Effect of Single Nucleotide Polymorphism on Chemotherapeutic Agents Efficacy and Safety (2023) - Mustansiriyah University PDF
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Mustansiriyah University
2023
Safa Salman Khazaal Mahdi
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Summary
This project investigates the effects of single nucleotide polymorphisms (SNPs) on the efficacy and safety of chemotherapeutic agents. It explores the impact of SNPs on the metabolism and transport of drugs like fluoropyrimidines, platinum derivatives, and taxanes. The study was conducted at Mustansiriyah University in Iraq during 2023.
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Republic of Iraq Ministry of Higher Education and Scientific Research Effect of Single Nucleotide Polymorphism on Chemotherapeutic Agents Efficacy and Safety A Project Submitted...
Republic of Iraq Ministry of Higher Education and Scientific Research Effect of Single Nucleotide Polymorphism on Chemotherapeutic Agents Efficacy and Safety A Project Submitted to College Of Pharmacy/Mustansiriyah University , Department of Pharmacology & Toxicology in Partial Fulfillment for the B.Sc.Pharmacy By : Safa Salman Khazaal Mahdi Supervised by : Professor Dr. Bahir Abdul Razzaq Ph.D. Pharmacology 2023 A.D 1444 A.H. 2 Acknowledgement : I would like to express my sincere thanks and appreciation to my Supervisor, Prof.Dr. Bahir Abdulrazzaq for his guidance, moral and scientific support before and throughout the preparation of this thesis. My deep gratitude to Dean of the College of Pharmacy/ Mustansiriyah University, Prof.Dr. Monther Faisal Alamery. Special thanks to Dean Assistant for scientific affairs , Assistant Prof. Dr. Inaam Samih Arif Best greetings and thanks to all Professors and staffs of Department of Pharmacology & Toxicology in our college for their spirit of cooperation and teamwork. I Dedication : اىل هي متٌث رات ٌْم اى جشاًً يف كلٍة الصٍذلَ ، ً هي بزلث الغايل ّالٌفٍس الجلً ّ ،الحً امتىن اى اكْى دّها عٌذ حسي ظٌِا بً ، اىل ّالذجً العضٌضٍ .. اىل هصذس العلن الزي ال ٌٌضب ّهثلً االعلى يف ّ الفاسهاكْلْجً ،هي علوًٌ الكثري خالل سحلحً الذساسٍَ ، ّالزي ميلؤًً الفخش كًًْ جحلوزت على ٌذٍ ، اسحاري ّهششف حبثً العضٌض " أ.د.باُش عبذ الشصاق " لكن اُذي حبث ختشجً ُزا ... II Supervisor Certificate : I certify that this project , entitled “Effect of Single Nucleotide Polymorphism on Chemotherapeutic Agents Efficacy and Safety” was prepared under my supervision at the Department of Pharmacology and Toxicology/ College of Pharmacy / Mustansiriyah University as a partial fulfillment for the degree of Bachelor in Pharmacy Sciences. Supervisor: Professor Dr. Bahir Abdulrazzaq Ph.D. Pharmacology Address: Department of Pharmacology and Toxicology, College of Pharmacy, Mustansiriyah University. SIGNATURE: III List of content : Number Title Page Number Acknowledgement I Dedication II Supervisor Certificate III Abstract VIII I. Introduction 1 II. Fluoropyrimidines 4 I.A) Mechanism of action 4 II.B) Metabolic pathway 5 III.C) Main SNPs that have been found 6 III. Platinum derivatives 8 III.A) Mechanism of action 8 III.B) Metabolic pathway 9 III.C) Main SNPs that have been found 9 IV. Topoisomerase inhibitors (Irinotecan) 12 IV.A) Mechanism of action 12 IV.B) Metabolic pathway 12 IV.C) Main SNPs that have been found 13 V. Taxanes 15 V.A) Mechanism of action 15 V.B) Metabolic pathway 15 V.C) Main SNPs that have been found 15 VI. Conclusion 17 Refrences 18 IV List of Tables : Table Number Title of the table Page Number 1 Synopses of the 4 major genes variants involved in the metabolism of fluoropyrimidines, platinum derivatives, irinotecan and taxanes. V List of Figures : Figure Number Figure Title Page Number 1 Single nucleotide polymorphisms 1 (SNPs) are genetic muta tions that alter single base in DNA, causing sequence modification in amino acids and malfunction of a corresponding protein 2 Types of SNP and their subsequent 2 effect on gene 3 Mechanism of action of 7 Fluoropyrimidines and the main enzymes included in the pathway 4 Mechanism of action of Platinum Drugs 11 and the main enzymes included in the pathway 5 Mechanism of action of Irinotecan and 14 the main enzymes included in the pathway 6 