Biology subjects

Perry, J. A.

Publications and source records attributed to Perry, J. A..

17 recordsLinked to original sources

bioRxiv2026

Tagging C. elegans septins disrupts cytoskeletal scaffolding but not post-embryonic roles

Septins are conserved polymer-forming proteins that scaffold the actomyosin cytoskeleton, its regulators, and other factors to cellular membranes. Septins also sense micron-scale curvature, bind microtubules, and establish membrane diffusion barriers. C. elegans is a powerful animal model to study septins roles because there are only two septin genes: unc-59 and unc-61. In many fungal and animal cell types, septins are required for proper cytokinesis. In the C. elegans zygote, septins scaffolding roles in cytokinesis manifest during the chiral rotation of the cell cortex and the asymmetry of cytokinetic ring closure. Originally named for the uncoordinated movement exhibited by hypomorphic alleles, UNC-59 and UNC-61 are also required for normal postembryonic development, germline development, and fertility. To study C. elegans septins in these various contexts, we sought a fluorescent-protein tagging strategy that minimally perturbed septin function. We examined strains in which GFP, mKate2 or wrmScarlet had been inserted at the unc-59 locus, or coupled to unc-61b/c at an exogenous locus, to encode fluorescently tagged fusion proteins. We compared these tagged septins to classical hypomorphic alleles, and to new null alleles. Null alleles phenocopied hypomorphic alleles in all our assays. Strains bearing fluorescently tagged septins exhibited defects in zygote cytokinesis, qualitatively phenocopying both hypomorphic and null alleles. These findings agreed with recent work with fission yeast, demonstrating the sensitivity of septin function to tagging. Interestingly, tagging septins did not perturb postembryonic development including animal mobility. This suggests that septins play distinct functions in the zygote versus later in development.

cell biology↗

bioRxiv2025

cellSTAAR: Incorporating single-cell-sequencing-based functional data to boost power in rare variant association testing of non-coding regions

Whole genome sequencing (WGS) studies have identified hundreds of millions of rare variants (RVs) and have enabled RV association tests (RVATs) of these variants with complex traits and diseases. Analysis of non-coding variants is challenged by the considerable variability in regulatory function which candidate Cis-Regulatory Elements (cCREs) exhibit across cell types. We propose cellSTAAR, which integrates WGS data with single-cell ATAC-seq data to capture variability in chromatin accessibility across cell types via the construction of cell-type-specific functional annotations and variant sets. To reflect the uncertainty in cCRE-gene linking, cellSTAAR also links cCREs to their target genes using an omnibus framework which aggregates results from a variety of popular linking approaches. We applied cellSTAAR on Freeze 8 (N = 60,000) of the NHLBI Trans-Omics for Precision Medicine (TOPMed) consortium data to four lipids phenotypes: LDL cholesterol, a binary variable corresponding to high LDL cholesterol, HDL cholesterol, and triglycerides. We also provide replication results for all four phenotypes using UK Biobank (N = 190,000). Evidence from simulation studies and our real data analysis demonstrates that cellSTAAR boosts power and improves interpretation of RVATs of cCREs.

genetics↗

bioRxiv2024

CEBPA repression by MECOM blocks differentiation to drive aggressive leukemias

Acute myeloid leukemias (AMLs) have an overall poor prognosis with many high-risk cases co-opting stem cell gene regulatory programs, yet the mechanisms through which this occurs remain poorly understood. Increased expression of the stem cell transcription factor, MECOM, underlies one key driver mechanism in largely incurable AMLs. How MECOM results in such aggressive AML phenotypes remains unknown. To address existing experimental limitations, we engineered and applied targeted protein degradation with functional genomic readouts to demonstrate that MECOM promotes malignant stem cell-like states by directly repressing pro-differentiation gene regulatory programs. Remarkably and unexpectedly, a single node in this network, a MECOM-bound cis-regulatory element located 42 kb downstream of the myeloid differentiation regulator CEBPA, is both necessary and sufficient for maintaining MECOM-driven leukemias. Importantly, targeted activation of this regulatory element promotes differentiation of these aggressive AMLs and reduces leukemia burden in vivo, suggesting a broadly applicable differentiation-based approach for improving therapy.

cancer biology↗

bioRxiv2023

Septins throughout phylogeny are predicted to have a transmembrane domain, which in Caenorhabditis elegans is functionally important.

