A Novel Tissue-Free Method to Estimate Tumor-Derived Cell-Free DNA Quantity Using Tumor Methylation Patterns

Estimating the abundance of cell-free DNA (cfDNA) fragments shed from a tumor (i.e., circulating tumor DNA (ctDNA)) can approximate tumor burden, which has numerous clinical applications. We derived a novel, broadly applicable statistical method to quantify cancer-indicative methylation patterns within cfDNA to estimate ctDNA abundance, even at low levels. Our algorithm identified differentially methylated regions (DMRs) between a reference database of cancer tissue biopsy samples and cfDNA from individuals without cancer. Then, without utilizing matched tissue biopsy, counts of fragments matching the cancer-indicative hyper/hypo-methylated patterns within DMRs were used to determine a tumor methylated fraction (TMeF; a methylation-based quantification of the circulating tumor allele fraction and estimate of ctDNA abundance) for plasma samples. TMeF and small variant allele fraction (SVAF) estimates of the same cancer plasma samples were correlated (Spearman's correlation coefficient: 0.73), and synthetic dilutions to expected TMeF of 10-3 and 10-4 had estimated TMeF within two-fold for 95% and 77% of samples, respectively. TMeF increased with cancer stage and tumor size and inversely correlated with survival probability. Therefore, tumor-derived fragments in the cfDNA of patients with cancer can be leveraged to estimate ctDNA abundance without the need for a tumor biopsy, which may provide non-invasive clinical approximations of tumor burden.

Megakaryocyte- and erythroblast-specific cell-free DNA patterns in plasma and platelets reflect thrombopoiesis and erythropoiesis levels

Circulating cell-free DNA (cfDNA) fragments are a biological analyte with extensive utility in diagnostic medicine. Understanding the source of cfDNA and mechanisms of release is crucial for designing and interpreting cfDNA-based liquid biopsy assays. Using cell type-specific methylation markers as well as genome-wide methylation analysis, we determine that megakaryocytes, the precursors of anuclear platelets, are major contributors to cfDNA (~26%), while erythroblasts contribute 1-4% of cfDNA in healthy individuals. Surprisingly, we discover that platelets contain genomic DNA fragments originating in megakaryocytes, contrary to the general understanding that platelets lack genomic DNA. Megakaryocyte-derived cfDNA is increased in pathologies involving increased platelet production (Essential Thrombocythemia, Idiopathic Thrombocytopenic Purpura) and decreased upon reduced platelet production due to chemotherapy-induced bone marrow suppression. Similarly, erythroblast cfDNA is reflective of erythrocyte production and is elevated in patients with thalassemia. Megakaryocyte- and erythroblast-specific DNA methylation patterns can thus serve as biomarkers for pathologies involving increased or decreased thrombopoiesis and erythropoiesis, which can aid in determining the etiology of aberrant levels of erythrocytes and platelets.

The DNA methylome of human vascular endothelium and its use in liquid biopsies

BACKGROUND

Vascular endothelial cells (VECs) are an essential component of each tissue, contribute to multiple pathologies, and are targeted by important drugs. Yet, there is a shortage of biomarkers to assess VEC turnover.

METHODS

To develop DNA methylation-based liquid biopsies for VECs, we determined the methylome of VECs isolated from freshly dissociated human tissues.

FINDINGS

A comparison with a human cell-type methylome atlas yielded thousands of loci that are uniquely unmethylated in VECs. These sites are typically gene enhancers, often residing adjacent to VEC-specific genes. We also identified hundreds of genomic loci that are differentially methylated in organotypic VECs, indicating that VECs feeding specific organs are distinct cell types with a stable epigenetic identity. We established universal and lung-specific VEC markers and evaluated their presence in circulating cell-free DNA (cfDNA). Nearly 2.5% of cfDNA in the plasma of healthy individuals originates from VECs. Sepsis, graft versus host disease, and cardiac catheterization are associated with elevated levels of VEC-derived cfDNA, indicative of vascular damage. Lung-specific VEC cfDNA is selectively elevated in patients with chronic obstructive pulmonary disease (COPD) or lung cancer, revealing tissue-specific vascular turnover.

