Circulating H3K27 Methylated Nucleosome Plasma Concentration: Synergistic Information with Circulating Tumor DNA Molecular Profiling

The molecular profiling of circulating tumor DNA (ctDNA) is a helpful tool not only in cancer treatment, but also in the early detection of relapse. However, the clinical interpretation of a ctDNA negative result remains challenging. The characterization of circulating nucleosomes (carrying cell-free DNA) and associated epigenetic modifications (playing a key role in the tumorigenesis of different cancers) may provide useful information for patient management, by supporting the contributive value of ctDNA molecular profiling. Significantly elevated concentrations of H3K27Me3 nucleosomes were found in plasmas at the diagnosis, and during the follow-up, of NSCLC patients, compared to healthy donors (p-value < 0.0001). By combining the H3K27Me3 level and the ctDNA molecular profile, we found that 25.5% of the patients had H3K27Me3 levels above the cut off, and no somatic alteration was detected at diagnosis. This strongly supports the presence of non-mutated ctDNA in the corresponding plasma. During the patient follow-up, a high H3K27Me3-nucleosome level was found in 15.1% of the sample, despite no somatic mutations being detected, allowing the identification of disease progression from 43.1% to 58.2% over molecular profiling alone. Measuring H3K27Me3-nucleosome levels in combination with ctDNA molecular profiling may improve confidence in the negative molecular result for cfDNA in lung cancer at diagnosis, and may also be a promising biomarker for molecular residual disease (MRD) monitoring, during and/or after treatment.

Abstract 2163: Circulating H3K27 nucleosomes to monitor lung cancer patients during treatment, a universal biomarker quantifying the molecular residual disease (MRD) in plasma samples

Introduction: Treatment options of lung cancer (LC) comprise radiotherapy, and/or combined treatment approaches, including chemotherapy, immunotherapy and targeted therapies based on the tumoral molecular profile. Following curative-intent first-line therapies, clinical surveillance involves serial CT imaging. However, such surveillance can detect only macroscopic disease recurrence and is frequently inconclusive. NGS has been utilized to help identify and monitor treatment plans. Nucleosomes, complexes of DNA and histones proteins, are released during cell death into blood circulation. Trimethylation of lysine 27 on histone H3 (H3K27Me3), catalyzed by enhancer of zeste homolog 2 (EZH2), is a crucial epigenetic process in tumorigenesis. We investigated if H3K27Me3-nucleosome concentration could be a biomarker for molecular residual disease (MRD).

Patients and Methods: Plasmas were retrospectively collected from patients with advanced LC during treatment (CIRCAN’s cohort, n= 200) and from healthy donors (n=100). We carried out standard targeted NGS on paired plasmas. Samples were divided in two sub-groups based on genetical results: ctDNA negative (n=120) or positive (n=80) for presence of somatic alterations. Concentration of circulating H3K27Me3-nucleosome was measured using chemiluminescent Nu.Q® immunoassay (Belgian Volition SRL, Belgium).

Results: Significantly elevated concentrations of H3K27Me3-nucleosomes were found in LC plasmas during the follow-up of patients compared to healthy donors (median 14.9 ng/ml vs 6.15 ng/ml, respectively, p&lt;0.001). In addition, H3K27Me3 levels is lower in the ctDNA-negative group compared to ctDNA-positive group (median 12.1 vs 24.8 ng/ml, respectively, p&lt;0.001). At a clinical cut-off of 14 ng/ml, 62% of samples were positive for either H3K27Me3 or ctDNA, or for both, suggesting an active disease progression compared to only 40% detection using the NGS assay alone. 38% of the patients have low levels of H3K27Me3 and were ctDNA-negative strongly suggesting a therapeutic response under treatment.

Conclusions: High levels of Nu.Q® H3K27Me3 could allow physicians to detect MRD in LC patients following treatment with curative intent. This could be achieved by monitoring testing of patients at defined intervals of treatment and recovery, alongside imaging, to incorporate analyses of evolving molecular landscapes during treatment. In this setting, the H3K27Me3-nucleosome quantification, to complete the molecular exploration of cfDNA is highly encouraging, especially in advanced NSCLC, where re-tissue biopsies are impractical, expensive, and may cause undue harm. H3K27Me3-nucleosome quantification may also be useful in patient identification for specific treatments such as EZH2 inhibitor, but this requires investigation.

