancestry with whole genome sequencing (WGS) data. We identified genetic variants at apolipoprotein E (APOE), BIN1, PSEN1, and LINC00320 associated with AD. We observed rare non-coding variants in the promoter of TOMM40 distinct of APOE.

Transmission of Carbapenem-Resistant Klebsiella pneumoniae in US Hospitals.

BACKGROUND: Carbapenem-resistant Klebsiella pneumoniae (CRKp) is the most prevalent carbapenem-resistant Enterobacterales in the United States. We evaluated CRKp clustering in patients in US hospitals. METHODS: From April 2016 to August 2017, 350 patients with clonal group 258 CRKp were enrolled in the Consortium on Resistance Against Carbapenems in Klebsiella and other Enterobacteriaceae, a prospective, multicenter, cohort study. A maximum likelihood tree was constructed using RAxML. Static clusters shared ≤21 single-nucleotide polymorphisms (SNP) and a most recent common ancestor. Dynamic clusters incorporated SNP distance, culture timing, and rates of SNP accumulation and transmission using the R program TransCluster. RESULTS: Most patients were admitted from home (n = 150, 43%) or long-term care facilities (n = 115, 33%). Urine (n = 149, 43%) was the most common isolation site. Overall, 55 static and 47 dynamics clusters were identified involving 210 of 350 (60%) and 194 of 350 (55%) patients, respectively. Approximately half of static clusters were identical to dynamic clusters. Static clusters consisted of 33 (60%) intrasystem and 22 (40%) intersystem clusters. Dynamic clusters consisted of 32 (68%) intrasystem and 15 (32%) intersystem clusters and had fewer SNP differences than static clusters (8 vs 9; P = .045; 95% confidence interval [CI]: -4 to 0). Dynamic intersystem clusters contained more patients than dynamic intrasystem clusters (median [interquartile range], 4 [2, 7] vs 2 [2, 2]; P = .007; 95% CI: -3 to 0). CONCLUSIONS: Widespread intrasystem and intersystem transmission of CRKp was identified in hospitalized US patients. Use of different methods for assessing genetic similarity resulted in only minor differences in interpretation.

Six-year experience of Australia's first dedicated cancer of unknown primary clinic.

BACKGROUND: Diagnosis and management of cancers of unknown primary (CUP) remain challenging. This study examines the referral patterns, management and outcomes of patients referred to Australia's first dedicated CUP clinic. METHODS: Retrospective medical record review was conducted for patients seen at the Peter MacCallum Cancer Centre CUP clinic between July 2014 and August 2020. Overall survival (OS) was analysed for patients with a CUP diagnosis where treatment information was available. RESULTS: Of 361 patients referred, fewer than half had completed diagnostic work-up at the time of referral. A diagnosis of CUP was established in 137 (38%), malignancy other than CUP in 177 (49%) and benign pathology in 36 (10%) patients. Genomic testing was successfully completed in 62% of patients with initial provisional CUP and impacted management in 32% by identifying a tissue of origin or actionable genomic alteration. The use of site-specific, targeted therapy or immunotherapy was independently associated with longer OS compared to empirical chemotherapy. CONCLUSION: Our specialised CUP clinic facilitated diagnostic work-up among patients with suspected malignancy and provided access to genomic testing and clinical trials for patients with a CUP diagnosis, all of which are important to improve outcomes in this patient population.

Novel loci for Alzheimer's disease identified by a genome-wide association study in Ashkenazi Jews.

