Epigenetic changes were defined as the changes at the protein level rather than in the DNA sequence. A British biologist Conrad Waddington in 1950s was the first time to discover the epigenetics. Conrad Waddington said that “some genetic alteration doesn’t cause new phenotype”. The differences between genetics and epigenetic is that the genetic processes are irreversible but the epigenetic is a reversible process (Kunysz et al. 2021). These changes lead to several diseases; including bone and skin with autoimmune diseases, neurodegenerative diseases as schizophrenia and cancer. It can be inherited from the daughter cells during the division (Esteller 2008; Josep and Maria 2022). The genome of an organism can be altered by many chemical compounds which can lead to gene expression alteration; These are called the “epigenome”. One thing that can lead to epigenetic changes is internal or external stress such as the oxidative stress in the cells which affect the organism’s genotype and phenotype (Allis and Jenuwein 2016; Rothstein et al. 2017).

Multiple forms of epigenetic changes like: DNA methylation, histone modifications, chromatin remodeling and microRNAs, that’s have a regulation function (Mikkelsen et al. 2007; Diane et al. 2011). All these mechanisms play a role in the regulation of genes as well as multiple biological functions that’s linked to several diseases (Skvortsova 2018).

Conventional therapies are ineffective for treatment the patients with epigenetic causes of disease. Because of that scientists can find personalized medicine or what is called “patient-specific medicine”. Cancer develops through many genetic accumulation changes, as point mutations, gene amplifications and genes deletions which are responsible for stimulation of “oncogenes” and inhibition of “tumor suppressor genes” (Peramaiyan et al. 2022). But on the other side, some studies mention that the cancer cells are “addicts oncogenes maintenance of the malignant phenotype” (Weinstein and Joe 2008). Due to the increasing the studies that demonstrate the concept of “oncogene addiction” by showing the efficacy of the antibodies and drugs that target the human cancer like EGFR mutation indicates sensitivity gefitinib (Lujambio and Lowe 2012). Now, how is the response to chemotherapy predicted? The answer is by knowing specifically the data about the gene expression, and basically the cancer cell expression gives a relationship between the gene expression inside the cells and the cell response to chemotherapy (Paster et al. 2021).

Epigenetic changes in term of “DNA methylation” are one of the hallmarks of the cancers that are responsible for inhibition a gene expression by using enzyme called DNA methyltransferases (DNMTs) and the processes reversed by using demethylation enzyme. The sensitivity to chemotherapeutic drug can be predicted by know specifically what the genetic alteration in the cancer is. (Orlando et al. 2012).

Several drugs can be developed just by understanding the role of epigenetic changes in the cells. Two DNMT inhibitors 5-azacytidine and decitabine, by the US FDA approval for the treatment of myelodysplastic syndromes (MDS) and hematologic malignancies (Kumer et al. 2020). Drug responses affected by DNA methylation that coding enzymes drug metabolism (EMD), drug transporters and drug targets (Cossio et al. 2020).

Another thing that affects gene expression is single Nucleotide Polymorphisms (SNPs) which are located adjacent to DNA methylation sites (Shoemaker et al. 2010). Both these mechanisms can lead to inter-individual differences in drug response. Here are multiple genes involved in methylation processes; in DNA repair and maintenance of genome integrity (as, MGMT, hMLH1, WRN, and FANCF), and genes checkpoint of the cell cycle (as RFHC and 14-3-3 σ, CDK10, and p73), all of them affect the response to chemotherapeutic agents (Castilho et al. 2017).

In this review, we focus on the consequences of epigenetic changes in term of DNA methylation in measuring a therapeutic effectiveness of the chemotherapeutic drugs in cancer treatment by giving a thiopurine methyltransferase as a model system for epigenetic and DNA methylation.

Pharmacogenomics is defined as the studying of the drug response in whole genome (RNA, DNA). It contributes with multiple factors correlated with drug metabolism, drug transporter, receptors and drug metabolizing enzymes with a deviation affect a responsiveness of drugs in different disease and this is called polymorphisms; All these things regulated by epigenetic mechanism (Pirmohamed 2011).