Citation Format: Emmanuel Grolleau, Julie Candiracci, Arnaud Gauthier, Gaelle Lescuyer, David Barthelemy, Christine Haon, Florence Geiguer, Margaux Raffin, Nathalie Hardat, Julie Balandier, Rémi Rabeuf, Anne-Sophie Wozny, Guillaume Rommelaere, Claire Rodriguez-Lafrasse, Fabien Subtil, Sébastien Couraud, Marielle Herzog, Lea Payen-Gay. Circulating H3K27 nucleosomes to monitor lung cancer patients during treatment, a universal biomarker quantifying the molecular residual disease (MRD) in plasma samples [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2163.

High specificity lung cancer test to rule out cancer in non-malignant lung nodules found at LDCT

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Background: Lung Cancer (LC) is the leading cause of cancer death worldwide and smoking is the leading risk factor. Only 15% of patients with LC are still alive 5 years after diagnosis due to advanced diseases stage at diagnosis. Low-Dose Computed Tomography (LDCT) is the widely accepted standard for screening of individuals at high risk of lung cancer. However, LDCT has several limitations including the high prevalence of non-malignant pulmonary nodules detected leading to overdiagnosis, the potential harms of cumulative radiation dose and poor adherence to recommended follow-up. Therefore, novel blood-based tests could offer a simple follow confirmation approach and this test is designed to find those patients who DO NOT have cancer. Methods: We measured levels of nucleosomes, CEA and CYFRA21-1in a cohort of 912 subjects and report data relating to 184 smoker subjects referred for CT scan at National Taiwan University Hospital. The smoker patients were later confirmed to have either a LC (n = 129, including 59 patients at early stage (stage 0-I), 15 at stage II, 47 at late stage (III and IV) and 8 with unknown stage), or non-malignant nodules (n = 41), or control with no-nodules (n = 14). Whole blood was collected in EDTA plasma tubes for analysis by six different Nu.Q chemiluminescent magnetic microparticle immunoassays (Belgian Volition, Belgium) targeting H3.1-nucleosomes or different histone modifications (H3K9Me3-, H3K27Me3-, H3K36Me3-, H3K9Ac-, H3K14Ac-nucleosomes). CEA was analyzed on the Abbott ARCHITECT analyzer. CYFRA21-1 was analyzed on the Roche Cobas E411 analyzer. We evaluated each biomarker levels individually and in a combinatorial approach by logistic regression for their performance in discriminating subject with a LC vs non-malignant nodules. Results: Among the eight individual markers evaluated, the best area under the curve (AUC) in discriminating LC vs non-malignant nodule were observed for CEA, H3K9Ac-nucleosomes and CYFRA21-1 with an AUC of 0.68, 0.69 and 0.74, respectively and a specificity at 95% sensitivity of 9.5%, 7.3% and 21.4%, respectively. A logistic regression approach defined H3K9Ac-nucleosomes, CEA and CYFRA21-1 as the best panel of biomarkers tested to improve the discrimination between LC and non-malignant nodules relatives to the markers alone, achieving a specificity of 34.1% at 95% sensitivity and an AUC of 0.80. 55 out of the 59 stage 0-I, 25/26 stage III and 20/21 stage IV LC were detected by this combination of markers while 34.1 % of the patients with benign nodules are found negative and not sent to unnecessary biopsy to ascertain the nodule status. Conclusions: Results of our proof-of-concept study indicate that a blood test combining H3K9Ac-nucleosome levels with CEA and CYFRA21-1 levels could help to rule-out patients with a non-malignant nodule offering a non-invasive tool as an aid to the decision-making process of the malignancy status of nodules detected by LDCT.

Circulating nucleosomes to identify non-smoker subjects at risk of lung cancer and triage them for low-dose CT scan

