Diagnostic and prognostic value of SHOX2 and SEPT9 DNA methylation and cytology in benign, paramalignant, and malignant ascites

Diagnosis of malignant body fluids via cancer-universal methylation in cell-free DNA

BACKGROUNDDifferentiating malignant from nonmalignant body fluids remains a clinical challenge because of the unsatisfying performance of conventional cytology. We aimed to improve the sensitivity and ubiquity of cancer cell detection by assaying universal cancer-only methylation (UCOM) markers in supernatant cell-free DNA (cfDNA).METHODSAn observational prospective cohort including 1,321 nonmalignant and malignant body fluids of multiple cancers was used to develop and validate a cfDNA UCOM methylation diagnostic assay. All samples were divided into 2 portions for cytology and supernatant cfDNA methylation analysis.RESULTSThe significant hypermethylation of a potentially novel UCOM marker, TAGMe, together with the formerly reported PCDHGB7, was identified in the cfDNA of malignant body fluid samples. The combined model, cell-free cancer-universal methylation (CUE), was developed and validated in a prospective multicancer cohort with markedly elevated sensitivity and specificity, and was further verified in a set containing additional types of malignant body fluids and metastases. In addition, it remained hypersensitive in detecting cancer cells in cytologically negative malignant samples.CONCLUSIONcfDNA methylation markers are robust in detecting tumor cells and are applicable to diverse body fluids and tumor types, providing a feasible complement to current cytology-based diagnostic analyses.TRIAL REGISTRATIONThis study was registered at Chictr.org.cn (ChiCTR2200060532).FUNDINGNational Natural Science Foundation of China (32270645, 31872814, 32000505, 82170088), the National Key R&D Program of Ningxia Hui Autonomous region (2022BEG01003), Shanghai Municipal Key Clinical Specialty (shslczdzk02201), Science and Technology Commission of Shanghai Municipality (20DZ2261200, 20DZ2254400), and Major Special Projects of Basic Research of Shanghai Science and Technology Commission (18JC1411101).

The emerging role of liquid biopsy in oral squamous cell carcinoma detection: advantages and challenges

INTRODUCTION

Oral Squamous Cell Carcinoma (OSCC), the sixth most widespread malignancy in the world, accounts for 90% of all cases of oral cancer. The primary risk factors are tobacco chewing, alcohol consumption, viral infection, and genetic modifications. OSCC has a high morbidity rate due to the lack of early diagnostic methods. Nowadays, liquid biopsy plays a vital role in the initial diagnosis of oral cancer. ctNAs extracted from saliva and serum/plasma offer meaningful insights into tumor genetics and dynamics. The interplay of these elements in saliva and serum/plasma showcases their significance in advancing noninvasive, effective OSCC detection and monitoring.

AREAS COVERED

This review mainly focused on the role of liquid biopsy as an emerging point in the diagnosis and prognosis of OSCC and the current advancements and challenges associated with liquid biopsy.

EXPERT OPINION

Liquid biopsy is regarded as a new, minimally invasive, real-time monitoring tool for cancer diagnosis and prognosis. Many biomolecules found in bodily fluids, including ctDNA, ctRNA, CTCs, and EVs, are significant biomarkers to identify cancer in its early stages. Despite these groundbreaking strides, challenges persist. Standardization of sample collection, isolation, processing, and detection methods is imperative for ensuring result reproducibility across diverse studies.

The prognostic impact of peritoneal tumour DNA in gastrointestinal and gynaecological malignancies: a systematic review

Peritoneal metastases from various abdominal cancer types are common and carry poor prognosis. The presence of peritoneal disease upstages cancer diagnosis and alters disease trajectory and treatment pathway in many cancer types. Therefore, accurate and timely detection of peritoneal disease is crucial. The current practice of diagnostic laparoscopy and peritoneal lavage cytology (PLC) in detecting peritoneal disease has variable sensitivity. The significant proportion of peritoneal recurrence seen during follow-up in patients where initial PLC was negative indicates the ongoing need for a better diagnostic tool for detecting clinically occult peritoneal disease, especially peritoneal micro-metastases. Advancement in liquid biopsy has allowed the development and use of peritoneal tumour DNA (ptDNA) as a cancer-specific biomarker within the peritoneum, and the presence of ptDNA may be a surrogate marker for early peritoneal metastases. A growing body of literature on ptDNA in different cancer types portends promising results. Here, we conduct a systematic review to evaluate the prognostic impact of ptDNA in various cancer types and discuss its potential future clinical applications, with a focus on gastrointestinal and gynaecological malignancies.

Ovarian hyperstimulation syndrome and pregnancy luteoma mimicking malignant ascites: a rare case report

BACKGROUND

During pregnancy, both ovarian hyperstimulation syndrome (OHSS) and pregnancy luteoma could manifest as massive ascites, enlarged ovaries, or elevated serum levels of cancer antigen 125 (CA125), and atypical cells may be found in the ascitic fluid of OHSS patients. Whether this should be treated aggressively as peritoneal carcinomatosis is controversial.

CASE PRESENTATION

A 35-year-old G2P1A1 woman with secondary infertility had a successful pregnancy after one cycle of assisted reproductive technology. The patient complained of lower abdominal distension, oliguria, and poor appetite 19 days after embryo transplantation. She was diagnosed with late-onset OHSS. Although the size of the ovaries decreased bilaterally to the normal range at 12 weeks of gestation after prompt medical care, the ascites increased again after an initial decreasing trend. Elevated serum levels of CA125 (191.1 IU/mL), and suspected adenocarcinoma cells were observed in the ascitic fluid. Although further magnetic resonance imaging examination or diagnostic laparoscopy was recommended, the patient was provided with supportive treatment and closely monitored upon her request. Surprisingly, her ascites diminished, and serum level of CA125 started to decline at 19 weeks of gestation. During cesarean section, pathological examination of the solid mass in the right ovary revealed pregnancy luteoma, which was presumably the other cause of the intractable ascites.

