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Abudukeremu M, Ayoufu A, Tuerhong A, Paizula X, Ou JH. Distribution of CYP2D6 and CYP2C19 gene polymorphisms in Han and Uygur populations with breast cancer in Xinjiang, China. Open Life Sci 2024; 19:20220728. [PMID: 38681733 PMCID: PMC11049739 DOI: 10.1515/biol-2022-0728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 08/18/2023] [Accepted: 08/24/2023] [Indexed: 05/01/2024] Open
Abstract
The aim of this study was to investigate the frequency distribution of the cytochrome P450 (CYP450) enzymes, CYP2D6 and CYP2C19, and the form of tamoxifen metabolisation in premenopausal patients with breast cancer in the Han and Uygur ethnic groups of Xinjiang to guide rational clinical drug use. A total of 125 Han patients and 121 Uygur patients with premenopausal hormone-receptor-positive breast cancer treated at the Xinjiang Uygur Autonomous Region Cancer Hospital between 1 June 2011 and 1 December 2013 were selected. The common mutation sites in CYP450 were analysed using TaqMan® minor groove binder technology. Genetic testing was performed to determine other metabolic types of tamoxifen, and the genotypes and metabolic types were compared using a Chi-squared test. Between the Han and Uygur groups, there were significant differences in the frequencies of the CYP2D6 (*10/*10) and CYP2C19 (*1/*1) genotypes, with P-values of 0.002 and 0.015, respectively. Genotypes of CYP2D6 (*1/*1), CYP2D6 (*1/*5), CYP2D6 (*5/*5), CYP2D6 (*5/*10) and CYP2C19 (*3/*3) were expressed in the two patient groups, and the difference was not statistically significant (P > 0.05). In the Han patients, the proportions of extensive, intermediate and poor metabolisers of tamoxifen were 72, 24 and 4%, respectively, whereas those in the Uygur patients were 76.9, 17.4 and 5.7%, respectively, with no significant difference (P > 0.05). In conclusion, There were partial differences in the CYP2D6 and CYP2C19 gene polymorphisms of CYP450 between the Han and Uygur patients with premenopausal breast cancer, but there was no significant difference between the CYP2D6 and CYP2C19 phenotypes. Further research is needed to determine the relationship between the enzyme genetic differences of CYP450 and the pharmacokinetics and efficacy of tamoxifen. Although there were some differences in genotypes, these did not result in differences in the predicted tamoxifen metabolisation phenotype between the Han and Uygur patients with breast cancer. Therefore, the doses should be adjusted according to the individual genotype data.
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Affiliation(s)
- Muzhapaer Abudukeremu
- Department of Breast and Thyroid Surgery, Affiliated Cancer Hospital of Xinjiang Medical University, Urumqi City, 830000, Xinjiang, China
| | - Aisikaer Ayoufu
- Department of Breast Cancer Surgery, Affiliated Tumor Hospital, Xinjiang Medical University, No. 789, Suzhou Road, Urumqi, Xinjiang, 830011, China
| | - Adila Tuerhong
- Department of Breast Cancer Surgery, Affiliated Tumor Hospital, Xinjiang Medical University, No. 789, Suzhou Road, Urumqi, Xinjiang, 830011, China
| | - Xuelaiti Paizula
- Department of Breast Cancer Surgery, Affiliated Tumor Hospital, Xinjiang Medical University, No. 789, Suzhou Road, Urumqi, Xinjiang, 830011, China
| | - Jiang-Hua Ou
- Department of Breast Cancer Surgery, Affiliated Tumor Hospital, Xinjiang Medical University, No. 789, Suzhou Road, Urumqi, Xinjiang, 830011, China
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Liu Y, Shao Y, Hao Z, Lei X, Liang P, Chang Q, Wang X. Cuproptosis gene-related, neural network-based prognosis prediction and drug-target prediction for KIRC. Cancer Med 2023; 13:e6763. [PMID: 38131663 PMCID: PMC10807644 DOI: 10.1002/cam4.6763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 10/23/2023] [Accepted: 11/16/2023] [Indexed: 12/23/2023] Open
Abstract
BACKGROUND Kidney renal clear cell carcinoma (KIRC), as a common case in renal cell carcinoma (RCC), has the risk of postoperative recurrence, thus its prognosis is poor and its prognostic markers are usually based on imaging methods, which have the problem of low specificity. In addition, cuproptosis, as a novel mode of cell death, has been used as a biomarker to predict disease in many cancers in recent years, which also provides an important basis for prognostic prediction in KIRC. For postoperative patients with KIRC, an important means of preventing disease recurrence is pharmacological treatment, and thus matching the appropriate drug to the specific patient's target is also particularly important. With the development of neural networks, their predictive performance in the field of medical big data has surpassed that of traditional methods, and this also applies to the field of prognosis prediction and drug-target prediction. OBJECTIVE The purpose of this study is to screen for cuproptosis genes related to the prognosis of KIRC and to establish a deep neural network (DNN) model for patient risk prediction, while also developing a personalized nomogram model for predicting patient survival. In addition, sensitivity drugs for KIRC were screened, and a graph neural network (GNN) model was established to predict the targets of the drugs, in order to discover potential drug action sites and provide new treatment ideas for KIRC. METHODS We used the Cancer Genome Atlas (TCGA) database, International Cancer Genome Consortium (ICGC) database, and