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Background: Lung cancer (LC) is the leading cause of cancer death worldwide and the most frequently occurring in men and the second most diagnosed cancer in woman after breast cancer. The primary risk factor leading to LC is tobacco smoke. Nevertheless, several studies in the US, UK and Asia reported an increasing rate of LC in non-smokers. 15-20% of LC patients worldwide are non-smokers with this percentage rising to 60% in non-smoking women in Asia. Current LC screening guidelines recommend a CT scan only for high-risk smokers. Despite there being no guidelines to recommend LC screening in non-smokers those with increased risk factors could be monitored. Therefore, a blood-test could offer a simple way to identify non-smokers at high-risk of LC and triage them to go for low-dose CT scan. Methods: We measured circulating levels of nucleosomes and CEA in 722 non-smoker subjects referred for CT scan at National Taiwan University Hospital. The patients were later confirmed to have either a LC (n = 509, including 401 patients at stage 0-1), non-malignant nodules (n = 142), or no-nodules (n = 71). Whole blood was collected in EDTA plasma tubes for analysis by six different Nu.Q chemiluminescent magnetic microparticle immunoassays (Belgian Volition SRL, Belgium) targeting H3.1-nucleosomes or different histone modifications (H3K9Me3-, H3K27Me3-, H3K36Me3-, H3K9Ac-, H3K14Ac-nucleosomes). CEA was analyzed on the Abbott ARCHITECT analyzer. We defined by logistic regression the best combination of biomarkers to identify LC cases in this non-smoking population in a rule-in approach. Results: At 95% specificity, none of the individual biomarkers exceed 24.8% of sensitivity for LC vs non-malignant nodules and no nodules. A combination of 2 nucleosome biomarkers: H3K9Me3- and H3K9Ac-nucleosomes with CEA in a logistic regression model showed improved sensitivity detecting 32.4% of LC in the non-smoker subjects at 95% specificity for LC vs non-malignant nodules and no nodules (area under the curve (AUC): 0.76, R2: 19.1%). In a non-smoking women sub-group by adding a third nucleosome biomarker: H3K36Me3-nucleosomes to the model we could detect 34.3% of the women who have lung cancer at 95% specificity (AUC: 0.75; R2: 20.2%). Conclusions: Our results indicate that a blood test combining circulating nucleosomes targeting different epigenetic modifications with CEA allow the detection of LC cases in a non-smokers population. This blood test could be part of the screening criteria for the non-smoking population at risk to develop LC and could help to triage them for low-dose CT scan.

Association of circulating nucleosomes levels with FIT performance for advanced adenomas in a symptomatic population

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Background: The effectiveness of screening using either fecal immunochemical testing (FIT) or colonoscopy in reducing colorectal cancer (CRC) mortality has been demonstrated in previous studies. Nevertheless, the single test sensitivity of FIT for relevant precursor lesions, especially high-risk neoplasms like invasive cancer or advanced adenomas (AA), is a concern. Improving the sensitivity for high-risk neoplasm is critical to improving the effectiveness of screening in reducing CRC incidence and mortality. Dysregulation of histone post-translational modifications (PTMs) has been linked with several cancers including CRC. We investigated the clinical performance of circulating nucleosome levels containing specific histone PTMs in blood, in combination with FIT from symptomatic subjects referred to colonoscopy to evaluate their discriminant power towards CRC and AA. Methods: 10mls whole blood was obtained prior to colonoscopy from 476 patients referred to colonoscopy in National Taiwan University Hospital for surveillance or secondary to bowel symptoms. Patients were classified into 5 groups based on their colonoscopy reports: (i) patient with CRC (n = 67), (ii) patients with AA (n = 60, including 22 with AA≥2cm); (iii) patients with non-AA (n = 123); (iv) patients with non-neoplastic polyps (n = 29); (vi) healthy controls with no endoscopic lesion (n = 197). Plasma samples were analyzed for nucleosome levels using 7 different quantitative immunoassays (Nu.Q assays; Belgian Volition SRL, Belgium) targeting H3.1-nucleosomes or different histone modifications (H3K27Me3-, H3K36Me3-, H3K9Me3-, H3K14Ac-, H3K27Ac- or H3R8Cit-nucleosomes). All study subjects were asked to collect a stool sample at home within 48-hours before the colonoscopy. The fecal samples were assayed with the OC-SENSOR FIT kit (Eiken Chemical Co., Ltd., Tokyo, Japan) for all subjects. Results: At a cut-off of 20µg/g feces, the FIT test showed a sensitivity of 83.5% at 82.1% specificity for CRC +AA vs. Controls. All the CRC patients were detected but 35% of AA were missed, and 7 of which were high-risk adenomas (AA≥2cm). A combination of 2 Nu.Q biomarkers: H3K36Me3 and H3K9Me3 with FIT in a decision tree model showed an improved sensitivity of 98.4% allowing the detection of all CRC patients and 97% of the patients with AA including all high-risk adenomas. The 2 missed AA were one AA below 1cm and one between 1 and 2cm. Unnecessary colonoscopies could be reduced by 28.9% of the control and 20.7% of the non-neoplastic polyps subgroups as both are found negative with this panel of assays. Conclusions: At present, all the symptomatic patients are sent to colonoscopy in clinical practice. Our results indicate that H3K36Me3- and H3K9Me3-nucleosome levels, in combination with FIT in a decision tree model, could detect all CRC patients and all high-risk adenomas and help reduce unnecessary colonoscopies.