Mechanism of action of Taxanes and 16 the main enzymes included in the pathway VI List of abbreviations : Abbreviation Full Meaning ABCB1 Adenosine triphosphate-Binding Cassette subfamily B member 1 AFBAL Alpha-Fluoro-Beta-Alanine BER Base Excision Repair CRC Colorectal Cancer CYP3A4 Cytochrome P450 3A4 DHFU Dihydrofluorouracil DPYD Dihydropyrimidine Dehydrogenase ERCC1 Excision Repair Cross Complementation group 1 FBAL Fluoro-Beta-Alanine FdUMP Fluoro-deoxyuridinemonophosphate FdUTP Fluoro-deoxyuridinetriphosphate 5-FU 5-Fluorouracil GSTP Glutathione S-Transferase Protein 1 MMR Mismatch repair MTHFR Methylentetrahydrofolate Reductase NER Nucleotide Excision Repair NHEJ Non-homologous end joining NSCLC Non-small cell lung cancer OS Overall-survival PFS Progression-free survival ROS Reactive Oxygen Species SNP Single Nucleotide Polymorphism TB Thymidine Phosphorylase TYMS Thymidylate Synthetase UDP Uridinediphosphate UGT Uridine Diphosphate Glucuronyltransferase XRCC1 X-ray Repair Cross Complementation group 1 VII Abstract : Single Nucleotides Polymorphism (SNP) is the most common type of genetic variation among people. It is a DNA sequence variation that occurs when a single nucleotide (adenine, thymine, cytosine, or guanine) in the genome sequence is altered. SNPs may change the encoded amino acids (nonsynonymous) or can be silent (synonymous) or simply occur in the noncoding regions. They may influence promoter activity (gene expression), messenger RNA (mRNA) conformation (stability), and subcellular localization of mRNAs and/or proteins and hence may produce disease. Single nucleotide polymorphism can also affect the efficacy and safety of anticancer drugs by altering drug metabolism, transport, and target receptor interactions. For example, single nucleotide polymorphism (SNP) in genes encoding drug-metabolizing enzymes such as Cytochrome P (CYP) can affect the metabolism of anticancer drugs such as Taxanes and Irinotecan chemotherapy agents, leading to inter-individual variability in drug response and toxicity. Similarly, Single nucleotide polymorphism (SNP) in genes encoding drug transporters such as Adenosin triphosphate binding cassette (ABC) can affect the distribution and elimination of anticancer drugs, influencing their efficacy and toxicity. Therefore, understanding the impact of single nucleotide polymorphism on anticancer drug pharmacokinetics and pharmacodynamics is important for personalized medicine and drug development. Overall, understanding the impact of SNPs in genes involved in chemotherapeutic agents metabolism and transport can help personalize chemotherapy regimens and improve treatment outcomes for cancer patients. Genetic testing for these SNPs may be useful in identifying patients who are at risk for treatment failure or toxicity and may benefit from alternative treatment options VIII I. Introduction : The human genome includes 3 billions of nucleotides, and inter-individual sequence variations are detected with a frequency of 1/300-1000 nucleotides. Single nucleotide polymorphisms (SNPs) is a variation in a single nucleotide that occurs at a specific position in the genome. For instance, at a specific base position in a chromosome of the human genome, while most individuals may present a thymine, in a minority of subjects the same base position can be occupied by a cytosine as shown in figure 1. This means that there is an SNP at that specific position, and the two possible nucleotides T or C are called alleles for that position. Figure 1 ;Figure 1 ; Single Nucleotide Single-nucleotide Polymorphism polymorphisms between (SNPs) are geneticindividuals alter mutaions that single base in DNA, causing sequence modification in amino acids and malfunction of a corresponding protein. 1 SNPs is observed in more than 1% of the general population, and account for approximately 80% of the overall genomic heterogeneity. SNPs may be located in different parts of the genome, with potentially different ―functional‖ implications : 1. Causative SNP , and it is further classified to : a) Coding SNP : located within coding sequences of genes. b) Non-coding SNP : located within noncoding regions of genes. 