Biology subjects

Curtis, M.

Publications and source records attributed to Curtis, M..

16 recordsLinked to original sources

bioRxiv2026

Hepatic Xanthine Oxidoreductase Sustains Antithrombotic Nitric Oxide Signalling Through the Nitrate-Nitrite-Nitric Oxide Pathway

Background: Tonic endothelium-derived nitric oxide (NO) suppresses platelet activation physiologically, and its loss underlies the thrombotic risk of endothelial dysfunction. Inorganic nitrate and nitrite provide an alternative NO source, and xanthine oxidoreductase (XOR) is a candidate nitrite reductase, but whether endogenous XOR sustains platelet NO signalling in vivo, and its source is unknown. Methods: Dietary nitrate (15 mmol/L KNO3) was given to eNOS-/- and ApoE-/- mice. XOR was interrogated pharmacologically (allopurinol) and genetically (global Xdh+/- and hepatocyte-specific XOR knockout, HXOR KO). Haemostasis and thrombosis were assessed by tail bleeding and intravital microscopy imaging of FeCl3-induced mesenteric arterial thrombosis, alongside aggregometry, flow cytometry, platelet VASPSer239 phosphorylation, cGMP and ozone chemiluminescence-based analysis of nitrate and nitrite. Results: Dietary nitrate raised plasma nitrate and nitrite levels in all genotypes. In eNOS-/- and ApoE-/- mice, it prolonged bleeding time and normalised thrombus burden. In ApoE-/- mice nitrate treatment improved vasorelaxation, without altering XOR or eNOS expression. Allopurinol suppressed nitrite reductase activity in liver and plasma but not aorta, elevated plasma nitrite, shortened bleeding time and reduced platelet P-VASPSer239 expression. Xdh+/- mice were spontaneously prothrombotic, showed reduced P-VASPSer239 and exaggerated calcium mobilisation, and were refractory to dietary nitrate treatment despite equivalent nitrite elevation. XOR was undetectable in platelets. HXOR KO mice phenocopied global deficiency, with blunted nitrite-induced vasorelaxation but preserved acetylcholine and spermine-NO responses, reduced P-VASPSer239, enhanced aggregation and shortened bleeding time. Conclusions: Hepatic XOR sustains platelet NO-cGMP signalling and thromboresistance through an inter-organ, endocrine-like axis. Dietary nitrate restores antithrombotic protection when endothelial NO generation fails, whereas XOR inhibition removes physiological tonic antithrombotic signal.

pharmacology and toxicology↗

bioRxiv2026

Defining strain variation in the maintenance of Borrelia turicatae during hyperparasitism and transovarial transmission in Ornithodoros turicata

Tick-borne relapsing fever (TBRF) spirochetes are maintained in nature through vector-associated transmission routes primarily in argasid ticks. However, the extent to which strain-level differences influence the maintenance of TBRF spirochetes remains unclear. We evaluated two Borrelia turicatae strains, Bt-SSK1 and Bt-FCB, in Ornithodoros turicata. Both strains were acquired by female ticks, and after mating we unexpectedly observed that they were hyperparasitized by uninfected and unfed male O. turicata. Bt- SSK1 was maintained in males while Bt-FCB was not. Transovarial transmission (TOT) of Bt-SSK1 and Bt-FCB was also evaluated and striking differences were observed between strains. Bt-SSK1 was vertically maintained in F1 progeny but we failed to detect TOT of Bt-FCB. TOT of Bt-SSK1 occurred inefficiently in early ovipositions but increasing in later or delayed reproductive events, indicating a timing-dependent barrier. Using a gfp-expressing Bt-FCB strain, we show that failure of vertical transmission is associated with a lack of persistent oocyte colonization despite dissemination to ovarian tissues. These findings demonstrate strain-dependent differences in oocyte colonization and represent a critical bottleneck governing vertical transmission and persistence of relapsing fever spirochetes in tick populations. ImportanceVector-borne pathogens rely on diverse transmission strategies to persist in nature, yet the biological factors that govern these processes remain poorly understood. In this study, we demonstrated that strains of Borrelia turicatae differ markedly in their ability to persist within Ornithodoros turicata ticks. We also discovered that male ticks frequently hyperparasitized engorged females, creating an unrecognized transmission route in which previously uninfected ticks can acquire, maintain, and transmitted the B. turicatae. We further showed phenotypic differences in vertical transmission and that it is temporally regulated and linked to successful colonization of developing oocytes, identifying a critical bottleneck in pathogen maintenance. Together, these findings revealed that strain-specific traits influence both horizontal maintenance within tick populations and vertical transmission to progeny. This work provides insight into the ecological and evolutionary processes that enable relapsing fever spirochetes to persist in nature.

