DNA Methylation

The prognosis of patients with esophageal squamous cell carcinoma (ESCC) who develop post-operative early tumor recurrence is often relatively poor. Therefore, biomarker that can detect micro metastases before the start of treatment is required. Epigenomic alterations such as DNA methylation have attracted attention as promising biomarkers. The investigators aim to predict early recurrence based on whole genome DNA methylation analysis of esophageal cancer.

Esophageal cancer remains a disease with a poor prognosis. Chemotherapy is an important part of its treatment, but there are cases in which chemotherapy is ineffective. The investigators aim to develop a model to predict the response to chemotherapy by DNA methylation of preoperative biopsy specimens to identify the chemotherapy ineffective group.

The MET-SELS study aims to revolutionize how we identify individuals for lung cancer screening by moving beyond the limitations of self-reported smoking history. Currently, eligibility for low-dose CT (LDCT) scans relies on "pack-years"-a metric often compromised by recall bias, under-reporting, and an inability to account for the biological nuances of smoke inhalation or environmental exposure. Consequently, current criteria miss nearly half of incidental lung cancers. To bridge this gap, the study investigates DNA methylation as a stable, objective "biological footprint" of smoking. Unlike short-term biomarkers like nicotine or CO levels, specific epigenetic changes in genes such as AHRR and F2RL3 persist long after cessation and correlate accurately with cumulative tobacco exposure. Led by Professor Dr. Annemiek Snoeckx and a multidisciplinary team at UZA and the Centre for Medical Genetics, the research will analyze saliva samples from two groups: roughly 900 participants from the ZORALCS screening trial and 150 volunteers. By comparing saliva-derived genomic signatures against both self-reported data and professional interviews, the team aims to validate a panel of methylation markers that can pinpoint high-risk individuals with far greater precision. The ultimate vision for MET-SELS is to implement a population-based "saliva-first" triage system, similar to the FIT test used for colorectal cancer. In this model, high-risk candidates would provide a saliva sample at home; only those with a confirmed epigenetic risk profile would be invited for a LDCT scan, significantly increasing the yield of early-stage lung cancer detection while streamlining healthcare resources.

Head and neck squamous cell carcinoma (HNSCC) are malignant tumors originating from the epithelial mucosa of the upper aerodigestive tract. The oral cavity is the most frequent location of HNSCC (oral squamous cell carcinoma: OSCC). Tobacco use and alcohol consumption are the greatest risk factors. The Hauts de France region has one of the highest incidence rates of OSCC. The overall survival of patients with OSCC remains low, with a 5-year overall survival rate of around 60%. In addition to the oncological prognosis, OSCCs and their treatment have a significant impact on the quality of life of patients. An early diagnosis of OSCC is recommended, but it remains difficult. It can be for example challenging to diagnose OSCC in a context of oral premalignant lesions. Identifying objective biomarkers of malignancy would be an advantage and would allow better progress in the field of precision medicine and surgery for these tumors. The investigators propose to establish the diagnostic use of an optimized DNA methylation profile detected in the saliva of OSCC patients by comparing these epigenetic marks before and after tumor resection. The investigators will construct a consolidated signature of 4 genes whose DNA is subject to methylation and gene expression is restricted to cancer cells, by crossing TCGA analysis with single-cell analysis (single-cell RNA sequencing). The investigators propose to analyse DNA methylation of the corresponding genes in the saliva of n=30 OSCC patients recruited for primary surgical resection in the Department of Maxillofacial Surgery vs controls. In addition, the investigators will examine the methylation profiles before / after complete excisional surgery of OSCC. This pilot study will aim to validate the analysis of DNA methylation markers in saliva of OSCC, with the aim of improving the diagnostic precision of OSCC and, secondly, to compare these markers before and after treatment by primary surgery.

This study aims to initially utilize machine learning on pan-cancer DNA methylation data from public databases to construct a DNA methylation classification model (PaCIFiC-CUP, pan-cancer integrated fingerprinting classifier of CUP) for diagnosing various types of cancer, particularly the primary site of cancer of unknown primary. The goal is to achieve diagnosis of cancer pathology type by analyzing the DNA methylation patterns of cancer specimens, thereby guiding subsequent precision treatment for cancer.

The goal of this observational study is to evaluate the accuracy of a novel molecular test for screening and monitoring endometrial lesions in women at medium-to-high risk for endometrial cancer. The main questions it aims to answer are: * What is the sensitivity and specificity of the CISENDO test (a DNA methylation test on cervical cytology samples) for detecting histologically confirmed endometrial intraepithelial neoplasia (EIN) or invasive endometrial cancer? * How do DNA methylation levels change during the follow-up of endometrial lesions? Researchers will compare the results of the CISENDO test to the results from the standard diagnostic procedure (hysteroscopy with histology) to see if the molecular test can reliably identify high-risk lesions and track disease progression. Participants will: * Provide a residual liquid-based cervical cytology sample for the CISENDO test. * Undergo a standard diagnostic hysteroscopy examination (with or without biopsy) for comparison. * Some participants will return for follow-up visits at 6 and 12 months for repeat methylation testing and/or hysteroscopy to monitor their condition.

The prognosis of patients with esophageal squamous cell carcinoma (ESCC) who develop post-operative early tumor recurrence is often relatively poor. Therefore, biomarker that can detect micro metastases before the start of treatment is required. Epigenomic alterations such as DNA methylation have attracted attention as promising biomarkers. The investigators aim to predict early recurrence based on whole genome DNA methylation analysis of esophageal cancer.

Esophageal cancer remains a disease with a poor prognosis. Chemotherapy is an important part of its treatment, but there are cases in which chemotherapy is ineffective. The investigators aim to develop a model to predict the response to chemotherapy by DNA methylation of preoperative biopsy specimens to identify the chemotherapy ineffective group.

The goal of this observational study is to test in patients with cystic tumor of pancreas. The main questions it aims to answer are: Screening of molecular diagnostic markers for pancreatic cystic tumors by cfDNA methylation sequencing of pancreatic cystic fluid and proteomic assays to distinguish benign from malignant and mucinous/non-mucinous, correlate with pathological features, and find molecular features associated with the degree of malignancy. Participants will Provide post-operative cyst fluid specimens.

Cervical cancer represents one of the foremost causes of cancer-related morbidity and mortality among women worldwide. Given the current limitations, such as the low specificity of human papillomavirus (HPV) testing and the relatively low sensitivity of cytological examinations, there is a pressing need for a novel, non-invasive, safe, and precise screening method. This study aims to undertake a multicentre, real-world investigation, incorporating at least 10 sub-centres and enrolling 30,000 participants. Histopathological examination results will serve as the 'gold standard' for evaluating the screening efficacy of human PAX1 and JAM3 gene methylation assays (PAX1m/JAM3m), HPV testing, and cytological examinations. Furthermore, the study seeks to elucidate the relationship between DNA methylation levels and persistent HPV infection, while also assessing the applicability of PAX1m/JAM3m across diverse clinical settings. By focusing on alterations in DNA methylation levels within cervical exfoliated cells as the primary research trajectory, this study aspires to furnish novel insights and theoretical foundations for the prevention and management of cervical cancer, targeting PAX1m/JAM3m. The ultimate objective is to facilitate the clinical implementation of an enhanced cervical cancer screening protocol, thereby addressing the deficiencies of current screening methodologies, achieving greater precision in cervical cancer screening, and effectively reducing the incidence of cervical cancer while mitigating the risks of overdiagnosis and overtreatment.