The hormonal derangement and other pathophysiology of endometriosis are partly due to epigenetic alterations in specific genes. Similar to the cancer cell, the progenitor endometriotic cell has to undergo similar hardships to establish a successful niche. This phenotypic change is mediated in part by deregulated gene expression, possibly as a result of epigenetic gene modification.

The epigenome in endometriosis is modified at the DNA, histone, and miRNA levels. In 2005, Wu et al. first demonstrated promoter hypermethylation of the homeobox gene, HOXA10, in eutopic endometrial tissues from women with endometriosis [1]. HOXA10 has functions in uterine physiology, being elevated in endometrial tissues at the mid-secretory phase of the menstrual cycle, coincident with the possible implantation of a fertilized ovum. Functionally, HOXA10 regulates progesterone receptor cofactors (e.g., KLP9) to mediate endometrial responsiveness to progesterone. Thus, decreased expression of HOXA10 in endometrial tissues from women with endometriosis could partly account for the associated infertility (lack of implantation). In support of endometriosis being a disease of epigenetic alteration is the overexpression of DNA methyltransferases (DNMT1, DNMT3A, and DNMT3B), in endometriotic tissues, which could mediate promoter hypermethylation of multiple genes. Thus, hypermethylation of progesterone receptor isoform B (PR-B) in endometriotic tissues is associated with progesterone resistance; reduced E-cadherin expression due to CDH1 promoter hypermethylation favors detachment and invasiveness. As a disease addicted to hormonal influence, altered expression of steroidogenic genes underlies the pathology of endometriosis. The expressions of steriodogenic genes are repressed in normal endometrial tissues partly due to promoter hypermethylation of steriodogenic factor-1 (SF-1), a transcription factor responsible for their expression. In contrast, endometriotic stromal cells have promoter hypomethylation of SF-1 leading to overexpression of these steriodogenic genes involved in estrogen biosynthesis. Finally, the overexpression of ERβ in endometriotic tissues is due to unregulated promoter hypomethylation.

Endometriosis may also be a disease of awry immunology at the molecular level. First, IL-6 and some other cytokines are elevated in endometriotic tissues. Second, epidemiologic evidence indicates the association of endometriosis with other autoimmune disorders. There are increased rates of fibromyalgia, autoimmune thyroiditis, hypothyroidism, multiple sclerosis, alopecia universalis, allergies, asthma, and chronic fatigue syndrome among women with endometriosis. Similarly, SNPs associated with rheumatoid arthritis (CCL21 rs2812378 and HLA-DRB1 rs660895) are associated with endometriosis.

Autoantibodies are also observed in tissues and circulation of women with endometriosis. Autoantibodies against laminin-1 are found in a vast majority (~90 %) of lesions from infertile-associated endometriosis. Consequently, elevated levels of anti-laminin-1 antibodies are in body fluids (serum and peritoneal fluid) of women with endometriosis and this could serve as a diagnostic biomarker. Autoantibodies against carbonic anhydrase are common in autoimmune diseases such as rheumatoid arthritis and systemic lupus erythematosus. In infertile women with endometriosis, circulating anti-carbonic anhydrase antibodies are equally present. Other autoantibodies implicated in endometriosis are those against endometrial transferrin and α-2-Heremans Schmidt glycoprotein.

A feature of endometriotic tissues that mimics some solid tumors is the high levels of vascularization. This is a necessary requirement for the endometriotic cell to sustain its existence as it proliferates and grows into a solid mass in its new environment. While the molecular mechanisms involved in new blood vessel formation in endometriotic lesions are poorly understood, hormonal signaling and immune response have been implicated. Estrogen signaling is involved in neovascularization, while inflammatory and other immune cells such as macrophages and dendritic cells contribute to the pro-angiogenic endometrial tissue environment. Additionally, angiogenic factors including VEGF, tissue factor, and its receptors are upregulated in endometriotic lesions.

Another feature of endometriosis is oxidative stress, as is common in solid tumors. Elevated free radicals in association with decreased antioxidant mechanisms play a role in endometriosis. Consistently, biomarkers of oxidative stress are elevated in sera from women with endometriosis compared to those without. Similarly, there are lower levels of the antioxidant, vitamin E, and its extracellular binding protein, afamin, in peritoneal fluid from women with endometriosis.

The Warburg phenomenon of aerobic glycolysis is also a feature of endometriosis. TGFβ1 signaling induces transcription of glycolytic gene (HIF-1α, PDK1, LDHA, and SLC2A1) expression accompanied by elevated lactate in peritoneal fluid and endometriotic tissues, and these levels are significantly higher than in eutopic endometrium from women without endometriosis.

