A mechanistic framework for cardiometabolic and coronary artery diseases

Coronary atherosclerosis results from the delicate interplay of genetic and exogenous risk factors, principally taking place in metabolic organs and the arterial wall. Here we show that 224 gene-regulatory coexpression networks (GRNs) identified by integrating genetic and clinical data from patients with (n = 600) and without (n = 250) coronary artery disease (CAD) with RNA-seq data from seven disease-relevant tissues in the Stockholm-Tartu Atherosclerosis Reverse Network Engineering Task (STARNET) study largely capture this delicate interplay, explaining >54% of CAD heritability. Within 89 cross-tissue GRNs associated with clinical severity of CAD, 374 endocrine factors facilitated inter-organ interactions, primarily along an axis from adipose tissue to the liver (n = 152). This axis was independently replicated in genetically diverse mouse strains and by injection of recombinant forms of adipose endocrine factors (EPDR1, FCN2, FSTL3 and LBP) that markedly altered blood lipid and glucose levels in mice. Altogether, the STARNET database and the associated GRN browser (http://starnet.mssm.edu) provide a multiorgan framework for exploration of the molecular interplay between cardiometabolic disorders and CAD.

Association of Breast Cancer Screening Behaviors With Stage at Breast Cancer Diagnosis and Potential for Additive Multi-Cancer Detection via Liquid Biopsy Screening: A Claims-Based Study

Purpose

To evaluate mammography uptake and subsequent breast cancer diagnoses, as well as the prospect of additive cancer detection via a liquid biopsy multi-cancer early detection (MCED) screening test during a routine preventive care exam (PCE).

Methods

Patients with incident breast cancer were identified from five years of longitudinal Blue Health Intelligence^® (BHI^®) claims data (2014-19) and their screening mammogram and PCE utilization were characterized. Ordinal logistic regression analyses were performed to identify the association of a biennial screening mammogram with stage at diagnosis. Additional screening opportunities for breast cancer during a PCE within two years before diagnosis were identified, and the method extrapolated to all cancers, including those without recommended screening modalities.

Results

Claims for biennial screening mammograms and the time from screening to diagnosis were found to be predictors of breast cancer stage at diagnosis. When compared to women who received a screening mammogram proximal to their breast cancer diagnosis (0-4 months), women who were adherent to guidelines but had a longer time window from their screening mammogram to diagnosis (4-24 months) had a 87% increased odds of a later-stage (stages III or IV) breast cancer diagnosis (p-value <0.001), while women with no biennial screening mammogram had a 155% increased odds of a later-stage breast cancer diagnosis (p-value <0.001). This highlights the importance of screening in the earlier detection of breast cancer. Of incident breast cancer cases, 23% had no evidence of a screening mammogram in the two years before diagnosis. However, 49% of these women had a PCE within that time. Thus, an additional 11% of breast cancer cases could have been screened if a MCED test had been available during a PCE. Additionally, MCED tests have the potential to target up to 58% of the top 5 cancers that are the leading causes of cancer death currently without a USPSTF recommended screening modality (prostate, pancreatic, liver, lymphoma, and ovarian cancer).

Conclusion

The study used claims data to demonstrate the association of cancer screening with cancer stage at diagnosis and demonstrates the unmet potential for a MCED screening test which could be ordered during a PCE.

Utilizing commercial health insurance claims data to identify the impact of cancer screening and estimate the added benefit of a multicancer liquid biopsy ordered during routine physical exams