2. Linked SNP : located outside of gene and has no effect on protein production or function as illustrated in figure 2. Figure 2 ; Types of SNP and their subsequent effect on gene. 2 As a consequence, many SNPs that can be found in the human genome are functionally ―silent‖ because they do not alter the expression of a gene or the function of a protein. Even SNPs located within a coding sequence are not necessarily associated with a change in the amino acid sequence of the protein because redundancy in the genetic code can imply that different DNA sequences can produce the same amino acid chain (a synonymous substitution is the substitution of one base for another in an exon of a gene coding for a protein, such that the produced amino acid sequence is not modified). Among the 10 million SNPs identified in the human genome, only 100,000 have a phenotypic and functional impact, since the majority of them is located in intronic portions of the DNA [5, 6] Functional SNPs are key determinants of inter-individual anthropometric differences, but may also activate the responses to environmental factors and predict the individual disease susceptibility [7, 8]. Moreover, a number of pharmacogenomic studies have demonstrated that both efficacy and toxicity of drugs are largely influenced by SNPs , and this event appears particularly relevant in cancer patients receiving chemotherapy since a definite correlation between chemotherapy efficacy/tolerability and survival outcomes, cannot be denied. The optimization of the so-called ―patient-therapy binomial‖ constitutes one of the main challenges of the modern oncology. 3 The major gene variants involved in the metabolism of anti-cancer drugs and the subsequent alteration in amino acid are mentioned in details in table 1. Table 1: Synopses of the major genes variants involved in the metabolism of fluoropyrimidines, platinum derivatives, irinotecan and taxanes Drug Gene Polymorphism Amino Acid SNP ID Fluoropyrimidines DPD G>A Splice donor rs3918290 variant MTHFR C677T Ala222Val rs1801133 TYMS 1494del6b I/D of TTAAAG rs151264360 sequence at 1494 rs869066439 position on the 3’UTR Platinum ERCC1 T19007C Asn118Asn rs11615 derivaties XRCC1 G28152A Arg399Gln rs25487 GSTP1 A313G Ile105Val rs1659 Irinotecan UGT1A 1*28 A(TA)6/7TAA rs34983651 ABCB1 C3435T Ile1145Ile rs1045642 CYP3A4*1B -392A>G Promoter rs2740574 CYP3A5*3 6986A>G Splicing defect rs776746 Taxanes ABCB1 C3435T Ile1145Ile rs1045642 CYP3A4*1B -392A>G Promoter rs2740574 CYP3A5*3 6986A>G Splicing defect rs776746 II) Fluoropyrimidines (Fluorouracil , Capecitabine , Tagafur) A)Mechanism Of Action : 5-FU is converted into an active metabolite that binds to and inhibits thymidylate synthase, leading to a decrease in the production of thymidine, a building block of DNA. This results in a decrease in DNA synthesis and cell division, ultimately leading to cell death. 4 Capecitabine is converted into 5-FU in the body and has a similar mechanism of action. Fluoropyrimidines are particularly effective against rapidly dividing cancer cells because they are more dependent on thymidine synthesis. However, these drugs can also affect normal cells in the body, leading to side effects such as nausea, vomiting, and diarrhea. B)Metabolic Pathway : Fluoropyrimidines are metabolized in the liver by enzymes called dihydropyrimidine dehydrogenase (DPD) and thymidine phosphorylase (TP). DPD converts 5-FU into its inactive form, dihydrofluorouracil (DHFU), which is then further metabolized into fluoro-beta-alanine (FBAL) and alpha-fluoro-beta- alanine (AFBAL). These metabolites are then excreted in the urine. TP converts capecitabine into 5-FU, which is then metabolized by DPD as described above. 5-FU is converted into its active form, fluorodeoxyuridine monophosphate (FdUMP), which inhibits DNA synthesis and cell division by inhibiting Thymidylate Synthase enzyme (TYMS). FdUMP is then converted into fluorodeoxyuridine triphosphate (FdUTP), which can be incorporated into DNA and cause further damage to cancer cells. as shown in figure 3 Overall, the metabolism of fluoropyrimidines is complex and involves multiple enzymes and pathways. This variability can contribute to differences in drug efficacy and toxicity among patients. 