CONCLUSIONS

VEC cfDNA biomarkers inform vascular dynamics in health and disease, potentially contributing to early diagnosis and monitoring of pathologies, and assessment of drug activity.

FUNDING

This work was supported by the Beutler Research Program, Helmsley Charitable Trust, JDRF, Grail and the DON Foundation (to Y.D.). Y.D holds the Walter & Greta Stiel Chair in heart studies. B.G., R.S., J.M., D.N., T.K., and Y.D. filed patents on cfDNA analysis.

Universal lung epithelium DNA methylation markers for detection of lung damage in liquid biopsies

BACKGROUND

Circulating biomarkers for lung damage are lacking. Lung epithelium-specific DNA methylation patterns can potentially report the presence of lung-derived cell-free DNA (cfDNA) in blood, as an indication of lung cell death.

METHODS

We sorted human lung alveolar and bronchial epithelial cells from surgical specimens, and obtained their methylomes using whole-genome bisulfite sequencing. We developed a PCR-sequencing assay determining the methylation status of 17 loci with lung-specific methylation patterns, and used it to assess lung-derived cfDNA in the plasma of healthy volunteers and patients with lung disease.

RESULTS

Loci that are uniquely unmethylated in alveolar or bronchial epithelial cells are enriched for enhancers controlling lung-specific genes. Methylation markers extracted from these methylomes revealed that normal lung cell turnover likely releases cfDNA into the air spaces, rather than to blood. People with advanced lung cancer show a massive elevation of lung cfDNA concentration in blood. Among individuals undergoing bronchoscopy, lung-derived cfDNA is observed in the plasma of those later diagnosed with lung cancer, and to a lesser extent in those diagnosed with other lung diseases. Lung cfDNA is also elevated in patients with acute exacerbation of chronic obstructive pulmonary disease (COPD) compared with patients with stable disease, and is associated with future exacerbation and mortality in these patients.

CONCLUSIONS

Universal cfDNA methylation markers of normal lung epithelium allow for mutation-independent, sensitive and specific detection of lung-derived cfDNA, reporting on ongoing lung injury. Such markers can find broad utility in the study of normal and pathologic human lung dynamics.

Remote immune processes revealed by immune-derived circulating cell-free DNA

Blood cell counts often fail to report on immune processes occurring in remote tissues. Here, we use immune cell type-specific methylation patterns in circulating cell-free DNA (cfDNA) for studying human immune cell dynamics. We characterized cfDNA released from specific immune cell types in healthy individuals (N = 242), cross sectionally and longitudinally. Immune cfDNA levels had no individual steady state as opposed to blood cell counts, suggesting that cfDNA concentration reflects adjustment of cell survival to maintain homeostatic cell numbers. We also observed selective elevation of immune-derived cfDNA upon perturbations of immune homeostasis. Following influenza vaccination (N = 92), B-cell-derived cfDNA levels increased prior to elevated B-cell counts and predicted efficacy of antibody production. Patients with eosinophilic esophagitis (N = 21) and B-cell lymphoma (N = 27) showed selective elevation of eosinophil and B-cell cfDNA, respectively, which were undetectable by cell counts in blood. Immune-derived cfDNA provides a novel biomarker for monitoring immune responses to physiological and pathological processes that are not accessible using conventional methods.