INTRODUCTION: Most Alzheimer's disease (AD) loci have been discovered in individuals with European ancestry (EA). METHODS: We applied principal component analysis using Gaussian mixture models and an Ashkenazi Jewish (AJ) reference genome-wide association study (GWAS) data set to identify Ashkenazi Jews ascertained in GWAS (n = 42,682), whole genome sequencing (WGS, n = 16,815), and whole exome sequencing (WES, n = 20,504) data sets. The association of AD was tested genome wide (GW) in the GWAS and WGS data sets and exome wide (EW) in all three data sets (EW). Gene-based analyses were performed using aggregated rare variants. RESULTS: In addition to apolipoprotein E (APOE), GW analyses (1355 cases and 1661 controls) revealed associations with TREM2 R47H (p = 9.66 × 10-9 ), rs541586606 near RAB3B (p = 5.01 × 10-8 ), and rs760573036 between SPOCK3 and ANXA10 (p = 6.32 × 10-8 ). In EW analyses (1504 cases and 2047 controls), study-wide significant association was observed with rs1003710 near SMAP2 (p = 1.91 × 10-7 ). A significant gene-based association was identified with GIPR (p = 7.34 × 10-7 ). DISCUSSION: Our results highlight the efficacy of founder populations for AD genetic studies.

Influence of water-level variability on fish assemblage and natural reproduction following connectivity enhancement in a Typha-dominated coastal wetland, USA.

We evaluated a wetland habitat modification strategy to contrast fish assemblage structure and the production of young-of-the-year (YOY) fish between different engineered habitats (i.e., spawning pool complexes and connectivity channels) relative to unmodified lateral channels in a large drowned river mouth tributary of the St Lawrence River. Prior to habitat modifications, the coastal wetland was impaired by water level regulations and dominance of the invasive hybrid cattail, Typha × glauca, which collectively replaced or created barriers to seasonally flooded spawning habitats important to fish. Connectivity enhancements provided fish access along a wetland habitat gradient from sedge-meadows to the deeper water robust emergent main channel. Across an 8-year fish emigration dataset (2012, 2013, 2016-2021) more than 90% of all captured fish (Ntotal = 218,086 fish) were YOY and modified habitats outperformed the unmodified channels in total fish catch-per-unit-effort (CPUE) per year (both YOY and non-YOY). Spawning pool complexes had higher YOY species richness than unmodified channel habitats. Fish assemblage structure differed between the modified habitats, where connectivity channels and unmodified channels shared a more similar fish assemblage than spawning pool complexes. Modified habitats, however, supported warmer water and higher dissolved oxygen than the unmodified channels. Redundancy analysis and linear mixed-effect modelling with abiotic variables (hydrology, temperature and dissolved oxygen) showed significant effects on fish assemblage structure, species richness and CPUE of fish emigrating from the modified and unmodified habitats. Historic flooding in 2017 and 2019 was a primary driver of YOY fish production and fish assemblage structure, but also appeared to be associated with near anoxic conditions systemwide. YOY fish for several species was inversely affected by floods at spawning pool complexes, but CPUE of YOY fish for these species appeared unaffected at the connectivity channels despite low dissolved oxygen. Diversified habitat structure (i.e., connectivity channels and spawning pool complexes) offers a management option to enhance habitat for fish that allowed compensatory effects on the capture of YOY fish of several species during floods. This multifaceted outcome from the habitat modifications resulted in unique fish assemblages between the channelized and spawning pool habitat. A connectivity-based habitat enhancement strategy provides adaptability for an uncertain climatic and regulatory future for the Laurentian Great Lakes and St Lawrence River.

Use of Exercise Training to Enhance the Power-Duration Curve: A Systematic Review.

ABSTRACT: Hurd, KA, Surges, MP, and Farrell, JW. Use of exercise training to enhance the power-duration curve: a systematic review. J Strength Cond Res 37(3): 733-744, 2023-The power/velocity-duration curve consists of critical power (CP), the highest work rate at which a metabolic steady state can obtained, and W' (e.g., W prime), the finite amount of work that can be performed above CP. Significant associations between CP and performance during endurance sports have been reported resulting in CP becoming a primary outcome for enhancement following exercise training interventions. This review evaluated and summarized the effects of different exercise training methodologies for enhancing CP and respective analogs. A systematic review was conducted with the assistance of a university librarian and in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. Ten studies met the criteria for inclusion and were reviewed. Four, 2, 2, 1, and 1 articles included swimming, cycling, resistance training, rowing, and running, respectively. Improvements in CP, and respective analogs, were reported in 3 swimming, 2 cycling, and 1 rowing intervention. In addition, only 2 cycling and 1 swimming intervention used CP, and respective analogs, as an index of intensity for prescribing exercise training, with one cycling and one swimming intervention reporting significant improvements in CP. Multiple exercise training modalities can be used to enhance the power/velocity-duration curve. Significant improvements in CP were often reported with no observed improvements in W' or with slight decreases. Training may need to be periodized in a manner that targets enhancements in either CP or W' but not simultaneously.