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Background: Cancer is the second leading cause of death in the United States. Survival varies by cancer type, but treatment of earlier stage cancer is consistently associated with improved survival relative to treatment of later stage cancers, highlighting that earlier detection is critical to improving patient outcomes. While most current cancer screening modalities require dedicated clinic visits, a multi-cancer liquid biopsy (i.e. a blood test) could enable screening for multiple cancers during routine physical exams. Methods: Five years of longitudinal data for 750,000 individuals from the Blue Health Intelligence national database were used to identify mammography utilization and breast cancer diagnoses. We identified incident cases and used univariate ordinal logistic regression to evaluate the association of breast cancer screening with earlier stage at diagnosis. We then identified all other incident cancers and characterized physical exam utilization in the two years prior to diagnosis. Results: Absence of claims for biennial screening mammograms as well as longer times from screening to diagnosis were associated with more advanced stage at breast cancer diagnosis. Women who were not screened (N = 400) had 155% increased odds of a later-stage (stage III or IV) breast cancer diagnosis when compared with women who were screened via mammography (N = 1,365) ( p < 0.001). Elapsed time from the most recent screening mammogram to breast cancer diagnosis was also significantly associated with cancer stage. Women with a longer time lapse ( > 4 months) between their most recent screening mammogram and diagnosis (N = 356) had 87% increased odds of a later-stage breast cancer diagnosis (p < 0.001). This is consistent with guidelines emphasizing the importance of screening to detect early-stage cancers. Among all incident breast cancer cases, 23% (N = 400) had no evidence of a screening mammogram in the two years before diagnosis. However, 49% (N = 196) of these women did have a routine physical examination during that same period. On this basis, we estimate that an additional 11% of breast cancer cases could have been screened for if a liquid biopsy test was utilized during those physical exams. Extending this analysis to include all incident cancer cases, 60% (N = 5,022) of the cohort had a routine physical exam in the two years prior to their cancer diagnosis. Conclusions: Our analyses confirm the association of cancer screening with earlier stage at diagnosis for breast cancer. Further, this research suggests opportunities to screen for and potentially intercept 60% of all incident cancer cases by incorporating a multi-cancer blood-based test into routine care. Given the importance of improving early cancer detection rates, additional clinical work extending the initial conclusions presented here is warranted.

Cancer screening utilization in patients diagnosed with cancer types with and without recommended screening modalities

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Background: Several studies have shown screening methods can detect cancer at earlier stages and improve cancer prognosis; however, only four cancer types (breast, colorectal, cervical, and lung) currently have screening methods recommended by the United States Preventive Services Taskforce (USPSTF). In 2021, these four cancers are expected to make up roughly 40% of new cases and cancer deaths, meaning that the majority of cancer deaths will be associated with cancer types lacking recommended screening. We sought to characterize patients who were diagnosed with cancer types with and without recommended screening modalities to demonstrate the gaps in screening faced by the majority of cancers today. Methods: The Geisinger Health System (GHS) Phenomics Initiative Database (PIDB) provides deidentified data from electronic health, billing, and imaging records, and a tumor registry. PIDB was used to identify patients aged 50 to 76 who had cancers diagnosed between 2008 and 2020 and a record of USPSTF-recommended cancer screenings within GHS prior to diagnosis. Analysis focused on patients who received care at GHS during their screening-eligible intervals. Results: Between 2008 and 2020, 13,347 incident invasive cancers were identified in the GHS tumor registry. Of these, 40% (N = 5,331) were cancer types with a recommended screening modality. 57% of these cases (N = 3,039; 23% of all incident cancers) occurred in patients who underwent screening in the interval preceding diagnosis. Screening adherence was significantly associated with stage at diagnosis; patients who were not screened for their diagnosed cancer were more than twice as likely to have a late-stage diagnosis as compared with patients who received screening (multivariate ordinal logistic regression, OR = 2.16, p < 0.001). Patterns of screening adherence in this population are complex; however, 57% of these patients had received screening for a different cancer type. The majority of incident cancers were of those types with no recommended screening modality (N = 8,016; 60% of all incident cancers). Of these, most (N = 6,252; 78%) had been screened for at least one of breast, lung, colon, or cervical cancer and nearly half (N = 3,607; 45%) were current for all guideline-recommended screenings. Not surprisingly, stage at diagnosis was not associated with adherence to any or all screening modalities (multivariate ordinal logistic regression, p = 0.11 and p = 0.45). Conclusions: The majority (79%) of individuals diagnosed with cancer had a history of adherence to at least one screening recommendation. Out of all cancer patients, only 23% were screened specifically for the cancer with which they were subsequently diagnosed, a group that is associated with a lower odds of a late-stage diagnosis. This suggests that the majority of cancer patients who underwent any cancer screening did not benefit from earlier stage diagnosis.

