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1.
Comput Biol Med ; 153: 106548, 2023 02.
Article in English | MEDLINE | ID: mdl-36652867

ABSTRACT

Existing warfarin dose prediction algorithms based on pharmacogenetics and clinical parameters have not been used clinically due to the absence of external validation, lack of assessment for clinical utility, and high risk of bias. Moreover, given the high degree of heterogeneity across different datasets used to develop these algorithms, it is unsurprising that prediction errors remain high, and dosing accuracy is dependent on specific ethnic populations. To circumvent these challenges, deep neural models are increasingly used to improve the precision and accuracy of warfarin dose predictions. Hence, this study sought to develop a deep learning-based model using a well-established curated dataset of over 6000 patients from the International Warfarin Pharmacogenomics Consortium (IWPC). Clinically-relevant input data such as physical attributes, medical conditions, concomitant medications, genotype status of functional warfarin genetic polymorphisms, and therapeutic INR were entered followed by applying a unique and robust training and validation method. The deep model yielded a low average mean absolute error (MAE) of 7.6 mg/week and a relatively low mean percentage of error of 40.9% in Asians, 14.2 mg/week MAE and 36.9% in African Americans, and 12.7 mg/week MAE and 45.4% mean percentage of error in White Caucasians. This model also resulted in 36.4% of all patients with a predicted dose within 20% of the administered dose. Hence, our proposed deep model provides an alternative to predicting warfarin dose in the clinical setting upon validation in ethnically-similar datasets.


Subject(s)
Anticoagulants , Deep Learning , Warfarin , Humans , Algorithms , Anticoagulants/administration & dosage , Dose-Response Relationship, Drug , Genotype , Pharmacogenetics/methods , Vitamin K Epoxide Reductases/genetics , Warfarin/administration & dosage
2.
Clin Pharmacol Ther ; 113(3): 712-723, 2023 03.
Article in English | MEDLINE | ID: mdl-36629403

ABSTRACT

The therapeutic efficacy of tamoxifen is predominantly mediated by its active metabolites 4-hydroxy-tamoxifen and endoxifen, whose formation is catalyzed by the polymorphic cytochrome P450 2D6 (CYP2D6). Yet, known CYP2D6 polymorphisms only partially determine metabolite concentrations in vivo. We performed the first cross-ancestry genome-wide association study with well-characterized patients of European, Middle-Eastern, and Asian descent (n = 497) to identify genetic factors impacting active and parent metabolite formation. Genome-wide significant variants were functionally evaluated in an independent liver cohort (n = 149) and in silico. Metabolite prediction models were validated in two independent European breast cancer cohorts (n = 287, n = 189). Within a single 1-megabase (Mb) region of chromosome 22q13 encompassing the CYP2D6 gene, 589 variants were significantly associated with tamoxifen metabolite concentrations, particularly endoxifen and metabolic ratio (MR) endoxifen/N-desmethyltamoxifen (minimal P = 5.4E-35 and 2.5E-65, respectively). Previously suggested other loci were not confirmed. Functional analyses revealed 66% of associated, mostly intergenic variants to be significantly correlated with hepatic CYP2D6 activity or expression (ρ = 0.35 to -0.52), and six hotspot regions in the extended 22q13 locus impacting gene regulatory function. Machine learning models based on hotspot variants (n = 12) plus CYP2D6 activity score (AS) increased the explained variability (~ 9%) compared with AS alone, explaining up to 49% (median R2 ) and 72% of the variability in endoxifen and MR endoxifen/N-desmethyltamoxifen, respectively. Our findings suggest that the extended CYP2D6 locus at 22q13 is the principal genetic determinant of endoxifen plasma concentration. Long-distance haplotypes connecting CYP2D6 with adjacent regulatory sites and nongenetic factors may account for the unexplained portion of variability.


Subject(s)
Breast Neoplasms , Cytochrome P-450 CYP2D6 , Humans , Female , Cytochrome P-450 CYP2D6/genetics , Cytochrome P-450 CYP2D6/metabolism , Genome-Wide Association Study , Antineoplastic Agents, Hormonal/therapeutic use , Tamoxifen , Breast Neoplasms/drug therapy , Breast Neoplasms/genetics , Breast Neoplasms/metabolism , Genotype
3.
JGH Open ; 6(10): 658-666, 2022 Oct.
Article in English | MEDLINE | ID: mdl-36262537

