Biology subjects

MacDonald, M.

Publications and source records attributed to MacDonald, M..

8 recordsLinked to original sources

bioRxiv2024

Genome report: First whole genome sequence of Triatoma sanguisuga (Le Conte, 1855), vector of Chagas disease

Triatoma sanguisuga is the most widespread triatomine bug species in the United States (US). The species vectors the human parasite Trypanosoma cruzi, which causes Chagas disease. Vector-borne Chagas disease is rarely diagnosed in the US, but T. sanguisuga has been implicated in a handful of cases. Despite its public health importance, little is known about the genomics or population genetics of T. sanguisuga. Here, we used long-read sequencing to assemble the first whole genome sequence for T. sanguisuga using DNA extracted from one adult specimen from Delaware. The final size of the genome was 1.162 Gbp with 77.7x coverage. The assembly consisted of 183 contigs with an N50 size of 94.97 Kb. The Benchmarking Universal Single-Copy Ortholog (BUSCO) complete score was 99.1%, suggesting a very complete assembly. Genome-wide GC level was 33.56%, and DNA methylation was 18.84%. The genome consists of 61.4% repetitive DNA and 17,799 predicted coding genes. The assembled T. sanguisuga genome was slightly larger than that of Triatominae species Triatoma infestans and Rhodnius prolixus (949 Mbp with 90.4% BUSCO score and 706 Mbp with 96.5% BUSCO score, respectively). The T. sanguisuga genome is the first North American triatomine species genome to be sequenced, and it is the most complete genome yet for any Triatominae species. The T. sanguisuga genome will allow for deeper investigations into epidemiologically relevant aspects of this important vector species, including blood feeding, host seeking, and parasite competence, thus providing potential vector-borne disease management targets and strengthening public health preparedness.

genomics↗

bioRxiv2024

Divergent gene expression in alcohol and opioid usedisorders results in consistent alterations in functional networks in the Dorsolateral Prefrontal Cortex

Substance Use Disorders (SUDs) manifest as persistent drug-seeking behavior despite adverse consequences, with Alcohol Use Disorder (AUD) and Opioid Use Disorder (OUD) representing prevalent forms associated with significant mortality rates and economic burdens. The co-occurrence of AUD and OUD is common, necessitating a deeper comprehension of their intricate interactions. While the causal link between these disorders remains elusive, shared genetic factors are hypothesized. Leveraging public datasets, we employed genomic and transcriptomic analyses to explore conserved and distinct molecular pathways within the dorsolateral prefrontal cortex associated with AUD and OUD. Our findings unveil modest transcriptomic overlap at the gene level between the two disorders but substantial convergence on shared biological pathways. Notably, these pathways predominantly involve inflammatory processes, synaptic plasticity, and key intracellular signaling regulators. Integration of transcriptomic data with the latest genome-wide association studies (GWAS) for problematic alcohol use (PAU) and OUD not only corroborated our transcriptomic findings but also confirmed the limited shared heritability between the disorders. Overall, our study indicates that while alcohol and opioids induce diverse transcriptional alterations at the gene level, they converge on select biological pathways, offering promising avenues for novel therapeutic targets aimed at addressing both disorders simultaneously.

neuroscience↗

bioRxiv2024

Increased TRPV4 channel expression enhances and impairs blood vessel function in hypertension

BackgroundEndothelial cell TRPV4 channels provide a control point that is pivotal in regulating blood vessel diameter by mediating the Ca2+-dependent release of endothelial-derived vasoactive factors. In hypertension, TRPV4-mediated control of vascular function is disrupted but the underlying mechanisms, and precise physiological consequences remain controversial. MethodsHere, using a comprehensive array of methodologies, endothelial TRPV4 channel function was examined in intact arteries from normotensive WKY and hypertensive SHR rats. ResultsOur results show there is a notable shift in vascular reactivity in hypertension, characterized by enhanced endothelium-dependent vasodilation at low levels of TRPV4 channel activation. However, at higher levels of TRPV4 activity, this vasodilatory response is reversed, contributing to the aberrant vascular tone observed in hypertension. The change in response, from dilation to constriction, was accompanied by a shift in intracellular Ca2+ signaling modalities arising from TRPV4 activity. Oscillatory TRPV4-evoked IP3-mediated Ca2+ release, which underlies dilation, decreased, while the contraction inducing sustained Ca2+ rise, arising from TRPV4-mediated Ca2+ influx, increased. Our findings also reveal that while the sensitivity of endothelial cell TRPV4 to activation was unchanged, expression of the channel is upregulated and IP3 receptors are downregulated in hypertension. ConclusionsThese data highlight the intricate interplay between endothelial TRPV4 channel expression, intracellular Ca2+ signaling dynamics, and vascular reactivity. Moreover, the data support a new unifying hypothesis for the vascular impairment that accompanies hypertension. Specifically, that endothelial cell TRPV4 channels play a dual role in modulating blood vessel function in hypertension.