Circulating nucleosomes for detection of colorectal cancer and high-risk advanced adenomas

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Background: Detection and treatment of early colorectal cancer (CRC) or advanced adenomas (AA) is the key for superior outcomes and fecal immunochemical testing (FIT)-based screening has proven effective in reducing CRC death and the risk of advanced-stage CRC but the discrepancy in the effectiveness was observed between proximal and distal cancers. On the other hand, false-positive results of FIT with 60 % of negative colonoscopy is another concern, considering the burden to the screening participants and the healthcare providers. A blood-based test as an alternative or supplement to FIT has the potential to concurrently enhance the detection of high-risk neoplasms and identify individuals at risk who should then be referred to colonoscopy. We investigated the levels of circulating free nucleosomes containing different epigenetic modifications in patients referred for colonoscopy. Methods: 10mls whole blood was obtained from 520 asymptomatic patients prior to colonoscopy at National Taiwan University Hospital. Patients were classified into 5 groups based on their colonoscopy reports: (i) patient with CRC (n = 33), (ii) patients with AA (n = 123, including 18 with AA > 2cm); (iii) patients with non-AA (n = 168); (iv) patients with non-neoplastic polyps (n = 30); (vi) healthy controls with no endoscopic lesion (n = 166). Plasma samples were analyzed for nucleosome levels using 7 different quantitative immunoassays (Nu.Q assays; Belgian Volition SRL, Belgium) targeting H3.1-nucleosomes or different histone modifications (H3K27Me3-, H3K36Me3-, H3K9Me3-, H3K14Ac-, H3K27Ac- or H3R8Cit-nucleosomes). All study subjects were asked to collect a stool sample at home within 48-hours before the colonoscopy. The fecal samples were assayed with the Eiken OC-SENSOR FIT kit (Eiken Chemical Co., Ltd., Tokyo, Japan) for all study subjects. Results: At a cut-off of 20µg/g feces, the FIT test showed a sensitivity of 92,9% at 17.5% specificity for CRC +AA vs. Controls. All the CRC patients and 83.3% of the high-risk AA (> 2cm) patients were FIT positive. A combination of 2 Nu.Q biomarkers: H3K27Me3 and H3R8Cit with FIT in a logistic regression model showed improved sensitivity of 95% at 20.6% specificity allowing the detection of all CRC patients and 94.3% of AA patients including all the high-risk adenomas. The FIT test detected 46 out of 55 proximal adenomas whereas the combined model could detect 50 proximal adenomas including 3 proximal AA > 2cm not being detected by FIT (p < 0.05). The same combination would reduce unnecessary colonoscopies by 21.8% of the control and 23.3% of the non-neoplastic polyps subgroups compared to 17.5% and 6.7%, respectively with the FIT test alone. Conclusions: Our results indicate that H3K27Me3 and H3R8Cit-nucleosome levels in combination with FIT could improve the detection of proximal high-risk AA and could also provide a non-invasive method to reduce unnecessary colonoscopy.

Evaluation of nucleosome concentrations in healthy dogs and dogs with cancer

INTRODUCTION

Nucleosomes consist of small fragments of DNA wrapped around a histone octamer core. Diseases such as cancer or inflammation lead to cell death, which causes fragmentation and release of nucleosomes into the blood. The Nu.Q™ technology measures circulating nucleosome levels and exploits the different compositions of cancer derived nucleosomes in blood to detect and identify cancer even at early stages. The objectives of this study are to identify the optimal sample type for the Nu.Q™ H3.1 assay and to determine if it can accurately detect nucleosomes in the blood of healthy canines as well as those with cancer.

MATERIALS AND METHODS

Blood samples from healthy canine volunteers as well as dogs newly diagnosed with lymphoma were used. The blood was processed at a variety of times under a variety of conditions to determine the most reliable sample type and conditions, and to develop an appropriate processing strategy to ensure reliably accurate results.

RESULTS

Nucleosomes could be detected using a variety of sample collection and processing protocols. Nucleosome signals were highest in EDTA plasma and serum samples and most consistent in plasma. Samples should be processed within an hour of collection. Experiments showed that samples were able to withstand several freeze thaw cycles. Processing time and tcollection tube type did affect nucleosome detection levels. Finally, significantly elevated concentrations of nucleosomes were seen in a small cohort of dogs that had been newly diagnosed with lymphoma.

CONCLUSIONS

When samples are collected and processed appropriately, the Nu.Q™ platform can reliably detect nucleosomes in the plasma of dogs. Further testing is underway to validate and optimize the Nu.Q™ platform for veterinary use.