CONCLUSIONS

Caution should be exercised in cases of suspicious malignant ascites during pregnancy. This may due to OHSS or pregnancy luteoma, in which abnormalities usually regress spontaneously.

A detection panel of novel methylated DNA markers for malignant pleural effusion

Background

Cytology remains the gold standard for the detection of malignant cells in pleural effusion. However, its sensitivity is limited. The aim of this study was to establish a novel panel of cancer-specific methylated genes for the differential diagnosis of malignant pleural effusion (MPE).

Methods

A cohort of 100 cancer patients (68 lung cancer, 32 other malignant tumors) and 48 patients with benign disease presenting with pleural effusion was prospectively enrolled. Pleural effusion was evaluated by means of cytopathological investigation and DNA methylation of SHOX2, RASSF1A, SEPTIN9 and HOXA9 in the cellular fraction. DNA methylation in bisulfite-converted DNA was determined using quantitative methylation-specific real-time PCR (MS-PCR). Cytopathological and DNA methylation results were evaluated with regard to the final clinical diagnosis.

Results

The LungMe® SHOX2 and RASSF1A Assay (Tellgen Corporation, China) has been reported to be highly sensitive and specific for lung cancer using bronchial aspirates. As expected, LungMe® detected metastases of lung cancer (sensitivity: 76.5%) as well as metastases of other malignant tumors (sensitivity: 68.8%). OncoMe, a novel combination of SHOX2, RASSF1A, SEPTIN9 and HOXA9 methylation, led to an additional 11% increase in the detection rate of MPE, resulting in a sensitivity of 85% and a specificity of 96%. Overall, OncoMe showed a higher positive detection rate in SCLC (100%), LUAC (87%), OC (100%), BC (92.9%), GC (80.0%), and MESO (80%) than in LUSC (50%). Cytopathological analyses only detected 23 positive samples, which were all positively measured by both LungMe® and OncoMe.

Conclusion

OncoMe has potential for use as a biomarker for the detection of MPE, even not limited to lung cancer.

Distinct Performance of Methylated SEPT9 in Upper and Lower Gastrointestinal Cancers and Combined Detection with Protein Markers

Background: The performance of methylated SEPT9 (mSEPT9) in lower gastrointestinal (GI) cancer (colorectal cancer) has been extensively investigated; however, its performance in upper GI cancer (esophageal cancer and gastric cancer) and the comparison with lower GI cancer have rarely been studied. Methods: A total of 1854 subjects, including 344 upper GI cancer patients, 459 lower GI cancer patients, and 1051 noncancer subjects, were recruited in this prospective cohort study. A modified single polymerase chain reaction test for detecting mSEPT9 was used for plasma detection. Results: The sensitivity of mSEPT9 for upper and lower GI cancers was 45.3% and 74.8%, and the corresponding specificities were 85.6% and 86.5%, with areas under curve (AUC) of 0.71 and 0.80, respectively. mSEPT9 exhibited lower sensitivity in stage I than stage II-IV cancer, while no difference in sensitivity was observed for different locations in upper or lower GI cancer. No difference in sensitivity was found among gross classifications, pathological classifications, and differentiation in upper GI cancer, but a higher sensitivity in infiltrative cancer and moderate and poorly differentiated cancers was observed in the lower GI. No difference in sensitivity was found between male and female in both cancers, while sensitivity increased with age for both cancers. Cancer antigen 724 (CA724) showed the highest sensitivity for upper GI cancers, and carcinoembryonic antigen (CEA) showed the highest sensitivity for lower GI cancers. The combination of CA724 with mSEPT9 increased the sensitivity to 67.5% in upper GI cancers, and the combination of mSEPT9 with CEA increased the sensitivity to 85.4% in lower GI cancers, with an AUC of 0.90 and 0.95, respectively. Conclusions: mSEPT9 exhibited a higher sensitivity in lower GI cancers than upper GI cancers. The combination of mSEPT9 with protein markers significantly enhanced the detection sensitivity in both cancers.

A functional methylation signature to predict the prognosis of Chinese lung adenocarcinoma based on TCGA

Background

Lung cancer is the leading cause of cancer morbidity and mortality worldwide, however, the individualized treatment is still unsatisfactory. DNA methylation can affect gene regulation and may be one of the most valuable biomarkers in predicting the prognosis of lung adenocarcinoma. This study was aimed to identify methylation CpG sites that may be used to predict lung adenocarcinoma prognosis.

Methods

The Cancer Genome Atlas (TCGA) database was used to detect methylation CpG sites associated with lung adenocarcinoma prognosis and construct a methylation signature model. Then, a Chinese cohort was carried out to estimate the association between methylation and lung adenocarcinoma prognosis. Biological function studies, including demethylation treatment, cell proliferative capacity, and gene expression changes in lung adenocarcinoma cell lines, were further performed.

