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Biology subjects

Evans, D.

Publications and source records attributed to Evans, D..

At least 19 recordsLinked to original sources

Fallopian Tube Organoid-Integrated Microfluidic Platform for Real-Time Imaging and Outflow Analysis

The fallopian tube is a dynamic, hormonally regulated epithelial conduit whose luminal microenvironment governs oocyte transport, fertilisation, early embryo development, and the initiation of gynaecological diseases including ectopic pregnancy, hydrosalpinx, and serous tubal intraepithelial carcinoma (STIC), yet existing models such as 2D monolayers, intact organoids, and static Transwell systems fail to recapitulate a polarised epithelium lining a perfused lumen under physiological fluid shear while preserving native organoid secretory function. We present a robust and accessible workflow integrating mechanically opened fallopian tube organoids into a custom-designed polydimethylsiloxane (PDMS) microfluidic device, in which organoid fragments form epithelial sheets and re-establish luminal-like architecture under controlled perfusion. The focus of this study is organoid integration and the characterisation of the resulting organoid-derived epithelium, rather than establishing chip cultures from individual cell lines. As this epithelium is built from expandable organoid stock rather than primary tissue, which typically survives only a few days in culture, the approach removes a major bottleneck to establishing organ-on-chip models, and we maintain viable cultures for up to 10 days. Epithelial sheets reproducibly covered more than 90% of the channel area by day 6 (n = 5 devices) and formed continuous ZO-1-positive tight junctions. The platform supports longitudinal brightfield and fluorescence microscopy at subcellular resolution, continuous collection of conditioned flow-through for ELISA, and quantitative analysis of cell coverage and health using CellProfiler software. We characterise the organoid-derived epithelium by benchmarking against tissue culture (TC) formats, comparing nuclear morphology on-chip with conventional well culture, and showing that the damage-associated cytokine interleukin-1 alpha (IL1 alpha) was undetectable in chip outflow, as in intact organoid secretions, indicating that cell health on-chip is comparable to that of intact organoids. Computational flow modelling characterises perfusion through the device and predicts how factors secreted by healthy epithelium and by tumour cells are distributed along the channel. The feasibility of tumour epithelium co culture was explored using OVCAR3 ovarian cancer spheroids as a proof of concept model of early tumour interaction with the tubal epithelium. Together, these results establish the technical feasibility of the platform and support its further development as an accessible system for studying reproductive health conditions affecting the fallopian tube, including tubal damage from infection, endometriosis, STIC lesions, and occlusion.

bioengineering↗

Metallothionein loss in cancer cells contributes to increased mutations through defective DNA repair and metabolic imbalance

Understanding which genes are involved in mutagenesis is essential for developing cancer prevention and treatment strategies; establishing protectors of the genome has revolutionized cancer biology. Here, we describe metallothionein (MT) proteins as previously uncharacterized protectors against mutagenesis. MT is a heavy metal binding protein essential for zinc homeostasis and protection against heavy metal cytotoxicity. Because zinc binds approximately 10-15% of the proteome and is critical for processes such as DNA repair and mitochondrial health, MT loss is expected to disrupt these processes. We hypothesized that MT loss induces genomic instability by impairing DNA repair and mitochondrial function. In this study, the consequences of MT deficiency in high-grade serous ovarian cancer (HGSC) were investigated by knockdown of the most highly expressed MT, MT2A. Loss of MT2A resulted in the impaired DNA repair pathway base excision repair (BER), leading to increased mutagenesis. MT2A deficiency produced mitochondrial dysfunction, characterized by a decrease in mitochondrial membrane potential, glycolysis, oxidative phosphorylation, amino acids, and an imbalance of nucleobases. Together, these defects reflect cellular states associated with increased cancer aggressiveness. These findings identify MT as a fundamental hub maintaining genomic and metabolic integrity. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=84 SRC="FIGDIR/small/736843v2_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@1af4adeorg.highwire.dtl.DTLVardef@15c588forg.highwire.dtl.DTLVardef@1ba5181org.highwire.dtl.DTLVardef@13d150b_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

MPXV Clade IIb virus infection in mice leads to prolonged viral replication, macrophage infiltration, and decreased spermatogenesis in the testes.