Septins, a conserved family of filament-forming proteins, contribute to eukaryotic cell division, polarity, and membrane trafficking. Septins scaffold other proteins to cellular membranes, but it is not fully understood how septins associate with membranes. We identified and characterized an isoform of Caenorhabditis elegans septin UNC-61 that was predicted to contain a transmembrane domain (TMD). The TMD isoform is expressed in a subset of tissues where the known septins were known to act, and TMD function was required for tissue integrity of the egg-laying apparatus. We found predicted TMD-containing septins across much of opisthokont phylogeny and demonstrated that the TMD-containing sequence of a primate TMD-septin is sufficient for localization to cellular membranes. Together, our findings reveal a novel mechanism of septin-membrane association with profound implications for septin dynamics and regulation.

cell biology↗

bioRxiv2022

PD-1 and CTLA-4 exert additive control of effector regulatory T cells

At homeostasis, a substantial proportion of Foxp3+ T regulatory cells (Tregs) have an activated phenotype associated with enhanced TCR signals and these effector Treg cells (eTregs) co-express elevated levels of PD-1 and CTLA-4. Short term in vivo blockade of the PD-1 or CTLA-4 pathways results in increased eTreg populations, while combination blockade of both pathways had an additive effect. Mechanistically, combination blockade resulted in a reduction of suppressive phospho-SHP2 Y580 in Treg cells which was associated with increased eTreg proliferation, enhanced production of IL-10, and altered dendritic cell expression of CD80 and MHC-II. Thus, at homeostasis, PD-1 and CTLA-4 function additively to regulate eTreg function and the ability to target these pathways in Treg cells may be useful to modulate inflammation.

immunology↗

bioRxiv2022

Engineered human cytokine/antibody fusion proteins expand regulatory T cells and confer autoimmune disease protection

Low dose human interleukin-2 (hIL-2) treatment is used clinically to treat autoimmune disorders due to the cytokines preferential expansion of immunosuppressive regulatory T cells (TRegs). However, high toxicity, short serum half-life, and off-target immune cell activation limit the clinical potential of IL-2 treatment. Recent work showed that complexes comprising hIL-2 and the anti-hIL-2 antibody F5111 overcome these limitations by preferentially stimulating TRegs over immune effector cells. Although promising, therapeutic translation of this approach is complicated by the need to optimize dosing ratios and by the instability of the cytokine/antibody complex. We leveraged structural insights to engineer a single-chain hIL-2/F5111 antibody fusion protein, termed F5111 immunocytokine (IC), that potently and selectively activates and expands TRegs. F5111 IC conferred protection in mouse models of colitis and checkpoint inhibitor-induced diabetes mellitus. These results provide a roadmap for IC design and establish a TReg-biased immunotherapy that could be clinically translated for autoimmune disease treatment.

bioengineering↗

bioRxiv2022

Impact of secondary TCR engagement on the heterogeneity of pathogen-specific CD8+ T cell response during acute and chronic toxoplasmosis