Tumor methylation patterns to measure tumor fraction in cell-free DNA

3052

Background: Cell-free DNA (cfDNA) tumor fraction (TF), the proportion of tumor molecules in a cfDNA sample, is a direct measurement of signal for cfDNA cancer applications. The Circulating Cell-free Genome Atlas study (CCGA; NCT02889978) is a prospective, multi-center, observational, case-control study designed to support development of a methylation-based, multi-cancer detection test in which a classifier is trained to distinguish cancer from non-cancer. Here we leveraged CCGA data to examine the relationship between cfDNA containing tumor DNA methylation patterns, TF, and cancer classification performance. Methods: The CCGA classifier was trained on whole-genome bisulfite sequencing (WGBS) and targeted methylation (TM) sequencing data to detect cancer versus non-cancer. 822 samples had biopsy WGBS performed; of those, 231 also had cfDNA targeted methylation (TM) and cfDNA whole-genome sequencing (WGS). Biopsy WGBS identified somatic single nucleotide variants (SNV) and methylation variants (MV; defined as methylation patterns in sequenced DNA fragments observed commonly in biopsy but rarely [ < 1/10,000] in the cfDNA of non-cancer controls [n = 898]). Observed tumor fragment counts (SNV in WGS; MV in TM), were modeled as a Poisson process with rate dependent on TF. TF and classifier limits of detection (LOD) were each assessed using Bayesian logistic regression. Results: Across biopsy samples, a median of 2,635 MV was distributed across the genome, with a median of 86.8% shared with ≥1 participant, and a median of 69.3% targeted by the TM assay. TF LOD from MV was 0.00050 (95% credible interval [CI]: 0.00041 - 0.00061); MV and SNV estimates were concordant (Spearman’s Rho: 0.820). MV TF estimates explained classifier performance (Spearman’s Rho: 0.856) and allowed determination of the classifier LOD (0.00082 [95% CI: 0.00057 - 0.00115]). Conclusions: These data demonstrate the existence of methylation patterns in tumor-derived cfDNA fragments that are rarely found in individuals without cancer; their abundance directly measured TF, and was a major factor influencing classification performance. Finally, the low classifier LOD (~0.1%) motivates further clinical development of a methylation-based assay for cancer detection. Clinical trial information: NCT02889978 .

Genome-wide cell-free DNA (cfDNA) methylation signatures and effect on tissue of origin (TOO) performance

3049

Background: For multi-cancer detection using cfDNA, TOO determination is critical to enable safe and efficient diagnostic follow-up. Previous array-based studies captured < 2% of genomic CpGs. Here, we report genome-wide fragment-level methylation patterns across 811 cancer cell methylomes representing 21 tumor types (97% of SEER cancer incidence), and define effects of this methylation database on TOO prediction within a machine learning framework. Methods: Genomic DNA from 655 formalin-fixed paraffin-embedded (FFPE) tumor tissues and 156 isolated cells from tumors was subjected to a prototype 30x whole-genome bisulfite sequencing (WGBS) assay, as previously reported in the Circulating Cell-free Genome Atlas (CCGA) study (NCT02889978). Two independent TOO models, one with and one without the methylation database, were fitted on training samples; each was used to predict on the test set. A WGBS classifier was used to detect cancer at 98% specificity; reported TOO results reflect percent agreement between predicted and true TOO among those detected cancers (166 cases: 81 stage I-III, 69 stage IV, 16 non-informative). Results: Genome-wide methylation data generated from this database allowed fragment-level analysis and coverage of ~30 million CpGs across the genome (~60-fold greater than array-based approaches). Incorrect TOO assignments decreased by 35% (20% to 13%) after incorporating methylation database information into TOO classification. Improvement was observed across all cancer types and was consistent in early-stage cancers (stage I-III). Respective performances in breast cancer (n = 23) were 87% vs 96%; in lung cancer (n = 32) were 85% vs 88%; in hepatobiliary (n = 10) were 70% vs 90%; and in pancreatic cancer (n = 17) were 94% vs 100%. Results using an optimized approach informed by these results in a large cohort of CCGA participants will be reported. Conclusions: Incorporating data from a large methylation database improved TOO performance in multiple cancer types. This supports feasibility of this methylation-based approach as an early cancer detection test across cancer types. Clinical trial information: NCT02889978.

