A mutation associated with resistance to synthetic pyrethroids is widespread in US populations of the tropical lineage of Rhipicephalus sanguineus s.l.

The brown dog tick, Rhipicephalus sanguineus sensu lato (s.l.), is an important vector for Rickettsia rickettsii, causative agent of Rocky Mountain spotted fever. Current public health prevention and control efforts to protect people involve preventing tick infestations on domestic animals and in and around houses. Primary prevention tools rely on acaricides, often synthetic pyrethroids (SPs); resistance to this chemical class is widespread in ticks and other arthropods. Rhipicephalus sanguineus s.l. is a complex that likely contains multiple unique species and although the distribution of this complex is global, there are differences in morphology, ecology, and perhaps vector competence among these major lineages. Two major lineages within Rh. sanguineus s.l., commonly referred to as temperate and tropical, have been documented from multiple locations in North America, but are thought to occupy different ecological niches. To evaluate potential acaricide resistance and better define the distributions of the tropical and temperate lineages throughout the US and in northern Mexico, we employed a highly multiplexed amplicon sequencing approach to characterize sequence diversity at: 1) three loci within the voltage-gated sodium channel (VGSC) gene, which contains numerous genetic mutations associated with resistance to SPs; 2) a region of the gamma-aminobutyric acid-gated chloride channel gene (GABA-Cl) containing several mutations associated with dieldrin/fipronil resistance in other species; and 3) three mitochondrial genes (COI, 12S, and 16S). We utilized a geographically diverse set of Rh sanguineus s.l. collected from domestic pets in the US in 2013 and a smaller set of ticks collected from canines in Baja California, Mexico in 2021. We determined that a single nucleotide polymorphism (T2134C) in domain III segment 6 of the VGSC, which has previously been associated with SP resistance in Rh. sanguineus s.l., was widespread and abundant in tropical lineage ticks (>50 %) but absent from the temperate lineage, suggesting that resistance to SPs may be common in the tropical lineage. We found evidence of multiple copies of GABA-Cl in ticks from both lineages, with some copies containing mutations associated with fipronil resistance in other species, but the effects of these patterns on fipronil resistance in Rh. sanguineus s.l. are currently unknown. The tropical lineage was abundant and geographically widespread, accounting for 79 % of analyzed ticks and present at 13/14 collection sites. The temperate and tropical lineages co-occurred in four US states, and as far north as New York. None of the ticks we examined were positive for Rickettsia rickettsii or Rickettsia massiliae.

Body weight, gonadectomy, and other risk factors for diagnosis of osteoarthritis in companion dogs.

Objective: The aim of this study is to evaluate age, sex, body weight, breed, neuter status, and age at neutering as risk factors for diagnosis of osteoarthritis in companion dogs. Animals: Dogs seen as patients at Banfield Pet Hospital in the United States from 1998 to 2019 with a date of death in 2019. The final cohort consisted of 131,140 dogs. Methods: In this retrospective cohort study, Cox proportional hazard models were used to test for associations between osteoarthritis incidence and age at baseline, sex, maximum body weight, maximum body condition score, neuter status, and age at neutering. The same model was used to test these associations in 12 representative breeds, chosen based on breed weight and sample size. Results: Older age, higher adult body weight, gonadectomy, and younger age at gonadectomy were significantly associated with higher risks of osteoarthritis in the total cohort and in all 12 breeds evaluated. Higher body condition scores and sex were also significantly associated with osteoarthritis but with minimal effect sizes in the overall cohort, and these risk factors were not consistently significant in all breeds tested. Clinical relevance: These results will assist veterinarians in identifying dogs at higher risk for osteoarthritis and applying appropriate diagnostic, preventative, and treatment interventions. An understanding of potentially modifiable risk factors, such as body condition and neutering, will support evidence-based discussions with dog owners about risk management in individual patients.

Somatic mutation as an explanation for epigenetic aging.

DNA methylation marks have recently been used to build models known as "epigenetic clocks" which predict calendar age. As methylation of cytosine promotes C-to-T mutations, we hypothesized that the methylation changes observed with age should reflect the accrual of somatic mutations, and the two should yield analogous aging estimates. In analysis of multimodal data from 9,331 human individuals, we find that CpG mutations indeed coincide with changes in methylation, not only at the mutated site but also with pervasive remodeling of the methylome out to ±10 kilobases. This one-to-many mapping enables mutation-based predictions of age that agree with epigenetic clocks, including which individuals are aging faster or slower than expected. Moreover, genomic loci where mutations accumulate with age also tend to have methylation patterns that are especially predictive of age. These results suggest a close coupling between the accumulation of sporadic somatic mutations and the widespread changes in methylation observed over the course of life.