Results

In the TCGA set, three methylation CpG sites were selected that were associated with lung adenocarcinoma prognosis (cg14517217, cg15386964, and cg18878992). The risk of mortality was increased in lung adenocarcinoma patients with the gradual increase level of methylation signature based on three methylation sites levels (HR = 45.30, 95% CI = 26.69–66.83; p < 0.001). The C‐statistic value increased to 0.77 when age, gender, and other clinical variables were added to the signature to prediction model. A similar situation was confirmed in Chinese lung adenocarcinoma cohort. In the biological function studies, the proliferative capacity of cell lines was inhibited when the cells were demethylated with 5‐aza‐2'‐deoxycytidine (5‐aza‐2dC). The mRNA and protein expression levels of SEPT9 and HIST1H2BH (cg14517217 and cg15386964) were downregulated with different concentrations of 5‐aza‐2dC treatment, while cg18878992 showed the opposite result.

Conclusion

This study is the first to develop a three‐CpG‐based model for lung adenocarcinoma, which is a practical and useful tool for prognostic prediction that has been validated in a Chinese population.

Liquid biopsy in head and neck squamous cell carcinoma: circulating tumor cells, circulating tumor DNA, and exosomes

Introduction: Head and neck squamous cell carcinoma (HNSCC) is one of the most common cancers worldwide. Due to a lack of reliable markers, HNSCC patients are usually diagnosed at a late stage, which will lead to a worse outcome. Therefore, it is critical to improve the clinical management of cancer patients. Nowadays, the development of liquid biopsy enables a minimally invasive manner to extract molecular information from HNSCCs. Thus, this review aims to outline the clinical value of liquid biopsy in early detection, real-time monitoring, and prognostic evaluation of HNSCC. Areas covered: This comprehensive review focused on the characteristics as well as clinical applications of three liquid biopsy markers (CTCs, ctDNA, and exosomes) in HNSCC. What is more, it is promising to incorporate machine learning and 3D organoid models in the liquid biopsy of HNSCC. Expert opinion: Liquid biopsy provides a noninvasive technique to reflect the inter and intra-lesional heterogeneity through the detection of tumor cells or materials released from the primary and secondary tumors. Recently, some evolving technologies have the potential to combine with liquid biopsy to improve clinical management of HNSCC patients.

Liquid biopsy in peritoneal fluid and plasma as a prognostic factor in advanced colorectal and appendiceal tumors after complete cytoreduction and hyperthermic intraperitoneal chemotherapy

Background

Positive cytology has been identified as an independent negative prognostic factor in patients with peritoneal metastases (PM) of colorectal origin. Liquid biopsy in plasma may detect increasing levels of circulating tumor DNA (ctDNA) and could help predict systemic relapse in patients with colorectal cancer, but little is known about the role of liquid biopsy in peritoneal fluid. The aim of this study was to evaluate the prognostic value of peritoneal fluid and plasma liquid biopsy in patients undergoing complete cytoreductive surgery and hyperthermic intraperitoneal chemotherapy (CC-HIPEC).

Methods

A longitudinal prospective study was designed in patients with KRAS-mutated colorectal or appendiceal primary tumor, including PM of colorectal origin, pseudomyxoma peritonei and patients at high risk of developing PM (selected for second-look surgery). Eleven patients were recruited according to inclusion and exclusion criteria. ctDNA from plasma and peritoneal fluid before and after HIPEC was studied by droplet digital PCR looking for KRAS mutation. A close follow-up was scheduled (mean of 28.5 months) to monitor for systemic and peritoneal recurrences.

Results

All patients with positive plasma postHIPEC had systemic relapse and four patients died as a result, while those with negative plasma postHIPEC did not relapse. Patients with negative peritoneal ctDNA after CC-HIPEC did not present peritoneal relapse. Of six patients with positive peritoneal ctDNA postHIPEC, two presented peritoneal recurrence and four systemic relapses.

Conclusions

Treatment with CC-HIPEC does not always neutralize ctDNA in peritoneal fluid, and its persistence after treatment may predict adverse outcome. Despite being a proof of concept, an adequate correlation between liquid biopsy in plasma and peritoneal fluid with both systemic and peritoneal relapse has been observed.

Liquid Biopsy is Instrumental for 3PM Dimensional Solutions in Cancer Management

One in every four deaths is due to cancer in Europe. In view of its increasing incidence, cancer became the leading cause of death and disease burden in Denmark, France, the Netherlands, and the UK. Without essential improvements in cancer prevention, an additional 775,000 cases of annual incidence have been prognosed until 2040. Between 1995 and 2018, the direct costs of cancer doubled from EUR 52 billion to EUR 103 billion in Europe, and per capita health spending on cancer increased by 86% from EUR 105 to EUR 195 in general, whereby Austria, Germany, Switzerland, Benelux, and France spend the most on cancer care compared to other European countries. In view of the consequent severe socio-economic burden on society, the paradigm change from a reactive to a predictive, preventive, and personalized medical approach in the overall cancer management is essential. Concepts of predictive, preventive, and personalized medicine (3PM) demonstrate a great potential to revise the above presented trends and to implement cost-effective healthcare that benefits the patient and society as a whole. At any stage, application of early and predictive diagnostics, targeted prevention, and personalization of medical services are basic pillars making 3PM particularly attractive for the patients as well as ethical and cost-effective healthcare. Optimal 3PM approach requires novel instruments such as well-designed liquid biopsy application. This review article highlights current achievements and details liquid biopsy approaches specifically in cancer management. 3PM-relevant expert recommendations are provided.