physiology↗

bioRxiv2020

Disrupted Endothelial Cell Heterogeneity and Network Organization Impairs Vascular Function in Prediabetic Obesity

RationaleObesity is a major risk factor for diabetes and cardiovascular diseases such as hypertension, heart failure, and stroke. Impaired endothelial function occurs in the earliest stages of obesity and underlies vascular alterations giving rise to cardiovascular disease. However, the mechanisms that link weight gain to endothelial dysfunction are ill-defined. Increasing evidence suggests that, rather than being a population of uniformly responding cells, neighboring endothelial cells are highly heterogeneous and are organized as a communicating multicellular network that controls vascular function. ObjectiveTo investigate the hypothesis that disrupted endothelial heterogeneity and network-level organization contributes to impaired vascular reactivity in obesity. Methods and ResultsTo study obesity-related vascular function without the complications associated with diabetes, we induced a state of prediabetic obesity in rats. Small artery diameter recordings confirmed nitric-oxide mediated vasodilator responses were dependent on increases in endothelial calcium levels and were impaired in obese animals. Single-photon imaging revealed a linear relationship between blood vessel relaxation and network-level calcium responses. Obesity did not alter the slope of this relationship, but impaired network-level endothelial calcium responses. The network itself was comprised of structural and functional components. The structural component, a hexagonal lattice network of endothelial cells, was unchanged in obesity. The functional network contained sub-populations of clustered agonist-sensing cells from which signals were communicate through the network. In obesity there were fewer but larger clusters of agonist-sensing cells and communication path lengths between clusters was increased. Communication between neighboring cells was unaltered in obesity. Altered network organization resulted in impaired, population-level calcium signaling and deficient endothelial control of vascular tone. Specialized subpopulations of endothelial cells had increased agonist sensitivity. These agonist-responsive cells were spatially clustered in a non-random manner and drove network level calcium responses. Communication between adjacent cells was unaltered in obesity, but there was a decrease in the size of the agonist-sensitive cell population and an increase in the clustering of agonist-responsive cells ConclusionsThe distribution of cells in the endothelial network is critical in determining overall vascular function. Altered cell heterogeneity and arrangement in obesity decrease endothelial function and provide a novel framework for understanding compromised endothelial function in cardiovascular disease.

cell biology↗

bioRxiv2020

Sox17 and β-catenin co-occupy Wnt-responsive enhancers to govern the endodermal gene regulatory network

Lineage specification is governed by gene regulatory networks (GRNs) that integrate the activity of signaling effectors and transcription factors (TFs) on enhancers. Sox17 is a key transcriptional regulator of definitive endoderm development, and yet, its genomic targets remain largely uncharacterized. Here, using genomic approaches and epistasis experiments, we define the Sox17-governed endoderm GRN in Xenopus gastrulae. We show that Sox17 functionally interacts with the canonical Wnt pathway to specify and pattern the endoderm while repressing alternative mesectoderm fates. Sox17 and {beta}-catenin co-occupy hundreds of key enhancers. In some cases, Sox17 and {beta}-catenin synergistically activate transcription independent of Tcfs, whereas on other enhancers, Sox17 represses {beta}-catenin/Tcf-mediated transcription to spatially restrict gene expression domains. Our findings establish Sox17 as a tissue-specific modifier of Wnt responses and point to a novel paradigm where genomic specificity of Wnt/{beta}-catenin transcription is determined through functional interactions between lineage-specific Sox TFs and {beta}-catenin/Tcf transcriptional complexes. Given the ubiquitous nature of Sox TFs and Wnt signaling, this mechanism has important implications across a diverse range of developmental and disease contexts. Key findingsO_LISox17 regulates germ layer segregation by promoting endoderm differentiation while simultaneously repressing mesectoderm fates. C_LIO_LIFunctional interactions between Sox17 and canonical Wnt-signaling is a major feature of the GRN controlling endoderm specification and patterning. C_LIO_LISox17 and {beta}-catenin co-occupy a subset of enhancers to synergistically stimulate transcription in the absence of Tcfs. C_LIO_LISox17 regulates the spatial expression domains of Wnt/{beta}-catenin-responsive transcription in the gastrula. C_LI

developmental biology↗

bioRxiv2019

Genetic overlap between psychiatric disorders and neuropsychiatric symptoms in HD