One of the applications of Pharmacogenomics is to determine a particular patient in the exact concentration and at the right time and this is called “precision medicine”. In the beginning, “one drug for all” arises but after studying the epigenetic and understanding what this term exactly means the second idea arises which is “patient specific dose”. Different factors contribute to epigenetic alteration like, diet, age, body weight, sex, genetic behavior, infections, co-medications, and organ function, all these important in drug therapy and disease treatment. However, new techniques used to determine that as medical computer science which focus on identifying disease targeted therapy.

Two terms used to determine drug response and drug variability, pharmacokinetics (PK) and pharmacodynamics (PD). Pharmacokinetics basically determines the dose and pharmacodynamics study effectiveness and toxicity (Rajasri 2017).

The major enzyme responsible for the metabolizing of drug is cytochrome CYP450, variation in this enzyme lead to different drug response either by increase efficient state or toxicity state. CYP450 has multiple polymorphisms, it’s about 38 families and different coding form (Shimizu and Kawano 2022). By using sensitive techniques like microarray, types of CYP450 genes can be determined whether CYP450 genes, CYP2D6, CYP2C19 etc. These genes affect the metabolism of 25% of all drugs (Megaraj et al. 2014).

Furthermore, multiple polymorphisms were detected within drug transporter and drug receptor. Mutations in transporters or receptors lead to different metabolism profiles, like the mutation within tyrosine kinases receptor encoded different cancers and neurodegenerative aberration. Another example of that is increasing the expression of ErbB2 (v-erb-b2 viral oncogene homolog 2 avian erythroblast leukemia) in breast cancer with trastuzumab treatment, the BCR / ABL fusion protein is very sensitive to imatinib in leukemia treatment and reactivating the mutations of the epidermal growth factor receptor (EGFR) shown to be correlated with gefitinib with different response (Corces et al. 2018).

Genotyping and phenotyping application are important to determine a disease-mutations “polymorphisms” and disease state. mRNA is a transcription product, genetic variation affects this product, also it’s affected splicing machinery, some mutation located in exon region and other located in intronic region or splicing site. Alternative splicing contributes about 40–60% of mammalian genome. Scientists studied gene expression at mRNA level, and a result of that was catechol-O-methyltransferase gene (COMT) which is a gene that higher found in schizophrenia patients, because this gene related into the autopsy brain tissue of patient (Gao et al. 2020).

Specific epigenetic biomarkers are used to classify cancer in histological parts of the hospital by using either tissue or cells. Also, by using microarray multiple cancer types can be detected whether breast, colon or any other type and their stages also can be detected. In microarray, cDNA, fluorescent labeling was used to determine specific stages for each type of cancer. The principle of microarray was based on analyzing mRNA expression (Lo et al. 2010). The most sample type used in cancer diagnosis is serum. For example, one of the epigenetic biomarkers in prostate cancer is hypermethylation of glutathione S-transferase gene (GSTP1) which is used to determine the cells if its benign or metastasis so, this is a clue for DNA methylation (Rodriguez and Esteller 2011). If GSTP1 higher in serum or urine that’s mean this biomarker become methylated and the cell get metastasis and vice a versa if GSTP1 level decreased in serum or urine that’s mean low level of methylation and the cells get benign, by controlling this pathway; by personalized medicine; benign cells get smaller (Richiardi et al. 2009; Xu et al. 2017).

New horizons about using monoclonal antibodies specific for each type of cancer and using specific inhibitors to inhibit some point in the cancer pathway; this can lead to improved cancer treatment. Different molecular targets and pathways like Aurora kinases, the FOXO FOXM1 axis and PI3K / mTOR signaling were contributed to human cancers. For example, the small molecule VX-680 shows an inhibitory effect and cause cell death in leukemic cells with a specific aurora expression profile by the Bax / Bcl-2 ratio to increase, what with a high aurora-A expression apoptosis acute in the myeloid leukemia induced (Yan and Liu 2013). In the same way, fork-head transcription factors (FOXO and FOXM1) a crucial play a major role in cell division, differentiation, angiogenesis, apoptosis, DNA repair and tissue homeostasis. As such, the FOXO FOXM1have a major role in drug resistance regulation and tumor- genesis (Gomes et al. 2013).

