The complexity of the relation between a genotype and phenotype is increasing with the advancement of cell and molecular biology techniques. The phenotype is the ultimate product of not only the number of genes but also of the intricate regulatory networks that affect or are associated with gene expression. In order to completely understand the pathology of both malignant and non-malignant disorders, it is imperative to focus on various regulatory networks associated with gene expression. This would ultimately benefit in finding new candidate markers for initiation, development or progression of the disease and identifying novel targets for therapeutic intervention as well. Epigenetic signatures are the basis of this regulatory network and methylation of CpG dinucleotides constitutes an important mechanism of gene silencing.
The mechanisms which contribute to progression of CML disease and drug response vary to a considerable extent and have not been clearly understood. The various events that have, till now, been found as culprits for the progression of CML to advanced clinical stages and drug response may be categorized at cellular and molecular levels. The culprits at cellular level include increased proliferation, decreased apoptosis, differentiation halt, abnormal immune surveillance while activation of oncogenes, tumor suppressor gene inactivation, genomic instability, impaired DNA repair mechanisms among others are the molecular culprits (25). The control of most of the above cited events can be attributed to changes in the genes that are at the heart of that particular event. Apoptosis, differentiation, DNA repair for example are controlled by the activity of genes related to these processes and among the various mechanisms, DNA methylation in the promoter regions of a gene is one of the important processes that controls gene expression. DNA hyper and hypomethylation are respectively associated with decreased and ectopic expression of the genes. Moreover, DNA methylation at CpG dinucleotides could also influence differential promoter usage influencing gene expression patterns (26).
In this study, we report promoter CpG hydroxymethylation status of various genes including cell cycle regulating genes, apoptosis related genes and cytokine signalling genes that act as the drivers and controlling arms of most of the processes cited above as mechanisms of CML disease progression and drug response. To find the association of methylation status of the genes with CML disease progression and drug response, we analysed the methylation differences among CML patients in different clinical stages and among age and gender matched healthy controls. It was found that CML patients possessed significant hypermethylation in all the genes studied, in comparison to healthy control subjects. Moreover, the proportion of CML patients with hypermethylation of promoter CpG dinucleotides of cell cycle regulating and apoptosis genes was significantly more in advanced disease (AP and BC) stages in comparison to early CML (CP) disease subjects. In addition, proportion of patients with promoter hypermethylation of cytokine signalling gene (SOCS1) was also found to be more in advanced CML disease compared to early CML disease, however, the differences were not statistically significant. These findings of our current study confirm and extend the reports of previous studies (3, 27–29). Methylation of cell cycle regulating genes like p16INK4A has been found to be associated with progression of CML disease and p16INK4A promoter hypermethylation is reported to be associated with late stage CML disease in other studies (29, 30). Moreover, progression to lymphoid blast crisis has been found to be associated with homozygous deletions of p16INK4A gene (30, 31). RASSF1 promoter methylation has been seen in CML-derived erythroleukaemia K562 cell line but not in CML patients at different clinical stages (32). However, this is not in accordance to our study, we report that RASSF1 methylation is associated with CML disease progression based on the finding that proportion of patients with RASSF1 methylation in advanced AP and BC CML disease was more than that of CP disease. This contradiction in our results to those of Avramouli A et al, 2009, might be because of smaller number of patients (n = 31) studied (32). One of the frequently altered cell cycle regulating genes is p14ARF which has been reported to be inactivated through various mechanisms viz, mutations, deletions and DNA methylation in variety of malignancies of diverse origin (33). p16INK4A and p14ARF inactivation through promoter methylation are reported to be important events associated with accelerated phase of CML disease (34). However, the results need to be validated in a large cohort of CML patients in all the three clinical stages since the total number of subjects in which the reports have been investigated by E Nagy et al, 2003, was too small (n = 30). In this study, the same results have been replicated in comparatively large number of subjects. Further, we have previously found that methylation of p16INK4A gene is one of the primary events in CML disease progression (35). The epigenetic changes of apoptosis related genes are reported to be associated with progression of both solid tumors and hematologic malignancies as well (36). Promoter methylation of DAPK1, for example, is a characteristic feature of breast cancer (37). In this study, the promoter methylation of apoptosis related gene DAPK1 was found to be related to accelerated phase and blast crisis. However, it is reported that promoter methylation of RIZ1, another apoptosis related gene, is not a characteristic feature of advanced CML disease which is in contrast to our findings in this study which could again be attributed to the smaller number of subjects included in the previous study (27). RIZ1 gene inactivation during blast crisis occurs through epigenetic silencing and has been suggested as a predictive marker for imatinib resistance and CML disease progression (38). Reduced expression of RIZ1 and DAPK1 due to promoter hypermethylation has been reported in other malignancies as well, such as cervical cancer/ cervical neoplasia (39, 40), thyroid tumorigenesis (41), stomach carcinogenesis (42), cervical cancer (39), lung cancer patients(43–45). Therefore, the above discussion of promoter methylation and disease progression of CML to advanced phases supports the idea of considering the use of epigenetic drugs along with tyrosine kinase inhibitor (TKI) therapy. This may help a significant number of CML patients in better management of the disease.