Treatment Response Monitoring in Patients with Advanced Malignancies Using Cell-Free SHOX2 and SEPT9 DNA Methylation in Blood: An Observational Prospective Study

Patients with incurable cancer usually receive palliative treatment with significant toxicity and limited efficacy. Methylation analysis of circulating cell-free DNA (ccfDNA) in blood from cancer patients represents a promising approach for minimally invasive, real-time monitoring of treatment response. Short stature homeobox 2 (SHOX2) and septin 9 (SEPT9) methylation was analyzed in N = 8865 malignant and N = 746 normal adjacent tissues across 33 different malignancies from The Cancer Genome Atlas. Furthermore, we performed quantitative SHOX2 and SEPT9 ccfDNA methylation analysis in plasma obtained before and consecutively during treatment from prospectively enrolled N = 115 patients with various advanced cancers. SHOX2 and/or SEPT9 hypermethylation in malignant tissues is present in various carcinomas, sarcoma, melanoma, brain tumors, mesothelioma, and hematopoietic malignancies. Among the prospectively enrolled cancer patients, 61% (70/115) of patients had a baseline-positive blood cumulative ccfDNA methylation score (CMS) and were eligible for response monitoring. Dynamic changes of CMS during treatment were strongly associated with treatment response. A CMS increase indicated response up to 80 days before conventional monitoring. SHOX2 and SEPT9 ccfDNA methylation represents a pan-cancer biomarker and has the potential to be a powerful tool for monitoring treatment response in patients with solid tumors and lymphomas. The early identification of nonresponders might allow for a timely change of treatment regimen.

Down-regulation of SEPT9 inhibits glioma progression through suppressing TGF-β-induced epithelial-mesenchymal transition (EMT)

Malignant glioma is a highly aggressive cancer, known as one of the most dangerous types of primary brain tumor occurring in the central nervous system (CNS). Septin 9 (SEPT9) has been involved in tumor growth. However, its exact roles in regulating glioma development have not been fully understood. In the present study, we found that SEPT9 expression levels were markedly up-regulated in glioma tissues and cell lines. High expression of SEPT9 predicted a poor overall survival in patients with glioma. SEPT9 knockdown significantly reduced the proliferation, migration and invasion of glioma cells. Moreover, epithelial-mesenchymal transition (EMT) markers, including N-cadherin, matrix metalloproteinase-9 (MMP9), Vimentin and Twist, were significantly reduced by SEPT9 knockdown; however, the expression of E-cadherin was elevated by SEPT9 silence. This EMT process in glioma cells was dependent on the expression transforming growth factor (TGF)-β1. In addition, the clinical analysis suggested that SEPT9 gene expression had a positive correlation with TGF-β1 in patients with primary glioma at different grades. Furthermore, knockdown of SEPT9 significantly reduced the glioma progression in vivo. The anti-metastasis regulated by the knockdown of SEPT9 was further confirmed in mouse model, as evidenced by the reduced number of lung metastatic nodules. Our results supported that reducing SEPT9 expression could inhibit glioma progression through the suppression of EMT induced by TGF-β1.

Novel methylation gene panel in adjacent normal tissues predicts poor prognosis of colorectal cancer in Taiwan

BACKGROUND

It is evident that current clinical criteria are suboptimal to accurately estimate patient prognosis. Studies have identified epigenetic aberrant changes as novel prognostic factors for colorectal cancer (CRC).

AIM

To estimate whether a methylation gene panel in different clinical stages can reflect a different prognosis.

METHODS

We enrolled 120 CRC patients from Tri-Service General Hospital in Taiwan and used the candidate gene approach to select six genes involved in carcinogenesis pathways. Patients were divided into two groups based on the methylation status of the six evaluated genes, namely, the < 3 aberrancy group and ≥ 3 aberrancy group. Various tumor stages were divided into two subgroups (local and advanced stages) on the basis of the pathological type of the following tissues: Tumor and adjacent normal tissues (matched normal). We assessed DNA methylation in tumors and adjacent normal tissues from CRC patients and analyzed the association between DNA methylation with different cancer stages and the prognostic outcome including time to progression (TTP) and overall survival.

RESULTS

We observed a significantly increasing trend of hazard ratio as the number of hypermethylated genes increased both in normal tissue and tumor tissue. The 5-year TTP survival curves showed a significant difference between the ≥ 3 aberrancy group and the < 3 aberrancy group. Compared with the < 3 aberrancy group, a significantly shorter TTP was observed in the ≥ 3 aberrancy group. We further analyzed the interaction between CRC prognosis and different cancer stages (local and advanced) according to the methylation status of the selected genes in both types of tissues. There was a significantly shorter 5-year TTP for tumors at advanced stages with the promoter methylation status of selected genes than for those with local stages. We found an interaction between cancer stages and the promoter methylation status of selected genes in both types of tissues.

CONCLUSION

Our data provide a significant association between the methylation markers in normal tissues with advanced stage and prognosis of CRC. We recommend using these novel markers to assist in clinical decision-making.

Hypermethylation of the SEPT9 Gene Suggests Significantly Poor Prognosis in Cancer Patients: A Systematic Review and Meta-Analysis

Background: Aberrant hypermethylation of the Septin 9 (SEPT9) is an early event in several human cancers, and increasing studies have reported good performance of methylated SEPT9 (mSEPT9) in cancer diagnosis. Recent studies further focused on its value in cancer prognosis, but results are not clearly elucidated.

Methods: A comprehensive search to identify relevant studies about the association between mSEPT9 and cancer prognosis was conducted through the EMBASE, PubMed, and Web of Science databases (up to January 2019). The main outcomes were overall survival (OS) and disease-free survival (DFS). The hazard ratio (HR) and 95% confidence interval (CI) for OS and DFS were extracted from each included study and pooled using a random-effects model.

