IMPRESS: Improved methylation profiling using restriction enzymes and smMIP sequencing, combined with a new biomarker panel, creating a multi-cancer detection assay

Sep 21, 2026

Uploaded by Rowan

Despite progress in cancer diagnostics, more sensitive biomarkers are still needed for routine, low-cost testing. A bisulfite-free, high-multiplex approach is presented to detect DNA methylation signatures by combining methylation-sensitive restriction enzymes with single-molecule molecular inversion probes (smMIP). The IMPRESS assay is developed for eight lethal cancer types using 1,791 CpG sites, analyzed across blood, tumor, and normal samples, and validated with ddPCR. A classifier using 358 CpG targets achieves sensitivity 0.95 and specificity 0.91, supporting liquid biopsy potential.

LanguageEnglish

CategoryResearch & Report

FormatPDF

Pages13

Reading Time33 min

AccessFree to download

Background

Methods

IMPRESS assay design and target selection

Sample analysis and classifier building

Results

ddPCR validation

Performance metrics and liquid biopsy potential

Conclusions

Introduction

Need for sensitive diagnostic biomarkers

Limitations of bisulfite and alternatives

[www.nature.com/bjc](www.nature.com/bjc British)[ British](www.nature.com/bjc British) Journal of Cancer ARTICLE OPEN Molecular Diagnostics IMPRESS: Improved methylation proﬁling using restriction enzymes and smMIP sequencing, combined with a new biomarker panel, creating a multi-cancer detection assay Janah Vandenhoeck 1,2,6, Isabelle Neefs 1,2,6, Thomas Vanpoucke1,2,6, Joe Ibrahim 1,2, Arvid Suls 1, Dieter Peeters3, Anne Schepers1, Alexander Hoischen4,5, Erik Fransen1, Marc Peeters2, Guy Van Camp1,2,7 and Ken Op de Beeck1,2,7 ✉ © The Author(s) 2024 BACKGROUND: Despite the worldwide progress in cancer diagnostics, more sensitive diagnostic biomarkers are needed. The methylome has been extensively investigated in the last decades, but a low-cost, bisulﬁte-free detection method for multiplex analysis is still lacking. METHODS: We developed a methylation detection technique called IMPRESS, which combines methylation-sensitive restriction enzymes and single-molecule Molecular Inversion Probes. We used this technique for the development of a multi-cancer detection assay for eight of the most lethal cancer types worldwide. We selected 1791 CpG sites that can distinguish tumor from normal tissue based on DNA methylation. These sites were analysed with IMPRESS in 35 blood, 111 tumor and 114 normal samples. Finally, a classiﬁer model was built. RESULTS: We present the successful development of IMPRESS and validated it with ddPCR. The ﬁnal classiﬁer model discriminating tumor from normal samples was built with 358 CpG target sites and reached a sensitivity of 0.95 and a speciﬁcity of 0.91 . Moreover, we provide data that highlight IMPRESS’s potential for liquid biopsies. CONCLUSIONS: We successfully created an innovative DNA methylation detection technique. By combining this method with anew multi-cancer biomarker panel, we developed a sensitive and speciﬁc multi-cancer assay, with potential use in liquid biopsies. British Journal of Cancer (2024) 131:1224–1236; [https://doi.org/10.1038/s41416-024-02809-1](https://doi.org/10.1038/s41416-024-02809-1) INTRODUCTION Cancer remains one of the most lethal diseases worldwide. Breast, lung, colorectal, and prostate cancer are amongst the most common cancers, with each over 1.4 million cases per year [1] . Diagnosis typically occurs in an advanced disease stage due to the lack of clear symptoms and the absence of effective screening programs for most cancer types [2] . This is reﬂected in the percentages of late-stage diagnoses, for example, 68% and 59% in lung and colorectal cancer respectively [3] . Clearly, there is anunfulﬁlled need for effective diagnostic biomarkers. An interesting biomarker candidate for cancer detection is DNA methylation. Genome wide epigenetic reprogramming of tumors occurs early in carcinogenesis. Methylation patterns of many tumor types are widely dysregulated compared to those of healthy cells, but the tumor type speciﬁc patterns are very distinctive [4–6] . Many studies have investigated the potential of the methylome in recent years but, to date, there are only a few successful methylation biomarkers for cancer in a clinical setting. Our research group has already shown the promise of methylationas a diagnostic biomarker [6] . We demonstrated the capability to discriminate 14 different cancer types from normal tissue and from each other using methylation biomarkers in silico, with high sensitivity and speciﬁcity. It is important to detect biomarkers in a sensitive and speciﬁc manner. Currently, bisulﬁte sequencing is still considered the gold standard for DNA methylation analysis. However, bisulﬁte is a harsh chemical that degrades DNA, limiting the sensitivity of downstream applications [7] . Alternative bisulﬁte-free techniques, such as afﬁnity-based methods (e.g. MeDIP-seq, Methyl Cap), are shown to have a lower accuracy compared to bisulﬁte sequencing [8] . Other bisulﬁte-free methods include restriction enzymes, which can eithe

FAQs

What problem does IMPRESS address in cancer diagnostics?

It targets the need for more sensitive diagnostic biomarkers while providing a low-cost, bisulfite-free method for multiplex methylation analysis.

How does IMPRESS detect DNA methylation?

IMPRESS combines methylation-sensitive restriction enzymes with single-molecule molecular inversion probes (smMIP) to assay methylation across selected CpG sites.

What performance did the final classifier achieve?

The classifier distinguishing tumor from normal samples used 358 CpG target sites and reached sensitivity 0.95 and specificity 0.91, validated with ddPCR.

Sep 21, 2026

Uploaded by Rowan