Abstract 4856: Transcriptome sequencing of circulating tumor cells reveals their heterogeneity

We have developed a novel sample preparation technology for complete purification of circulating tumor cells (CTCs). The target cells are magnetically labeled with anti-EpCAM particles and then immunostained with anti-EpCAM antibodies. CTCs have been selectively captured by applying absorption magnetic forces and desorbing fluidic shear force to the cells (MagSweeper technology). CTCs, defined as EpCAM+ CD45- cells are then picked individually for nucleic acid analysis.

We have utilized this platform for isolation of CTCs from prostate cancer patients. From each case, 7.5ml blood sample is processed within 24hr of collection. The purified CTCs have been validated to be EpCAM+ CD45- by immunostaining and qPCR analysis (91%± 6% specificity). So far we have isolated CTCs from 14 out of 35 cases. The CTC counts isolated by MagSweeper have correlated well with the counts obtained from the same cases using FDA-cleared CellSearch system.

We are also developing new genomic technologies for whole-genome expression profiling of single CTCs. The purified CTCs are lysed under control conditions, and then processed with our whole transcriptome amplification (WTA) protocol. The amplified cDNA are used for SBS sequencing library preparation. Our WTA protocol has been validated through mRNA-sequencing of cultured single prostate LNCaP and bladder T24 cells. We found that more than 66% of all genes are reproducibly sequenced and the expression profile of single LNCaP and T24 cells correlated well within each cell line (R⁁2=0.75 for LNCaP and R⁁2=0.87 for T24 cells).

We have sequenced the whole transcriptome of 7 CTCs and one leukocyte cell isolated from blood sample of a metastatic prostate cancer patient. We found that 7/7 CTC cells express KLK3, AR and EpCAM, 6/7 express CD24 and AMACR, 5/7 express MYC and 0/7 express CD45. On the other hand, the WBC does not express any of these genes except CD45. At present we are analyzing the data for the presence of fusion genes. So far we have not detected the TMPRSS2-ERG fusion gene in any of the CTCs analyzed; however, the search for looking into other known fusion genes is currently under progress. In addition, we clustered CTCs with LNCaP and T24 single cells. We found that the 5/7 CTC cells cluster together, and are different from LNcap or T24 clusters. 2/7 CTCs show different expression profile, demonstrating expected heterogeneity between CTCs.

We have introduced a new end-to-end integrated workflow for CTC genomic analysis. The workflow has been successfully tested in isolation and mRNA-seq profiling of CTCs from prostate cancer patient samples. This novel workflow will open up new opportunities in studying CTC biology.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4856. doi:10.1158/1538-7445.AM2011-4856

Abstract 1144: High-throughput genetic and expression analysis of circulating tumor cells

We are developing novel sample preparation technologies for genomic analysis of circulating tumor cells (CTCs): a new cell-sorting device for purification of single CTCs from a tube of blood; and highly sensitive and quantitative genomic technologies for single cell analysis using Illumina's microarray and next-generation sequencing platforms.

We have prototyped a new ultra-rare cell enrichment device that produces cell samples compatible with Illumina's nucleic-acid analysis platforms. Sorting is performed on whole blood samples with no pre-fractionation, to minimize the genetic alteration of CTCs. To validate the performance of our cell sorting device, we have monitored the recovery of LNCaP prostate cancer cells spiked into 7.5ml normal blood samples at concentration of 10 cells/7.5ml. For ease of analysis, the cancer cells were labeled with cell tracker dye and leukocyte nuclei in blood were labeled with Hoechst 33342 dye. Cancer cells were immunomagnetically labeled in blood with EpCAM beads and then isolated by our cell sorter. We found that the capturing efficiency of our platform was 60% ± 24% for 10 cells/7.5ml samples. The purity of cancer cells among contaminating white blood cells was 91% ± 6%, after a second round of extraction of individual cancer cells. The entire purification protocol of CTCs from 7.5ml blood samples takes 2 hours. This platform has been earlier validated for CTC isolation from blood samples of breast cancer patients and is currently under evaluation for prostate and ovarian cancer patients.