Inter-individual variation in drug-response-genes is very important to study drug response (toxicity or effectiveness). These differences are shown in ADME expression, drug carriers, drug targets and downstream signaling molecules. (Table 1).

Cytochrome P450 super-family play a role in phase I metabolism of approximately 75% drugs approved by FDA. Different studies have shown the robust role of epigenetic (DNA methylation) in the regulation of CYP1, CYP2 and CYP3 gene expression. CYP1A2; one enzyme belongs to CYP450 superfamilies. It’s contributed to metabolism of drugs, steroid, hormones, and other lipid synthesis. Another member of the CYP450 family is CYP1A2, which is involved in drug metabolism and cholesterol, steroids, and other lipids synthesis (Bjornsson et al. 2004).

Study done by Miyajima et al, showed that a strong relationship between methylation and CYP1A2 expression in liver. When methylation increases, mRNA expression of this enzyme decreased in liver and vises a versa in case DNA methylation level increases (Miyajima et al. 2009).

Another enzyme from CYP450 families is CYP1B1 called “estrogen metabolite”. It’s more potent to study its effect in female because this enzyme plays a role in breast cancer. It regulates 4-hydroxy estradiol formation. Recent studies done by De Montellano, whose said that the methylation pattern within CYP1B1 promoter affect binding of transcription factor (AhR / ARNT and SP-1). Another type of cancer related to this enzyme is prostate cancer. When methylation status increases for this enzyme, level of expression becomes lower or decreased and cancer will develop (De Montellano 2013).

In general, all CYP450 families are regulated by epigenetic alteration (DNA methylation) such as CYP2A6, CYP2C19, CYP2D6, CYP2E1, CYP2J2, CYP2R1, CYP2S1 and CYP2W1. Remember that acetylation processes or demethylation mechanisms are responsible for increased expression of these genes. One of the largest CYP450 families is CYP3A that’s making about 70% of drug metabolizing in liver. Methylation is inhibited by small molecules of DNMT inhibitor, it’s a sensitive mechanism affected by CYP3 expression whether CYP3A4, CYP3A5 or CYP3A7 in HepG2 cells. In vivo studies showed that the CpG hot spot regions are highly different within individual and within fatal, adult tissue. Methylation status is different in adults than fatal; high methylation status in fatal liver indicates low CYP3A4 expression. Drug response regulated by the methylation status of CYP3A, low level of DNA methylation required to get higher response. For this idea to complete, small DNMT inhibitors can be used in disease treatment and increase drug effectiveness.

As mentioned before, epigenetic affected by external factors like nutrition intake and diet like ingestion of vitamin D. One of the CYP450 enzymes that are responsible for vitamin D metabolism is CYP24A1. This enzyme is considered as “tissue specific”. According to Novakovic et al studies that provided a clue for methylation relationship to CYP24A1 expression in human placenta samples that’s related to gestation abnormalities. As such, one marker to determine inter-individual differences for calcitriol “active form of vitamin D3” is CYP24A1 that expressed on the endothelial cells. By using this enzyme, normal and tumor endothelial cells can be detected (Johnson et al. 2010).

One cause of DNA methylation is smoking. Smoking or occupational exposure are recognized as a major source of lung cancer. One of the compounds that are found within cigarette smoking is Polycyclic Aromatic Hydrocarbons (PAHs), which is an organic matter. This matter was considered as carcinogenic compound and it was used for inter-individual differences. Polymorphisms within the enzyme that metabolize PAHs are very important in studying drug response and effectiveness.