Toward a fine-scale population health monitoring system

Understanding population health disparities is an essential component of equitable precision health efforts. Epidemiology research often relies on definitions of race and ethnicity, but these population labels may not adequately capture disease burdens and environmental factors impacting specific sub-populations. Here, we propose a framework for repurposing data from electronic health records (EHRs) in concert with genomic data to explore the demographic ties that can impact disease burdens. Using data from a diverse biobank in New York City, we identified 17 communities sharing recent genetic ancestry. We observed 1,177 health outcomes that were statistically associated with a specific group and demonstrated significant differences in the segregation of genetic variants contributing to Mendelian diseases. We also demonstrated that fine-scale population structure can impact the prediction of complex disease risk within groups. This work reinforces the utility of linking genomic data to EHRs and provides a framework toward fine-scale monitoring of population health.

Mammography utilization among women with a negative circulating tumor DNA-based early cancer detection test

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Background: Blood-based tests may enable minimally invasive detection of multiple cancer types. One such test, CancerSEEK, employs ctDNA and protein biomarkers for this purpose. Test performance has been evaluated in women without a history of cancer in an ongoing prospective study called DETECT-A. The introduction of such blood tests holds promise, and their future utility lies in augmenting, not displacing, standard-of-care (SOC) cancer screening. One important safety concern is that a negative test result could provide false reassurance that discourages adherence to SOC cancer screening. To investigate this possibility, we studied delivery of mammography to DETECT-A participants before and after receipt of a negative CancerSEEK result. Methods: DETECT-A screened 10,000 women aged 65-75 using CancerSEEK. Participants completed a survey about cancer screening at enrollment and at one-year post-enrollment. We analyzed only those participants who had received a negative CancerSEEK result, were insured by Geisinger Health Plan (GHP), and had completed both surveys. GHP claims data were used to identify mammograms performed within one year prior-to and post-enrollment. Overall utilization was determined by combining claims and survey data at enrollment and one-year post-enrollment. In addition to comparing SOC screening rates pre- versus post-testing, we evaluated the impact of primary care physician (PCP) type (Geisinger versus any other institution), as screening reminder mechanisms differ between institutions. Results: Of the 2,241 participants who met analysis criteria, 73.6% (n = 1,650) had a mammogram in the year before enrollment while a significantly great number (79.3%, n = 1,777) did so during the one-year follow-up (χ2(1) = 59.05, p < 0.001). At enrollment, there were 591 participants who had not had a mammogram completed in the previous year, but 404 (68.4%) of them did have a mammogram during the one-year follow-up. The rate of change in mammography utilization did not differ between those who had a Geisinger versus a non-Geisinger PCP (χ2(2) = 1.83, p = 0.40). Conclusions: Participants in a study using a novel blood test for earlier cancer detection had a significantly higher rate of annual mammography after study enrollment and testing. These results indicate that introduction of a minimally invasive ctDNA and protein biomarker-based cancer screening test may engender greater, not lesser, utilization of SOC cancer screening. Further study is required to understand the root causes of increased utilization in this context.

Carbonyl reductase 1 catalyzes 20β-reduction of glucocorticoids, modulating receptor activation and metabolic complications of obesity

Carbonyl Reductase 1 (CBR1) is a ubiquitously expressed cytosolic enzyme important in exogenous drug metabolism but the physiological function of which is unknown. Here, we describe a role for CBR1 in metabolism of glucocorticoids. CBR1 catalyzes the NADPH- dependent production of 20β-dihydrocortisol (20β-DHF) from cortisol. CBR1 provides the major route of cortisol metabolism in horses and is up-regulated in adipose tissue in obesity in horses, humans and mice. We demonstrate that 20β-DHF is a weak endogenous agonist of the human glucocorticoid receptor (GR). Pharmacological inhibition of CBR1 in diet-induced obesity in mice results in more marked glucose intolerance with evidence for enhanced hepatic GR signaling. These findings suggest that CBR1 generating 20β-dihydrocortisol is a novel pathway modulating GR activation and providing enzymatic protection against excessive GR activation in obesity.

Corrigendum: Endothelial to mesenchymal transition is common in atherosclerotic lesions and is associated with plaque instability

Nature Communications 8: Article number: 11853 (2016); Published: 24 June 2016; Updated: 16 February 2017 In this Article, the catalogue number for the anti-Fap-Alexa Fluor 647 antibody is listed incorrectly and should have read bs-5758R-A647 instead of bs-5760R-A647.