Initial TCR engagement of CD8+ T cells results in T cell expansion, and these early events influence the generation of diverse effector and memory populations. During infection, some activated T cells re-encounter cognate antigen, but how these events influence local effector responses or formation of memory populations is unclear. To address this issue, OT-I T cells which express the Nur77-GFP reporter of TCR activation were paired with T. gondii that express OVA to assess the impact of TCR activation on CD8+ T cell responses. During acute infection, TCR stimulation in affected tissues correlated with parasite burden and was associated with markers of effector cells while Nur77-GFP- OT-I showed signs of effector memory potential. However, adoptive transfer of Nur77-GFP negative or positive OT-I from infected mice into naive recipients resulted in formation of similar memory populations. During the chronic stage of infection in the CNS, TCR activation was associated with large scale transcriptional changes and the acquisition of an effector T cell phenotype as well as the generation of a population of CD103+ CD69+ Trm like cells. However, while inhibition of parasite replication resulted in reduced effector responses it did not alter the Trm population. These data sets highlight the contribution of recent TCR activation on the phenotypic heterogeneity of the CD8+ T cell response but suggest that this process has a limited impact on memory populations at acute and chronic stages of infection. Author SummaryCD8+ T cells are important to control many acute and chronic infections, however the role that recent T cell receptor stimulation plays in the formation of ongoing T cell responses is unclear. Here, we utilize a genetic reporter of TCR stimulation and high parameter flow cytometry to characterize TCR-driven phenotypes of pathogen specific T cell responses to the parasite Toxoplasma gondii during acute and chronic infection in the periphery and central nervous system. This work demonstrates the importance of recent TCR stimulation in driving local effector CD8+ T cell responses in peripheral tissues during infection, as well as the plasticity of the formation of memory T cells. Additionally, we utilize static and live imaging to investigate how Toxoplasma gondii life cycle impacts the ability to present antigen to CD8+ T cells. These studies aid in our understanding of how effector and memory CD8+ T cell responses are generated and maintained during an infection.

immunology↗

bioRxiv2021

Leveraging a founder population to identify novel rare-population genetic determinants of lipidome

Identifying the genetic determinants of inter-individual variation in lipid species (lipidome) may provide deeper understanding and new insight into the mechanistic effect of complex lipidomic pathways in CVD risk and progression beyond simple traditional lipids. Previous studies have been largely population based and thus only powered to discover associations with common genetic variants. Founder populations represent a powerful resource to accelerate discovery of novel biology associated with rare population alleles that have risen to higher frequency due to genetic drift. We performed a GWAS of 355 lipid species in 650 individuals from the Old Order Amish founder population including 127 lipid species not previously tested. We report for the first time the lipid species associated with two rare-population but Amish-enriched lipid variants: APOB_rs5742904 and APOC3_rs76353203. We also identified novel associations for 3 rare-population Amish-enriched loci with several sphingolipids and with proposed potential functional/causal variant in each locus including GLPTD2_rs536055318, CERS5_rs771033566, and AKNA_rs531892793. We replicated 7 previously known common loci including novel associations with two sterols: androstenediol with UGT locus on chromosome 2 and estriol with SLC22A8/A24 locus on chromosome 11. Our results show the power of founder populations to discover novel biology due to genetic drift that can increase the frequency of an allele from only few copies in large sample cohorts such as the UK Biobank to dozens of copies in sample size as small as 650.

genetics↗

bioRxiv2021

An Omics Analysis Search and Information System (OASIS) for Enabling Biological Discovery in the Old Order Amish

The "Omics Analysis Search and Information System" (OASIS), developed at the University of Maryland School of Medicine, enables discovery by allowing researchers to mine results from genome wide association studies (GWAS). When interesting signals are found, the research can immediately ask follow-up questions and get answers in real-time. OASIS provides this unique capability with a web-based, scientist-friendly search system and a variety of real-time analysis tools (linkage disequilibrium calculations, conditional analysis, and direct variant comparison) plus on-demand visualizations (boxplots, histograms, LocusZoom & Haploview plots, and pedigree charts). Because OASIS uses a web-based user interface, an understanding of programming or the UNIX operating system is not required. The OASIS application has been used to enable discovery from whole-exome, whole-genome, metabolome, transcriptome and methylome association results for Old Order Amish studies at the University of Maryland School of Medicine.

bioinformatics↗

bioRxiv2021

Identification of Novel Genetic Susceptibility Loci for Thoracic and Abdominal Aortic Aneurysms Via Genome-Wide Association Study Using the UK Biobank Cohort