DrugBank database for our study. Differentially expressed genes (DEGs) were screened using TCGA data, and then a DNN-based risk prediction model was built and validated using ICGC data. Subsequently, the differences between high- and low-risk groups were analyzed and KIRC-sensitive drugs were screened, and finally a GNN model was trained using DrugBank data to predict the relevant targets of these drugs. RESULTS A prognostic model was built by screening 10 significantly different cuproptosis-related genes, the model had an AUC of 0.739 on the training set (TCGA data) and an AUC of 0.707 on the validation set (ICGC data), which demonstrated a good predictive performance. Based on the prognostic model in this paper, patients were also classified into high- and low-risk groups, and functional analyses were performed. In addition, 251 drugs were screened for sensitivity, and four drugs were ultimately found to have high sensitivity, with 5-Fluorouracil having the best inhibitory effect, and subsequently their corresponding targets were also predicted by GraphSAGE, with the most prominent targets including Cytochrome P450 2D6, UDP-glucuronosyltransferase 1A, and Proto-oncogene tyrosine-protein kinase receptor Ret. Notably, the average accuracy of GraphSAGE was 0.817 ± 0.013, which was higher than that of GAT and GTN. CONCLUSION Our KIRC risk prediction model, constructed using 10 cuproptosis-related genes, had good independent prognostic ability. In addition, we screened four highly sensitive drugs and predicted relevant targets for these four drugs that might treat KIRC. Finally, literature research revealed that four drug-target interactions have been demonstrated in previous studies and the remaining targets are potential sites of drug action for future research.
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Affiliation(s)
- Yixin Liu
- Department of Surgery, Shanghai Key Laboratory of Gastric NeoplasmsShanghai Institute of Digestive Surgery, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of MedicineShanghaiChina
- School of Health Science and EngineeringUniversity of Shanghai for Science and TechnologyShanghaiChina
| | - Yuan Shao
- Department of UrologyRuijin Hospital Affiliated to Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Zezhou Hao
- School of Health Science and EngineeringUniversity of Shanghai for Science and TechnologyShanghaiChina
| | - Xuanzi Lei
- Graduate SchoolShanghai University of Traditional Chinese MedicineShanghaiChina
| | - Pengchen Liang
- School of MicroelectronicsShanghai UniversityShanghaiChina
| | - Qing Chang
- Department of Surgery, Shanghai Key Laboratory of Gastric NeoplasmsShanghai Institute of Digestive Surgery, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of MedicineShanghaiChina
- School of Health Science and EngineeringUniversity of Shanghai for Science and TechnologyShanghaiChina
| | - Xianjin Wang
- Department of UrologyRuijin Hospital Affiliated to Shanghai Jiao Tong University School of MedicineShanghaiChina
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The Expression Quantitative Trait Loci in Immune Response Genes Impact the Characteristics and Survival of Colorectal Cancer. Diagnostics (Basel) 2022; 12:diagnostics12020315. [PMID: 35204406 PMCID: PMC8871427 DOI: 10.3390/diagnostics12020315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/24/2022] [Accepted: 01/24/2022] [Indexed: 02/05/2023] Open
Abstract
The impact of germline variants on the regulation of the expression of tumor microenvironment (TME)-based immune response genes remains unclear. Expression quantitative trait loci (eQTL) provide insight into the effect of downstream target genes (eGenes) regulated by germline-associated variants (eVariants). Through eQTL analyses, we illustrated the relationships between germline eVariants, TME-based immune response eGenes, and clinical outcomes. In this study, both RNA sequencing data from primary tumor and germline whole-genome sequencing data were collected from patients with stage III colorectal cancer (CRC). Ninety-nine high-risk subjects were subjected to immune response gene expression analyses. Seventy-seven subjects remained for further analysis after quality control, of which twenty-two patients (28.5%) experienced tumor recurrence. We found that 65 eQTL, including 60 germline eVariants and 22 TME-based eGenes, impacted the survival of cancer patients. For the recurrence prediction model, 41 differentially expressed genes (DEGs) achieved the best area under the receiver operating characteristic curve of 0.93. In total, 19 survival-associated eGenes were identified among the DEGs. Most of these genes were related to the regulation of lymphocytes and cytokines. A high expression of HGF, CCR5, IL18, FCER1G, TDO2, IFITM2, and LAPTM5 was significantly associated with a poor prognosis. In addition, the FCER1G eGene was associated with tumor invasion, tumor nodal stage, and tumor site. The eVariants that regulate the TME-based expression of FCER1G, including rs2118867 and rs12124509, were determined to influence survival and chromatin binding preferences. We also demonstrated that FCER1G and co-expressed genes in TME were related to the aggregation of leukocytes via pathway analysis. By analyzing the eQTL from the cancer genome using germline variants and TME-based RNA sequencing, we identified the eQTL in immune response genes that impact colorectal cancer characteristics and survival.