Association of Body Mass Index with DNA Methylation and Gene Expression in Blood Cells and Relations to Cardiometabolic Disease: A Mendelian Randomization Approach

BACKGROUND

The link between DNA methylation, obesity, and adiposity-related diseases in the general population remains uncertain.

METHODS AND FINDINGS

We conducted an association study of body mass index (BMI) and differential methylation for over 400,000 CpGs assayed by microarray in whole-blood-derived DNA from 3,743 participants in the Framingham Heart Study and the Lothian Birth Cohorts, with independent replication in three external cohorts of 4,055 participants. We examined variations in whole blood gene expression and conducted Mendelian randomization analyses to investigate the functional and clinical relevance of the findings. We identified novel and previously reported BMI-related differential methylation at 83 CpGs that replicated across cohorts; BMI-related differential methylation was associated with concurrent changes in the expression of genes in lipid metabolism pathways. Genetic instrumental variable analysis of alterations in methylation at one of the 83 replicated CpGs, cg11024682 (intronic to sterol regulatory element binding transcription factor 1 [SREBF1]), demonstrated links to BMI, adiposity-related traits, and coronary artery disease. Independent genetic instruments for expression of SREBF1 supported the findings linking methylation to adiposity and cardiometabolic disease. Methylation at a substantial proportion (16 of 83) of the identified loci was found to be secondary to differences in BMI. However, the cross-sectional nature of the data limits definitive causal determination.

CONCLUSIONS

We present robust associations of BMI with differential DNA methylation at numerous loci in blood cells. BMI-related DNA methylation and gene expression provide mechanistic insights into the relationship between DNA methylation, obesity, and adiposity-related diseases.

EXPLORING THE REPRODUCIBILITY OF PROBABILISTIC CAUSAL MOLECULAR NETWORK MODELS

Network reconstruction algorithms are increasingly being employed in biomedical and life sciences research to integrate large-scale, high-dimensional data informing on living systems. One particular class of probabilistic causal networks being applied to model the complexity and causal structure of biological data is Bayesian networks (BNs). BNs provide an elegant mathematical framework for not only inferring causal relationships among many different molecular and higher order phenotypes, but also for incorporating highly diverse priors that provide an efficient path for incorporating existing knowledge. While significant methodological developments have broadly enabled the application of BNs to generate and validate meaningful biological hypotheses, the reproducibility of BNs in this context has not been systematically explored. In this study, we aim to determine the criteria for generating reproducible BNs in the context of transcription-based regulatory networks. We utilize two unique tissues from independent datasets, whole blood from the GTEx Consortium and liver from the Stockholm-Tartu Atherosclerosis Reverse Network Engineering Team (STARNET) study. We evaluated the reproducibility of the BNs by creating networks on data subsampled at different levels from each cohort and comparing these networks to the BNs constructed using the complete data. To help validate our results, we used simulated networks at varying sample sizes. Our study indicates that reproducibility of BNs in biological research is an issue worthy of further consideration, especially in light of the many publications that now employ findings from such constructs without appropriate attention paid to reproducibility. We find that while edge-to-edge reproducibility is strongly dependent on sample size, identification of more highly connected key driver nodes in BNs can be carried out with high confidence across a range of sample sizes.

Cardiometabolic risk loci share downstream cis- and trans-gene regulation across tissues and diseases

Genome-wide association studies (GWAS) have identified hundreds of cardiometabolic disease (CMD) risk loci. However, they contribute little to genetic variance, and most downstream gene-regulatory mechanisms are unknown. We genotyped and RNA-sequenced vascular and metabolic tissues from 600 coronary artery disease patients in the Stockholm-Tartu Atherosclerosis Reverse Networks Engineering Task study (STARNET). Gene expression traits associated with CMD risk single-nucleotide polymorphism (SNPs) identified by GWAS were more extensively found in STARNET than in tissue- and disease-unspecific gene-tissue expression studies, indicating sharing of downstream cis-/trans-gene regulation across tissues and CMDs. In contrast, the regulatory effects of other GWAS risk SNPs were tissue-specific; abdominal fat emerged as an important gene-regulatory site for blood lipids, such as for the low-density lipoprotein cholesterol and coronary artery disease risk gene PCSK9 STARNET provides insights into gene-regulatory mechanisms for CMD risk loci, facilitating their translation into opportunities for diagnosis, therapy, and prevention.