Current status of neuroprotective and neuroregenerative strategies in multiple sclerosis: A systematic review.

BACKGROUND: Immune-mediated demyelination and consequent degeneration of oligodendrocytes and axons are hallmark features of multiple sclerosis (MS). Remyelination declines in progressive MS, causing permanent axonal loss and irreversible disabilities. Strategies aimed at enhancing remyelination are critical to attenuate disease progression. OBJECTIVE: We systematically reviewed recent advances in neuroprotective and regenerative therapies for MS, covering preclinical and clinical studies. METHODS: We searched three biomedical databases using defined keywords. Two authors independently reviewed articles for inclusion based on pre-specified criteria. The data were extracted from each study and assessed for risk of bias. RESULTS: Our search identified 7351 studies from 2014 to 2020, of which 221 met the defined criteria. These studies reported 262 interventions, wherein 92% were evaluated in animal models. These interventions comprised protein, RNA, lipid and cellular biologics, small molecules, inorganic compounds, and dietary and physiological interventions. Small molecules were the most highly represented strategy, followed by antibody therapies and stem cell transplantation. CONCLUSION: While significant strides have been made to develop regenerative treatments for MS, the current evidence illustrates a skewed representation of the types of strategies that advance to clinical trials. Further examination is thus required to address current barriers to implementing experimental treatments in clinical settings.

Association of mitochondrial variants and haplogroups identified by whole exome sequencing with Alzheimer's disease.

INTRODUCTION: Findings regarding the association between mitochondrial DNA (mtDNA) variants and Alzheimer's disease (AD) are inconsistent. METHODS: We developed a pipeline for accurate assembly and variant calling in mitochondrial genomes embedded within whole exome sequences (WES) from 10,831 participants from the Alzheimer's Disease Sequencing Project (ADSP). Association of AD risk was evaluated with each mtDNA variant and variants located in 1158 nuclear genes related to mitochondrial function using the SCORE test. Gene-based tests were performed using SKAT-O. RESULTS: Analysis of 4220 mtDNA variants revealed study-wide significant association of AD with a rare MT-ND4L variant (rs28709356 C>T; minor allele frequency = 0.002; P = 7.3 × 10-5 ) as well as with MT-ND4L in a gene-based test (P = 6.71 × 10-5 ). Significant association was also observed with a MT-related nuclear gene, TAMM41, in a gene-based test (P = 2.7 × 10-5 ). The expression of TAMM41 was lower in AD cases than controls (P = .00046) or mild cognitive impairment cases (P = .03). DISCUSSION: Significant findings in MT-ND4L and TAMM41 provide evidence for a role of mitochondria in AD.

Management of anaphylaxis due to COVID-19 vaccines in the elderly.

Older adults, especially men and/or those with diabetes, hypertension, and/or obesity, are prone to severe COVID-19. In some countries, older adults, particularly those residing in nursing homes, have been prioritized to receive COVID-19 vaccines due to high risk of death. In very rare instances, the COVID-19 vaccines can induce anaphylaxis, and the management of anaphylaxis in older people should be considered carefully. An ARIA-EAACI-EuGMS (Allergic Rhinitis and its Impact on Asthma, European Academy of Allergy and Clinical Immunology, and European Geriatric Medicine Society) Working Group has proposed some recommendations for older adults receiving the COVID-19 vaccines. Anaphylaxis to COVID-19 vaccines is extremely rare (from 1 per 100,000 to 5 per million injections). Symptoms are similar in younger and older adults but they tend to be more severe in the older patients. Adrenaline is the mainstay treatment and should be readily available. A flowchart is proposed to manage anaphylaxis in the older patients.