5 C)Main SNPs that have been found : Several SNPs in genes involved in fluoropyrimidine metabolism and transport have been shown to affect the efficacy and safety of these drugs. For example, a common SNP in dihydropyrimidine dehydrogenase (DPD) IVS14+1G>A c.1905+1G>A DPYD * 2A (rs3918290) has been associated with increased toxicity of fluoropyrimidines. This SNP reduces the activity of the DPD enzyme of 30-70% than normal , this enzyme involved in the metabolism of fluoropyrimidines, causing persistence of high concentrations of the drug in the body and increased risk of side effects such as myelosuppression and gastrointestinal toxicity. In this case , it is recommended to administer 50% of total fluoroprimidines dose. [13,14] Another SNP in methylenetetrahydrofolate reductase (MTHFR) C677T Ala222Val (rs1801133) has been associated with decreased drug efficacy of fluoropyrimidines. This SNP reduces the activity of the MTHFR enzyme, which is involved in folate metabolism, leading to decreased availability of folate for DNA synthesis and repair. A third SNP is in thymidylate synthase (TYMS) (1494 ins/del 6b rs16430/ rs34489327). 1494 del allele causes TYMS mRNA instability with lower protein expression. It has also been associated with greater sensitivity to fluoropyrimidine- based therapy and increased cytotoxicity. 6 Excretion DNA Synthesis Figure 3 ; Mechanism of action of Fluoropyrimidines and the main. enzymes included in its pathway DPYD - dihydropyrimidine dehydrogenase; DHFU - dihydrofluorouracil; FUTP - fluorouridine triphosphate; FdUTP - fluorodeoxyuridine triphosphate; FdUMP - fluorouridine monophosphate; TYMS - thymidylate synthase; MTHFR - methylene tetrahydrofolate reductas 7 III) Platinum Derivatives (Cisplatin , Carboplatin , Oxaliplatin) : A)Mechanism Of Action : Platinum derivatives promote the Reactive Oxygen Species (ROS) synthesis, that cause the alteration of cell membranes permeability , the deregulation of different signal transduction pathways and calcium homeostasis but overall the DNA damage. When platinum derivatives reach the nucleus, they form intra and interstrand DNA cross-links that block the cell cycle by activating tumor cell apoptosis through different pathways. DNA adducts however may activate sensor proteins and DNA repair systems by avoiding cytotoxicity. Excision repair cross complementation group 1 (ERCC1) is the main endonuclease of DNA NER (Nucleotide Excision Repair) pathway but it also interacts with the BER (Base Excision Repair) function in maintaining chromosomal stability and telomers integrity. X-ray repair cross-complementing group 1 (XRCC1) is another enzyme of BER pathway that repairs DNA bases damaged by X-rays, ROS and mostly alkylating agents. The efficiency of the GSTP1 detoxification reaction and of DNA repairing systems affects the platinum-based treatments response. as shown in figure 4. 8 B)Metabolic Pathway : Platinum drugs are primarily eliminated from the body through the kidneys, with up to 90% of the drug being excreted in the urine within 24 hours of administration. The metabolism of platinum drugs involves several steps: 1. Activation : Platinum drugs are activated by the forming a complexes that can bind to DNA and form cross-links. 2. Inactivation : Platinum drugs can be inactivated by binding to proteins or other molecules in the body before they have a chance to bind to DNA. 3. Detoxification : Platinum drugs can be detoxified by enzymes such as glutathione S-transferase (GST), which conjugates the drug with glutathione and makes it more water-soluble for excretion. 