Results: Ten eligible studies comprising 1,266 cancer patients were included. Results demonstrated that mSEPT9 was associated with poor OS (HR = 2.07, 95% CI = 1.40–3.06). Specially, mSEPT9 detected in preoperative plasma predicted worse OS in cancer patients (HR = 3.25, 95% CI = 1.93–5.48). In addition, we also identified a significant association of mSEPT9 with decreased DFS of cancer (HR = 3.24, 95% CI = 1.81–5.79).

Conclusion: Our meta-analysis supports that mSEPT9 is associated with reduced OS and DFS in cancer patients. Moreover, detection of mSEPT9 using plasma appears to be a convenient and promising way to predict long-term survival of cancer patients.

Are we ready to develop a tiered scheme for the effusion cytology? A comprehensive review and analysis of the literature

BACKGROUND

Cytology is widely utilized in the initial evaluation of fluid accumulation in the body cavities. The aim of this study was to determine the accuracy of cytology in distinguishing between benign and malignant (MAL) effusions.

METHODS

A comprehensive and systematic review of the literature was conducted to evaluate the accuracy of serous effusion cytology (SEC) against tissue biopsy/resection histology, imaging, or clinical follow-up as the reference test. Risk of publication bias and level of heterogeneity in the included studies was assessed. Meta-regression was performed to assess the effect of various variables on the accuracy of SEC.

RESULTS

Eighty studies met the inclusion criteria for meta-analysis comprising of 34 941 samples; of which 52 (0.2%), 22 202 (72.7%), 194 (0.6%), 711 (2.3%), and 6507 (21.3%) could be reclassified as nondiagnostic (ND), negative for malignancy (NFM), atypical (atypia of uncertain significance-AUS), suspicious for malignancy (SFM), and malignant (MAL), respectively. On follow-up, the mean risk of malignancy for ND, NFM, AUS, SFM, MAL was 17.4%, 20.7%, 65.9%, 81.8%, and 98.9%, respectively. A total of 73 studies were included in estimating the diagnostic accuracy of SEC. The bivariate mixed-effect model estimated the SEC sensitivity, specificity, diagnostic odds ratio, positive likelihood ratio, and negative likelihood ratio as 73.1%, 99.9%, 7850.6%, 2112.2%, and 0.27%, respectively.

CONCLUSION

Serous effusion cytology shows high specificity and moderate sensitivity in the evaluation of serous effusions. A tiered classification scheme can improve the consistency of terminology for reporting SEC results, thus improving communication between the pathologists and clinical team, and quality of patient care.

The mSHOX2 is capable of assessing the therapeutic effect and predicting the prognosis of stage IV lung cancer

Background

Instant monitoring of the therapeutic effect of systematic therapy in late-stage lung cancer is crucial for response assessment and strategy adjustment. Previous study found that specific plasma methylation markers may be applied to therapeutic effect assessment. In order to investigate the performance of plasma mSHOX2 in assessing the therapeutic effect and predicting the prognosis of stage IV lung cancer, we performed the study focusing on patients underwent chemotherapy or tyrosine kinase inhibitor (TKI)-based targeted therapy.

Methods

Blood samples from 163 subjects, including 30 stage I, 29 stage II, 26 stage III and 68 stage IV lung cancer patients, were recruited in this study. Quantitative relationship between primary tumor size and the plasma mSHOX2 level was established. Blood samples before therapy and two cycles after therapy were obtained from 68 stage IV patients, and the mSHOX2 level was quantified as ΔΔCt.

Results

Sharp decrease of plasma mSHOX2 level was seen in patients with partial response (PR) while not in those with stable disease (SD). The plasma mSHOX2 level change reflected the degree of response and correlated with the maximal diameter of primary tumors in linear relationship. The mSHOX2 levels before and two cycles after therapy were predictors of the overall survival, while the mSHOX2 level change or the tumor size change were not predictors of the overall survival. Furthermore, univariable and multivariable Cox regression revealed that mSHOX2 level before therapy was the only independent predictor of the overall survival with a hazard ratio of 1.414.

Conclusions

mSHOX2 is effective for therapeutic effect assessment and prognosis prediction of stage IV lung cancer patients underwent systematic therapy.

Applying circulating tumor DNA methylation in the diagnosis of lung cancer

Lung cancer is the leading cause of cancer-related deaths worldwide. Low dose computed tomography (LDCT) is commonly used for disease screening, with identified candidate cancerous regions further diagnosed using tissue biopsy. However, existing techniques are all invasive and unavoidably cause multiple complications. In contrast, liquid biopsy is a noninvasive, ideal surrogate for tissue biopsy that can identify circulating tumor DNA (ctDNA) containing tumorigenic signatures. It has been successfully implemented to assist treatment decisions and disease outcome prediction. ctDNA methylation, a type of lipid biopsy that profiles critical epigenetic alterations occurring during carcinogenesis, has gained increasing attention. Indeed, aberrant ctDNA methylation occurs at early stages in lung malignancy and therefore can be used as an alternative for the early diagnosis of lung cancer. In this review, we give a brief synopsis of the biological basis and detecting techniques of ctDNA methylation. We then summarize the latest progress in use of ctDNA methylation as a diagnosis biomarker. Lastly, we discuss the major issues that limit application of ctDNA methylation in the clinic, and propose possible solutions to enhance its usage.