Correction: Whole exome sequencing study identifies novel rare and common Alzheimer's-Associated variants involved in immune response and transcriptional regulation.

A correction to this paper has been published and can be accessed via a link at the top of the paper.

Whole exome sequencing study identifies novel rare and common Alzheimer's-Associated variants involved in immune response and transcriptional regulation.

The Alzheimer's Disease Sequencing Project (ADSP) undertook whole exome sequencing in 5,740 late-onset Alzheimer disease (AD) cases and 5,096 cognitively normal controls primarily of European ancestry (EA), among whom 218 cases and 177 controls were Caribbean Hispanic (CH). An age-, sex- and APOE based risk score and family history were used to select cases most likely to harbor novel AD risk variants and controls least likely to develop AD by age 85 years. We tested ~1.5 million single nucleotide variants (SNVs) and 50,000 insertion-deletion polymorphisms (indels) for association to AD, using multiple models considering individual variants as well as gene-based tests aggregating rare, predicted functional, and loss of function variants. Sixteen single variants and 19 genes that met criteria for significant or suggestive associations after multiple-testing correction were evaluated for replication in four independent samples; three with whole exome sequencing (2,778 cases, 7,262 controls) and one with genome-wide genotyping imputed to the Haplotype Reference Consortium panel (9,343 cases, 11,527 controls). The top findings in the discovery sample were also followed-up in the ADSP whole-genome sequenced family-based dataset (197 members of 42 EA families and 501 members of 157 CH families). We identified novel and predicted functional genetic variants in genes previously associated with AD. We also detected associations in three novel genes: IGHG3 (p = 9.8 × 10-7), an immunoglobulin gene whose antibodies interact with ß-amyloid, a long non-coding RNA AC099552.4 (p = 1.2 × 10-7), and a zinc-finger protein ZNF655 (gene-based p = 5.0 × 10-6). The latter two suggest an important role for transcriptional regulation in AD pathogenesis.

Effects of Group Running on the Training Intensity Distribution of Collegiate Cross-Country Runners.

ABSTRACT: Farrell III, JW, Dunn, A, Cantrell, GS, Lantis, DJ, Larson, DJ, and Larson, RD. Effects of group running on the training intensity distribution of collegiate cross-country runners. J Strength Cond Res 35(10): 2862-2869, 2021-Collegiate cross-country training is often conducted and prescribed in a group setting. This may result in the application of an inappropriate training stimulus to athletes due to potentially different physiological responses to the same training prescription. The aim of this investigation was to quantify the training intensity distribution (TID) of a collegiate cross-country team and the associated physiological adaptions. Sixteen subjects, 8 male subjects and 8 female subjects, performed a graded exercise test before and after observational period to determine peak oxygen consumption (V̇o2peak), the speed (S@), heart rate (HR@), and oxygen consumption (V̇o2@) associated with 2 and 4 mmol·L-1 of blood lactate. Training intensity distribution was quantified by assessing time spent in 3 intensity zones calculated as zone 1 (low intensity, HR values HR@2 and HR@4). No statistical differences were observed between male subjects and female subjects for percent of training time spent in zones 1, 2, and 3. No significant interactions were observed between sex and time for performance variables. Male subjects and female subjects improved V̇o2peak, S@4, and V̇o2@4 with male subjects also increasing V̇o2@2. No significant differences were observed between male subjects and female subjects when comparing percent changes for variables. Examining individual data showed that 2 female subjects experienced performance decrements and trained proportionally more in zones 2 and 3 compared with the overall group. The TID and performance decrements of the 2 highlighted subjects suggest that conducting training in a group setting may potentially be detrimental for some collegiate runners.

PopCluster: an algorithm to identify genetic variants with ethnicity-dependent effects.