microbiology↗

bioRxiv2026

Human neurons stimulated with IFNγ present HLA class I-restricted autoantigens to cytotoxic CD8+ T cells

Interferon-{gamma} (IFN{gamma}) signaling is prominent in inflammatory CNS microenvironments across many neurological disorders, but the neuronal peptides presented on HLA class I under these conditions and their functional consequences for CD8+ T cells remain incompletely defined. Here we combine human iPSC-derived human neural aggregates (HNAs), HLA class I immunoprecipitation coupled to LC-MS/MS immunopeptidomics, and microfluidic co-culture assays to map IFN{gamma}-induced neuronal antigen presentation and test antigen-specific cytotoxicity. IFN{gamma} stimulation induced robust HLA class I expression in HNAs and enabled recovery of a canonical 8-12-mer class I ligandome enriched for 9-mers. Neuron-restricted expression of a synapsin-driven polyepitope cassette yielded presentation of defined neoantigen 9-mer peptides on donor HLA class I molecules and, in the presence of IFN{gamma}, elicited activation of autologous antigen-specific CD8+ T cells and consequent antigen-dependent neurite injury. Across four donors, comparative immunopeptidomics identified large IFN{gamma}-unique neural peptide repertoires distinct from matched fibroblasts and revealed a consistent enrichment of predicted high-affinity binders on HLA-B allotypes. Finally, {beta}2-microglobulin deletion ablated peptide recovery, and neuron-restricted {beta}2-microglobulin reconstitution enabled identification of neuron-derived peptides, including peptides derived from neurofilament light (NEFL) that were shared across donors and presented on multiple HLA allotypes. Together, these data provide an integrated platform for neuronal autoantigen discovery and functional validation and support a model in which IFN{gamma}-driven neuronal HLA class I presentation creates an HLA-B-weighted epitope landscape that can be recognized by autoreactive cytotoxic CD8+ T cells.

immunology↗

bioRxiv2026

Loss of interruption in the HTT CAG repeat is associated with increased somatic expansion and loss of medium spiny neurons in HD

Synonymous loss of interruption variants in the expanded CAG repeat sequence of Huntingtin (HTT) accelerate the clinical onset and progression of Huntington disease (HD). Medium spiny neurons (MSNs) are gradually lost in HD and undergo selective somatic CAG expansion, but it is unclear how CAG expansion in MSNs relates to HD pathology. Here, we show that MSNs with large (111-150 CAG) and very large (>150 CAG) somatic expansions are rare in early manifest HD, but accumulate in proportion with duration of disease and inherited CAG repeat length. In patients with the deleterious CAG-CCG loss-of-interruption (CAG-CCG LOI) modifier, the proportion of MSNs with large and very large expansions is increased [~]5-fold despite reduced small somatic expansions in blood, and direct caudate MSN counts are reduced. Our findings suggest that increased somatic CAG expansion contributes to accelerated striatal MSN pathology and hastened onset of HD, but that MSNs with very large genomic CAG expansions can persist among surviving neurons of the HD brain.

neuroscience↗

bioRxiv2025

Brain Microstructure and Obesity Risk in Early Childhood: Insights from Restriction Spectrum Imaging

Pediatric obesity is a growing public health concern, yet little is known about the neurobiological underpinnings of obesity risk in early childhood. Using restriction spectrum imaging (RSI), we examined associations between adiposity and brain microstructure in a cross-sectional sample of 159 children aged 4-7 years, including 81 with ADHD and 78 typically developing (TD) peers. We focused on RSI-derived measures of restricted diffusion--specifically restricted normalized isotropic (RNI), directional (RND), and total (RNT) signals--as indicators of cellular density in subcortical and cortical regions implicated in reward and salience processing. Body mass index (BMI), percent body fat, waist circumference, and obesity status were assessed. Higher BMI, but not other adiposity measures, was significantly associated with increased RNI in the right insula, nucleus accumbens (NAcc), and putamen, as well as increased RNT in the right insula and pallidum. These findings suggest early microstructural alterations in reward-related circuits, consistent with theories of diet-related neuroinflammation. Contrary to hypotheses, ADHD diagnosis did not moderate the associations, and anthropometric profiles were similar between groups. This suggests a shared neural pathway linking early adiposity and brain structure, independent of diagnostic status. Our findings replicate and extend prior work in older children, highlighting BMI as the most sensitive marker of obesity-related brain differences in early childhood. These results underscore the potential of RSI as a tool for identifying early neural risk markers of obesity and inform future efforts to design preventive interventions during critical developmental windows.