Potential of quantitative SEPT9 and SHOX2 methylation in plasmatic circulating cell-free DNA as auxiliary staging parameter in colorectal cancer: a prospective observational cohort study

Background

Septin 9 (SEPT9) and short stature homeobox 2 (SHOX2) methylation in circulating cell-free DNA (ccfDNA) are powerful biomarkers for colorectal cancer (CRC) screening, as well as head and neck squamous cell carcinoma staging and monitoring. In the present study, we investigated SEPT9 and SHOX2 ccfDNA methylation as auxiliary pre and post-therapeutic staging parameters in CRC patients.

Methods

ccfDNA methylation was quantified in 184 prospectively enrolled patients prior to and 3–10 days after surgery, and biomarker levels were associated with clinico-pathological parameters.

Results

Pre-therapeutic levels of SHOX2 and SEPT9 ccfDNA methylation were strongly associated with Union for International Cancer Control (UICC) stages, tumour (T), nodal (N), and metastasis (M) categories, and histological grade (all P ≤ 0.001), as well as lymphatic invasion and extracapsular lymph node extension (all P< 0.05). Post-therapeutic SHOX2 and SEPT9 ccfDNA methylation levels correlated with UICC stage (all P  <0.01). SEPT9 ccfDNA methylation further allowed for an accurate pre- and post-therapeutic detection of distant metastases (AUC_{pre-therapeutic} = 0.79 (95%CI 0.69–0.89), AUC_{post-therapeutic} = 0.93 (95% CI 0.79–1.0)).

Conclusions

DNA methylation analysis in plasma is a powerful pre and post-therapeutic diagnostic tool for CRC and may add valuable information to current TNM staging, thereby holding the potential to assist in the development of individually tailored treatment protocols.

Comparison of quantification algorithms for circulating cell-free DNA methylation biomarkers in blood plasma from cancer patients

Background

SHOX2 and SEPT9 methylation in circulating cell-free DNA (ccfDNA) in blood are established powerful and clinically valuable biomarkers for diagnosis, staging, prognosis, and monitoring of cancer patients. The aim of the present study was to evaluate different quantification algorithms (relative quantification, absolute quantification, quasi-digital PCR) with regard to their clinical performance.

Methods

Methylation analyses were performed in a training cohort (141 patients with head and neck squamous cell carcinoma [HNSCC], 170 control cases) and a testing cohort (137 HNSCC cases, 102 controls). DNA was extracted from plasma samples, bisulfite-converted, and analyzed via quantitative real-time PCR. SHOX2 and SEPT9 methylations were assessed separately and as panel [mean_SEPT9/SHOX2] using the ΔCT method for absolute quantification and the ΔΔCT-method for relative quantification. Quasi-digital PCR was defined as the number of amplification-positive PCR replicates. The diagnostic (sensitivity, specificity, area under the curve (AUC) of the receiver operating characteristic (ROC)) and prognostic accuracy (hazard ratio (HR) from Cox regression) were evaluated.

Results

Sporadic methylation in control samples necessitated the introduction of cutoffs resulting in 61–63% sensitivity/90–92% specificity (SEPT9/training), 53–57% sensitivity/87–90% specificity (SHOX2/training), and 64–65% sensitivity/90–91% specificity (mean_SEPT9/SHOX2/training). Results were confirmed in a testing cohort with 54–56% sensitivity/88–90% specificity (SEPT9/testing), 43–48% sensitivity/93–95% specificity (SHOX2/testing), and 49–58% sensitivity/88–94% specificity (mean_SEPT9/SHOX2/testing). All algorithms showed comparable cutoff-independent diagnostic accuracy with largely overlapping 95% confidence intervals (SEPT9: AUC_training = 0.79–0.80; AUC_testing = 0.74–0.75; SHOX2: AUC_training = 0.78–0.81, AUC_testing = 0.77–0.79; mean_SEPT9/SHOX2: AUC_training = 0.81–0.84, AUC_testing = 0.80). The accurate prediction of overall survival was possible with all three algorithms (training cohort: HR_SEPT9 = 1.23-1.90, HR_SHOX2 = 1.14-1.85, HR_{meanSEPT9/SHOX2} =1.19-1.89 ; testing cohort: HR_SEPT9 =1.22-1.67, HR_SHOX2 = 1.15-1.71, HR_{meanSEPT9/SHOX2} = 1.12-1.77).

Conclusion

The concordant clinical performance based on different quantification algorithms allows for the application of various diagnostic platforms for the analysis of ccfDNA methylation biomarkers.

Electronic supplementary material

The online version of this article (10.1186/s13148-017-0425-4) contains supplementary material, which is available to authorized users.

Clinical value of serum miR-21/miR-24 detection combined with quantitative analysis of DNA content in differential diagnosis of benign and malignant ascites

AIM

To assess the clinical value of serum miR-21/miR-24 detection combined with quantitative analysis of DNA content in the differential diagnosis of benign and malignant ascites.

METHODS

A total of 58 patients with ascites treated at Yueyang Second People's Hospital from January to October 2016 were included. These cases were divided into either a malignant ascites group (27 cases) or a benign ascites group (31 cases). Serum miR-21/miR-24 levels were quantified by real-time quantitative polymerase chain reaction. DNA content in ascites was determined by quantitative analysis. The receiver operating characteristic (ROC) curves were plotted to calculate the area under the ROC curve (AUC) to evaluate the significance of each index or their combination in the differential diagnosis of benign and malignant ascites.