Mpox (formerly monkeypox) is caused by monkeypox virus (MPXV) and has prompted two recent global health emergencies. Clade IIb MPXV, a recently recognized subclade, has been associated with oral and genital lesions and transmission among men who have sex with men (MSM); however, mechanisms of genital pathogenesis and sexual transmission are not understood. We investigated several routes of MPXV Clade IIb virus infection (intranasal, oral, anal, and intraperitoneal) and found high and prolonged viral titres in the testes after IP inoculation still detectable at 21 days. The testes had significant changes to tissue architecture including loss of spermatogenesis, disorganization of spermatozoa, loss of Leydig cells, and breakdown of the seminiferous tubule membranes. Viral antigen positive cells were present in the interstitial spaces between the seminiferous tubules with macrophage infiltration also evident. This work provides insights into potential of sexual transmission for MPXV viruses as well as mechanisms of Mpox disease which may significantly impact long-term fertility or sex organ health of infected males. Author SummaryMpox (formerly monkeypox) is a painful disease similar to smallpox caused by the monkeypox virus (MPXV) which is an emerging/re-emerging virus. Recently the WHO has declared two global health emergencies due to human-to-human transmission of MPXV. Clade IIb MPXV is a newly recognized subclade that has been associated with genital lesions and sexual transmission/contact; however, how the virus causes disease in sex-organs or how it is passed from person-to-person is not understood. We investigated several routes of MPXV Clade IIb inoculation and found IP inoculation in male mice led to high and prolonged viral titres in testes. Additionally, the testes were significantly affected having loss of sperm and cellular organization. Evidence of inflammatory cell infiltration, specifically, macrophages, are suspected to be the cause of testes specific disease. This work provides insights into potential of sexual transmission for MPXV viruses as well as mechanisms of Mpox disease.

microbiology↗

Systematic elucidation and pharmacologic targeting on non-oncogene dependencies in imatinib-resistant gastrointestinal stromal tumor

Treatment of gastrointestinal stromal tumor (GIST) with imatinib and other KIT-targeting drugs has improved outcomes significantly. However, most patients with advanced GIST eventually develop imatinib resistance and succumb to disease. We have developed mutation-agnostic, network-based methodologies to systematically elucidate and pharmacologically target Master Regulator (MR) proteins--critical non-oncogene dependencies--in cancer cells. Unsupervised, MR-based clustering of 34 GIST patient tumor samples produced two clusters, one of which contained all imatinib-resistant tumors. Analysis of 9 single-cell RNA profiles of high-risk GIST revealed that tumors with clinical progression on imatinib harbored large subpopulations enriched for the MR-activity signature of imatinib-resistant tumors, while tumors with resistance-associated mutations but without overt progression showed smaller, variably sized enriched subpopulations. High-throughput profiling of transcriptional responses by two GIST cell lines to FDA-approved and late-stage experimental drugs identified six candidate drugs that reversed the MR activity of imatinib-resistant GIST. Predictions were validated in two imatinib-resistant, patient-derived xenograft (PDX) models. The top prediction, linifanib, induced marked tumor growth inhibition in both PDXs across a wide dose range; selinexor and selumetinib were also effective compared to imatinib. We confirmed in vivo MR-activity reversal by these drugs, but not by ineffective drugs.

cancer biology↗

Differential methylation clock ages across buffy coat (BC), peripheral blood mononuclear cells (PBMC), and saliva in individuals approaching midlife