Although, in addition to constitutively active tyrosine kinase; BCR/ABL1, the root cause of CML pathogenesis, a considerable amount of factors come into play when one talks of CML progression, prognosis and drug response. During the recent couple of decades; we have witnessed a huge surge for the identification of mechanisms and factors that decide patients’ response to TKI therapy. A variety of factors including gene amplification, additional chromosomal aberrations, point mutations, epigenetic changes, to name a few, have been cited as mechanisms underlying drug response in CML disease. These factors might help in defining the outcome of therapy and decide the treatment strategy of a patient; however each of these factors and mechanisms need to be extensively studied and validated by conducting further studies so that they may help in predicting drug response and prognosis among patients with CML disease. In this study, we evaluated hydroxymethylation status at promoter CpG dinucleotides of six genes in concert with imatinib response. It was observed that methylation at promoter CpG dinucleotide regions of cell cycle regulating genes including RASSF1, p16INK4A and p14ARF and apoptosis related genes DAPK1 and RIZ-1 are characteristics of poor respondents of imatinib drug. We found significant association of increased methylation patterns of the above cited genes with poor imatinib response as judged by the proportion of patients with hypermethylation of the genes to be more in warning and failure groups as compared to optimal response group. The identification of methylation of apoptosis related DAPK1 and RIZ1 genes in concert with drug response and prognosis is utmost important. We observed that DAPK1 and RIZ1 promoter methylation is significantly associated with poor imatinib response in CML patients. Methylation of DAPK1 is reported in other cancers like gastric cancer (46–50). There are contradictory reports regarding methylation of DAPK1 in concert with drug response and prognosis for example no correlation of DAPK1 methylation was found with prognosis in ovarian cancer (51) and non small cell lung cancer(52). However, there are reports suggesting a strong association of DAPK1 hypermethylation with poor disease specific survival and therapy response (53). Hypermethylation of RIZ1 has been reported for its inactivation and silencing (54). In one of the studies from our lab, we have reported that RIZ1 promoter methylation increases progressively in CML disease in advanced phases and that its expression may be a cause, among others, for poor drug response in CML patients on imatinib treatment (55). In another study, we have reported that decrease in RIZ1 gene is responsible for increased IGF1 expression in K562 CML blast crisis cell line and in advanced disease CML patients (56). Yet another report from our lab has observed that inactivation of RIZ1 gene by insertion/deletion polymorphism and promoter hypermethylation is associated with CML disease progression and imatinib resistance (57). In the present study, we observed that promoter hypermethylation of RIZ1 is significantly more frequent in advanced CML disease compared to early disease and that RIZ1 hypermethylation at promoter CpG dinucleotides is a characteristic feature of poor imatinib respondents. But we could not find any statistical difference in proportion of patients having hyper and hypomethylation of RIZ1 gene promoter in relation to overall survival. RIZ1 reduced expression has been reported in other haematological malignancies (58). In adult acute lymphoblastic leukaemia, reduced RIZ1 gene expression has been found to be associated with leukemogenesis. Inactivation of RIZ1 is a characteristic feature of T-ALL (58). However, further studies are required for elucidation of the inactivation mode of RIZ1 and its intricate role in development and progression of different types of malignancies and drug response. RASSF1A promoter methylation is speculated to influence drug sensitivity of tumors like non small cell lung carcinoma (59), esophageal squamous carcinoma tumorigenesis (60), breast cancer patients (61). In addition, there are reports suggesting utilization of RASSF1A methylation for monitoring response to adjuvant therapy in the clinic as RASSF1A methylation depletion has been found to be linked with good response to adjuvant regimens(62). Apparent methylation patterns of RASSF1A gene is reported as biomarker of