neuroscience↗

bioRxiv2025

An Inflammatory and Quiescent HSC Subpopulation Expands with Age in Humans

Aging of the blood system impacts systemic health and can be traced to hematopoietic stem cells (HSCs). Despite multiple reports on human HSC aging, a unified map detailing their molecular age-related changes is lacking. We developed a consensus map of gene expression in HSCs by integrating seven single-cell datasets. This map revealed previously unappreciated heterogeneity within the HSC population. It also links inflammatory pathway activation (TNF/NF{kappa}B, AP-1) and quiescence within a single gene expression program. This program dominates an inflammatory HSC subpopulation that increases with age, highlighting a potential target for further experimental studies and anti-aging interventions.

cell biology↗

bioRxiv2025

A population-scale atlas of blood and tissue in lupus nephritis

One Sentence SummaryA single-cell atlas of paired blood and tissue samples from Lupus Nephritis patients and healthy controls identified stromal and immune populations within renal tissue, including the scar-associated macrophage populations, which correlate with and may drive renal disease activity. Lupus nephritis (LN), a severe manifestation of Systemic Lupus Erythematosus (SLE), is a heterogeneous disease driven by diverse immune and tissue cell types. We obtained 538K single-cell and 140K single-nuclear profiles from kidney biopsies of 155 LN patients and 30 pre-implantation transplant biopsy controls, along with 325K single-cell blood profiles overlapping many of these patients. We identified key tissue cell types and cell states, and immune cell states; we were able to determine cell states that were tissue specific, and those that were present in the blood. We observed that LN pathological features are significantly associated with cell states using differential gene expression and Covarying Neighborhood Analysis (CNA). These analyses revealed broad changes in cell states associated with irreversible chronic tissue damage. After controlling for the effects of ongoing tissue damage, we observed that expansion of key glomerular and Scar Associated Macrophages (SAMs) populations tracked with increasing inflammatory disease activity. SAMs appear to drive LN fibrosis and, in active disease, infiltrate the glomeruli more than other myeloid cells. These observations strongly support that therapeutic targeting of myeloid populations may offer an as-of-yet unproven strategy to prevent renal inflammation and ongoing kidney damage in LN.

molecular biology↗

bioRxiv2025

Defining effective strategies to integrate multi-sample single-nucleus ATAC-seq datasets via a multimodal-guided approach

BackgroundChromatin accessibility, measured via single-nucleus Assay for Transposase-Accessible Chromatin with sequencing (snATAC-seq), can reveal the underpinnings of transcriptional regulation across heterogeneous cell states. As the number and scale of snATAC-seq datasets increases, we need robust computational pipelines to integrate samples within a dataset and datasets across studies. These integration pipelines should correct cell-state-obfuscating technical effects while conserving underlying biological cell states, as has been shown for single-cell RNA-seq (scRNA-seq) pipelines. However, scRNA-seq integration methods have performed inconsistently on snATAC-seq datasets, potentially due to sparsity and genomic feature differences. ResultsUsing single-nucleus multimodal datasets profiling ATAC and RNA simultaneously, we can measure snATAC-seq integration method performance by comparison to independently integrated snRNA-seq gold standard embeddings and annotations. Here, we benchmark 58 pipelines, incorporating 7 integration methods plus 1 embedding correction method with 5 feature sets. Using our command-line tool, we assessed 5 multimodal datasets at 3 different resolutions using 2 novel metrics to determine the best practices for multi-sample snATAC-seq integration. ATAC features outperformed Gene Activity Score (GAS) features, and embedding correction with Harmony was generally useful. SnapATAC2, PeakVI, and ArchRs iterative Latent Semantic Indexing (LSI) performed well. ConclusionsWe recommend SnapATAC2 + Harmony with pre-defined ENCODE candidate cis-regulatory element (cCRE) features as a first-pass pipeline given its metric performance, generalizability of features, and method resource-efficiency. This and other high-performing pipelines will guide future comprehensive gene regulation maps.