We are also developing new genomic technologies for whole-genome expression profiling, somatic mutation analysis, and transcriptome sequencing of purified CTCs: a) using a Multiple Displacement Amplification (MDA)-based protocol and a 300K-SNP chip readout, we were able to obtain 88.3% and 93.9% call rate, and 97.4% and 99.9% call accuracy with direct cell lysis from 1 and 5 LNCaP cells, respectively. We also detected the chromosomal amplification and loss-of-heterozygosity; b) with our current RNA amplification protocol, we were able to generate reproducible expression profiles, R2 = 0.37 and 0.75, from 1 and 10 cell inputs, respectively. In addition, the expression profiles correlated well with those obtained with standard 100 ng total RNA input, R2 = 0.36 and 0.72, respectively; c) we have also developed next-generation sequencing protocols to profile single-cell transciptomes.

We have introduced a new platform for isolation of small numbers of CTCs from patient blood samples that are compatible with Illumina genomic assays. Our gDNA and RNA amplification protocols work with direct cell lysates; no need to extract DNA or RNA from single cells. The protocols are compatible with Illumina microarray and next-gen sequencing platforms.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 1144.

Abstract 1149: Genetic analysis of single cells

We are developing highly sensitive and quantitative genomic technologies for genetic and expression analysis of single cells or trace amount of DNA/RNA materials, using microarray and next-generation sequencing platforms. We have tested various Multiple Displacement Amplification (MDA)-based protocols under a variety of reaction conditions. With our current protocol and a 300K-SNP chip readout, we were able to obtain 88.3% and 93.9% call rate, and 97.4% and 99.9% call accuracy with direct cell lysis from 1 cell and 5 cells, respectively. We are also developing RNA amplification methods for high-throughput expression profiling of single cells. With our current protocol, we were able to generate reproducible expression profiles, R2 = 0.73 and 0.77, using 10 pg and 50 pg total RNA input, respectively. In addition, the profiles correlated well with those obtained with standard 100 ng total RNA input, R2 = 0.61 and 0.77, respectively. Our data show that sequencing of single-cell transcriptomes can clearly distinguish embryonic stem cells from embryonic fibroblasts and tumor cells. We are currently using these technologies to study medical specimens such as circulating tumor cells and cancer stem cells.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 1149.

SF/HGF is a mediator between limb patterning and muscle development

Scatter factor/hepatocyte growth factor (SF/HGF) is known to be involved in the detachment of myogenic precursor cells from the lateral dermomyotomes and their subsequent migration into the newly formed limb buds. As yet, however, nothing has been known about the role of the persistent expression of SF/HGF in the limb bud mesenchyme during later stages of limb bud development. To test for a potential role of SF/HGF in early limb muscle patterning, we examined the regulation of SF/HGF expression in the limb bud as well as the influence of SF/HGF on direction control of myogenic precursor cells in limb bud mesenchyme. We demonstrate that SF/HGF expression is controlled by signals involved in limb bud patterning. In the absence of an apical ectodermal ridge (AER), no expression of SF/HGF in the limb bud is observed. However, FGF-2 application can rescue SF/HGF expression. Excision of the zone of polarizing activity (ZPA) results in ectopic and enhanced SF/HGF expression in the posterior limb bud mesenchyme. We could identify BMP-2 as a potential inhibitor of SF/HGF expression in the posterior limb bud mesenchyme. We further demonstrate that ZPA excision results in a shift of Pax-3-positive cells towards the posterior limb bud mesenchyme, indicating a role of the ZPA in positioning of the premuscle masses. Moreover, we present evidence that, in the limb bud mesenchyme, SF/HGF increases the motility of myogenic precursor cells and has a role in maintaining their undifferentiated state during migration. We present a model for a crucial role of SF/HGF during migration and early patterning of muscle precursor cells in the vertebrate limb.