Endothelial to mesenchymal transition is common in atherosclerotic lesions and is associated with plaque instability

Endothelial to mesenchymal transition (EndMT) plays a major role during development, and also contributes to several adult cardiovascular diseases. Importantly, mesenchymal cells including fibroblasts are prominent in atherosclerosis, with key functions including regulation of: inflammation, matrix and collagen production, and plaque structural integrity. However, little is known about the origins of atherosclerosis-associated fibroblasts. Here we show using endothelial-specific lineage-tracking that EndMT-derived fibroblast-like cells are common in atherosclerotic lesions, with EndMT-derived cells expressing a range of fibroblast-specific markers. In vitro modelling confirms that EndMT is driven by TGF-β signalling, oxidative stress and hypoxia; all hallmarks of atherosclerosis. 'Transitioning' cells are readily detected in human plaques co-expressing endothelial and fibroblast/mesenchymal proteins, indicative of EndMT. The extent of EndMT correlates with an unstable plaque phenotype, which appears driven by altered collagen-MMP production in EndMT-derived cells. We conclude that EndMT contributes to atherosclerotic patho-biology and is associated with complex plaques that may be related to clinical events.

Assembly and diploid architecture of an individual human genome via single-molecule technologies

We present the first comprehensive analysis of a diploid human genome that combines single-molecule sequencing with single-molecule genome maps. Our hybrid assembly markedly improves upon the contiguity observed from traditional shotgun sequencing approaches, with scaffold N50 values approaching 30 Mb, and we identified complex structural variants (SVs) missed by other high-throughput approaches. Furthermore, by combining Illumina short-read data with long reads, we phased both single-nucleotide variants and SVs, generating haplotypes with over 99% consistency with previous trio-based studies. Our work shows that it is now possible to integrate single-molecule and high-throughput sequence data to generate de novo assembled genomes that approach reference quality.

Integrated genome-wide association, coexpression network, and expression single nucleotide polymorphism analysis identifies novel pathway in allergic rhinitis

BACKGROUND

Allergic rhinitis is a common disease whose genetic basis is incompletely explained. We report an integrated genomic analysis of allergic rhinitis.

METHODS

We performed genome wide association studies (GWAS) of allergic rhinitis in 5633 ethnically diverse North American subjects. Next, we profiled gene expression in disease-relevant tissue (peripheral blood CD4+ lymphocytes) collected from subjects who had been genotyped. We then integrated the GWAS and gene expression data using expression single nucleotide (eSNP), coexpression network, and pathway approaches to identify the biologic relevance of our GWAS.

RESULTS

GWAS revealed ethnicity-specific findings, with 4 genome-wide significant loci among Latinos and 1 genome-wide significant locus in the GWAS meta-analysis across ethnic groups. To identify biologic context for these results, we constructed a coexpression network to define modules of genes with similar patterns of CD4+ gene expression (coexpression modules) that could serve as constructs of broader gene expression. 6 of the 22 GWAS loci with P-value ≤ 1x10-6 tagged one particular coexpression module (4.0-fold enrichment, P-value 0.0029), and this module also had the greatest enrichment (3.4-fold enrichment, P-value 2.6 × 10-24) for allergic rhinitis-associated eSNPs (genetic variants associated with both gene expression and allergic rhinitis). The integrated GWAS, coexpression network, and eSNP results therefore supported this coexpression module as an allergic rhinitis module. Pathway analysis revealed that the module was enriched for mitochondrial pathways (8.6-fold enrichment, P-value 4.5 × 10-72).

CONCLUSIONS

Our results highlight mitochondrial pathways as a target for further investigation of allergic rhinitis mechanism and treatment. Our integrated approach can be applied to provide biologic context for GWAS of other diseases.