ABSTRACT

Background and Aim: Thiopurines are recommended for maintenance of steroid-free remission (SFR) in inflammatory bowel disease (IBD). Thiopurine metabolite monitoring (MM) is increasingly used in the West but remains novel in Singapore, with limited information on its therapeutic and economic benefits. Hence, this study aims to investigate MM's clinical utility and its impact on healthcare resource utilization in Singaporean IBD patients. Methods: A retrospective observational study was conducted at Singapore General Hospital outpatient IBD Centre. Patients with IBD, baseline MM during 2014-2017, and weight-based thiopurine doses for ≥4 weeks were followed up for 1 year. Actions were taken to optimize therapy, and metabolite levels before and after the first action were documented. Outcomes assessed included SFR, no therapy escalation or surgery, healthcare resource utilization, and direct healthcare costs. Results: Ninety IBD patients (50 Crohn's disease, 40 ulcerative colitis) were included. Among them, 40% had baseline metabolite levels within therapeutic range, 31.1% sub-therapeutic, 21.1% supra-therapeutic, and 7.8% shunters. Repeated MM with subsequent dose optimization helped 67.2% of patients achieve therapeutic levels after 1 year. Overall, 87.8% of patients achieved SFR and 90% had no therapy escalation or surgery. Despite greater outpatient visits and laboratory investigations with MM, the median total healthcare costs at 1 year only increased marginally (S$6407.66 [shunters] vs S$5215.20 [supra-therapeutic] vs S$4970.80 [sub-therapeutic] vs S$4370.48 [control (within therapeutic range)], P = 0.592). Conclusion: MM guided timely therapy escalation for non-responders, identification of non-adherence, and reversal of shunting. Therefore, it is a useful clinical tool to optimize thiopurines without significantly increasing healthcare costs.

4.
Int J Cancer ; 151(3): 435-449, 2022 08 01.
Article in English | MEDLINE | ID: mdl-35415893

ABSTRACT

Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal and debilitating disease with limited therapeutic options. The aim of this clinical study was to evaluate the safety, efficacy and pharmacokinetics of a novel regimen comprised of metronomic oxaliplatin (O), chronomodulated capecitabine (X) and UGT1A1 genotype-guided dosing of irinotecan (IRI) [OXIRI] as well as its immunomodulatory effects. Thirty-six patients were enrolled into either dose-escalation or expansion cohorts. In the dose escalation phase, capecitabine doses (2000, 2650, 3500 and 4500 mg/day) were administered at midnight on days 1 to 14 while oxaliplatin and irinotecan were intravenously infused at fixed doses of 50 and 75 mg/m2 respectively on days 1, 8 in a 21-day cycle. The maximum tolerated dose of capecitabine was 2650 mg/day and the most common grade 3 adverse events were neutropenia (30.6%) and diarrhea (13.9%). No grade 4 toxicity was observed. UGT1A1-genotype directed dosing resulted in similar exposure levels of irinotecan, SN-38 and SN-38G in all patients. Objective response rate was 22.2%. Median overall survival and progression-free survival were 8.1 and 5.2 months, respectively. Exploratory immunoprofiling by flow cytometry and quantitative spatial localization analysis of infiltrated immune cells performed on biopsy and plasma samples revealed significant declines in CCL22, CCL2 and TNFα levels at end of first cycle and an active host immune response. Our study showed that OXIRI was well-tolerated and exhibited good efficacy, with immunomodulatory effects. It may be considered as an alternative to FOLFIRINOX in patients intolerant to the latter.


Subject(s)
Adenocarcinoma , Pancreatic Neoplasms , Adenocarcinoma/pathology , Antineoplastic Combined Chemotherapy Protocols/adverse effects , Camptothecin , Capecitabine/therapeutic use , Fluorouracil/therapeutic use , Humans , Immunity , Irinotecan , Oxaliplatin , Pancreatic Neoplasms/pathology , Treatment Outcome , Pancreatic Neoplasms
6.
J Paediatr Child Health ; 58(3): 397-403, 2022 Mar.
Article in English | MEDLINE | ID: mdl-34477275

ABSTRACT

AIM: This pilot study aimed to compare the pharmacokinetic profiles of oral (PO) and intravenous (IV) ibuprofen for treatment of patent ductus arteriosus (PDA) in preterm neonates. METHODS: In a single-centre, parallel, randomised open-label trial, neonates ≤35 weeks, weight <1800 g with haemodynamically significant PDA during the first week of life were recruited between June 2017 and February 2019 and randomised to receive either PO or IV ibuprofen at standard dosage of 10, 5 and 5 mg/kg every 24 h for three consecutive days. Plasma concentrations of ibuprofen were quantified using a validated high-performance liquid chromatography method and pharmacokinetic parameters were calculated. Treatment outcomes were recorded. RESULTS: Eleven neonates participated in the trial, six and five patients receiving PO and IV ibuprofen, respectively. Pharmacokinetic analysis reveals similar ibuprofen exposure levels in treatment groups. Median dose- and weight-normalised Cmax values of PO and IV groups were 2.12 and 2.53 g/mL respectively (P = 0.082) and median AUC0-24 levels were comparable (PO: 34.6 g*h/mL vs. IV: 50.7.6 g*h/mL, P = 0.25). CONCLUSION: This exploratory study demonstrates comparable pharmacokinetics of PO and IV formulations of ibuprofen in preterm neonates. Larger prospective studies are required to validate these findings.