RESULTS

The relative expression of serum miR-21/miR-24 in malignant ascites patients was significantly higher than those in benign ascites patients (P < 0.05). Multivariate Logistic regression analysis showed that conventional cytology, DNA quantitative analysis, and serum miR-21/miR-24 were sensitive indicators for the differential diagnosis of benign and malignant ascites. Conventional cytology and serum miR-21/miR-24 were positively correlated with DNA quantitative analysis (P < 0.05). The AUCs of conventional cytology, DNA quantitative analysis, and their combination were 0.766, 0.857, and 0.873, respectively (P < 0.001). The AUCs of serum miR-21, serum miR-24, and their combination were 0.857, 0.866, and 0.890, respectively (P < 0.001). Notably, the AUC was significantly increased to 0.910 (or 0.932) when DNA quantitative analysis was combined with serum miR-21 (or miR-24). The expression of serum miR-21and miR-24 was significantly higher in DNA positive patients than in DNA negative patients.

CONCLUSION

The relative expression of serum miR-21/miR-24 is significantly increased in malignant ascites patients. Combined determination of serum miR-21/miR-24 and DNA quantitative analysis can improve the effectiveness of differential diagnosis of benign and malignant ascites.

DNA Methylation Analysis of the SHOX2 and RASSF1A Panel in Bronchoalveolar Lavage Fluid for Lung Cancer Diagnosis

Introduction: Currently the majority of lung cancer patients are diagnosed as advanced diseases for no sensitive and specific biomarkers exist, noninvasive biomarkers with high sensitivity and specificity are urgently needed in lung cancer diagnosis. Bronchoscopy is a standard procedure of the diagnostic work-up of patients with suspected lung cancer despite of the limited diagnostic accuracy. Besides, epigenetic changes through DNA methylation play an important role in tumorigenesis. Thus, we examined the aberrant methylation of the SHOX2 and RASSF1A in bronchoalveolar lavage fluid (BALF) in comparing with conventional cytology examination and serum CEA in order to evaluate the new diagnostic method.

Patients and Methods: BALF and serum samples were collected from 322 patients at the time of diagnosis, 284 of them were pathologically confirmed lung cancer, 35 were benign lung diseases and 3 were malignancies in other systems. For all of the 322 patients, the methylation status of the SHOX2 and RASSF1A gene were detected by a new RT-PCR platform and then confirmed by sanger sequencing. Serum CEA were detected using electrochemiluminescence immunoassay.

Results: Profiling data showed the consistency of RT-PCR and sanger sequencing in detecting the methylation of the SHOX2 and RASSF1A. Besides, the combination of SHOX2 and RASSF1A methylation in BALF yielded a diagnostic sensitivity of 81.0% and specificity of 97.4%. When compared with established cytology examination (sensitivity: 68.3%, specificity: 97.4%) and serum biomarker carcinoembryonic antigen (CEA) (sensitivity: 30.6%, specificity: 100.0%), the SHOX2 and RASSF1A methylation panel showed the highest diagnostic efficiency. Notably, the combination of cytology and the SHOX2 and RASSF1A methylation panel could significantly improve the diagnostic efficacy.

Conclusion: The methylation analysis of the SHOX2 and RASSF1A panel in BALF with RT-PCR achieved a satisfactory sensitivity and specificity in lung cancer diagnosis, especially in an early stage. It could be used as a promising noninvasive biomarker for auxiliary diagnosis of lung cancer.

DNA methylation profiles in cancer diagnosis and therapeutics

Cancer initiation and proliferation is regulated by both epigenetic and genetic events with epigenetic modifications being increasingly identified as important targets for cancer research. DNA methylation catalyzed by DNA methyltransferases (DNMTs) is one of the essential epigenetic mechanisms that control cell proliferation, apoptosis, differentiation, cell cycle, and transformation in eukaryotes. Recent progress in epigenetics revealed a deeper understanding of the mechanisms of tumorigenesis and provided biomarkers for early detection, diagnosis, and prognosis in cancer patients. Although DNA methylation biomarker possesses potential contributing to precision medicine, there are still limitations to be overcome before it reaches clinical setting. Hence, the current status of DNA methylation biomarkers was reviewed and the future use in clinic was also predicted.

Free-Circulating Methylated DNA in Blood for Diagnosis, Staging, Prognosis, and Monitoring of Head and Neck Squamous Cell Carcinoma Patients: An Observational Prospective Cohort Study

BACKGROUND

Circulating cell-free DNA methylation testing in blood has recently received regulatory approval for screening of colorectal cancer. Its application in other clinical settings, including staging, prognosis, prediction, and recurrence monitoring is highly promising, and of particular interest in head and neck squamous cell carcinomas (HNSCCs) that represent a heterogeneous group of cancers with unsatisfactory treatment guidelines.

METHODS

Short stature homeobox 2 (SHOX2) and septin 9 (SEPT9) DNA methylation in plasma from 649 prospectively enrolled patients (training study: 284 HNSCC/122 control patients; testing study: 141 HNSCC/102 control patients) was quantified before treatment and longitudinally during surveillance.

RESULTS

In the training study, 59% of HNSCC patients were methylation-positive at 96% specificity. Methylation levels correlated with tumor and nodal category (P < 0.001). Initially increased methylation levels were associated with a higher risk of death [SEPT9: hazard ratio (HR) = 5.27, P = 0.001; SHOX2: HR = 2.32, P = 0.024]. Disease recurrence/metastases were detected in 47% of patients up to 377 days earlier compared to current clinical practice. The onset of second cancers was detected up to 343 days earlier. In the testing study, sensitivity (52%), specificity (95%), prediction of overall survival (SEPT9: HR = 2.78, P = 0.022; SHOX2: HR = 2.50, P = 0.026), and correlation with tumor and nodal category (P <0.001) were successfully validated.