A new nucleosomic-based model to identify and diagnose SSc-ILD

BACKGROUND

Systemic sclerosis (SSc) is a rare connective tissue disease associated with rapid evolving interstitial lung disease (SSc-ILD), driving its mortality. Specific biomarkers associated with the evolution of the lung disease are highly needed. We aimed to identify specific biomarkers of SSc-ILD to predict the evolution of the disease. Nucleosomes are stable DNA/protein complexes that are shed into the blood stream making them ideal candidates for biomarkers.

METHODS

We studied circulating cell-free nucleosomes (cf-nucleosomes) in SSc patients, 31 with ILD (SSc-ILD) and 67 without ILD. We analyzed plasma levels for cf-nucleosomes and investigated whether global circulating nucleosome levels in association with or without other biomarkers of interest for systemic sclerosis or lung fibrosis (e.g., serum growth factors: IGFBP-1 and the MMP enzyme: MMP-9), could be suitable potential biomarkers for the correct identification of SSc-ILD disease.

RESULTS

We found that H3.1 nucleosome levels were significantly higher in patients with SSc-ILD compared SSc patients without ILD (p < 0.05) and levels of MMP-9 were significantly increased in patients with SSc-ILD compared to SSc patients without ILD (p < 0.05). Conversely, IGFBP-1 was significantly reduced in patients with SSc-ILD compared to SSc without ILD (p < 0.001). The combination of cf-nucleosomes H3.1 coupled to MMP-9 and IGFBP-1 increased the sensitivity for the differential detection of SSc-ILD. High levels of accuracy were reached with this combined model: its performances are strong with 68.4% of positive predictive value and 77.2% of negative predictive value for 90% of specificity. With our model, we identified a significant negative correlation with FVC % pred (r = -0.22) and TLC % pred (r = -0.31). The value of our model at T1 (baseline) has a predictive power over the Rodnan score at T2 (after 6-18 months), showed by a significant linear regression with R2 = 19% (p = 0.013). We identified in the sole group of SSc-ILD patients a significant linear regression with a R2 = 54.4% with the variation of DLCO between T1 and T2 (p < 0.05).

CONCLUSION

In our study, we identified a new blood-based model with nucleosomic biomarker in order to diagnose SSc-ILD in a SSc cohort. This model is correlated with TLC and FVC at baseline and predictive of the skin evolution and the DLCO. Further longitudinal exploration studies should be performed in order to evaluate the potential of such diagnostic and predictive model.

Altered epigenetic features in circulating nucleosomes in idiopathic pulmonary fibrosis

BACKGROUND

Idiopathic pulmonary fibrosis (IPF) is a progressive, fatal lung disorder of unknown origin with a highly variable and unpredictable clinical course. Polymorphisms and environmentally induced epigenetic variations seem to determine individual susceptibility to the development of lung fibrosis.

METHODS

We have studied circulating epitopes on cell-free nucleosomes (cfnucleosomes) in 50 IPF patients. We have compared untreated IPF (n = 23) with IPF receiving antifibrotic therapy (n = 27) and healthy subjects (HS) (n = 27). We analyzed serum levels of five cfnucleosomes including bound HMGB1 (nucleosomes adducted to high-mobility growth protein B1), mH2A1.1 (nucleosomes containing the histone variant mH2A1.1), 5mC (nucleosomes associated with methylated DNA), and H3K9Ac and H3K27Ac (nucleosomes associated with histone H3 acetylated at lysine 9 or 27 residue).

RESULTS

Our findings showed that serum levels of bound HMGB1, mH2A1.1, 5mC, H3K9Ac, and H3K27Ac were significantly lower in IPF patients than in HS (p < 0.001, p < 0.001, p < 0.01, p < 0.001, and p < 0.0001, respectively). Moreover, we found differences in epigenetic profiles between untreated IPF patients and those receiving anti-fibrotic therapy with mH2A1.1 and 5mC being significantly lower in untreated than in treated patients (p < 0.01 and p < 0.05, respectively). Combination of four cfnucleosomes (HMGB1, 5mC, H3K9Ac, and H3K27Ac) allow to discriminate IPF vs HS with a good coefficient of determination (R² = 0.681). The AUC for the ROC curve computed by this logistic regression was 0.93 (p < 0.001) with 91% sensitivity at 80% specificity.

CONCLUSION

Our observations showed that cfnucleosomes (bound HMGB1, mH2A1.1, 5mC, H3K9Ac, and H3K27Ac) might have potential as biomarkers for diagnosis and treatment response. These results deserve further validation in longitudinal cohorts.