Epigenetic aging prior to midlife is gaining interest as an intervenable period to address health and cognitive aging. Epigenetic changes may index DNA methylation aging rates, but methylation profiles may not be substitutable across tissues. We compared DNA methylation clocks and age acceleration in saliva, buffy coat (BC), and peripheral blood mononuclear cells (PBMC) collected in 91 individuals (7 unpaired, 20 siblings, 64 twins; 18 monozygotic (MZ), 14 dizygotic (DZ) pairs) from the Colorado Adoption/Twin Study of Lifespan behavioral development and cognitive aging (CATSLife1; Mean age=30.90 years [range=28.07-41.13]; 50.5% female). Across 15 DNA methylation clocks, chronological age and DNA methylation ages were moderately associated (mean Spearman correlations: r=0.37, Saliva; r=0.41, BC; r=0.38, PBMC). In mixed-effects models, saliva showed higher DNA methylation ages (B=3.83-16.46 years vs BC, p<0.001), whereas PBMC and BC were comparable (B=-0.06-0.39 years vs BC, p>0.447). The exception was the next-generation clock DunedinPace showing comparability (p=0.486). Similar patterns were observed for age acceleration estimates. Altogether, MZ pairs (meta-analytic r=0.49, 95%CI=0.32,0.66) and DZ pairs (meta-analytic r=0.38, 95%CI=0.25,0.52) were moderately correlated (Spearman), but MZ pairs showed heterogeneity across tissues (p<0.020): saliva was lower (mean r=0.33, SD=0.25) than BC (mean r=0.64, SD=0.10) and PBMC (mean r=0.49, SD=0.18). Next-generation PCGrimAge and DunedinPace clocks showed consistent zygosity correlations across tissues, while multi-tissue clocks (e.g., ZhangQ) showed comparable MZ-DZ correlations. While saliva-based DNA methylation is not a direct substitute for blood-based DNA methylation, BC and PBMC show comparability; nevertheless, all tissue types may be appropriate for DNA methylation aging studies when compared within tissues. Key Policy HighlightsO_LISaliva-based methylation is not a direct substitute for blood-based methylation. C_LIO_LISaliva-based DNA methylation clocks demonstrated relatively older methylation ages and faster age accelerations relative to blood-based DNA methylation clocks. C_LIO_LIBlood-based DNA methylation clocks were comparable across buffy coat and peripheral blood mononuclear cell tissues. C_LIO_LITwin similarity, particularly among identical twins, was higher for blood-based DNA methylation clocks and newer generation DNA methylation clocks. C_LIO_LIThree clocks (one first-generation multi-tissue and two next-generation) showed consistency and/or comparability across tissues and showed moderate to strong correlations among identical and fraternal twins, supporting the importance of tool development. C_LI

genetics↗

The Green Band: Using Production and Catch to Judge Distortive Pressure on an Ecosystem

Ecosystem based fisheries management is an increasingly accepted approach for many fisheries management agencies. Indicators and methods that can usefully support the aspiration of making ecosystem based fisheries management decisions on tactical time frames are slowly accumulating, but have primarily focused on biomass status and trends. We first verify that fishing can distort the cumulative distribution of connections within an ecosystem, and then show (via theoretical testing and application to four contrasting case study locations) how relating catch with production by defining an acceptable band of exploitation pressure - the "Green Band" - can help inform fisheries decision makers as to whether an ecosystem is under distortive patterns of fishing pressure that will ultimately undermine the structure of the ecosystem.

ecology↗

Single Nuclei-Derived Molecular Subtypes of Gastrointestinal Stromal Tumors Correlate with Clinicopathologic Features and Predict Clinical Outcomes

Historically, gastrointestinal stromal tumor (GIST) has been subtyped by oncogenic driver mutations. However, tumors with the same mutational profile can have variable biology. To further explore the impact of molecular diversity on GIST biology, we performed single nucleus RNA sequencing on 16 primary GIST and utilized an integrated single cell atlas of the normal GI tract composed from multiple publicly available datasets to identify six distinct GIST cell states. We then statistically estimated the relative abundances of these profiles in bulk transcriptomic data. These were used to define six common GIST molecular subtypes based upon one or two predominant tumor cell states. We found that these molecular subtypes correlate with tumor locations, mutational profiles, and patient outcomes, and validated these subtypes in an independent international cohort. These molecular subtypes have the potential to be used for clinical prognostication for patients with GIST, identifying new therapeutic targets, and studying the cell of transformation of GIST.

cancer biology↗

MYC is sufficient to generate mid-life high-grade serous ovarian and uterine serous carcinomas in a p53-R270H mouse model