Subject(s)
Ductus Arteriosus, Patent , Ibuprofen , Cyclooxygenase Inhibitors/therapeutic use , Ductus Arteriosus, Patent/drug therapy , Humans , Ibuprofen/therapeutic use , Infant, Newborn , Infant, Premature , Pilot Projects
7.
Nat Nanotechnol ; 16(6): 734-742, 2021 06.
Article in English | MEDLINE | ID: mdl-33686255

ABSTRACT

Current technologies to measure drug-target interactions require complex processing and invasive tissue biopsies, limiting their clinical utility for cancer treatment monitoring. Here we develop an analytical platform that leverages circulating extracellular vesicles (EVs) for activity-based assessment of tumour-specific drug-target interactions in patient blood samples. The technology, termed extracellular vesicle monitoring of small-molecule chemical occupancy and protein expression (ExoSCOPE), utilizes bio-orthogonal probe amplification and spatial patterning of molecular reactions within matched plasmonic nanoring resonators to achieve in situ analysis of EV drug dynamics. It measures changes in drug occupancy and protein composition in molecular subpopulations of EVs. When used to monitor various targeted therapies, the ExoSCOPE revealed EV signatures that closely reflected cellular treatment efficacy. We further applied the technology for clinical cancer diagnostics and treatment monitoring. Using a small volume of blood, the ExoSCOPE accurately classified disease status and rapidly distinguished between targeted treatment outcomes, within 24 h after treatment initiation.


Subject(s)
Antineoplastic Agents/pharmacology , Extracellular Vesicles/drug effects , Lung Neoplasms/drug therapy , Molecular Targeted Therapy/methods , Antineoplastic Agents/pharmacokinetics , Biomarkers, Tumor/blood , Biosensing Techniques/instrumentation , Biosensing Techniques/methods , Case-Control Studies , Cell Line, Tumor , ErbB Receptors/genetics , Erlotinib Hydrochloride/blood , Erlotinib Hydrochloride/therapeutic use , Extracellular Vesicles/chemistry , Feasibility Studies , Humans , Lung Neoplasms/blood , Signal-To-Noise Ratio
8.
Cancer Res ; 81(7): 1802-1812, 2021 04 01.
Article in English | MEDLINE | ID: mdl-33547160

ABSTRACT

Signaling between cancer and nonmalignant (stromal) cells in the tumor microenvironment (TME) is a key to tumor progression. Here, we deconvoluted bulk tumor transcriptomes to infer cross-talk between ligands and receptors on cancer and stromal cells in the TME of 20 solid tumor types. This approach recovered known transcriptional hallmarks of cancer and stromal cells and was concordant with single-cell, in situ hybridization and IHC data. Inferred autocrine cancer cell interactions varied between tissues but often converged on Ephrin, BMP, and FGFR-signaling pathways. Analysis of immune checkpoints nominated interactions with high levels of cancer-to-immune cross-talk across distinct tumor types. Strikingly, PD-L1 was found to be highly expressed in stromal rather than cancer cells. Overall, our study presents a new resource for hypothesis generation and exploration of cross-talk in the TME. SIGNIFICANCE: This study provides deconvoluted bulk tumor transcriptomes across multiple cancer types to infer cross-talk in the tumor microenvironment.


Subject(s)
Neoplasms , Receptor Cross-Talk/physiology , Tumor Microenvironment , Autocrine Communication/physiology , Cell Communication/genetics , Computational Biology , Datasets as Topic , Female , Genomics/methods , Humans , Ligands , Male , Neoplasms/genetics , Neoplasms/metabolism , Neoplasms/pathology , Receptors, Cytoplasmic and Nuclear/physiology , Tumor Microenvironment/genetics , Exome Sequencing
9.
Clin Pharmacol Ther ; 108(3): 661-670, 2020 09.
Article in English | MEDLINE | ID: mdl-32578187

ABSTRACT

Endoxifen is one of the most important metabolites of the prodrug tamoxifen. High interindividual variability in endoxifen steady-state concentrations (CSS,min ENDX ) is observed under tamoxifen standard dosing and patients with breast cancer who do not reach endoxifen concentrations above a proposed therapeutic threshold of 5.97 ng/mL may be at a 26% higher recurrence risk compared with patients with endoxifen concentrations exceeding this value. In this investigation, 10 clinical tamoxifen studies were pooled (1,388 patients) to investigate influential factors on CSS,min ENDX using nonlinear mixed-effects modeling. Age and body weight were found to significantly impact CSS,min ENDX in addition to CYP2D6 phenotype. Compared with postmenopausal patients, premenopausal patients had a 30% higher risk for subtarget CSS,min ENDX at tamoxifen 20 mg per day. In treatment simulations for distinct patient subpopulations, young overweight patients had a 3.1-13.8-fold higher risk for subtarget CSS,min ENDX compared with elderly low-weight patients. Considering ever-rising obesity rates and the clinical importance of tamoxifen for premenopausal patients, this subpopulation may benefit most from individualized tamoxifen dosing.