genomics↗

bioRxiv2025

Powerful and accurate case-control analysis of spatial molecular data with deep learning-defined tissue microniches

As spatial molecular data grow in scope and resolution, there is a pressing need to identify key spatial structures associated with disease. Current approaches typically make restrictive assumptions such as representing tissue regions by local abundances of manually typed, discrete cell types, or representing samples in terms of abundances of manually called, discrete spatial structures; this risks overlooking important signals. Here we introduce variational inference-based microniche analysis (VIMA), a method that combines deep learning with principled statistics to discover associated spatial features with greater flexibility and precision. VIMA trains an ensemble of variational autoencoders to extract numerical "fingerprints" from small tissue patches that capture their biological content. It uses these fingerprints to define a large number of data-dependent "microniches" - small, potentially overlapping groups of tissue patches with highly similar biology that span multiple samples. It then meta-analyzes across the autoencoders to identify microniches whose abundance correlates with case-control status while controlling for multiple testing. We show in simulations that VIMA is well calibrated. We then apply VIMA to spatial datasets spanning three different diseases and spatial modalities: a 7-marker immunofluorescence (IF) microscopy dataset in rheumatoid arthritis (RA), a 52-marker CO-Detection by indEXing (CODEX) dataset in ulcerative colitis (UC), and a 140-gene spatial transcriptomics dataset in dementia. In each case, we recapitulate known biology and identify novel spatial features of disease that were not discoverable with current state-of-the-art methods.

genomics↗

bioRxiv2024

Structural Development of Speech Networks in Young Children at Risk for Speech Disorder

Characterizing the structural development of the neural speech network in early childhood is important to understand speech acquisition. To investigate speech in the developing brain, 94 children aged 4-7-years-old were scanned using diffusion weighted imaging (DWI) magnetic resonance imaging (MRI). In order to increase sample size and performance variability, we included children who were diagnosed with attention-deficit hyperactivity disorder (ADHD) from a larger ongoing study. Additionally, each child completed the Syllable Repetition Task (SRT), a validated measure of phoneme articulation. The DWI data were modeled using restriction spectrum imaging (RSI) to measure restricted and hindered diffusion properties in both grey and white matter. Consequently, we analyzed the diffusion data using both whole brain analysis, and automated fiber quantification (AFQ) analysis to establish tract profiles for each of six fiber pathways thought to be important for supporting speech development. In the whole brain analysis, we found that SRT performance was associated with restricted diffusion in bilateral inferior frontal gyrus, pars opercularis, right pre-supplementary and supplementary motor area, and bilateral cerebellar grey matter (p < .005). Age moderated these associations in left pars opercularis and frontal aslant tract (FAT). However, in both cases only the cerebellar findings survived a cluster correction. We also found associations between SRT performance and restricted diffusion in cortical association fiber pathways, especially left FAT, and in the cerebellar peduncles. Analyses using automated fiber quantification (AFQ) highlighted differences in high and low performing children along specific tract profiles, most notably in left but not right FAT, in bilateral SLFIII, and in the cerebellar peduncles. These findings suggest that individual differences in speech performance are reflected in structural grey and white matter differences as measured by restricted and hindered diffusion metrics, and offer important insights into developing brain networks supporting speech in very young children.

neuroscience↗

bioRxiv2024

Reproducible single cell annotation of programs underlying T-cell subsets, activation states, and functions

T-cells recognize antigens and induce specialized gene expression programs (GEPs) enabling functions including proliferation, cytotoxicity, and cytokine production. Traditionally, different classes of helper T-cells express mutually exclusive responses - for example, Th1, Th2, and Th17 programs. However, new single-cell RNA sequencing (scRNA-Seq) experiments have revealed a continuum of T-cell states without discrete clusters corresponding to these subsets, implying the need for new analytical frameworks. Here, we advance the characterization of T-cells with T-CellAnnoTator (TCAT), a pipeline that simultaneously quantifies pre-defined GEPs capturing activation states and cellular subsets. From 1,700,000 T-cells from 700 individuals across 38 tissues and five diverse disease contexts, we discover 46 reproducible GEPs reflecting the known core functions of T-cells including proliferation, cytotoxicity, exhaustion, and T helper effector states. We experimentally characterize several novel activation programs and apply TCAT to describe T-cell activation and exhaustion in Covid-19 and cancer, providing insight into T-cell function in these diseases.