Dissection of immune gene networks in primary melanoma tumors critical for antitumor surveillance of patients with stage II-III resectable disease

Patients with resected stage II-III cutaneous melanomas remain at high risk for metastasis and death. Biomarker development has been limited by the challenge of isolating high-quality RNA for transcriptome-wide profiling from formalin-fixed and paraffin-embedded (FFPE) primary tumor specimens. Using NanoString technology, RNA from 40 stage II-III FFPE primary melanomas was analyzed and a 53-immune-gene panel predictive of non-progression (area under the curve (AUC)=0.920) was defined. The signature predicted disease-specific survival (DSS P<0.001) and recurrence-free survival (RFS P<0.001). CD2, the most differentially expressed gene in the training set, also predicted non-progression (P<0.001). Using publicly available microarray data from 46 primary human melanomas (GSE15605), a coexpression module enriched for the 53-gene panel was then identified using unbiased methods. A Bayesian network of signaling pathways based on this data identified driver genes. Finally, the proposed 53-gene panel was confirmed in an independent test population of 48 patients (AUC=0.787). The gene signature was an independent predictor of non-progression (P<0.001), RFS (P<0.001), and DSS (P=0.024) in the test population. The identified driver genes are potential therapeutic targets, and the 53-gene panel should be tested for clinical application using a larger data set annotated on the basis of prospectively gathered data.

Immune gene expression in primary melanomas to predict lower risk of recurrence and death

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Background: Improved biomarkers are needed to define recurrence risk in patients with completely resected skin melanomas. Standard prognostic indicators used in staging, including depth, ulceration, and mitotic rate, while useful, often fail to accurately predict recurrence for individual patients. The immune system may prevent recurrence in this population, but no evidence-based immune biomarkers are in clinical use. Biomarker development has been hindered by clinical standards necessitating that the entire specimen be formalin fixed and paraffin embedded (FFPE) for morphology evaluation, a process damaging to RNA. Methods: To define a biomarker for melanoma recurrence, mRNA copy number of immune-related genes from FFPE melanoma was measured using NanoString, a hybridization assay suited for analysis of partially degraded RNA. Genes predictive of non-recurrence were defined using receiver operating characteristic (ROC) curves in a training cohort and then validated in an independent patient cohort. Results: A panel of 21 genes predictive of non-recurrence were defined using ROC curves in a training cohort (N=44). This result was validated in an independent patient cohort (N=37, AUC=0.794). Protein levels of the most differentially expressed gene, CD2, also associated with non-recurrence (p<0.001). The immune gene panel and CD2 staining associated with prolonged survival (p<0.001 and p=0.019, respectively). Conclusions: mRNA copy number of immune-related genes in primary FFPE melanomas predicts non-recurrence and prolonged survival. This data highlights the impact of immunosurveillance in primary human melanoma and the identified gene panel may be a useful tool for patient stratification for adjuvant immunotherapy studies.

Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease

Crohn’s disease (CD) and ulcerative colitis (UC), the two common forms of inflammatory bowel disease (IBD), affect over 2.5 million people of European ancestry with rising prevalence in other populations¹. Genome-wide association studies (GWAS) and subsequent meta-analyses of CD and UC^2,3 as separate phenotypes implicated previously unsuspected mechanisms, such as autophagy⁴, in pathogenesis and showed that some IBD loci are shared with other inflammatory diseases⁵. Here we expand knowledge of relevant pathways by undertaking a meta-analysis of CD and UC genome-wide association scans, with validation of significant findings in more than 75,000 cases and controls. We identify 71 new associations, for a total of 163 IBD loci that meet genome-wide significance thresholds. Most loci contribute to both phenotypes, and both directional and balancing selection effects are evident. Many IBD loci are also implicated in other immune-mediated disorders, most notably with ankylosing spondylitis and psoriasis. We also observe striking overlap between susceptibility loci for IBD and mycobacterial infection. Gene co-expression network analysis emphasizes this relationship, with pathways shared between host responses to mycobacteria and those predisposing to IBD.

Deciphering the transcriptional network of the dendritic cell lineage

Although much progress has been made in the understanding of the ontogeny and function of dendritic cells (DCs), the transcriptional regulation of the lineage commitment and functional specialization of DCs in vivo remains poorly understood. We made a comprehensive comparative analysis of CD8(+), CD103(+), CD11b(+) and plasmacytoid DC subsets, as well as macrophage DC precursors and common DC precursors, across the entire immune system. Here we characterized candidate transcriptional activators involved in the commitment of myeloid progenitor cells to the DC lineage and predicted regulators of DC functional diversity in tissues. We identified a molecular signature that distinguished tissue DCs from macrophages. We also identified a transcriptional program expressed specifically during the steady-state migration of tissue DCs to the draining lymph nodes that may control tolerance to self tissue antigens.