Methylation Profile Test (Methylscape) in Body Fluids for Multi-Cancer Detection and Monitoring in Colombia

Official title

Evaluation of a Rapid Test for the Detection of Methylation Profiles (Methylscape) in Various Body Fluids as a Universal Biomarker for Cancer Detection and Monitoring

Overview

DNA methylation changes occur early and broadly during carcinogenesis. Methylscape is a rapid assay that detects global DNA methylation patterns in body fluids (blood, urine, and saliva) and may detect a cancer signal and predict the cancer signal origin (CSO) from a single fluid sample, using the differential interaction between methylated and unmethylated DNA and gold nanoparticles. This prospective observational study evaluates the diagnostic performance (sensitivity and specificity) of the Methylscape test in Colombian patients with various biopsy-confirmed solid tumors compared with age- and sex-matched cancer-free (healthy) volunteers. The study is conducted in three parts: Phase 1 validates the assay in 250 patients with cancer; Sub-study 2a compares 1,500 patients with cancer against 1,500 matched cancer-free volunteers; and Sub-study 2b uses serial blood and urine sampling in 300 patients with early-stage disease to assess detection of disease relapse during follow-up, in parallel with standard imaging. The study also estimates positive and negative predictive values (PPV/NPV) and projects the budget impact and cost-effectiveness of Methylscape as a multi-cancer early detection (MCED) tool in an upper-middle-income Latin American setting.

Detailed description

Background. Most cancers lack reliable screening methods, often leading to advanced-stage diagnosis. Multi-cancer early detection (MCED) tests based on body fluids can screen for several cancer types from a single sample. DNA methylation, which occurs early in carcinogenesis and is tissue-specific, is the most commonly used marker in MCED assays. Methylscape leverages global differences in the genomic distribution of methylation between cancerous and normal tissues, detected electrochemically through differential adsorption of DNA on gold electrodes.

Objective. To determine whether Methylscape can detect the methylation landscape across multiple cancer types with sufficiently high specificity to predict the cancer signal origin (CSO), and to assess its potential application as a population-scale MCED test among Colombians.

Design. Single-center prospective observational study conducted at CTIC (Bogotá, Colombia), with sample processing at CTIC and Columbia University. Phase 1 (N=250 patients with cancer) provides initial validation across solid tumor types selected by local incidence. Sub-study 2a (1,500 patients with cancer and 1,500 matched cancer-free volunteers) provides large-scale clinical validation. Sub-study 2b (N=300 early-stage patients) evaluates serial blood/urine Methylscape testing for relapse detection during follow-up every 6 months. Phase 1 participants may enter Sub-studies 2a/2b only if they meet the corresponding criteria and provide new informed consent; cross-phase participation is flagged in the database to adjust statistical estimates.

Biospecimens \& reference standards. Blood/plasma (K2EDTA), urine, saliva, and FFPE tumor tissue are collected and stored at -80 °C in the CTIC biobank. Cancers are coded with WHO ICD-O-3; stage per AJCC 8th edition. Reference standards: histopathology (MCED), RECIST 1.1 or biopsy (relapse), and absence of cancer by record review plus 12-month follow-up (cancer-free).

Statistical analysis. Sensitivity and specificity are estimated overall and by stage/type (expected sensitivity 85-90%, specificity 98%; 95% confidence, 80% power). PPV/NPV are derived via Bayes' theorem with prevalence from GLOBOCAN 2022; 95% CIs by stratified bootstrap (1,000 resamples). Budget impact and cost-effectiveness (QALYs) are projected via microsimulation and Markov models.

Interventions

• Diagnostic test Methylscape DNA methylation assay
  Rapid assay measuring global DNA methylation patterns in body fluids (blood/plasma, urine, saliva) and FFPE tumor tissue via differential adsorption of methylated vs. unmethylated DNA on gold electrodes (differential pulse voltammetry), to detect a cancer signal and predict the cancer signal origin (CSO). Applied to both groups; no therapeutic intervention is administered.

Primary outcome measures

• Sensitivity of the Methylscape test for cancer-signal detection, as assessed against histopathological confirmation as the reference standard [Time frame: Baseline]
• Specificity of the Methylscape test for cancer-signal detection, as assessed against absence of cancer confirmed by medical-record review and 12-month follow-up [Time frame: 12 months]

Secondary outcome measures (2)

• Accuracy of Methylscape cancer-signal-origin (CSO) prediction, measured as the percentage of cases in which the predicted tissue of origin matches the histopathologically confirmed primary tumor site [Time frame: Baseline]
• Sensitivity and specificity of serial Methylscape testing for detection of disease relapse, as assessed against imaging response (RECIST 1.1) or biopsy of local recurrence [Time frame: At 6, 12, 18, and 24 months]

Eligibility criteria

Inclusion criteria

• Adults aged 18 years or older.
• Willing and able to participate and to provide the required samples (blood, urine, saliva) and demographic information (age, sex, race/ethnicity, BMI).
• Able to provide written informed consent for participation and for use of biological samples. For CTIC Biobank samples, prior research-use consent is verified.
• Demographic/anthropometric comparability (race, ethnicity, BMI) with other participants; race/ethnicity by self-identification (WHO and national census categories); BMI per WHO categories.