Subject(s)
Antineoplastic Agents, Hormonal/pharmacokinetics , Breast Neoplasms/drug therapy , Models, Theoretical , Obesity/complications , Tamoxifen/analogs & derivatives , Adult , Age Factors , Aged , Aged, 80 and over , Antineoplastic Agents, Hormonal/administration & dosage , Antineoplastic Agents, Hormonal/blood , Body Weight , Breast Neoplasms/blood , Breast Neoplasms/complications , Computer Simulation , Cytochrome P-450 CYP2D6/genetics , Cytochrome P-450 CYP2D6/metabolism , Female , Humans , Middle Aged , Obesity/blood , Pharmacogenomic Variants , Tamoxifen/administration & dosage , Tamoxifen/blood , Tamoxifen/pharmacokinetics , Young Adult
10.
Pharmacogenomics J ; 20(3): 505-515, 2020 06.
Article in English | MEDLINE | ID: mdl-31813937

ABSTRACT

Thiopurines are used in the treatment of inflammatory bowel disease (IBD) but remain clinically challenging to manage due to wide interpatient variability in clinical outcomes and adverse events. Apart from genetic variants in thiopurine S-methyltransferase (TPMT) and nudix hydrolase 15 (NUDT15) genes, polymorphisms in FTO alpha-ketoglutarate dependent dioxygenase (FTO) were found predictive of thiopurine-induced leukopenia, albeit with conflicting results. To clarify the role of FTO variants in a multiethnic Asian IBD cohort, we recruited 149 patients on thiopurine-based therapy and genotyped two FTO variants p.Ala134Thr (rs79206939) and rs16952570 T > C using Sanger sequencing. FTO p.Ala134Thr (rs79206939) was non-polymorphic and absent whereas intronic rs16952570 T > C was equally prevalent in Chinese (22%) and Indians (18%) and higher in Malays (28%). Higher nadir white blood cell (WBC) and absolute neutrophil count (ANC) levels were observed in patients harboring FTO rs16952570 CC genotypes compared with TT carriers at 4, 8, and 12 weeks after start of thiopurine therapy (P < 0.05). A similar trend was observed in patients carrying the previously well-characterized NUDT15 rs116855232 wild-type CC genotypes. Further in silico analysis suggests that FTO variants linked to rs16952570, particularly rs74018601, may play a regulatory role in altering the FTO expression. The findings from this study indicate a novel protective association with the FTO variant rs16952570 CC genotype and hematological parameters.


Subject(s)
Alpha-Ketoglutarate-Dependent Dioxygenase FTO/genetics , Asian People/genetics , Azathioprine/adverse effects , Genetic Variation/genetics , Inflammatory Bowel Diseases/genetics , Introns/genetics , Adolescent , Adult , Aged , Aged, 80 and over , Asian People/ethnology , Female , Humans , Inflammatory Bowel Diseases/drug therapy , Inflammatory Bowel Diseases/ethnology , Leukopenia/chemically induced , Leukopenia/ethnology , Leukopenia/genetics , Male , Mercaptopurine/adverse effects , Middle Aged , Neutropenia/chemically induced , Neutropenia/ethnology , Neutropenia/genetics , Retrospective Studies , Young Adult
11.
Pharmacogenomics ; 19(1): 31-43, 2018 Jan.
Article in English | MEDLINE | ID: mdl-29210335