CYP1A1 (Cytochrome P4501A1) is a reactive HAP metabolite, that can play a role in starting of carcinogenesis by the formation of PAH-DNA bulky in adducts. From PAHs, CYP1A1 was formed, when PAHs level increased that’s indicate lung cancer and vice versa if PAHs level low in human lung. CYP1A1 contain multiple polymorphisms and according to these polymorphisms drugs was adjusted. Everyone has specific polymorphism, which means specific dose (Mittal et al. 2015). Here, one of the biological markers that can be used to determine toxic dose threshold in the tissue is PAH-DNA adducts. One type of tumor suppressor gene is TP5, mutation in this gene plus K- Ras oncogene was shown about 50% in non-small cell lung cancerous (NSCLC). Higher expression of PAH-DNA adducts in TP53, and K-Ras mutations were considered as a molecular marker for lung cancer.

As such, CYP1A1 is an enzyme which is regulated by specific enhancer and may alter gene expression. Enhancer of this enzyme contains specific region called xenobiotic response elements (XREs), located upstream of start site of transcription, this region considered as transcriptional control region. XREs binds with AHR complex (aryl hydrocarbon classical motifs receptor) which is a grouped of enhancer domain. Gene expression can be altered based on this thing, silencing states occur when enhancer is absent and in other hand, when AHR binds to enhancer CYP1A1 activated and the transcription will begin (Tekpli et al. 2012). In addition, DNA methylation here plays a role in regulating gene expression, the methylation of CpG islands leads to down regulate CYP1A1. Acetylation is a mechanism that enables AHR to XRE binding which is responsible for CYP1A1 activation and expression (Gomez and Ingelman-Sundberg 2009).

The conclusion from that; smoking alters methylation states and modifies the histone protein that surrounded the DNA, methylation alteration affects AHR binding to CYP1A1 enhancer that’s lead to higher expression shown in lung cancerous tissue (Androutsopoulos et al. 2009).

The transporter responsible either for efflux or influx of drugs across the cell. To show how DNA methylation affects drug metabolizing enzymes, epigenetic mechanisms must be investigated. All the individuals worldwide have a difference in drug response due to variability in either genes or enzyme. Different drug responses are due to different genes which are called pharmacogenetics that involved pharmacokinetics which plays a role in absorption, distribution, metabolism, and excretion (ADME) of the drugs. So, more than one factor affects the changes in drug and drug metabolizing. (Zhang et al. 2008).

Juliana et al., showed that 2 genes (CYP1B1, CYP3A4) have a direct relationship between methylation and the transcription process. For example, up regulation in CYP1B1 was explained by hypermethylation in the 5’-promoter end of this gene (1B1) and Pregnane X Receptor (PXR) genes. To date scientists have discovered more than 50 ADME-related genes that target epigenetic regulation. Also, these ADME genes were controlled by epigenetic mechanisms in both tumor and normal cells. This is developed by several research about tumor suppressor genes field. One example of anticancer drug cation transporter is SLC22A1 in hepatocellular carcinoma. Hepatocellular carcinoma is one type of cancer that occurs by genetic and epigenetic alteration that collected in regulatory genes leading to inhibit tumor suppressor genes and activate oncogenes. And because the environmental factor in addition to genome alteration can affect the epigenetic mechanism, deregulation of epigenome by environmental stresses such as: (hepatitis B and C virus, chronic alcohol intake, and aflatoxins) could disrupt the cellular processes and increase the rash of hepatocellular carcinoma. Juliana et al showed how the gene expression of solute carrier families (SLC) regulated by DNA methylation. SLC is called organic cation transporter genes SLC22A1, SLC22A2, SLC22A3 encoding OCT1, OCT2, OCT3 respectively. In the case of normal hepatocytes this SLC solute carrier family 22, member 1, that encodes for organic cation transport 1 (OCT1), it’s highly expressed due to nutrients, metabolite uptake. Also, this transporter could uptake drugs and some antineoplastic agents like imatinib, cisplatin, irinotecan and oxaliplatin. OCT1 transports these drugs and increase cancerous cells risk for these antineoplastic drugs. Methylation of OCT1 in hepatocellular carcinoma leads to inhibit its function of uptake some anticancer drugs. Because the potent role of OCT1 in increase efficiency of many anticancer drugs, SLC22A1 methylation may be used as epigenetic biomarker in disease diagnosis and drug response (Srijib et al. 2014; Falero-Perez et al. 2018).

