For the first time, we described methylation alterations in genes FAM19A4, EPB41L3 and PAX1 in HPV-positive patients with cervical lesions and explored their relationship with disease progression. The major new findings of this study were: (i) methylation levels of these three genes were markedly elevated in HSIL and CC patients and could be considered as new biomarkers accurately distinguishing between HSIL + CC cases and control + LSIL cases; (ii) The methylation degree of all three genes had high sensitivity and specificity for the diagnosis and prediction of HSIL + CC, especially the diagnostic performance of the tri-gene methylation assay was more prominent; (iii) methylation levels of the three genes were positively correlated with the severity of cervical lesions, and they had significant differences in group HSIL and CC. Although slightly inferior, methylation assay of the three genes still had considerable sensitivity and specificity for distinguishing between HSIL and CC, which could act as novel indicators to monitor disease progression; (iv) Although all of the included subjects were HPV-positive, patients in groups HSIL and CC seemed to have a higher proportion of hrHPV16/18 infection.
CC is one of the most common malignant tumors in wome with extremely high morbidity and mortality rate [13]. Although the incidence rate of CC in China has been dramatically increasing in recent years, the screening rate in China is markedly lower than those in developed countries [14]. HPV has emerged as a primary cause of CC worldwide. To date, 228 genotypes of HPV have been identified. Persistent infection of hrHPV (mainly with HPV16 and HPV18) usually results in the development of malignancy of cervix [15].
Scientific screening, rational triage of risk groups and active interventions are critical to effectively prevent disease progression, improve prognosis and reduce fatality. Cervical liquid-based cytology examination is mainly used to stain the exfoliated cells from the cervix to observe morphological changes and then determine whether the cells are cancerous. The specificity of cytology examination is high, but the sensitivity is low, which is easy to lead to missed diagnosis and treatment. The judgment of cytology results needs to be interpreted by professional pathologists under the microscope, and as a result, results are susceptible to subjective decisions [3]. HPV testing is an etiological examination to detect whether the cervix is infected with HPV virus through nucleic acid testing for pathogens [4]. The sensitivity of HPV testing is high, but the specificity is poor. The false-positive rate is relatively high, and it is impossible to distinguish between transient infection and pathogenic infection. Transient HPV infection will not develop into cervical precancerous lesions or CC, which is easy to increase the rate of colposcopy referral and cervical tissue biopsy, causing unnecessary suffering to women [16].
Aberrant genomic DNA methylation of cervical exfoliated cells is a common epigenetic alteration in the process of CC. HPV can induce hypermethylation of the promoter of certain tumor suppressor genes in the host, thereby causing gene silencing and participating in the occurrence of CC [17]. The quantitative detection of DNA methylation of related genes can act as a new means for CC screening, which has important clinical value for monitoring high-risk populations [18–23].
FAM19A4 gene is a member of the TAFA family, which is low in most normal tissues and slightly higher in brain tissues, and is generally considered to be involved in immune response as immunomodulators, with the function of preventing pathogen invasion [24, 25]. It was found that the promoter of FAM19A4 gene had a high degree of abnormal methylation in cervical precancerous lesions and CC, and the methylation detection of FAM19A4 gene promoter had a higher specificity than cytology examination and HPV testing in CC screening [26]. Luttmer et al. [27] found that the sensitivity of FAM19A4 methylation assay, cytology examination and HPV16/18-genotyping testing for the detection of cervical lesion (grade ≥ CIN 3) was 75.6%, 85.6% and 72.2%, respectively, and the specificity was 71.1%, 49.8% and 57.4%, respectively. According to another study, patients with a positive FAM19A4 methylation test could be directly referred for colposcopy, while a negative test could predict a transient HPV infection and a low risk of CC [28]. In our study, methylation levels of FAM19A4 gene promoter had a higher sensitivity and specificity for the diagnosis of HSIL + CC, at 84.6% and 96.1%, respectively. The sensitivity and specificity of further differentiating HSIL from CC were 68.1% and 66.9%, respectively.
EPB41L3 (erythrocyte membrane protein band 4.1 like 3), also known as 4.1B or DAI-1, is an important membrane skeleton protein belonging to the protein 4.1 family. As a candidate tumor suppressor gene, EPB41L3 inhibits cell overgrowth by inducing cell apoptosis and arresting the cell cycle [29]. It was found that the expression of EPB41L3 in various malignant tumors such as CC was significantly down-regulated compared with that in normal tissues, and the aberrant methylation of its promoter played an important role in the regulation of the expression of EPB41L3 genes [30]. Boers et al. [31] showed that the sensitivity and specificity of EPB41L3 promoter methylation for the screening of CIN3 cervical precancerous lesions reached 79% and 88%, respectively, with good shunt guidance significance for HPV-positive patients. In our study, methylation levels of EPB41L3 gene promoter had a higher sensitivity and specificity for the prediction of HSIL + CC, at 86.3% and 95.3%, respectively. The sensitivity and specificity of further differentiating HSIL from CC were 54.9% and 81.8%, respectively.
PAX1 has been revealed to be a key tumor suppressor gene that regulates cell differentiation and maturation. In cervical cells, once the PAX1 gene promoter is methylated, it will cause the gene to be silenced or inactivated, thus losing the function of inhibiting tumor growth and resulting in CC, which has been widely recognized and studied internationally [32]. In 2010, Lai's research team [33] found that PAX1 methylation assay has a sensitivity of 78% and a specificity of 91% for CIN3 + cervical precancer. In 2014, Kan's study [34] confirmed that methylation detection of PAX1 has an 86% sensitivity and 85% specificity for CIN3 + cervical precancer. In another study, Yang L et al. [35] found that in non-HPV16/18 hrHPV-positive populations, PAX1 methylation detection had a sensitivity and specificity of 86.2% and 75.5%, respectively, for CIN2 cervical precancerous lesions, while CIN3 cervical precancerous lesions had a sensitivity and specificity of 90% and 69.3%, respectively, which were significantly better than cytology detection. According to the latest research, hypermethylation of PAX1 was positively associated with high HPV viral load, especially HPV16/18, and PAX1 methylation had a specificity of 86.6% for detecting CIN2+ [36]. From our experimental data, the methylation detection of gene PAX1 also had high sensitivity and specificity for the diagnosis of HSIL + CC, which is 88.0% and 97.7%, respectively. The sensitivity and specificity of further differentiating HSIL from CC were 81.4% and 58.7%, respectively.
Meanwhile, there were also some limitations in this study. First, due to the fact that there was no difference in methylation degree of the three genes in the control cases and the LSIL cases, other screening indicators need to be further explored and confirmed for cervical lesions below HSIL. Second, on the basis that both HSIL and CC cases had high methylation levels of FAM19A4, EPB41L3 and PAX1 and high rates of hrHPV16/18 infection, further studies are needed to investigate the relationship between methylation alterations and hrHPV16/18 viral load. Last but not least, further basic researches are needed to explore the mechanism of these tumor suppressor genes with abnormal methylation status in the pathogenesis of CC, so as to provide more effective and precise therapies and interventions.