lung cancer diagnosis, treatment and prognosis(63). RASSF1A and its epigenetics have gained much attention due to its increasing occurrence in diverse cancer types. Promoter methylation of RASSF1A, which is preceded by histone modifications, has been reported as an epigenetic candidate marker in a variety of cancers with diverse origin. There are reports which suggest that its epigenetic abrogation may promote expression of RASSF1C which is a putative oncogenic isoform (64). However, some studies discuss RASSF1A methylation in non small cell lung carcinoma and associate it with good response (65). Therefore, a better understanding of the significance of RASSF1A methylation pattern in various cancer types becomes imperative for its clinical and drug behaviour role. Our results indicate that RASSF1A hypermethylation characterizes poor imatinib response and poor survival of CML patients treated with imatinib. p16INK4a expression has been found to be associated with poor prognosis in ER-positive, PR-negative and HER2- negative tumors and hence reported as a predictive prognostic indicator to predict treatment response for hormonal therapy (66). Hypermethylation of p16INK4A and p14ARF has been suggested to possess predictive properties for a variety of clinicopathological outcomes. Moreover, p14ARF and p16INK4A gene inactivation has been reported in development of colon carcinoma (67), cervical cancer (68), hematological malignancies(69). It is suggested that methylation profile of p14ARF and p16INK4A might be playing an important role in distinct subsets of colon carcinoma(70). The observation from our present study that hypermethylation of these two genes accumulate in patients with poor drug response and poor overall survival and the reports from previous studies discussed above indicate that methylation status of p16INK4A and p14ARF can definitely be used as promising candidate predictors of response to therapy and clinical outcome.
Suppressor of cytokine signaling1 (SOCS1) gene has been recognised as tumor suppressor gene and found to be related to lymphatic metastasis and disease progression of liver cancer (71). Silencing of SOCS1 by methylation is reported in hepatocellular carcinoma and other tumors like cervical cancer (72), hepatoblastoma(73), esophageal squamous cancers(74), melanoma, squamous cell carcinoma of the head and neck, pancreatic carcinoma and breast and ovarian cancer (75). SOCS1 gene methylation has been reported to cause gene silencing which is accompanied by downstream JAK/STAT signalling and promotion of cell proliferation in acute myeloid leukaemia (76). In this study, although we found a higher proportion of patients with SOCS1 methylation in advanced disease stages and poor imatinib respondents, but the difference was not statistically significant. Our results are slightly different from the previous study by Ta Chih Liu et al (2003) (77) which reports that SOCS1 gene methylation plays an important role in the pathogenesis of CML disease progression. This discrepancy might be attributed to the environmental effects and ethnicity of the cases being studied. The methylation status of the DNA and histone proteins depends on ethnicity of population (78). However, we did observe that hydroxyrmethylation of SOCS1 gene was significantly associated with poor overall survival of CML patients on imatinib therapy. Therefore, we suggest that there is need of more studies to conduct for studying the exact role of SOCS1 methylation and expression patterns that will provide more detailed insight of the role of SOCS1 methylation in CML disease progression and imatinib response. The major limitation of our study was that we did not characterize the methylation pattern of the genes quantitatively. Another limitation of our study was that we were not able to include homogenous number of patients in each clinical stage of the disease.
Based on the present study and from the above discussion, it may be suggested that hydroxymethylation of cell cycle regulating and apoptosis related genes are the main characteristics of a variety of malignancies including haematological ones. Therefore, more accurate and site specific methylation pattern of genomic loci should be focussed in future studies. These studies would benefit to identify the methylation patterns of the genes involved in cancer development, progression and prognosis and illustrate the feasibility of epigenome target therapy.