ABSTRACT

BACKGROUND: Genetic variants of TPMT and NUDT15 have been reported to predict the inter-patient variability in response and toxicity profiles of patients receiving thiopurine therapy. However, the clinical utility of TPMT genotyping in guiding thiopurine doses has been questionable, in part due to underlying differences in the prevalence of TPMT variants in both Caucasian and Asian populations. Several NUDT15 variants have been associated with thiopurine-induced leukopenia, particularly in Asian cohorts. So far, none have been reported in a multiethnic Asian population. AIM: To investigate the associations between TPMT and NUDT15 variants with thiopurine-induced myelotoxicity in 129 Asian inflammatory bowel disease patients. MATERIALS & METHODS: Pyrosequencing was performed to screen for TPMT and NUDT15 variants. Intracellular steady-state metabolite concentrations were quantified using liquid chromatography-tandem mass spectrometry. RESULTS: Significant declines in nadir white blood cell, absolute neutrophil count and platelet counts were observed with increasing copy numbers of the risk T allele at NUDT15 c.415C>T locus (overall p < 0.05) within 4, 8 and 12 weeks and 6 months after thiopurine initiation. Patients with low and intermediate NUDT15 activity, as inferred from haplotype pairs, had significantly higher risks of leukopenia (p = 0.000253) and neutropenia (p = 0.002) compared with patients with normal NUDT15 activity. CONCLUSION: These findings highlight the critical relevance of NUDT15 pharmacogenetics in predicting for thiopurine-induced myelotoxicity and confirm the lack of significance of TPMT variants in Asian inflammatory bowel disease patients.


Subject(s)
Azathioprine/adverse effects , Genetic Variation/genetics , Inflammatory Bowel Diseases/genetics , Pyrophosphatases/genetics , Adult , Alleles , Asian People , Azathioprine/therapeutic use , Female , Haplotypes/genetics , Humans , Inflammatory Bowel Diseases/drug therapy , Leukopenia/chemically induced , Leukopenia/genetics , Male , Methyltransferases/genetics , Neutrophils/drug effects , Pharmacogenetics/methods , Platelet Count/methods , Risk Factors
12.
Nat Med ; 23(10): 1167-1175, 2017 Oct.
Article in English | MEDLINE | ID: mdl-28920960

ABSTRACT

Targeting EGFR is a validated approach in the treatment of squamous-cell cancers (SCCs), although there are no established biomarkers for predicting response. We have identified a synonymous mutation in EGFR, c.2361G>A (encoding p.Gln787Gln), in two patients with head and neck SCC (HNSCC) who were exceptional responders to gefitinib, and we showed in patient-derived cultures that the A/A genotype was associated with greater sensitivity to tyrosine kinase inhibitors (TKIs) as compared to the G/A and G/G genotypes. Remarkably, single-copy G>A nucleotide editing in isogenic models conferred a 70-fold increase in sensitivity due to decreased stability of the EGFR-AS1 long noncoding RNA (lncRNA). In the appropriate context, sensitivity could be recapitulated through EGFR-AS1 knockdown in vitro and in vivo, whereas overexpression was sufficient to induce resistance to TKIs. Reduced EGFR-AS1 levels shifted splicing toward EGFR isoform D, leading to ligand-mediated pathway activation. In co-clinical trials involving patients and patient-derived xenograft (PDX) models, tumor shrinkage was most pronounced in the context of the A/A genotype for EGFR-Q787Q, low expression of EGFR-AS1 and high expression of EGFR isoform D. Our study reveals how a 'silent' mutation influences the levels of a lncRNA, resulting in noncanonical EGFR addiction, and delineates a new predictive biomarker suite for response to EGFR TKIs.


Subject(s)
Carcinoma, Squamous Cell/drug therapy , ErbB Receptors/genetics , Esophageal Neoplasms/drug therapy , Head and Neck Neoplasms/drug therapy , Mouth Neoplasms/drug therapy , Protein Kinase Inhibitors/therapeutic use , Quinazolines/therapeutic use , RNA, Long Noncoding/genetics , Adult , Aged , Aged, 80 and over , Carcinoma, Squamous Cell/genetics , Cell Proliferation , Drug Resistance, Neoplasm/genetics , Esophageal Neoplasms/genetics , Esophageal Squamous Cell Carcinoma , Female , Gefitinib , Gene Knockdown Techniques , Head and Neck Neoplasms/genetics , Humans , In Vitro Techniques , Male , Middle Aged , Molecular Targeted Therapy , Mouth Neoplasms/genetics , RNA Isoforms , RNA Splicing , Squamous Cell Carcinoma of Head and Neck , Xenograft Model Antitumor Assays
13.
Front Pharmacol ; 8: 582, 2017.
Article in English | MEDLINE | ID: mdl-28955222