Huntingtons disease (HD) is an inherited neurodegenerative disorder caused by an expanded CAG repeat in the HTT gene. It is diagnosed following a standardized exam of motor control and often presents with cognitive decline and psychiatric symptoms. Recent studies have detected genetic loci modifying the age at onset of motor symptoms in HD, but genetic factors influencing cognitive and psychiatric presentations are unknown. We tested the hypothesis that psychiatric and cognitive symptoms in HD are influenced by the same common genetic variation as in the general population by constructing polygenic risk scores from large genome-wide association studies of psychiatric and neurodegenerative disorders, and of intelligence, and testing for correlation with the presence of psychiatric and cognitive symptoms in a large sample (n=5160) of HD patients. Polygenic risk score for major depression was associated specifically with increased risk of depression in HD, as was schizophrenia risk score with psychosis and irritability. Cognitive impairment and apathy were associated with reduced polygenic risk score for intelligence. In general, polygenic risk scores for psychiatric disorders, particularly depression and schizophrenia, are associated with increased risk of the corresponding psychiatric symptoms in HD, suggesting a common genetic liability. However, the genetic liability to cognitive impairment and apathy appears to be distinct from other psychiatric symptoms in HD. No associations were observed between HD symptoms and risk scores for other neurodegenerative disorders. These data provide a rationale for treatments effective in depression and schizophrenia to be used to treat depression and psychotic symptoms in HD.

genetics↗

bioRxiv2019

Synaptic Proteome Alterations in the Primary Auditory Cortex of Schizophrenia

ImportanceFindings from unbiased genetic studies have consistently implicated synaptic protein networks in Schizophrenia (Sz), but the molecular pathology at these networks and their potential contribution to the synaptic and circuit deficits thought to underlie disease symptoms remain unknown.\n\nObjectiveTo determine if protein levels are altered within synapses from primary auditory cortex (A1) of subjects with Sz; and if so, are these differences restricted to the synapse or present throughout the grey matter?\n\nDesignA paired case-control design was utilized for this study. Biochemical fractional - targeted Mass Spectrometry (MS) was used to measure the levels of >350 proteins in A1 grey matter homogenate and synaptosome preparations, respectively. All experimenters were blinded to diagnosis at every stage of sample preparation, MS analysis, and raw data processing. The effects of postmortem interval (PMI) and antipsychotic drug treatment on protein levels were assessed in mouse and monkey models, respectively.\n\nSettingAll cases were recruited from a single site, The Allegheny County Office of the Medical Examiner, and all tissues were processed at the University of Pittsburgh.\n\nParticipantsBrain specimens from all subjects were obtained during autopsies conducted at the Allegheny County Office of the Medical Examiner after receiving consent from the next-of-kin. An independent panel of experienced clinicians made consensus Diagnostic and Statistical Manual of Mental Disorders Fourth Edition diagnoses. Unaffected comparison subjects underwent identical assessments and were determined to be free of lifetime psychiatric illness. Each Sz subject was matched by sex, and as closely as possible for age and PMI, with one unaffected comparison subject.\n\nMain Outcomes and MeasuresPrimary measures were homogenate and synaptosome protein levels and their co-regulation network features. Prior to data collection we hypothesized: 1. That levels of canonical postsynaptic proteins in A1 synaptosome preparations would differ between Sz and control subjects; and 2. That these differences would not be explained by changes in total A1 homogenate protein levels.\n\nResultsMean subject age was 48 years for both groups with a range of 17-83; each group included 35 males and 13 females; mean PMI was 17.7 hours in controls and 17.9 in Sz. We observed robust alterations (q < 0.05) in synaptosome levels of canonical mitochondrial and postsynaptic proteins that were highly co-regulated and not readily explained by postmortem interval, antipsychotic drug treatment, synaptosome yield, or underlying alterations in homogenate protein levels.\n\nConclusions and RelevanceOur findings indicate a robust and highly coordinated rearrangement of the synaptic proteome likely driven by aberrant synaptic, not cell-wide, proteostasis. In line with unbiased genetic findings, our results identified alterations in synaptic levels of postsynaptic proteins, providing a road map to identify the specific cells and circuits that are impaired in Sz A1.

neuroscience↗

bioRxiv2016

Genome-scale transcriptional regulatory network models for the mouse and human striatum predict roles for SMAD3 and other transcription factors in Huntington’s disease

Transcriptional changes occur presymptomatically and throughout Huntingtons Disease (HD), motivating the study of transcriptional regulatory networks (TRNs) in HD. We reconstructed a genome-scale model for the target genes of 718 TFs in the mouse striatum by integrating a model of the genomic binding sites with transcriptome profiling of striatal tissue from HD mouse models. We identified 48 differentially expressed TF-target gene modules associated with age- and Htt allele-dependent gene expression changes in the mouse striatum, and replicated many of these associations in independent transcriptomic and proteomic datasets. Strikingly, many of these predicted target genes were also differentially expressed in striatal tissue from human disease. We experimentally validated a key model prediction that SMAD3 regulates HD-related gene expression changes using chromatin immunoprecipitation and deep sequencing (ChIP-seq) of mouse striatum. We found Htt allele-dependent changes in the genomic occupancy of SMAD3 and confirmed our models prediction that many SMAD3 target genes are down-regulated early in HD. Importantly, our study provides a mouse and human striatal-specific TRN and prioritizes a hierarchy of transcription factor drivers in HD.

systems biology↗