Genetically engineered mouse models (GEMM) have fundamentally changed how ovarian cancer etiology, early detection, and treatment is understood. However, previous GEMMs of high-grade serous ovarian cancer (HGSOC) have had to utilize genetics rarely or never found in human HGSOC to yield ovarian cancer within the lifespan of a mouse. MYC, an oncogene, is amongst the most amplified genes in HGSOC, but it has not previously been utilized to drive HGSOC GEMMs. We coupled Myc and dominant negative mutant p53-R270H with a fallopian tube epithelium-specific promoter Ovgp1 to generate a new GEMM of HGSOC. Female mice developed lethal cancer at an average of 15.1 months. Histopathological examination of mice revealed HGSOC characteristics including nuclear p53 and nuclear MYC in clusters of cells within the fallopian tube epithelium and ovarian surface epithelium. Unexpectedly, nuclear p53 and MYC clustered cell expression was also identified in the uterine luminal epithelium, possibly from intraepithelial metastasis from the fallopian tube epithelium (FTE). Extracted tumor cells exhibited strong loss of heterozygosity at the p53 locus, leaving the mutant allele. Copy number alterations in these cancer cells were prevalent, disrupting a large fraction of genes. Transcriptome profiles most closely matched human HGSOC and serous endometrial cancer. Taken together, these results demonstrate the Myc and Trp53-R270H transgene was able to recapitulate many phenotypic hallmarks of HGSOC through the utilization of strictly human-mimetic genetic hallmarks of HGSOC. This new mouse model enables further exploration of ovarian cancer pathogenesis, particularly in the 50% of HGSOC which lack homology directed repair mutations. Histological and transcriptomic findings are consistent with the hypothesis that uterine serous cancer may originate from the fallopian tube epithelium.

cancer biology↗

E7-mediated repression of miR-203 promotes LASP1-dependent proliferation in HPV-positive cervical cancer

Human papillomaviruses (HPV) are a major cause of malignancy, contributing to [~]5% of all human cancers worldwide, including most cervical cancer cases and a growing number of ano-genital and oral cancers. The major HPV viral oncogenes, E6 and E7, manipulate many host cellular pathways that promote cell proliferation and survival, predisposing infected cells to malignant transformation. Despite the availability of highly effective vaccines, there are still no specific anti-viral therapies targeting HPV or treatments for HPV-associated cancers. As such, a better understanding of viral-host interactions may allow the identification of novel therapeutic targets. Here, we demonstrate that the actin-binding protein LASP1 is upregulated in cervical cancer and significantly correlates with a poorer overall survival. In HPV positive cervical cancer, LASP1 depletion significantly inhibited proliferation in vitro, whilst having minimal effects in HPV negative cervical cancer cells. Furthermore, we show that the LASP1 SH3 domain is essential for LASP1-mediated proliferation in these cells. Mechanistically, we show that HPV E7 regulates LASP1 at the post-transcriptional level by repressing the expression of miR-203, which negatively regulated LASP1 mRNA levels by binding to its 3UTR. Finally, we demonstrated that LASP1 expression is required for the growth of HPV positive cervical cancer cells in an in vivo tumourigenicity model. Together, these data demonstrate that HPV induces LASP1 expression to promote proliferation and survival role in cervical cancer, thus identifying a potential therapeutic target in these cancers.

cancer biology↗

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.

genomics↗

Temporal control by co-factors prevents kinetic trapping in retroviral Gag lattice assembly

For retroviruses like HIV to proliferate, they must form virions shaped by the self-assembly of Gag polyproteins into a rigid lattice. This immature Gag lattice has been structurally characterized and reconstituted in vitro, revealing the sensitivity of lattice assembly to multiple co-factors. Due to this sensitivity, the energetic criterion for forming stable lattices is unknown, as are their corresponding rates. Here, we use a reaction-diffusion model designed from the cryo-ET structure of the immature Gag lattice to map a phase diagram of assembly outcomes controlled by experimentally constrained rates and free energies, over experimentally relevant timescales. We find that productive assembly of complete lattices in bulk solution is extraordinarily difficult due to the large size of this [~]3700 monomer complex. Multiple Gag lattices nucleate before growth can complete, resulting in loss of free monomers and frequent kinetic trapping. We therefore derive a time-dependent protocol to titrate or activate the Gag monomers slowly within the solution volume, mimicking the biological roles of co-factors. This general strategy works remarkably well, yielding productive growth of self-assembled lattices for multiple interaction strengths and binding rates. By comparing to the in vitro assembly kinetics, we can estimate bounds on rates of Gag binding to Gag and the cellular co-factor IP6. Our results show that Gag binding to IP6 can provide the additional time-delay necessary to support smooth growth of the immature lattice with relatively fast assembly kinetics, mostly avoiding kinetic traps. Our work provides a foundation for predicting and disrupting formation of the immature Gag lattice via targeting specific protein- protein binding interactions.