The alpha4 subunit of integrin is important for neural crest cell migration

We identify the alpha4 subunit of integrin as a predominant integrin expressed by neural crest cells in both avian and murine embryos. Using degenerate primers, we obtained a PCR fragment of the chick integrin alpha4 subunit that was subsequently used to clone the full-length subunit with a predicted amino acid sequence 60% identical to human and mouse alpha4 subunits. In situ hybridization demonstrates that chick integrin alpha4 mRNA is expressed at high levels by migrating neural crest cells and neural crest-derived ganglia at both cranial and trunk levels. An antibody against the murine alpha4 subunit revealed similar distribution patterns in mouse to chick. In addition to neural crest cells, the integrin alpha4 subunit was later observed on the muscle masses of the limb, the apical ectodermal ridge, and the developing liver. To examine the functional role of the integrin alpha4 subunit in neural crest cell migration, we used an explant preparation that allows visualization of neural crest cells in their normal environment with or without perturbing reagents. In the presence of a blocking antibody against the mouse integrin alpha4 subunit, there was a profound abrogation of neural crest cell migration at trunk and hindbrain levels. Both the numbers of migrating neural crest cells and the total distance traversed were markedly reduced. Similarly, avian embryos injected with synthetic peptides that contain the integrin alpha4 binding site in fibronectin displayed abnormal neural crest cell migration. Our results suggest that the integrin alpha4 subunit is important for normal neural crest cell migration and may be one of the primary alpha subunits used for neural crest cell migration in vivo. Furthermore, the integrin alpha4 subunit represents a useful neural crest marker in the mouse.

What happens to patients following open access gastroscopy? An outcome study from general practice

BACKGROUND

Open access gastroscopy allows general practitioners to request a gastroscopy without prior referral to a specialist. The effect of open access gastroscopy upon patient management is poorly explored. Most studies have been hospital based and have focused on diagnostic yields and on means of tightening requests to reduce inefficient use. A user evaluation can only be made by measuring outcomes in primary care.

AIM

A study was undertaken to determine the impact of open access gastroscopy in general practice and in particular, the value of a normal result.

METHOD

All general practices in South Tees District Health Authority were asked to participate. Any of their patients who had had open access gastroscopy in the year prior to July 1990 were identified from the hospital computer and their general practitioner notes examined. Patient management during the year prior to the open access gastroscopy was compared with the year after. The main outcome measures were: detection rate and grade of lesion, change in graded score of prescribed drugs, consultation rate for dyspepsia and non-dyspepsia problems, and further hospital referral and investigations. Outcomes among those with normal and abnormal gastroscopy results were compared.

RESULTS

The study sample comprised 715 patients, 36% of whom had a normal gastroscopy result, 34% a major abnormality and 26% a minor abnormality (4% of patients had miscellaneous diagnoses). It was found that 39% of all patients, and 60% of those with normal findings on open access gastroscopy had their drug treatment stopped or reduced in grade after the investigation. Of those with a major endoscopic abnormality 58% increased their treatment score. Consultations for dyspepsia in the year before and after gastroscopy fell by 57% overall among those with a normal gastroscopy result, by 37% among those with a minor finding and by 33% in those with a major finding. There was a 21% fall in consultations for all reasons among those with a normal gastroscopy result but those with a minor abnormality had a 23% increase in non-dyspepsia consultations. Of all patients 19% were referred to hospital subsequently.

CONCLUSION

Open access gastroscopy has a major effect upon patient management in general practice, and a normal endoscopy result has an important an impact as an abnormal one. Open access gastroscopy is associated with a rationalization of drug therapy, reduced consultations and a low hospital referral rate.