Schaeffler et al., that exhibit the individuals with higher SLC22A1 methylation phenotype showed transport inhibition and chemoresistance, and vice versa in case of individuals with low methylation phenotype and respond to chemotherapy due to transporter activation. He suggests the DNA methylation of MIR193A promoter might be used as a molecular marker to detect how hepatocellular carcinoma response to 5-flourouracil (5-Fu). MIR193A promoter hypomethylation induced microRNA 193a-3p transcription that targets both serine/arginine rich splicing factor (SRSF2). This factor sensitizes hepatocellular carcinoma to 5-Fu chemotherapeutic drugs (Srijib et al. 2014).

Glutathione S-transferase P1 (GSTP1) is one of the most potent DME phase II that regulate drug metabolism of Oxaliplatin and Adriamycin. Mostly, GSTP1 promoter is highly regulated, because if this enzyme downregulated or hypermethylated this indicates prostate cancer. 5-azacytidine and decitabine GSTM1 and GSTP1are DNMT inhibitors that lead to reactivation of the GSTP1 promoter and its expression. Generally, GSTP1 can be used as epigenetic biomarkers to study the response of tissue for 5-azacytidine (Goering et al. 2012).

N-acetyltransferase 1 (NAT1) is a DME phase II which is more potent in the metabolism of drugs and other xenobiotics. NAT1 was observed, inside the tissue of breast cancer, to be methylated in 62.2% tamoxifen-resistant tumors, significantly greater than 33.8% shown in normal tissues proportion. In addition, in the case of tamoxifen therapy, NAT1 is seen to get a lower expression in comparison to normal cells. These studies showed that the NAT1 methylation can be subscribed to tamoxifen resistance, after addition studies will do (Levesque et al. 2019).

DNA methylation can alter drug sensitivity and it can change the drug target expression, also the downstream signaling molecules. Hypermethylation of some transcription factors can affect cancer development and metastasis. One example of that is Transcription factor AP-2 epsilon (TFAP2E) which belongs to AP-2 transcription factor family. DNA methylation of the TFAP2E causes low level of TFAP2E expression in benign cancer which leads to metastatic cancer. Dickkopf homolog 4 protein (DKK4) is one of the target proteins for TFAP2E, over expression of the gene coding DKK4 can be developed for fluorouracil resistance. Nowadays, several studies have seen that the TFAP2E methylation causes fluorouracil resistance due to DKK4 higher expression. Additionally, patients whose suffer from colorectal cancer showed TFAP2E hypermethylation (Ebert et al. 2012).

The best example of colorectal cancer causing is a hypermethylation of tumor suppressor genes (TSG) and transcription silencing. Hypermethylation and inhibition of TSG can be affected the responsiveness for drugs. Several studies in colorectal-cancer field show that patient whose have a hypermethylated epidermal growth factor receptor (EGFR) promoter, treated with both irinotecan and cetuximab exhibit a higher resistance, increase disease metastasis and shorter median overall survival (OS) (Scartozzi et al. 2011).

Furthermore, Camptothecin (CPT) is involved Glucocorticoid-induced protein-coding gene (DEXI) showed a resistance by apoptosis inhibition. So, inhibition of DEXI gene using small interference RNA (siRNA), a type of non-coding RNA which plays a role in gene regulation, decreased CPT-induced apoptosis. In comparison, reactivation of DEXI expression via 5-aza-2’-deoxycytidine increases CPT sensitivity. DEXI is hypermethylated in both colorectal and gastric cancer (49%, 31% patients respectively). Patients with colorectal cancer have a not good response and get worse after 5-Fluorouracil +CPT- 11 treatments. From that, DEXI was used as a molecular marker in disease prognosis after CPT-11-based chemotherapy (Miyaki et al. 2012).

One of the best examples of tumor suppressor genes is the breast cancer genes BRCA1 and BRCA2 which encoding for proteins responsible for DNA repair. A hypermethylation in BRCA1 promoter leads to loss BRCA1 expression, while a silencing mutation in these two genes leads to increased sensitivity to Poly-ADP ribose polymerase-inhibitors (Ibragimova and Cairns 2011).