MOTIVATION: Over the last decade, more diverse populations have been included in genome-wide association studies. If a genetic variant has a varying effect on a phenotype in different populations, genome-wide association studies applied to a dataset as a whole may not pinpoint such differences. It is especially important to be able to identify population-specific effects of genetic variants in studies that would eventually lead to development of diagnostic tests or drug discovery. RESULTS: In this paper, we propose PopCluster: an algorithm to automatically discover subsets of individuals in which the genetic effects of a variant are statistically different. PopCluster provides a simple framework to directly analyze genotype data without prior knowledge of subjects' ethnicities. PopCluster combines logistic regression modeling, principal component analysis, hierarchical clustering and a recursive bottom-up tree parsing procedure. The evaluation of PopCluster suggests that the algorithm has a stable low false positive rate (∼4%) and high true positive rate (>80%) in simulations with large differences in allele frequencies between cases and controls. Application of PopCluster to data from genetic studies of longevity discovers ethnicity-dependent heterogeneity in the association of rs3764814 (USP42) with the phenotype. AVAILABILITY AND IMPLEMENTATION: PopCluster was implemented using the R programming language, PLINK and Eigensoft software, and can be found at the following GitHub repository: https://github.com/gurinovich/PopCluster with instructions on its installation and usage. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Modification of the cyclopropyl moiety of abacavir provides insight into the structure activity relationship between HLA-B*57:01 binding and T-cell activation.

BACKGROUND: Abacavir is associated with hypersensitivity reactions in individuals positive for the HLA-B*57:01 allele. The drug binds within the peptide binding groove of HLA-B*57:01 altering peptides displayed on the cell surface. Presentation of these HLA-abacavir-peptide complexes to T-cells is hypothesized to trigger a CD8+ T-cell response underpinning the hypersensitivity. Thus, the aim of this study was to explore the relationship between the structure of abacavir with HLA-B*57:01 binding and the CD8+ T-cell activation. METHODS: Seventeen abacavir analogues were synthesized and cytokine secretion from abacavir/abacavir analogue-responsive CD8+ T-cell clones was measured using IFN-γ ELIspot. In silico docking studies were undertaken to assess the predicted binding poses of the abacavir analogues within the HLA-B*57:01 peptide binding groove. In parallel, the effect of selected abacavir analogues on the repertoire of self-peptides presented by cellular HLA-B*57:01 was characterized using mass spectrometry. RESULTS: Abacavir and ten analogues stimulated CD8+ T-cell IFN-γ release. Molecular docking of analogues that retained antiviral activity demonstrated a relationship between predicted HLA-B*57:01 binding orientations and the ability to induce a T-cell response. Analogues that stimulated T-cells displayed a perturbation of the natural peptides displayed by HLA-B*57:01. The antigen-specific CD8+ T-cell response was dependent on the enantiomeric form of abacavir at both cyclopropyl and cyclopentyl regions. CONCLUSION: Alteration of the chemical constitution of abacavir generates analogues that retain a degree of pharmacological activity, but have variable ability to activate T-cells. Modelling and immunopeptidome analysis delineate how drug HLA-B*57:01 binding and peptide display by antigen presenting cells relate to the activation of CD8+ T-cells.

Pseudomonas poae-Associated Fatal Septic Transfusion Reaction, Peoria, Illinois, USA, 2017.

In the United States, fatal transfusion-transmitted infections from red blood cell units are rare. Although this pattern mostly reflects how inhospitable refrigerated red blood cell units are to contaminant growth, fatalities caused by microorganisms that can grow at storage temperature (4°C), but not in standard clinical blood cultures at 37°C, are probably underestimated. We analyzed a fatal red blood cell transfusion in Peoria, Illinois, USA, that occurred in 2017. Samples from the patient's whole blood and the red blood cell unit remained culture-negative during the investigation, despite direct visualization of gram-negative bacilli within the unit immediately after transfusion. We identified the bacteria as Pseudomonas poae, a nonpathogenic pseudomonad carrying multiple cold-shock domain protein genes, and confirmed its cold tolerance and inability to grow at 37°C. Our work indicates transfusion reaction workups need to include testing for psychrophilic organisms, which could explain the cause of other apparently culture-negative transfusion reactions.