ABSTRACT

Purpose: Prediction of impaired tamoxifen (TAM) to endoxifen metabolism may be relevant to improve breast cancer treatment, e.g., via TAM dose increase. The polymorphic cytochrome P450 2D6 (CYP2D6) strongly determines an individual's capacity for endoxifen formation, however, CYP2D6 phenotype assignments inferred from genotype widely differ between studies. Thus, we modeled plasma endoxifen predictability depending on variable CYP2D6 genotype groupings. Methods: CYP2D6 diplotype and metabolite plasma concentrations were assessed in 908 pre- and post-menopausal estrogen receptor (ER)-positive, TAM treated early breast cancer patients of Caucasian (N = 678), Middle-Eastern Arab (N = 77), and Asian (N = 153) origin. Robust coefficients of determination (R2) were estimated for endoxifen (E) or metabolic ratio endoxifen/desmethyl-TAM (E/DMT) as dependent and different CYP2D6 phenotype assignments as independent variables. Allele activity scores (ASs) were modified with respect to a reduced ∗10 allele activity. Predictability of endoxifen plasma concentrations above the clinical threshold of 5.9 ng/mL was investigated by receiver operating characteristic (ROC) analysis. Results: CYP2D6 diplotypes (N = 898) were strongly associated with E and E/DMT independent of age (P < 10-15). Across all ethnicities, 68-82% inter-patient variability of E/DMT was explained by CYP2D6 diplotype, while plasma endoxifen was predictable by 39-58%. The previously used codeine specific phenotype classification showed worse prediction for both endpoints particularly in Asians (median R2< 20%; P < 10-9). Downgrading of ∗10 activity slightly improved the explanatory value of metabolizer phenotype (P < 0.002). Endoxifen plasma concentrations above the clinical threshold of 5.9 ng/mL were achieved in 82.3% of patients and were predictable (96% sensitivity, 57% specificity) by CYP2D6 diplotypes with AS > 0.5, i.e., omitting PM/PM and PM/IM patients. Conclusion: The CYP2D6 explanatory power for active drug level assessment is maximized by TAM-specific phenotype assignments while a genotype cutoff that separates PM/PM and PM/IM from the remaining patients may improve clinical benefit via increased endoxifen concentrations.

14.
Sci Rep ; 7(1): 1540, 2017 05 08.
Article in English | MEDLINE | ID: mdl-28484248

ABSTRACT

Small molecules targeting the EGFR tyrosine kinase domain have been used with some success at treating patients with non-small cell lung cancer driven by activating mutations in the kinase domain. The initial class of inhibitors displaced ATP noncovalently but were rendered ineffective due to the development of resistance mutations in the kinase domain. These were overcome by the development of covalent inhibitors such as afatinib which also bind in the ATP pocket. However pooled analysis of two recent clinical trials LUX-3 and LUX-6 demonstrated an unprecedented overall survival benefit of afatinib over chemotherapy for the EGFR 19del , but not the EGFR L858R . In the current study we use modelling and simulations to show that structural constraints in EGFR 19del deletion result in significantly attenuated flexibilities in the binding pocket resulting in strong hydrogen and halogen bonds with afatinib in the EGFR 19del ; these constraints are modulated by buried water and result in the differential affinities of afatinib for the different mutants. SNP analysis of residues surrounding the buried water points to the likelihood of further differential effects of afatinib and provides a compelling case for investigating the effects of the SNPs towards further stratification of patients for ensuring the most effective use of afatinib.


Subject(s)
Afatinib/pharmacology , ErbB Receptors/antagonists & inhibitors , Mutation/genetics , Water/chemistry , Binding Sites , Enzyme Activation , Humans , Ligands , Molecular Dynamics Simulation
15.
Pharmacogenet Genomics ; 27(3): 120-123, 2017 03.
Article in English | MEDLINE | ID: mdl-28059867

ABSTRACT

The critical role of lysine demethylase 4A (KDM4A), in regulating chromatin structure and consequently in driving cellular proliferation and oncogenesis has been the focus of recent studies. Non-small-cell lung cancer (NSCLC) patients with adenocarcinoma histology who were homozygous for KDM4A single nucleotide polymorphism (SNP)-A482 (rs586339) were recently shown to have significantly worse overall survival (OS) compared with patients with the wild-type or the heterozygous genotype at this locus (hazard ratio=1.68, P=0.042). In the current study, we investigated the association between the same polymorphism with OS in our Asian NSCLC-adenocarcinoma patients comprising Chinese (N=572), Malays (N=50), and Indians (N=22). KDM4A SNP-A482 genotype status was determined by Sanger sequencing. OS was calculated from the date of diagnosis to date of death or censored at the date of last follow-up. Kaplan-Meier analysis, log-rank test, and Cox regression methods were utilized to evaluate OS outcomes. KDM4A SNP-A482 had a minor allele (C) frequency of 18.8% and a major allele (A) frequency of 81.2% in our Asian NSCLC (adenocarcinoma) patients. However, the OS in our Asian NSCLC patients homozygous for KDM4A SNP-A482 was not significantly different from those who were wild type or heterozygous at this locus [CC vs. AA/AC: median OS (95% confidence interval): 40.2 (18.7-61.6) vs. 29.6 (26.9-32.3) months; P=0.858]. The results remained statistically nonsignificant even after adjustment for epidermal growth factor receptor mutational status, suggesting that KDM4A SNP-A482 does not significantly influence OS in Asian NSCLC patients.


Subject(s)
Asian People/ethnology , Carcinoma, Non-Small-Cell Lung/genetics , Jumonji Domain-Containing Histone Demethylases/genetics , Lung Neoplasms/genetics , Polymorphism, Single Nucleotide , Adult , Aged , Aged, 80 and over , Asian People/genetics , Carcinoma, Non-Small-Cell Lung/ethnology , Female , Genetic Association Studies , Humans , Kaplan-Meier Estimate , Lung Neoplasms/ethnology , Male , Middle Aged , Sequence Analysis, DNA , Survival Analysis
16.
Cancer Lett ; 388: 328-333, 2017 03 01.
Article in English | MEDLINE | ID: mdl-28003122

ABSTRACT

Metronomic administration of chemotherapy has long been recognized as having a different biological effect from maximal tolerated dose (MTD) administration. Preclinical studies have demonstrated these differences quite elegantly and many clinical trials have also demonstrated reproducible activity albeit small, in varied solid malignancies even in patients who were heavily pretreated. However, the concept of metronomic chemotherapy has been plagued by lack of a clear definition resulting in the published literature that is rather varied and confusing. There is a need for a definition that is mechanism(s)-based allowing metronomics to be distinguished from standard MTD concept. With significant advances made in understanding cancer biology and biotechnology, it is now possible to attain that goal. What is needed is both a concerted effort and adequate funding to work towards it. This is the only way for the oncology community to determine how metronomic chemotherapy fits in the overall cancer management schema.


Subject(s)
Administration, Metronomic , Antineoplastic Combined Chemotherapy Protocols/therapeutic use , Neoplasms/drug therapy , Humans
17.
J Thorac Oncol ; 12(3): 529-538, 2017 03.
Article in English | MEDLINE | ID: mdl-27908825

ABSTRACT

INTRODUCTION: Activating mutations in the EGFR gene have been shown to confer sensitivity to EGFR tyrosine kinase inhibitors in patients with advanced NSCLC. However, wide interpatient variability in treatment outcomes in response to EGFR tyrosine kinase inhibitors in these patients remains unaccounted for. This study aimed to evaluate the influence of EGFR mutation types and subtypes on survival outcomes in advanced Asian patients with NSCLC receiving first-line gefitinib therapy. METHODS: Patients with stage IIIB or IV NSCLC who were harboring EGFR mutations, receiving first-line gefitinib treatment, and of Asian descent (N = 383) were evaluated. Overall survival (OS) and progression-free survival (PFS) were estimated by Kaplan-Meier analysis. Log-rank tests and Cox proportional hazards models were implemented to evaluate the differences in PFS and OS. RESULTS: Significant differences in PFS were observed between patients carrying EGFR mutations in exons 18, 19, 20, and 21, with patients carrying EGFR exon 19 mutations having the longest median PFS (overall p = 8.88 × 10-15). Comparison of PFS among the five different exon 19 mutation subtypes and among the two exon 19 deletion start codons did not reveal any significant differences. No significant difference was observed in OS among patients carrying EGFR mutations on different exons (overall p = 0.054); however, OS was found to be significantly different among the various subtypes of exon 19 mutations, with the 15-nucleotide deletion "non-ELREA" group having the shortest OS of 11.3 months (overall p = 0.025). CONCLUSIONS: EGFR mutation types and subtypes significantly influence survival outcomes in patients with advanced NSCLC who are receiving first-line gefitinib treatment.


Subject(s)
Adenocarcinoma/mortality , Carcinoma, Non-Small-Cell Lung/mortality , ErbB Receptors/genetics , Lung Neoplasms/mortality , Mutation , Quinazolines/therapeutic use , Adenocarcinoma/genetics , Adenocarcinoma/secondary , Adult , Aged , Aged, 80 and over , Asian People/genetics , Biomarkers, Tumor/genetics , Carcinoma, Non-Small-Cell Lung/genetics , Carcinoma, Non-Small-Cell Lung/secondary , Female , Follow-Up Studies , Gefitinib , Humans , Lung Neoplasms/genetics , Lung Neoplasms/pathology , Lymphatic Metastasis , Male , Middle Aged , Neoplasm Staging , Prognosis , Protein Kinase Inhibitors/therapeutic use , Retrospective Studies , Survival Rate
18.
Pharmacogenomics ; 17(17): 1941-1955, 2016 Nov.
Article in English | MEDLINE | ID: mdl-27804783

ABSTRACT

The use of imatinib in the treatment of BCR-ABL-positive chronic myeloid leukemia and gastrointestinal stromal tumors has significantly improved survival outcomes in patients afflicted by these malignancies. However, a substantial proportion of imatinib-treated patients still experience treatment failure. Suboptimal concentrations of imatinib have been postulated to contribute at least partially to the development of resistance against imatinib. Indeed, variations in the genes encoding drug transporters have been reported to markedly influence imatinib disposition and treatment outcomes in various populations. This review aims to consolidate and critically assess the studies conducted to date which have investigated the influence of pharmacogenetic variants in drug transporters on the disposition of imatinib and treatment outcomes in Asians and other populations.