One of the genes that control the cell division processes is mitotic checkpoint with fork head-associated and ring finger (CHFR) gene. Again, CHFR gene can be used as biomarker for gastric cancer and endometrial cancer prognosis by studying the methylation pattern (Hiraki et al. 2010).

Nowadays, evaluated hypermethylation within CpG hot spot region correlated to 35 mammalian cell lines from the National Cancer Institute (NCI) Drug Screening Panel (NCI-60 panel). Hypermethylation profile of some tumor suppressor genes (TIMP3, APC, and IGSF4) in the NCI panel-60 has been found to show a strong relationship with sensitivity for antimetabolites like fluorouracil (5-FU) (Duan and Maki 2016).

Abaan and his colleagues (Aban et al. 2013) determine a strong pattern between hypermethylation profile of P15, CDH (E-cadherin) and HIC (hypermethylated in cancer 1) gene in the outcome of traditional chemotherapy in myelodysplastic syndromes high risk (MDS) and acute myelogenous leukemia (Abaan et al. 2013).

To date, pharmacogenomics has two main approaches: candidate gene approach and whole genome approach. Both resolve the genetic alteration like SNPs to determine the response for drugs. Besides variations within DNA sequences, heritable epigenetic is a non-genetic system even though they include have been involved in gene regulation which can be affected the drug response.

In the beginning, all research concentrates on DNA sequence studying rather than DNA methylation on the drug response. Nowadays, several studies arise to focus on epigenetic alteration. Epigenetic or methylation mechanism is a reversible process unlike genetic variants; it’s correlated with drug response alteration. In addition, genetic alteration like polymorphism changes the cancerous cell response for chemotherapy which can be predicted by different methods like microarrays and next generation sequencing. From that, analyzing promoter methylation status was very important thing before using any type of chemotherapy or drug treatment.

This article focuses on precision “personalized” medicine related to epigenetic or methylation status in the case of cancer treatment. Nowadays, there is no treatment without epigenetic analysis because epigenetics is considered as a basal level in the clinical trials of cancer treatment. Not all the patients have the same response to drug treatment; discontinuation or toxicity that developed is due to one-dose giving for all patients. By analyzing epigenetic factors, dose-specific patients can be determined, increase efficiency, and reduce adverse drug reactions and toxicity.

Although still some patients have a failure in drug therapy because until now low of information about epigenetic and genetic variants may developed. The term pharmacogenetics developed to include pharmacogenomics because “omics” is a term used generally to predict all the things in the genome whether DNA or RNA. By using this term, drug response detection becomes easier. As such, molecular biomarkers make this process easier. Proteomics must obtain an enormous potential to answer directly about the pharmacological issues such as transcription profiling. While inconsistency for the modification of proteins makes the application of proteomic markers for personalized medicine limited.

“Omics” term includes lipidomic, transcriptomics, and “Epigenomics” which play an important role in the development of personalized medicine, which covered both internal and external like food, environment conditions, etc.…, that produce SNPs affected gene regulation. However, pharmacogenetics and epigenetics until now has been the most studied in cancer treatment. Because there is a relationship or some information between chemotherapy and epigenetic or DNA methylation by selecting specific epigenetic markers to get a better therapy. Chemotherapy if it’s given to all patients may produce efficient in person and toxicity in another. But epigenetic biomarkers that determine the specific dose for each person will reduce the toxicity. So, represent epigenetic alteration completely personalized features and demonstrate specifically the reason for the collaboration of epigenetic personalized area improves medicine.

Overall, the final thing for pharmaco-epigenomics with personalized medicine is to be contemplated the cancer treatment. A dynamic movement between cancerous cells, normal cells, and immune system. One of the barriers in this article is using epigenetic and personalized medicine to treat not just cancer but also for heart failure and osteoarthritis disease. In general, information patient-proteome, epigenetic and drug metabolism can be integrated to adapt individual health care.