BackgroundThoracic aortic aneurysm (TAA) and abdominal aortic aneurysm (AAA) are known to have a strong genetic component. Methods and ResultsIn a genome-wide association study (GWAS) using the UK Biobank, we analyzed the genomes of 1,363 individuals with AAA compared to 27,260 age, ancestry, and sex-matched controls (1:20 case:control study design). A similar analysis was repeated for 435 individuals with TAA compared to 8,700 controls. Polymorphism with minor allele frequency (MAF) >0.5% were evaluated. We identified novel loci near LINC01021, ATOH8 and JAK2 genes that achieved genome-wide significance for AAA (p-value <5x10-8), in addition to three known loci. For TAA, three novel loci in CTNNA3, FRMD6 and MBP achieved genome-wide significance. There was no overlap in the genes associated with AAAs and TAAs. Additionally, we identified a linkage group of high-frequency variants (MAFs [~]10%) encompassing FBN1, the causal gene for Marfan syndrome, which was associated with TAA. In Finngen PheWeb, this FBN1 haplotype was associated with aortic dissection. Finally, we found that baseline bradycardia was associated with TAA, but not AAA. ConclusionsOur GWAS found that AAA and TAA were associated with distinct sets of genes, suggesting distinct underlying genetic architecture. We also found association between baseline bradycardia and TAA. These findings, including JAK2 association, offer plausible mechanistic and therapeutic insights. We also found a common FBN1 linkage group that is associated with TAA and aortic dissection in patients who do not have Marfan syndrome. These FBN1 variants suggest shared pathophysiology between Marfan disease and sporadic TAA. Condensed AbstractIn genome-wide association study (GWAS) of thoracic aortic aneurysm (TAA) and abdominal aortic aneurysm (AAA) using UK Biobank database, we found 3 novel loci associated with TAA, and 3 novel loci associated AAA. We also found significant association between baseline bradycardia and TAA. These findings, including JAK2 association, offer plausible mechanistic and therapeutic insights. Additionally, we identified a common FBN1 linkage group associated with TAA in patients who do not have Marfan syndrome. In the FinnGen cohort, this haplotype is associated with aortic dissection. These results suggest a shared pathophysiology between Marfan disease and sporadic TAA. Study LimitationsAs with any GWAS study, the discovery of novel loci associated with aortopathies does not prove functional causality, and the findings described herein needs to be validated by analysis of other databases, ideally in a patient population of more diverse genetic origins than the UK Biobank. The use of the ICD10 codes to classify disease carriers and noncarriers in a population cohort may not be the most accurate assessment of prevalence of aortopathies. The association between baseline bradycardia and TAA does not take into account the concurrent use of medications that may impact heart rate. HighlightsO_LIIdentification of 3 novel AAA-associated loci near LINC01021, ATOH8 and JAK2 genes. C_LIO_LIIdentification of 3 novel TAA-associated loci near CTNNA3, FRMD6 and MBP genes. C_LIO_LIIdentification of a linkage group of common FBN1 variants associated with non-syndromic TAA in the UK Biobank and with aortic dissection in the FinnGen cohort, strengthening the evidence for a shared pathophysiology between Marfan disease and nonsyndromic aortopathy. C_LIO_LIAssociation between baseline bradycardia and TAA but not AAA. C_LI

genomics↗

bioRxiv2021

IL-33 promotes innate lymphoid cell-dependent IFN-γ production required for innate immunity to Toxoplasma gondii

IL-33 is an alarmin required for resistance to the parasite Toxoplasma gondii, but its role in innate resistance to this infection is unclear. T. gondii infection promotes increased stromal cell expression of IL-33 and levels of parasite replication correlate with IL-33 release. In response to infection, a subset of innate lymphoid cells (ILC) emerges composed of IL-33R+ NK cells and ILC1s. In Rag-/- mice, where NK cells and ILC1 provide an innate mechanism of resistance to T. gondii, the loss of IL-33R reduced ILC responses and increased parasite replication. Furthermore, administration of IL-33 to Rag-/- mice resulted in a marked decrease in parasite burden, increased production of IFN-{gamma} and the recruitment and expansion of inflammatory monocytes associated with parasite control. These protective effects of exogenous IL-33 were dependent on endogenous IL-12p40 and the ability of IL-33 to enhance ILC production of IFN-{gamma}. These results highlight that IL-33 synergizes with IL-12 to promote ILC-mediated resistance to T. gondii.

immunology↗

bioRxiv2020

PD-L1 - PD-1 interactions limit effector Treg cell populations at homeostasis and during infection