biophysics↗

The City Nature Challenge - A global citizen science phenomenon contributing to biodiversity knowledge and informing local government practices

The bioblitz phenomenon has recently branched into cities, presenting exciting opportunities for local governments to channel participants efforts toward local issues. The City Nature Challenge (CNC) is one such initiative that has been quickly uptaken by hundreds of municipalities worldwide. Despite high participation, we still lack a framework for evaluating how the CNC contributes to local biodiversity knowledge and to inform local government practices. Here, we develop such a tool and present a case study that illustrates its applicability. We demonstrate that the collected records contributed to a better understanding of contemporary, local biodiversity patterns and provided a more realistic representation of understudied groups such as insects and fungi. Importantly, we show that the CNC presented local governments with a cost-effective tool to make informed, evidence-based management and policy decisions, improve education and engagement programs, foster cross-council collaborations, and support a stronger sense of environmental stewardship within the local community.

scientific communication and education↗

Exploitation of ATP-sensitive potassium ion (KATP) channels by HPV promotes cervical cancer cell proliferation by contributing to MAPK/AP-1 signalling

Persistent infection with high-risk human papillomaviruses (HPVs) is the causal factor in multiple human malignancies, including >99% of cervical cancers and a growing proportion of oropharyngeal cancers. Prolonged expression of the viral oncoproteins E6 and E7 is necessary for transformation to occur. Although some of the mechanisms by which these oncoproteins contribute to carcinogenesis are well-characterised, a comprehensive understanding of the signalling pathways manipulated by HPV is lacking. Here, we present the first evidence to our knowledge that the targeting of a host ion channel by HPV can contribute to cervical carcinogenesis. Through the use of pharmacological activators and inhibitors of ATP-sensitive potassium ion (KATP) channels, we demonstrate that these channels are active in HPV-positive cells and that this activity is required for HPV oncoprotein expression. Further, expression of SUR1, which forms the regulatory subunit of the multimeric channel complex, was found to be upregulated in both HPV+ cervical cancer cells and in samples from patients with cervical disease, in a manner dependent on the E7 oncoprotein. Importantly, knockdown of SUR1 expression or KATP channel inhibition significantly impeded cell proliferation via induction of a G1 cell cycle phase arrest. This was confirmed both in vitro and in in vivo tumourigenicity assays. Mechanistically, we propose that the pro-proliferative effect of KATP channels is mediated via the activation of a MAPK/AP-1 signalling axis. A complete characterisation of the role of KATP channels in HPV-associated cancer is now warranted in order to determine whether the licensed and clinically available inhibitors of these channels could constitute a potential novel therapy in the treatment of HPV-driven cervical cancer.

microbiology↗

Rapid, Reference-Free Human Genotype Imputation with Denoising Autoencoders

Genotype imputation is a foundational tool for population genetics. Standard statistical imputation approaches rely on the co-location of large whole-genome sequencing-based reference panels, powerful computing environments, and potentially sensitive genetic study data. This results in computational resource and privacy-risk barriers to access to cutting-edge imputation techniques. Moreover, the accuracy of current statistical approaches is known to degrade in regions of low and complex linkage disequilibrium. Artificial neural network-based imputation approaches may overcome these limitations by encoding complex genotype relationships in easily portable inference models. Here we demonstrate an autoencoder-based approach for genotype imputation, using a large, commonly-used reference panel, and spanning the entirety of human chromosome 22. Our autoencoder-based genotype imputation strategy achieved superior imputation accuracy across the allele-frequency spectrum and across genomes of diverse ancestry, while delivering at least 4-fold faster inference run time relative to standard imputation tools.

bioinformatics↗

Universal and Programmable Thinning and Thickening of Topologically-Active DNA Fluids

Understanding and controlling the rheology of polymeric complex fluids that are pushed out-of-equilibrium is a fundamental problem in both industry and biology. For example, to package, repair, and replicate DNA, cells use enzymes to constantly manipulate DNA topology, length, and structure. Inspired by this, here we engineer and study DNA-based complex fluids that undergo enzymatically-driven topological and architectural alterations via restriction endonuclease (RE) reactions. We show that these systems display time-dependent rheological properties that depend on the concentrations and properties of the comprising DNA and REs. Through time-resolved microrheology experiments and Brownian Dynamics simulations, we show that conversion of supercoiled to linear DNA topology leads to a monotonic increase in viscosity. On the other hand, the viscosity of entangled linear DNA undergoing fragmentation displays a universal decrease that we rationalize using living polymer theory. Finally, to showcase the tunability of these behaviours, we design a DNA fluid that exhibits a time-dependent increase, followed by a temporally-gated decrease, of its viscosity. Our results present a class of polymeric fluids that leverage naturally occurring enzymes to drive diverse time-varying rheology by performing architectural alterations to the constituents.