genomics↗

bioRxiv2024

Defining the function of disease variants with CRISPR editing and multimodal single cell sequencing

Abstract / Summary ParagraphGenetic studies have identified thousands of individual disease-associated non-coding alleles, but identification of the causal alleles and their functions remain critical bottlenecks. Even though CRISPR-Cas editing has enabled targeted modification of DNA, inefficient editing leads to heterogeneous outcomes across individual cells, limiting the ability to detect functional consequences of disease alleles. To overcome these challenges, we present a multi-omic single cell sequencing approach that directly identifies genomic DNA edits, assays the transcriptome, and measures cell surface protein expression. We apply this approach to investigate the effects of gene disruption, deletions in regulatory regions, and non-coding single nucleotide polymorphisms. We identify the specific effects of individual SNPs, including the state-specific effects of an IL2RA autoimmune variant in primary human T cells. Multimodal functional genomic single cell assays including DNA sequencing bridge a crucial gap in our understanding of complex human diseases by directly identifying causal variation in primary human cells.

genomics↗

bioRxiv2022

A statistical genetics guide to identifying HLA alleles driving complex disease

The human leukocyte antigen (HLA) locus is associated with more human complex diseases than any other locus. In many diseases it explains more heritability than all other known loci combined. Investigators have now demonstrated the accuracy of in silico HLA imputation methods. These approaches enable rapid and accurate estimation of HLA alleles in the millions of individuals that are already genotyped on microarrays. HLA imputation has been used to define causal variation in autoimmune diseases, such as type I diabetes, and infectious diseases, such as HIV infection control. However, there are few guidelines on performing HLA imputation, association testing, and fine-mapping. Here, we present comprehensive statistical genetics guide to impute HLA alleles from genotype data. We provide detailed protocols, including standard quality control measures for input genotyping data and describe options to impute HLA alleles and amino acids including a web-based Michigan Imputation Server. We updated the HLA imputation reference panel representing global populations (African, East Asian, European and Latino) available at the Michigan Imputation Server (n = 20,349) and achived high imputation accuracy (mean dosage correlation r = 0.981). We finally offer best practice recommendations to conduct association tests in order to define the alleles, amino acids, and haplotypes affecting human traits. This protocol will be broadly applicable to the large-scale genotyping data and contribute to defining the role of HLA in human diseases across global populations.

genetics↗

bioRxiv2022

PP4 inhibition sensitizes ovarian cancer to NK cell-mediated cytotoxicity via STAT1 activation and inflammatory signaling

BackgroundIncreased infiltration of T cells into ovarian tumors has been repeatedly shown to be predictive of enhanced patient survival. However, despite the evidence of an active immune response in ovarian cancer (OC), the frequency of responses to immune checkpoint blockade (ICB) therapy in OC is much lower than other cancer types. Recent studies have highlighted that deficiencies in the DNA damage response (DDR) can drive increased genomic instability and tumor immunogenicity, which leads to enhanced responses to ICB. Protein phosphatase 4 (PP4) is a critical regulator of the DDR; however, its potential role in anti-tumor immunity is currently unknown. ResultsOur results show that the PP4 inhibitor, fostriecin, combined with carboplatin leads to increased carboplatin sensitivity, DNA damage, and micronuclei formation. Using multiple ovarian cancer cell lines, we show that PP4 inhibition or PPP4C knockdown combined with carboplatin triggers inflammatory signaling via NF{kappa}B and STAT1 activation. This resulted in increased expression of the pro-inflammatory cytokines and chemokines: CCL5, CXCL10, and IL6. In addition, IFNB1 expression was increased suggesting activation of the type I interferon response. Conditioned media from OC cells treated with the combination of PP4 inhibitor and carboplatin significantly increased migration of both CD8 T cell and NK cells over carboplatin treatment alone. Knockdown of STING in OC cells significantly abrogated the increase in CD8 T cell migration induced by PP4 inhibition. Co-culture of NK-92 cells and OC cells with PPP4C or PPP4R3B knockdown resulted in strong induction of NK cell activation as measured by IFN-{gamma} levels. Further, we also observed increased degranulation and NK cell-mediated cytotoxicity against OC cells with PPP4C or PPP4R3B knockdown. ConclusionsOur work has identified a role for PP4 inhibition in promoting inflammatory signaling and enhanced immune cell effector function. These findings support the further investigation of PP4 inhibitors to enhance chemo-immunotherapy for ovarian cancer treatment.