While much is known about the factors that promote the development of diverse Treg cell responses, less is known about the pathways that constrain Treg cell activities. The studies presented here reveal that at homeostasis there is a population of effector Treg cells that express PD-1, and that blockade of PD-L1 or loss of PD-1 results in increased Treg cell activity. In response to infection with the parasite T. gondii, the early production of IFN-{gamma} results in widespread upregulation of PD-L1. Moreover, blockade of PD-L1, whole body deletion of PD-1, or lineage-specific deletion of PD-1 in Foxp3+ cells prevented the loss of the effector Treg cells but resulted in reduced pathogen specific CD4+ T cell responses during infection. Thus, at homeostasis basal PD-L1 expression constrains and tunes the pool of Treg cells, but during infection the upregulation of PD-L1 provides a mechanism to contract the Treg cell population required to maximize the development of pathogen specific CD4+ T cell responses.

immunology↗

bioRxiv2020

Septins and a formin have distinct functions in chiral cortical rotation in the anaphase C. elegans zygote.

Many cells and tissues exhibit chirality that stems from the chirality of proteins and polymers. In the C. elegans zygote actomyosin contractility drives chiral rotation of the entire cortex circumferentially around the division plane during anaphase. How contractility is translated to cell-scale chirality, and what dictates handedness, are unknown. Septins are candidate contributors to cell-scale chirality because they anchor and crosslink the actomyosin cytoskeleton. We report that septins are required for anaphase cortical rotation. In contrast, the formin CYK-1, which we found to be enriched in the posterior in early anaphase, is not required for cortical rotation, but contributes to its chirality. Simultaneous loss of septin and CYK-1 function led to abnormal and often reversed cortical rotation. Our results suggest that anaphase contractility leads to chiral rotation by releasing torsional stress generated during formin-based polymerization, which is polarized along the cell anterior-posterior axis, and which accumulates due to actomyosin network connectivity. Our findings shed light on the molecular and physical bases for cellular chirality in the C. elegans zygote. We also identify conditions in which chiral rotation fails but animals are developmentally viable, opening avenues for future work on the relationship between early embryonic cellular chirality and animal body plan.

cell biology↗

bioRxiv2020

Conditional Analysis Cakewalk

SummarySequential conditional analysis is an important tool for identifying the unique signals in single-variant association analysis between genomic variants and various phenotypic outcomes. With large datasets, it is tedious and time-consuming to manually run the sequential steps which require the association analysis, computation of linkage disequilibrium (LD) between the variants, generation of a visualization graphic, and identification of the "top hit" to be inserted as an additional covariate for the next iteration. The Conditional Analysis Cakewalk automates this process, making it easy and fast, while only requiring user input in the initial configuration steps. Availability and ImplementationThe Conditional Analysis Cakewalk is implemented as a Linux shell script utilizing MMAP or PLINK and LocusZoom. Source code and documentation are available at https://github.com/jennetics/Cakewalk.

bioinformatics↗

bioRxiv2019

Impact of rare and common genetic variants on diabetes diagnosis by hemoglobin A1c in multi-ancestry cohorts: The Trans-Omics for Precision Medicine Program.

Hemoglobin A1c (HbA1c) is widely used to diagnose diabetes and assess glycemic control in patients with diabetes. However, nonglycemic determinants, including genetic variation, may influence how accurately HbA1c reflects underlying glycemia. Analyzing the NHLBI Trans-Omics for Precision Medicine (TOPMed) sequence data in 10,338 individuals from five studies and four ancestries (6,158 Europeans, 3,123 African-Americans, 650 Hispanics and 407 East Asians), we confirmed five regions associated with HbA1c (GCK in Europeans and African-Americans, HK1 in Europeans and Hispanics, FN3K/FN3KRP in Europeans and G6PD in African-Americans and Hispanics) and discovered a new African-ancestry specific low-frequency variant (rs1039215 in HBG2/HBE1, minor allele frequency (MAF)=0.03). The most associated G6PD variant (p.Val98Met, rs1050828-T, MAF=12% in African-Americans, MAF=2% in Hispanics) lowered HbA1c (-0.88% in hemizygous males, -0.34% in heterozygous females) and explained 23% of HbA1c variance in African-Americans and 4% in Hispanics. Additionally, we identified a rare distinct G6PD coding variant (rs76723693 - p.Leu353Pro, MAF=0.5%; -0.98% in hemizygous males, -0.46% in heterozygous females) and detected significant association with HbA1c when aggregating rare missense variants in G6PD. We observed similar magnitude and direction of effects for rs1039215 (HBG2) and rs76723693 (G6PD) in the two largest TOPMed African-American cohorts and replicated the rs76723693 association in the UK Biobank African-ancestry participants. These variants in G6PD and HBG2 were monomorphic in the European and Asian samples. African or Hispanic ancestry individuals carrying G6PD variants may be underdiagnosed for diabetes when screened with HbA1c. Thus, assessment of these variants should be considered for incorporation into precision medicine approaches for diabetes diagnosis.