CONCLUSIONS

Methylation testing in plasma is a powerful diagnostic tool for molecular disease staging, risk stratification, and disease monitoring. Patients with initially high biomarker levels might benefit from intensified treatment and posttherapeutic surveillance. The early detection of a recurrent/metastatic disease or a second malignancy could lead to an earlier consecutive treatment, thereby improving patients' outcomes.

Promoter hypermethylation of SHOX2 and SEPT9 is a potential biomarker for minimally invasive diagnosis in adenocarcinomas of the biliary tract

BACKGROUND

Biliary tract carcinoma (BTC) is a fatal malignancy which aggressiveness contrasts sharply with its relatively mild and late clinical presentation. Novel molecular markers for early diagnosis and precise treatment are urgently needed. The purpose of this study was to evaluate the diagnostic and prognostic value of promoter hypermethylation of the SHOX2 and SEPT9 gene loci in BTC.

METHODS

Relative DNA methylation of SHOX2 and SEPT9 was quantified in tumor specimens and matched normal adjacent tissue (NAT) from 71 BTC patients, as well as in plasma samples from an independent prospective cohort of 20 cholangiocarcinoma patients and 100 control patients. Receiver operating characteristic (ROC) curve analyses were performed to probe the diagnostic ability of both methylation markers. DNA methylation was correlated to clinicopathological data and to overall survival.

RESULTS

SHOX2 methylation was significantly higher in tumor tissue than in NAT irrespective of tumor localization (p < 0.001) and correctly identified 71% of BTC specimens with 100% specificity (AUC = 0.918; 95% CI 0.865-0.971). SEPT9 hypermethylation was significantly more frequent in gallbladder carcinomas compared to cholangiocarcinomas (p = 0.01) and was associated with large primary tumors (p = 0.01) as well as age (p = 0.03). Cox proportional hazard analysis confirmed microscopic residual tumor at the surgical margin (R1-resection) as an independent prognostic factor, while SHOX2 and SEPT9 methylation showed no correlation with overall survival. Elevated DNA methylation levels were also found in plasma derived from cholangiocarcinoma patients. SHOX2 and SEPT9 methylation as a marker panel achieved a sensitivity of 45% and a specificity of 99% in differentiating between samples from patients with and without cholangiocarcinoma (AUC = 0.752; 95% CI 0.631-0.873).

CONCLUSIONS

SHOX2 and SEPT9 are frequently methylated in biliary tract cancers. Promoter hypermethylation of SHOX2 and SEPT9 may therefore serve as a minimally invasive biomarker supporting diagnosis finding and therapy monitoring in clinical specimens.

SEPT9 and SHOX2 DNA methylation status and its utility in the diagnosis of colonic adenomas and colorectal adenocarcinomas

Background

Colorectal cancer (CRC) appear to arise from precursor lesions in a well-characterized adenoma-carcinoma sequence. Significant efforts have been invested to develop biomarkers that identify early adenocarcinomas and adenomas with high-grade dysplasia, since these are believed to harbor a particularly high risk for malignant transition and thus require resection. Promoter methylation of SEPT9 and SHOX2 has been suggested as a biomarker for various solid malignant tumors. Hence, the present study aimed to test their biomarker potential in CRC and precursor lesions.

Results

Assessment of promoter methylation of SEPT9 distinguished adenomas and CRC from controls as well as advanced from non-advanced adenomas (all p < 0.001). Correspondingly, SHOX2 methylation levels in adenomas and colorectal carcinomas were significantly higher compared to those in normal control tissues (p < 0.001). Histologic transition from adenomas to CRC was paralleled by amplification of the SEPT9 gene locus.

Conclusions

SEPT9/SHOX2 methylation assays may help to distinguish colorectal cancer and adenomas from normal and inflammatory colonic tissue, as well as advanced from non-advanced adenomas. Further studies need to validate these findings before introduction in clinical routine.

Analysen epigenetischer Marker aus Liquid Biopsies: Informationen von jenseits des Genoms

Die Analyse epigenetischer Marker aus Liquid Biopsies erlaubt Einblicke in physiologische und pathologische Prozesse im Körper einer Person, die über die reine Sequenzinformation hinausgehen. Insbesondere das DNA-Methylierungsmuster sowie die Expressionsmuster von mRNA und ncRNA sind aus Liquid Biopsies erfassbar. Damit werden ganze Gruppen neuer potenzieller Biomarker einer nicht invasiven und ökonomischen Diagnostik zugänglich. Darüber hinaus und im Gegensatz zur reinen DNA-Sequenzanalyse von Liquid Biopsies erlaubt die hohe Gewebespezifität epigenetischer Marker auch die Bestimmung der Herkunft der analysierten Nukleinsäuren z. B. in Bezug auf ein betroffenes Organ. Angesichts der fallenden Kosten für Sequenzierungen und des technologischen Fortschritts, der die Nachweisgrenzen immer weiter zu immer sensitiveren Anwendungen verschiebt, könnten epigenetische Untersuchungen aus Liquid Biopsies den Trend zu einer Individualisierung in der Medizin weiter forcieren.

Current status and future perspectives of circulating cell-free DNA methylation in clinical diagnostics

Aberrant DNA methylation is a hallmark of malignancies and can be detected in circulating cell-free DNA (ccfDNA) in bodily fluids, i.e. blood plasma, serum and urine. The availability of technologies that allow for an accurate and sensitive quantification of ccfDNA DNA methylation enables the precise monitoring of dynamic pathologic processes and pharmacodynamics. Recently, the first ccfDNA methylation biomarker