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Karimi F, Amiri-Moghaddam SM, Bagheri Z, Bahrami AR, Goshayeshi L, Allahyari A, Mirsadraee M, Fanipakdel A, Bari A, Emadi-Torghabeh A, Kerachian MA, Rahimi H, Matin MM. Investigating the association between rs6983267 polymorphism and susceptibility to gastrointestinal cancers in Iranian population. Mol Biol Rep 2021; 48:2273-2284. [PMID: 33713253 DOI: 10.1007/s11033-021-06249-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 02/24/2021] [Indexed: 11/28/2022]
Abstract
Genome-wide association studies have revealed that some single nucleotide polymorphisms at 8q24, such as rs6983267, might be effective in susceptibility to various cancers in different populations. Therefore, rs6983267 might be useful as a marker for multiple cancers. In this study, we considered a population, including 478 gastrointestinal cancer cases from the Iranian population, to investigate the association between rs6983267 and susceptibility to gastrointestinal cancers. The samples were genotyped using the TaqMan real-time PCR method while 10% of them were also confirmed by sequencing. Higher frequency of G allele was associated with higher grades of tumors in esophageal cancer and the tumors located in the lower portion of the esophagus (OR 3.56; 95% CI 1.13-11.24; P = 0.03) and cardia (OR 5.24; 95% CI 1.26-21.83; P = 0.02), which both locations are involved in esophageal adenocarcinomas with poor prognosis. The results indicated that in the male subgroup, the rs6983267 GG genotype significantly enhanced the gastric cancer susceptibility (OR 4.76; 95% CI 1.57-14.45; P = 0.01). GG genotype also increased the risk of intestinal-type gastric cancer, located in non-cardia (OR 4.62; 95% CI 1.25-17.04; P = 0.02). Moreover, gastric cancer cases and controls with a family history of gastrointestinal tumors were mostly genotyped with the G allele (OR 3.61; 95% CI = 1.09-12.01; P = 0.04). There were no remarkable associations between rs6983267 and susceptibility to esophageal and colon cancers in the Iranian population. However, different genotypes of rs6983267 had significant correlations with tumor grade, cancer type, and family history of gastrointestinal cancers. Further investigations in a larger population and other ethnicities are required to confirm these results.
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Affiliation(s)
- Farzaneh Karimi
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | | | - Zakieh Bagheri
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Ahmad Reza Bahrami
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran.,Novel Diagnostics and Therapeutics Research Group, Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Ladan Goshayeshi
- Department of Gastroenterology and Hepatology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Surgical Oncology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Abolghasem Allahyari
- Hematology and Oncology Department, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Azar Fanipakdel
- Cancer Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Alireza Bari
- Hematology and Oncology Department, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ali Emadi-Torghabeh
- Cancer Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Amin Kerachian
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Cancer Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran
| | - Hossein Rahimi
- Hematology and Oncology Department, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Maryam M Matin
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran. .,Novel Diagnostics and Therapeutics Research Group, Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran.