19.
Drugs R D ; 16(4): 317-326, 2016 Dec.
Article in English | MEDLINE | ID: mdl-27681888

ABSTRACT

Des-aspartate-angiotensin I (DAA-I) is an endogenous angiotensin peptide and a prototype angiotensin receptor agonist (ARA). It acts on the angiotensin AT1 receptor and antagonises the deleterious actions of angiotensin II. DAA-I attenuates animal models of human disease in which angiotensin II has been implicated, such as cardiac hypertrophy, neointima formation, arteriosclerosis, renal failure, post-infarction injuries, diabetes, viral infection, chemical-induced inflammation, heat stroke, cancer, and gamma radiation lethality. DAA-I crosses Caco-2 cells and is effective at sub-nanomolar concentrations. These two properties are responsible for its oral efficacy. A single dose-escalation study was conducted to evaluate the safety, tolerability and pharmacokinetics of orally administered DAA-I in 18 healthy subjects. DAA-I was safe and well tolerated by the subjects, who were administered either 0.08, 0.70 or 1.50 mg/kg of the compound. The heart rate and systolic and diastolic blood pressures determined at each post-dose measurement remained within the clinically acceptable range. Across all cohorts, DAA-I had no substantial effect on blood pressures compared with placebo. Electrocardiographs (ECGs) were normal, and none of the subjects complained of chest discomfort. All clinical laboratory tests obtained before and after DAA-I and placebo treatment were normal. Pharmacokinetic analysis over a 12-h period following DAA-I administration did not show any increase of its level beyond basal concentration. This is in line with studies showing that intravenously administered DAA-I is rapidly metabolized and has a short half-life. We postulate that, during its short systemic sojourn, DAA-I exerts its actions via biased agonism on the angiotensin AT1 receptor.The ClinicalTrial.gov assignment number for this study is NCT02666196.


Subject(s)
Angiotensin I/analogs & derivatives , Administration, Oral , Adult , Angiotensin I/administration & dosage , Angiotensin I/pharmacokinetics , Dose-Response Relationship, Drug , Female , Humans , Male , Middle Aged , Young Adult
20.
Drug Metab Rev ; 48(4): 502-540, 2016 11.
Article in English | MEDLINE | ID: mdl-27546072

ABSTRACT

Drug efflux and influx transporters play critical roles in regulating the cellular drug disposition and modulating the pharmacokinetics and pharmacodynamics of anti-cancer agents, which may potentially alter treatment outcomes. The efficiency of drug transport is often dependent on the expression and activity of these membrane-bound proteins, factors which have been shown to be regulated by genes that are known to be highly polymorphic in different ethnic populations. The role of drug transporters becomes even more critical for anti-cancer agents due to the narrow therapeutic windows that separate treatment response and toxicities for these agents. Moreover, high inter-individual variability in the disposition of anti-cancer agents often results in variable treatment outcomes among patients receiving standard doses of the same drug. Such variability has been attributed at least in part to polymorphisms in genes encoding drug-metabolizing enzymes and transporter. To date, numerous pharmacogenetic studies have investigated the associations between variants in the ABC and SLC transporters genes with drug disposition, treatment outcomes and drug-induced toxicities. However, the strengths of these associations and their clinical relevance in different ethnic populations have not been critically examined. This review aims to summarize and evaluate the implications of pharmacogenetic variants in the ABC and SLC transporters genes on the pharmacokinetics and clinical outcomes of three anti-cancer agents: irinotecan, docetaxel and doxorubicin in Caucasian and Asian patients.


Subject(s)
Asian People/genetics , Camptothecin/analogs & derivatives , Doxorubicin/pharmacokinetics , Neoplasms/genetics , Neoplasms/metabolism , Taxoids/pharmacokinetics , White People/genetics , ATP-Binding Cassette Transporters/genetics , Antineoplastic Agents/pharmacokinetics , Antineoplastic Agents/therapeutic use , Camptothecin/pharmacokinetics , Camptothecin/therapeutic use , Docetaxel , Doxorubicin/therapeutic use , Humans , Irinotecan , Polymorphism, Genetic/genetics , Solute Carrier Proteins/genetics , Taxoids/therapeutic use , Treatment Outcome
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