cancer biology↗

bioRxiv2020

Recycling old drugs: cardiac glycosides as therapeutics to target barrier inflammation of the vasculature, meninges and choroid plexus

Neuroinflammation is a key component of virtually all neurodegenerative diseases; preceding neuronal loss and associating directly with cognitive impairment. Neuroinflammatory signals can originate and be amplified at barrier tissues such as brain vasculature, surrounding meninges and the choroid plexus. We designed a high-throughput screening system to target inflammation in cells of the blood-brain barrier (primary human pericytes and endothelia) and microglia enabling us to target human disease-specific inflammatory modifiers. Screening an FDA-approved drug library we identified digoxin and lanatoside C, members of the cardiac glycoside family as inflammatory modulating drugs that work in blood-brain barrier cells. A novel ex vivo assay of leptomeningeal and choroid plexus explants further confirmed that these drugs maintain their function in 3D cultures of brain border tissues. While current therapeutic strategies for the treatment of neurodegenerative diseases are missing the mark in terms of targets, efficacy and translatability, our innovative approach using in vitro and ex vivo human barrier cells and tissues to target neuroinflammatory pathways is a step forward in drug development and testing, and brings us closer to translatable treatments for human neurodegenerative disease. One Sentence SummaryWe have identified cardiac glycosides as powerful regulators of neuroinflammatory pathways in brain-barrier tissues such as vasculature, meninges and choroid plexus.

neuroscience↗

bioRxiv2020

Genes and pathways implicated in tetralogy of Fallot revealed by ultra-rare variant burden analysis in 231 genome sequences

Recent genome-wide studies of rare genetic variants have begun to implicate novel mechanisms for tetralogy of Fallot (TOF), a severe congenital heart defect (CHD). To provide statistical support for case-only data without parental genomes, we re-analyzed genome sequences of 231 individuals with TOF or related CHD. We adapted a burden test originally developed for de novo variants to assess singleton variant burden in individual genes, and in gene-sets corresponding to functional pathways and mouse phenotypes, accounting for highly correlated gene-sets, and for multiple testing. The gene burden test identified a significant burden of deleterious missense variants in NOTCH1 (Bonferroni-corrected p-value <0.01). These NOTCH1 variants showed significant enrichment for those affecting the extracellular domain, and especially for disruption of cysteine residues forming disulfide bonds (OR 39.8 vs gnomAD). Individuals with NOTCH1 variants, all with TOF, were enriched for positive family history of CHD. Other genes not previously implicated in TOF had more modest statistical support and singleton missense variant results were non-significant for gene-set burden. For singleton truncating variants, the gene burden test confirmed significant burden in FLT4. Gene-set burden tests identified a cluster of pathways corresponding to VEGF signaling (FDR=0%), and of mouse phenotypes corresponding to abnormal vasculature (FDR=0.8%), that suggested additional candidate genes not previously identified (e.g., WNT5A and ZFAND5). Analyses using unrelated sequencing datasets supported specificity of the findings for CHD. The findings support the importance of ultra-rare variants disrupting genes involved in VEGF and NOTCH signaling in the genetic architecture of TOF. These proof-of-principle data indicate that this statistical methodology could assist in analyzing case-only sequencing data in which ultra-rare variants, whether de novo or inherited, contribute to the genetic etiopathogenesis of a complex disorder. Author summaryWe analyzed the ultra-rare nonsynonymous variant burden for genome sequencing data from 231 individuals with congenital heart defects, most with tetralogy of Fallot. We adapted a burden test originally developed for de novo variants. In line with other studies, we identified a significant truncating variant burden for FLT4 and deleterious missense burden for NOTCH1, both passing a stringent Bonferroni multiple-test correction. For NOTCH1, we observed frequent disruption of cysteine residues establishing disulfide bonds in the extracellular domain. We also identified genes with BH-FDR <10% that were not previously implicated. To overcome limited power for individual genes, we tested gene-sets corresponding to functional pathways and mouse phenotypes. Gene-set burden of truncating variants was significant for vascular endothelial growth factor signaling and abnormal vasculature phenotypes. These results confirmed previous findings and suggested additional candidate genes for experimental validation in future studies. This methodology can be extended to other case-only sequencing data in which ultra-rare variants make a substantial contribution to genetic etiology.

genomics↗