4.Resistance : Cancer cells can develop resistance to platinum drugs through various mechanisms, such as increased expression of GST or decreased uptake of the drug into the cell. C)Main SNPs that have been found : Several SNPs in ERCC1 have been identified that can affect the activity of the ERCC1 protein. One of the most studied SNPs is C8092A (rs321298). A allele is associated with an increased risk of grade 3 or 4 gastrointestinal toxicity and with anemia in advanced non-small cell lung cancer patients and colorectal cancer patients. [18,19] 9 Another SNP that has been found is in XRCC1 G28152A Arg399Gln(rs25487) , and it’s associated with lower XRCC1 expression and increase platinum toxicity (including grade 3-4 gastrointestinal and haematological toxicity in patient with non-small cell lung cancer) as well as increase in tumor aggressiveness.A allele is associated with worse overall survival compared with C allele. Third SNP is in GSTP A313G Ile105Val (rs1659) and it caused lower GSTP1 activity which lead to increase platinum drugs neurotoxicity in patient with colorectal cancer while in patient with non-small cell lung cancer , it has no toxicities associations.This SNP is associated with better outcome and overall survival in breast, colorectal cancer, non-small cell lung cancer and gastric cancer patients 10 Figure 4 ; Mechanism of action of Platinum Drugs and the main enzymes included in its pathway ROS : reactive oxygen species; NHEJ : Non-homologous end joining GSTP1 : glutathione s-transferases protein 1; MMR : Mismatch Repair ERCC1: excision repair cross complementation group 1; NER : Nucleotide Excision Repair; BER : Base Excision Repair; XRCC1 : X-ray repair cross-complementing group 1. 11 IV)Topoisomerase Inhibitors ( Irinotecan) A)Mechanism Of Action : In cancer cell nuclei, the active form of Irinotecan (SN-38) inhibits topoisomerase I, a key enzyme in DNA replication. Topoisomerase I is responsible for unwinding and separating the DNA strands during replication. Irinotecan binds to the enzyme and prevents it from re-ligating the DNA strands, leading to the formation of single-strand breaks in the DNA. This results in the accumulation of DNA damage and ultimately leads to cell death. B)Metabolic Pathway : Irinotecan is a prodrug that, that is after administration, is activated in liver by the hydrolysis reaction catalyzed by carboxylesterases (CES1, CES2) of the microsomal system of hepatocytes, with the release of the more active metabolite SN-38. In liver cells, irinotecan and SN-38 may be oxidated by hepatic cytochrome P-450 (CYP 3A4 and 3A5) to form pharmacologically inactive metabolites (NPC, APC). The Uridine diphosphate (UDP) glucuronosyltransferases (UGT) catalyzes the subsequent conjugation reaction of SN-38 with glucuronic acid making its excretion possible through the bile in the intestinal lumen. 12 Adenosine-triphosphate binding cassettes (ABC) transporters (ABCB1/ABCB2) are transmembrane proteins which make possible the absorption of SN-38 from plasma into hepatocytes and hence in interstitial and the excretion of irinotecan and its metabolites by bile into the intestinal lumen. An increased bioavailability of SN-38, i.e. for the reduced efficiency of UGT and CYP 3A4/3A5 reactions, seems to justify the onset of diarrhea and neutropenia as specific side effects of chemotherapy. as illustrated in Figure 5 C)Main SNPs that have been found : One of the most studied SNP is in UGT1A 1 * 28 A(TA) 6/7 TAA (rs34983651). This SNP (if it is inherited as homozygous genotype) , will cause reduction in glucuronation efficiency of 30-50% than the normal leading to increased risk of developing grade 3-4 diarrhea and severe neutropenia, especially in case of dosage >200-250 mg/m 2. In this case , dose reduction of 30% than the total dose (for doses >250mg/m 2 ) is required.[14,22] Another SNP is CYP3A4*1B -392A>G (rs2740574) , It is correlates with CYP3A4 * 1B higher expression which will increase the drug oxidative detoxification leading to lower Irinotecan toxicities. CYP3A5*3 6986A>G (rs776746) is another SNP that is correlated with protein splicing defect and lower CYP3A5 * 3 expression, reducing the drug oxidative detoxification leading to lower response rate in patient with colorectal cancer. 13 The last SNP is ABCB1 C3435T Ile1145Ile (rs1045642) , which affects mRNA stability and protein structure by reducing its function and expression and causes the reduction of drug clearance resulting in increased risk of chemotherapy- associated toxicities and with worst objective response rate and overall survival in colorectal cancer patients. In non-small cell lung cancer patients treated with Irinotecan-Cisplatin regimen 3435T allele correlates with higher irinotecan efflux with lower AUC, higher clearance and higher incidence of grade 3 diarrhea. Figure 5 ; Mechanism of action of Irinotecan and the main enzymes included in its pathway CES – carboxylesterases ; CYP - cytochrome P-450 ; UGT - uridine diphosphate glucuronosyltransferases ; ABC - adenosine-triphosphate binding cassettes. 