genetics↗

bioRxiv2019

De novo mutations across 1,465 diverse genomes reveal novel mutational insights and reductions in the Amish founder population.

de novo Mutations (DNMs), or mutations that appear in an individual despite not being seen in their parents, are an important source of genetic variation whose impact is relevant to studies of human evolution, genetics, and disease. Utilizing high-coverage whole genome sequencing data as part of the Trans-Omics for Precision Medicine (TOPMed) program, we directly estimate and analyze DNM counts, rates, and spectra from 1,465 trios across an array of diverse human populations. Using the resulting call set of 86,865 single nucleotide DNMs, we find a significant positive correlation between local recombination rate and local DNM rate, which together can explain up to 35.5% of the genome-wide variation in population level rare genetic variation from 41K unrelated TOPMed samples. While genome-wide heterozygosity does correlate weakly with DNM count, we do not find significant differences in DNM rate between individuals of European, African, and Latino ancestry, nor across ancestrally distinct segments within admixed individuals. However, interestingly, we do find significantly fewer DNMs in Amish individuals compared with other Europeans, even after accounting for parental age and sequencing center. Specifically, we find significant reductions in the number of T[->]C mutations in the Amish, which seems to underpin their overall reduction in DNMs. Finally, we calculate near-zero estimates of narrow sense heritability (h2), which suggest that variation in DNM rate is significantly shaped by non-additive genetic effects and/or the environment, and that a less mutagenic environment may be responsible for the reduced DNM rate in the Amish. SignificanceHere we provide one of the largest and most diverse human de novo mutation (DNM) call sets to date, and use it to quantify the genome-wide relationship between local mutation rate and population-level rare genetic variation. While we demonstrate that the human single nucleotide mutation rate is similar across numerous human ancestries and populations, we also discover a reduced mutation rate in the Amish founder population, which shows that mutation rates can shift rapidly. Finally, we find that variation in mutation rates is not heritable, which suggests that the environment may influence mutation rates more significantly than previously realized.

genetics↗

bioRxiv2017

Deep-coverage whole genome sequences and blood lipids among 16,324 individuals

Deep-coverage whole genome sequencing at the population level is now feasible and offers potential advantages for locus discovery, particularly in the analysis rare mutations in non-coding regions. Here, we performed whole genome sequencing in 16,324 participants from four ancestries at mean depth >29X and analyzed correlations of genotypes with four quantitative traits - plasma levels of total cholesterol, low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol, and triglycerides. We conducted a discovery analysis including common or rare variants in coding as well as non-coding regions and developed a framework to interpret genome sequence for dyslipidemia risk. Common variant association yielded loci previously described with the exception of a few variants not captured earlier by arrays or imputation. In coding sequence, rare variant association yielded known Mendelian dyslipidemia genes and, in non-coding sequence, we detected no rare variant association signals after application of four approaches to aggregate variants in non-coding regions. We developed a new, genome-wide polygenic score for LDL-C and observed that a high polygenic score conferred similar effect size to a monogenic mutation (~30 mg/dl higher LDL-C for each); however, among those with extremely high LDL-C, a high polygenic score was considerably more prevalent than a monogenic mutation (23% versus 2% of participants, respectively).

genomics↗