A framework for group-wise summarization and comparison of chromatin state annotations.

MOTIVATION: Genome-wide maps of epigenetic modifications are powerful resources for non-coding genome annotation. Maps of multiple epigenetics marks have been integrated into cell or tissue type-specific chromatin state annotations for many cell or tissue types. With the increasing availability of multiple chromatin state maps for biologically similar samples, there is a need for methods that can effectively summarize the information about chromatin state annotations within groups of samples and identify differences across groups of samples at a high resolution. RESULTS: We developed CSREP, which takes as input chromatin state annotations for a group of samples. CSREP then probabilistically estimates the state at each genomic position and derives a representative chromatin state map for the group. CSREP uses an ensemble of multi-class logistic regression classifiers that predict the chromatin state assignment of each sample given the state maps from all other samples. The difference in CSREP's probability assignments for the two groups can be used to identify genomic locations with differential chromatin state assignments. Using groups of chromatin state maps of a diverse set of cell and tissue types, we demonstrate the advantages of using CSREP to summarize chromatin state maps and identify biologically relevant differences between groups at a high resolution. AVAILABILITY AND IMPLEMENTATION: The CSREP source code and generated data are available at http://github.com/ernstlab/csrep. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Epigenetic aging: Biological age prediction and informing a mechanistic theory of aging.

Numerous studies have shown that epigenetic age-an individual's degree of aging based on patterns of DNA methylation-can be computed and is associated with an array of factors including diet, lifestyle, genetics, and disease. One can expect that still further associations will emerge with additional aging research, but to what end? Prediction of age was an important first step, but-in our view-the focus must shift from chasing increasingly accurate age computations to understanding the links between the epigenome and the mechanisms and physiological changes of aging. Here, we outline emerging areas of epigenetic aging research that prioritize biological understanding and clinical application. First, we survey recent progress in epigenetic clocks, which are beginning to predict not only chronological age but aging outcomes such as all-cause mortality and onset of disease, or which integrate aging signals across multiple biological processes. Second, we discuss research that exemplifies how investigation of the epigenome is building a mechanistic theory of aging and informing clinical practice. Such examples include identifying methylation sites and the genes most strongly predictive of aging-a subset of which have shown strong potential as biomarkers of neurodegenerative disease and cancer; relating epigenetic clock predictions to hallmarks of aging; and using longitudinal studies of DNA methylation to characterize human disease, resulting in the discovery of epigenetic indications of type 1 diabetes and the propensity for psychotic experiences.

Inter-hemispheric Asymmetry Patterns in the ADHD Brain: A Neuroimaging Replication Study.

Attention-deficit/ hyperactivity disorder (ADHD) is the most common neurodevelopment disorder in children, and many genetic markers have been linked to the behavioral phenotypes of this highly heritable disease. The neuroimaging correlates are similarly complex, with multiple combinations of structural and functional alterations associated with the disease presentations of hyperactivity and inattentiveness. Thus far, neuroimaging studies have provided mixed results in ADHD patients, particularly with respect to the laterality of findings. It is possible that hemispheric asymmetry differences may help reconcile the variability of these findings. We recently reported that inter-hemispheric asymmetry differences were more sensitive descriptors for identifying differences between ADHD and typically developing (TD) brains (n=849) across volumetric, morphometric, and white matter neuroimaging metrics. Here, we examined the replicability of these findings across a new data set (n=202) of TD and ADHD subjects at the time of diagnosis (medication naive) and after a six week course of either stimulant drugs, non-stimulant medications, or combination therapy. Our findings replicated our earlier work across a number of volumetric and white matter measures confirming that asymmetry is more robust at detecting differences between TD and ADHD brains. However, the effects of medication failed to produce significant alterations across either lateralized or symmetry measures. We suggest that the delay in brain volume maturation observed in ADHD youths may be hemisphere dependent. Future work may investigate the extent to which these inter-hemispheric asymmetry differences are causal or compensatory in nature.