Proteomic profiling of samples to uncover diagnostic signatures of endometriosis has demonstrated potential. Jing et al. used SELDI-TOF MS to identify two serum proteins peaks that were associated with endometriosis [6]. As diagnostic biomarkers of endometriosis, these achieved a sensitivity of 86.67 % and specificity of 96.7 %. Importantly, these peaks declined to levels in control women following surgery. Zheng and colleagues uncovered three peptide peaks that were used in a diagnostic model to detect endometriosis [7]. This peptide-peak model achieved a sensitivity of 91.4 % and specificity of 95 % when applied to women with (n = 126) and without (n = 120) endometriosis. In an independent validation set, this model performed at a similarly high sensitivity and specificity of 89.3 % and 90 %, respectively, in detecting endometriosis. Another study using SELDI-TOF MS uncovered five peptide peaks that achieved a sensitivity of 88% and specificity of 84 % in stratifying women with and without endometriosis [8]. Thirteen and twelve peptide peaks were found deregulated in women with endometriosis and adenomyosis, respectively, when compared to healthy controls. Five common peaks were decreased in both patient groups, and the two conditions could not be separated based on these serum peptide peak profiles [9].

Currently, the only circulating biomarker used by some centers to help detect endometriosis is CA125. Circulating CA125 is well studied as a diagnostic biomarker of endometriosis. It has demonstrated clinical utility in endometriosis management, but the sensitivity limits its general recommendation as a screening biomarker. A meta-analytical study revealed a sensitivity of 50 % at a specificity of 72 % for all stages of endometriosis, with a slight increased performance in women with late stage III/IV disease (sensitivity of 60 % and specificity of 80 %) [10]. Other members of the CA family, especially CA19-9 and CA15-3, are significantly elevated in circulation of women with endometriosis. In the analysis by Tuten et al., CA125 achieved a better AUROCC of 0.928 for the detection of endometriosis; however, levels of CA19-9 and copeptin were significantly much higher in stage III/IV than stage I/II disease patients [11]. Copeptin levels correlated with disease burden in terms of stage and size of endometriosis.

Aside from CA, many other glycoproteins are evaluated singly as potential diagnostic biomarkers. These include glycodelin (sICAM-1), follistatin, Zn-α2-glycoprotein, and several others. Serum levels of glycodelin failed to delineate adolescent women with endometriosis from those without [12]. However, in women with endometrioma, glycodelin was elevated in patients compared to controls and achieved a diagnostic sensitivity and specificity of 82.1 % and 78.4 %, respectively [13]. The levels of circulating follistatin, an inhibitor of activin, were elevated in women with endometriosis [14], but this data could not be reproduced [15]. In a pilot study using mass spectrometry, Zn- α2-glycoprotein was identified as differentially expressed between cases and controls. An ELISA assay was developed for this biomarker and confirmed the significant differential expression in women with and without endometriosis (p = 0.019). When applied to samples from 120 cases and controls (n = 20), this assay could detect endometriosis at a sensitivity of 69.4 % and specificity of 100 % [16]. A panel of biomarkers including glycodelin, annexin V, VEGF, and CA125 achieved a sensitivity of 74–94 % and specificity of 55–75 % in a training set [17].

As a disease of inflammation, circulating levels of immunologic mediators have been explored as biomarkers of endometriosis. Cytokines, chemokines, and cells of the immune system have all been explored as diagnostic biomarkers with mixed outcomes. With the exception of RANTES, IL-4, IL-8, MCP-1, TNF-α, YKL-40, and copeptin, many immunologic circulating biomarkers have demonstrated no discrimination between women with and without endometriosis. In adolescent women with endometriosis, IL-4 is significantly elevated in their sera [18]. Tuten et al. performed a pilot study of the circulating levels of the inflammatory mediator, copeptin, between cases and controls [11]. Levels were significantly increased in cases compared to controls. As a potential circulating biomarker of endometriosis, copeptin performed at a sensitivity and specificity of 65 % and 58.3 %, respectively, when using a cutoff value of 251.18 pg/ml. Another inflammatory biomarker identified by Tuten et al. is YKL-40, which is significantly elevated in women with and without endometriosis [19]. In a comprehensive review by May et al., significant increases in circulating levels of RANTES (concordant in 75 % of the studies), MCP-1 (concordant in 50 % of the studies), and IL-8 (concordant in 46.1 % of the studies) were uncovered in women with endometriosis, and may have potential as early detection biomarkers, especially if used in a panel [20]. A panel of three plasma biomarkers including IL-8, TNF-α, and CA125 impressively achieved a sensitivity and specificity of 89.7% and 71.1%, respectively, in differentiating between women with (n = 201) and without (n = 93) endometriosis [21].