health care provider standing in front of gynecology stirrups holding swabs for Pap smear
health care provider standing in front of gynecology stirrups holding swabs for Pap smear

DNA Methylation Could Predict Ovarian, Breast Cancers

A pair of new studies finds that analyzing material from a Pap smear can reveal tumor risk in distant parts of the body, potentially allowing early interventions.

smiling woman with curly hair and glasses
Anna Napolitano

Anna Napolitano is a freelance science writer based in London with bylines in several outlets. As a PhD student and as a postdoc, she published several peer-reviewed papers in the immunology field.

View full profile.


Learn about our editorial policies.

Feb 11, 2022

ABOVE: © ISTOCK.COM, ANASTAS_

Malignancies that affect internal reproductive organs are a leading cause of global cancer incidence worldwide. Breast, cervical, ovarian, and uterine tumors account for more than half of cancers in women. However, cervical cancer is the only one of these cancer types with a reliable screening system. Routine Pap smears offer a simple, non-invasive way to detect precancerous cells and have reduced the incidence and mortality from cervical cancer by more than 50 percent.  

New findings published in Nature Communications last week (February 1) suggest that a version of the Pap smear could be used to provide early warning of some other cancer types as well. In two studies, a group of researchers tested the ability of a new scoring system that the authors call WID-index, or women’s cancer risk identification index, based on the DNA methylation footprint in cervical samples, to predict the risk of developing ovarian and breast cancer.  

“Both studies highlight that looking at the epigenome is a promising tool for indicating cancer risk,” says Sarah Blagden, a cancer researcher at the University of Oxford who was not involved in the work but has previously collaborated with one of the authors. “But, as a cancer diagnostic, it still needs to be optimized and prospectively and temporally validated against existing methods before determining whether it is a meaningful clinical tool.”  

Analyzing DNA methylation to screen for cancer is not a new concept. While DNA is the cells’ instruction booklet, its methylation status tells each cell which chapter it needs to read to have a specific identity and function. Unlike the DNA itself, the methylation status is not fixed but can be affected by life experience and disease. For those reasons, altered DNA methylation has long been regarded as a hallmark of cancer, and some researchers have suggested it could become the basis for early-stage cancer detection. For cancers that mainly affect internal reproductive organs, previous studies have demonstrated that environmental or nongenetic factors play a crucial role, and are as much a factor as genetic predisposition. Analyses of the DNA methylation state could potentially capture the effects of such environmental factors on cells.   

In the view of Martin Widschwendter, a researcher at University College London’s Institute for Women’s Health and the senior author of both new papers, “DNA methylation is the best possible tool for diagnoses, recording and integrating all risk factors that leads to women’s cancer.” He tells The Scientist that the studies grew out of a project that began in 2014 with the aim of developing an epigenetic test that could screen for four cancers: uterine, cervical, breast, and ovarian. 

The team started with breast and ovarian cancers, since these account for the most deaths of the four. The researchers wanted to look at the methylation state of epithelial cells, as both cancers studied in the papers originate in this cell type. However, sampling tissue from the breasts or ovaries requires invasive surgery, so they tried using the cervix as a surrogate organ for assessing the state of distant epithelial cells. The cervix undergoes similar hormonal control to the ovaries and breasts, it allows access to epithelial cells without surgery, and many countries already have routine cervical screening programs.  

The researchers analyzed samples taken during routine smear tests from more 3,000 women from 15 European medical centers to test their hypotheses. They measured the epigenetic changes for 850,000 sites in the genome, then team used a machine learning system to sift through the data to focus specifically on DNA from epithelial cells, excluding possible interference from DNA derived from immune cells or cell-free DNA. Comparing the DNA methylation in patients with breast or ovarian cancer versus healthy controls, the researchers identified unique signature of epigenetic marks found in people with each kind of cancer, which they then validated in a second set of data. They found that the WID-index incorporating the epigenetic data for breast cancer correctly identified 76 percent of women within the highest risk group, while a current test based on a panel of genes that increase the risk of breast cancer in people with a family history or recurrent malignancies correctly identifies 47.5 percent of women in this group. For ovarian cancer, the WID-index identified 71 percent of women under 50 and 55 percent of woman over the age of 50 in the highest risk group. The current genetic test identifies 35.1 percent of women over 50 in this group, and there is currently no screening method used for patients under 50.  

“The study demonstrates a fascinating biology, and the use of a surrogate tissue is an interesting novelty,” says Jason Ross, a bioinformatician at CSIRO Health and Biosecurity in Australia who was not involved in the study. 

The result is particularly significant for breast cancer as mammography, the current screening method for breast cancer, performs poorly in young people, leads to over-diagnosis, and doesn’t reach all patients who could benefit from it. Widschwendter says that applying a scoring system such as the WID-index in the clinic could help in make informed decisions about whether a lump detected in a patient’s breast should be biopsied or simply monitored.  

Retrospective analyses on smear samples from Sweden’s biobank allowed the team to test whether the WID-index could be used as prognostic index as well as screening tool. “Something like the WID-index presented in the paper can help as a precision tool to better quantify the degree of risk for who has already an innate genetic risk,” says Ross. For example, people with BRCA1/BRCA2 mutations, who have a high risk of developing certain cancers, commonly undergo multiple screenings over their lives and face difficult decisions about their reproductive lives such as whether to undergo mastectomy. In patients with either BRCA1 or BRCA2 mutations, the team found that their breast cancer WID-index was roughly as accurate in predicting the presence of cancer with a poor prognosis as it had been in the population without such mutations that was used to construct the index, suggesting that it could yield valuable information for these patients. However, there was a high signal-to-noise ratio for the samples analyzed from the biobank due to their storage conditions, so the study authors not that more work is needed to validate the prognostic value of the WID-index. 

According to Ross, several factors will determine whether these academic findings can be translated to clinical application. One is the technology the authors used for DNA methylation screening, the Illumina InfiniumMethylation, will soon be retired, so the research team will need to re-calibrate their findings on newer technology. Another consideration is that, thanks to the success of vaccination in reducing infection rates with human papilloma virus (HPV), which causes cervical cancer, the need for a regular smear test for that disease will fade over time. Blagden tells The Scientist that she agrees that cervical sampling is changing and, looking ahead, the deep cervical brushing needed for the DNA methylation analyses might not be a routine screening method anymore.  

These two papers establish a proof-of-concept for women’s cancers, Blagden says. Widschwendter says the team is working on further confirming the results, as well as expanding the index to other cancers. “We have great hope that looking at the methylation profiles, we will be able to predict the risk for multiple cancers” concludes Widschwendter.