Inclusion - Cancer cohort:

• Cancer diagnosis confirmed within 90 days prior to sample collection.
• Biopsy-proven malignancy with radiological staging.
• No anticancer treatment at the time of collection or within the previous 3 years.
• Inclusion - Cancer-free (healthy) cohort:
• No cancer diagnosis or treatment in the previous 3 years (ICD-O-3 behavior code 2 or 3).
• Not under evaluation for suspected cancer (verified by medical record review or additional medical evaluation).
• Subjects with benign tumors (code 0) or tumors of uncertain behavior (code 1) may be included if there is no clinical evidence of progression or malignancy.

Additional criteria - tumor-burden monitoring (Sub-study 2b):

• Biopsy-confirmed cancer.
• ECOG performance status ≤ 2.

Exclusion Criteria (both cohorts):

• Failure to meet the general or cohort-specific inclusion criteria.
• Pregnancy.
• Organ transplant recipients.
• Use of demethylating agents (azacitidine, decitabine) or cytotoxic agents (including for autoimmune/inflammatory conditions).
• Prior or ongoing anticancer therapy: cancer surgery beyond that needed for diagnosis; local, regional, or systemic chemotherapy (including chemoembolization); targeted therapy; immunotherapy (including cancer vaccines); hormonal therapy; or radiotherapy.

Criteria are shown verbatim from the registry (in English). Final eligibility is always assessed by the study center.

Healthy volunteers: Yes

Study design

Observational model

Case-control

Study locations

Colombia · 1 center

• Fundación CTIC Centro de Tratamiento e Investigación sobre Cáncer Luis Carlos Sarmiento An — Bogotá

Publications

• Sina AA, Carrascosa LG, Liang Z, Grewal YS, Wardiana A, Shiddiky MJA, Gardiner RA, Samaratunga H, Gandhi MK, Scott RJ, Korbie D, Trau M. Epigenetically reprogrammed methylation landscape drives the DNA self-assembly and serves as a universal cancer biomarker. Nat Commun. 2018 Dec 4;9(1):4915. doi: 10.1038/s41467-018-07214-w. PMID 30514834
• Bretthauer M, Wieszczy P, Loberg M, Kaminski MF, Werner TF, Helsingen LM, Mori Y, Holme O, Adami HO, Kalager M. Estimated Lifetime Gained With Cancer Screening Tests: A Meta-Analysis of Randomized Clinical Trials. JAMA Intern Med. 2023 Nov 1;183(11):1196-1203. doi: 10.1001/jamainternmed.2023.3798. PMID 37639247
• Welch HG, Bergmark R. Cancer Screening, Incidental Detection, and Overdiagnosis. Clin Chem. 2024 Jan 4;70(1):179-189. doi: 10.1093/clinchem/hvad127. PMID 37757858
• Tafazzoli A, Ramsey SD, Shaul A, Chavan A, Ye W, Kansal AR, Ofman J, Fendrick AM. The Potential Value-Based Price of a Multi-Cancer Early Detection Genomic Blood Test to Complement Current Single Cancer Screening in the USA. Pharmacoeconomics. 2022 Nov;40(11):1107-1117. doi: 10.1007/s40273-022-01181-3. Epub 2022 Aug 30. PMID 36038710
• Nicholson BD, Oke J, Virdee PS, Harris DA, O'Doherty C, Park JE, Hamady Z, Sehgal V, Millar A, Medley L, Tonner S, Vargova M, Engonidou L, Riahi K, Luan Y, Hiom S, Kumar H, Nandani H, Kurtzman KN, Yu LM, Freestone C, Pearson S, Hobbs FR, Perera R, Middleton MR. Multi-cancer early detection test in symptomatic patients referred for cancer investigation in England and Wales (SYMPLIFY): a large-scale PMID 37352875
• Minasian LM, Pinsky P, Katki HA, Dickherber T, Han PKJ, Harris L, Patriotis C, Srivastava S, Weil CJ, Prorok PC, Castle PE. Study design considerations for trials to evaluate multicancer early detection assays for clinical utility. J Natl Cancer Inst. 2023 Mar 9;115(3):250-257. doi: 10.1093/jnci/djac218. PMID 36458902
• Klein EA, Richards D, Cohn A, Tummala M, Lapham R, Cosgrove D, Chung G, Clement J, Gao J, Hunkapiller N, Jamshidi A, Kurtzman KN, Seiden MV, Swanton C, Liu MC. Clinical validation of a targeted methylation-based multi-cancer early detection test using an independent validation set. Ann Oncol. 2021 Sep;32(9):1167-1177. doi: 10.1016/j.annonc.2021.05.806. Epub 2021 Jun 24. PMID 34176681
• LeeVan E, Pinsky P. Predictive Performance of Cell-Free Nucleic Acid-Based Multi-Cancer Early Detection Tests: A Systematic Review. Clin Chem. 2024 Jan 4;70(1):90-101. doi: 10.1093/clinchem/hvad134. PMID 37791504

Identifiers

NCT: NCT07741435 · Methylscape · CEI-183

Primary sources (government registries)

• ClinicalTrials.gov (US NIH)

View this study on ClinicalTrials.gov ↗