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Mou P, Wang H, An L, Yin Q, Chang J. RS7435335 located in the UGT2B7 gene may be a possible genetic marker for the clinical response and prognosis of breast cancer patients receiving neoadjuvant chemotherapy. J Cell Biochem 2019; 120:7167-7173. [PMID: 30552707 DOI: 10.1002/jcb.27990] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 10/08/2018] [Indexed: 01/24/2023]
Abstract
OBJECTIVE To evaluate the predictive efficacy and prognostic value of rs7435335 located in the UGT2B7 gene as a genetic marker in breast cancer patients receiving neoadjuvant chemotherapy (NAC). METHODS A total of 190 patients with breast cancer treated with NAC were enrolled to detect the rs7435335 SNP by sequenom. Miller-Payne grades were used to evaluate the treatment efficacy. The association between rs7435335 and chemotherapy efficacy and prognosis was analyzed. RESULTS Altogether, 42 cases (22.1%) achieved pathologic complete response (pCR). The results of the univariate analysis showed that rs7435335 had no statistically significant difference with pCR and Miller-Payne grades (P > 0.05). When grouping was done in accordance with the ER status, the pCR and Miller-Payne grades significantly associated with rs7435335 ( P < 0.05) only in the ER-negative group. Multivariate logistic regression analysis suggested that rs7435335 in the ER-negative group was an independent predictor of pCR ( P < 0.05). Survival analysis showed that the disease-free survival (DFS) time in patients with GA genotype was longer than that of GG genotype, and rs7435335 predicted the DFS in the ER-negative group. CONCLUSION The UGT2B7 rs7435335 is associated with the NAC efficacy and prognosis. Patients with GA genotype have better efficacy and prognosis. Rs7435335 was found to be a possible gene marker for pCR and prognosis in ER-negative patients who received NAC.
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Affiliation(s)
- Peng Mou
- Breast Surgery Department, People's Hospital of Rizhao, Rizhao, Shandong, China
| | - HuiJun Wang
- Breast Surgery Department, People's Hospital of Rizhao, Rizhao, Shandong, China
| | - Liping An
- Oncology Department, People's Hospital of Rizhao, Rizhao, Shandong, China
| | - Qiang Yin
- Breast Surgery Department, People's Hospital of Rizhao, Rizhao, Shandong, China
| | - Juan Chang
- Department of Nursing, Rizhao LanShan of People's Hospital, Rizhao, Shandong, China
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Perdomo-Pantoja A, Mejía-Pérez SI, Reynoso-Noverón N, Gómez-Flores-Ramos L, Soto-Reyes E, Sánchez-Correa TE, Guerra-Calderas L, Castro-Hernandez C, Vidal-Millán S, Sánchez-Corona J, Taja-Chayeb L, Gutiérrez O, Cacho-Diaz B, Alvarez-Gomez RM, Gómez-Amador JL, Ostrosky-Wegman P, Corona T, Herrera-Montalvo LA, Wegman-Ostrosky T. Angiotensinogen rs5050 germline genetic variant as potential biomarker of poor prognosis in astrocytoma. PLoS One 2018; 13:e0206590. [PMID: 30383794 PMCID: PMC6211735 DOI: 10.1371/journal.pone.0206590] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 10/16/2018] [Indexed: 01/11/2023] Open
Abstract
Introduction Renin-angiotensin system (RAS) in brain cancer represents a scarcely explored field in neuro-oncology. Recently, some pre- and clinical studies have reported that RAS components play a relevant role in the development and behavior of gliomas. The angiotensinogen (AGT) rs5050 genetic variant has been identified as a crucial regulator of the transcription of AGT mRNA, which makes it a logical and promising target of research. The aim of this study was to determine the relationship between the AGT rs5050 genetic variant in blood with prognosis in astrocytoma. Methods A prospective pilot study was performed on forty-eight astrocytoma patients, who received the standard-of-care treatment. Blood samples were taken prior to surgery and DNA was sequenced using Ion Torrent next-generation sequencing and analyzed by Ion Reporter software. Descriptive, bivariate, multivariate, and survival analyses were performed using SPSS v21, STATA 12 and GraphPad Prism 7. Results Median follow-up was 41 months (range 1–48). Survival analysis showed a significant difference between the rs5050 genotypes (p = .05). We found lower survival rates in individuals with the GG-genotype of rs5050 AGT compared to patients with the TT- and TG-genotype (2 months vs. 11.5 months, respectively [p = .01]). In bivariate and multivariate analyses, GG-genotype was negatively associated with survival. Conclusions In patients with astrocytoma, AGT rs5050 GG-genotype was associated with poor prognosis. We propose this germline genetic variant as a complementary biomarker, which can be detected practically and safely in blood samples or saliva.
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Affiliation(s)
- Alexander Perdomo-Pantoja
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, United States of America
- Departamento de Neurocirugía, Instituto Nacional de Neurología y Neurocirugía, "Manuel Velasco Suarez", Mexico City, Mexico
| | - Sonia Iliana Mejía-Pérez
- Departamento de Neurocirugía, Instituto Nacional de Neurología y Neurocirugía, "Manuel Velasco Suarez", Mexico City, Mexico
| | | | | | - Ernesto Soto-Reyes
- Dirección de Investigación, Instituto Nacional de Cancerología, Mexico City, