Host Genome Methylation: a Screening Tool in Anal Cancer Detection

1. Current state of knowledge on the pathology

In 2020, 30,000 cases of squamous cell carcinoma of the anus were reported worldwide. These cancers affect women in 2/3 of cases. They are fairly rare in the general population, with an age-standardised incidence rate of 0.35 per 100,000 person-years (p.a.) in men and 0.57 in women.

The population of men who have sex with men (MSM) living with HIV is at greater risk of anal cancer: studies in 2012 reported an 80-fold increase in the relative risk compared with the non-HIV-infected male population. This population is also more exposed to anal HPV infections, which adds to the dysimmunity associated with HIV infection. As a result, this population was already the subject of specific recommendations concerning anal canal cancer screening based on cytology. A recent meta-analysis has stratified the risk of anal cancer in different populations. It confirms the excess risk of anal cancer in the MSM population living with HIV (up to 100 per 100,000 pa in MSM living with HIV aged over 45).

It has also identified other groups at risk of anal cancer. A higher incidence rate of anal cancer in women who have already had cervical or vulvovaginal cancer is clearly established. But this meta-analysis by Clifford et al. shows a different stratification of anal cancer risk according to the type of previous HPV-induced cancer. Thus, the incidence rate of anal cancer is highest in the case of a history of vulvar cancer, equal to 50 per 100,000 pa, whereas it is close to 10 per 100,000 pa in the case of a history of vaginal or cervical cancers. Another group at risk of anal cancer is made up of immunosuppressed people not infected with HIV, and in particular solid transplant recipients, with different incidence rates of anal cancer depending on the type of transplant and above all the time since the transplant.

Overall, incidence rates of anal cancer, regardless of sex, are higher in high-income countries. In 2018, 1,532 new cases of anal cancer were reported in women in France, corresponding to an incidence rate of 2.4 per 100,000 woman-years, and 479 new cases in men, corresponding to an incidence rate of 0.8 per 100,000 man-years. As in many high-income countries, an overall increase in the incidence of this cancer has been observed in France, both in women (+3.4% and +5.7% between 1990 and 2018 and between 2010 and 2018 respectively) and in men (+1.5% and +3.3% between 1990 and 2018 and between 2010 and 2018 respectively). Trends by age for anal cancer show an increase in the number of cases, mainly in women aged 50 and 60.

Analysis of human genome methylation in anal swabs is a promising biomarker for anal cancer risk. Methylation is an epigenetic physiological phenomenon that regulates the expression of certain genes. The viral oncoproteins E6 and E7 of high-risk oncogenic HPVs (notably HPV16) have been shown to induce activation or increased expression of the cellular enzymes responsible for these methylation phenomena. As a general rule, hypermethylation of gene promoters leads to their inactivation. Repression of genes involved in the antiviral or anti-tumour response may contribute to immune escape, whereas hypermethylation inducing repression of tumour suppressor genes favours the cancerous process.

With regard to anal cancer, two studies demonstrated that the methylation markers previously developed for the cervix were not discriminatory for anal cancer. Subsequently, cross-sectional analysis of anal biopsies at different stages (normal cytology, low-grade or high-grade lesions, cancer) has revealed methylation markers specific to anal carcinogenesis in anal biopsies (invasive tissue sampling).

These markers are extremely promising, and methylation could therefore constitute a robust predictive marker of progression to an invasive lesion, and would therefore be a decisive factor in the decision of invasive treatment versus surveillance.

II. State of knowledge on reference procedures

The evolution of anal pre-cancerous lesions is less well described than that of cervical lesions due to the absence of screening programmes to date.

For the first time, the American ANCHOR study of nearly 5,000 PLHIV demonstrated the impact of treatment of high-grade lesions, with a 57% reduction in the rate of cancer in the treated arm (incidence 173 per 100,000 pa vs 402 per 100,000 pa in the simple surveillance arm). Following this study, recommendations for screening for precancerous anal lesions in asymptomatic at-risk populations are beginning to emerge.

In January 2023, the French National Society of Colo-Proctology (SNFCP) issued recommendations for anal cancer screening of asymptomatic individuals in three at-risk populations: MSM living with HIV aged over 30, women with a history of pre-cancerous lesion or cancer of the vulva and women who have received a solid organ transplant for more than 10 years. These recommendations target populations with an incidence of anal cancer greater than 40 per 100,000 pa according to the meta-analysis by Clifford et al. In this context, screening for anal cancer is based on primary HPV16 screening, in particular by anal self-sampling and, if positive, an anal smear for cytology and a standard proctology examination. In the event of abnormal cytology, patients will be referred for a proctology consultation with high-resolution anoscopy (HRA).

There are few proctologists in France who carry out AHR examinations, and waiting times for consultations are already very high. The major stumbling block to the introduction of anal cancer screening is the anticipated worsening of the overcrowding of AHR examinations and proctology consultations. For example, a recent meta-analysis reported a prevalence of 27% to 35% of HPV16 infection in the anal region of MSM living with HIV. The development of triage tools enabling only those patients most at risk of high-grade anal dysplasia to be referred for this examination is therefore crucial.

The aim of this new study is to validate the predictive capacity of anal smear methylation markers for screening patients at risk of progressing to high-grade dysplasia and to define appropriate thresholds in this sample, including patients targeted by the new SNFCP screening recommendations and therefore with no history of AIN3 lesions.

III. Hypothesis

This study is based on the hypothesis that the level of methylation of the markers ASCL1 and ZNF582 will be predictive of the risk of asymptomatic patients developing high-grade anal lesions and therefore anal cancer.