14 V) Taxanes (Paclitaxel , Tocetaxel) A)Mechanism Of Action : Taxanes are a class of chemotherapy drugs that work by disrupting the normal function of microtubules, which are essential for cell division. Specifically, taxanes bind to the microtubules and prevent them from disassembling, leading to the accumulation of microtubules and inhibition of mitosis. This ultimately results in cell death. B)Metabolic Pathway In hepatocytes, these drugs are subjected to oxidation reactions by specific isoforms of the Cytochrome P450 enzymes. In particular, CYP3A4 and CYP3A5 have docetaxel as substrate while CYP3A4 and CYP2C8 have paclitaxel. These reactions result in the synthesis of inactive metabolites that pass from the liver microsomal system into bile and then are excreted via fecal. The bioavailability of taxanes is also influenced by the functioning of ABCB1 adenosine-triphosphate binding cassettes (ABC), energy-dependent drug efflux pumps that regulate the drug clearance by influencing the balance between reabsorption from the hepatocellular system and intestinal excretion. as illustrated in figure 6. C) Main SNPs that have been found : SNP in ABCB1 C3435T Ile1145Ile (rs1045642) affects mRNA stability and protein structure by reducing its function and expression also causes the reduction of drug clearance by increasing toxicity risk. This SNP is associated with diarrhea (> grade 2) in Non-small cell lung cancer (NSCLC) and breast patients and with more severe neutropenia in ovarian, breast and prostate cancer patients and correlates with lower Progression-Free survival (PFS) and higher mucositis frequency in gastric cancer patients and with dose- limiting neuropathy in breast cancer patients while C allele correlates with increased risk of hematological oxicity. 15 CYP3A4 * 1B -392A>G (rs2740574) is another SNP that correlates with higher expression of the enzyme , increasing the drug oxidative detoxification , it is correlates with decreased Overall Survival (OS) and worse clinical outcome and associated in breast cancer patients with infusion reactions but with lower risk of neuropathy. [27,28] CYP3A5 * 3 6986A>G (rs776746) correlates with protein splicing defect and lower CYP3A5 * 3 expression reducing the drug oxidative detoxificatio causing neutropenia in breast cancer patients while in another study it is associated with lower risk of taxanes-induced neuropathy Excretion Figure 6 ; Mechanism of action of Taxanes and the main enzymes included in its pathway CYP - Cytochrome P450 ; ABC - adenosine-triphosphate binding cassette 16 VI.Conclusion : In most cases these polymorphisms are associated with a demonstrated and significantly increased or decreased chemotherapeutic exposure and can be used in pretreatment screening for optimizing dosage regimens. A genotyping test can be used to identify single nucleotide polymorphism in genes involved in anticancer metabolism and transport. This test involves analyzing a patient's DNA sample to determine their genetic makeup at specific locations in these genes. The test can be performed using a variety of methods, including polymerase chain reaction (PCR), DNA sequencing, and microarray technology. Results from the test can be used to guide treatment decisions and help predict a patient's response to chemotherapy. Genotyping tests for these SNPs are available commercially and can be ordered by healthcare providers. However, it is important to note that genetic testing should always be done in conjunction with clinical evaluation and should not be used as the sole basis for treatment decisions. 17 Refrences : 1. Syvänen AC. Accessing genetic variation: genotyping single nucleotide polymorphisms. Nat Rev Genet. 2001; 2:930–42. 2. Camp, K. M.; Trujillo, E. J. Acad. Nutr. Diet. 2014, 114, 299–312. doi:10.1016/j.jand.2013.12.001 3. https://learn.genetics.utah.edu/content/precision/snips 4. 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