biophysics↗

Recombination in enteroviruses is a ubiquitous event independent of sequence homology and RNA structure

Genetic recombination in RNA viruses is an important evolutionary mechanism. It contributes to population diversity, host/tissue adaptation and compromises vaccine efficacy. Both the molecular mechanism and initial products of recombination are relatively poorly understood. We used an established poliovirus-based in vitro recombination assay to investigate the roles of sequence identity and RNA structure, both implicated or inferred from analysis of circulating recombinant viruses, in the process. In addition, we used next generation sequencing to investigate the early products of recombination after cellular co-infection with different poliovirus serotypes. In independent studies we find no evidence for a role for RNA identity or structure in determining recombination junctions location. Instead, genome function and fitness are of greater importance in determining the identity of recombinant progeny. These studies provide further insights into this important evolutionary mechanism and emphasise the critical nature of the selection process on a mixed virus population.

microbiology↗

Detection of Chemotherapy-Resistant Pancreatic Cancer Using a Glycan Biomarker

Background and AimsA subset of pancreatic ductal adenocarcinomas (PDACs) is highly resistant to systemic chemotherapy, but no markers are available in clinical settings to identify this subset. We hypothesized that chemotherapy-resistant PDACs express a glycan biomarker called sTRA. Methods. We tested this marker to identify treatment-resistant PDAC in multiple systems: sets of cell lines, organoids, and isogenic cell lines; primary tumors; and blood plasma from cohorts of human subjects. Results. Among a panel of 27 cell lines, high levels of cell-surface sTRA identified higher resistance to seven chemotherapeutics used against PDAC. Using primary tumors from two different cohorts, patients who were positive for a gene-expression classifier for sTRA received no statistically significant benefit from adjuvant chemotherapy, in contrast to those negative for the signature. In another cohort, using direct measurements of sTRA in tissue microarrays by quantitative immunofluorescence, patients who were high in sTRA again had no statistically significant benefit from adjuvant chemotherapy. Further, a blood-plasma test for the sTRA glycan identified the PDACs that showed rapid relapse following neoadjuvant chemotherapy. This blood test performed with 96% specificity and 56% sensitivity in a blinded cohort using samples collected before the start of treatment. Conclusion. These findings establish that tissue or plasma sTRA can identify PDACs that are resistant to neoadjuvant or adjuvant chemotherapy. This capability could help apply systemic treatments more precisely and facilitate biomarker-guided trials targeting resistant PDAC.

cancer biology↗

Decoding the transcriptome of atherosclerotic plaque at single-cell resolution

Atherogenesis involves an interplay of inflammation, tissue remodeling and cellular transdifferentiation (CTD), making it especially difficult to precisely delineate its pathophysiology. Here we examine the single-cell transcriptome of entire atherosclerotic core (AC) plaques and patient-matched proximal adjacent (PA) portions of carotid artery tissue from patients undergoing carotid endarterectomy. We use a novel tissue dissociation strategy, single-cell RNA sequencing, and systems-biology approaches to analyze the transcriptional profiles of six main cell populations and identify key gene drivers of pathogenic biological processes in vascular smooth muscle cells (VSMCs) and endothelial cells (ECs). Our results reveal an anatomic continuum whereby PA cells promote and respond to inflammatory processes and eventually transition through CTD into matrix-secreting cells in the AC. Inflammatory signaling in PA ECs is driven by IL6, while TNFa signaling defines inflammation in both PA ECs and VSMCs. Furthermore, we identify POSTN, SPP1 and IBSP in AC VSMCs, and ITLN1, SCX and S100A4 in AC ECs as key drivers of CTD in the atherosclerotic core. These results establish an anatomic framework for atherogenesis and suggest a site-specific strategy for disruption of disease progression.

genomics↗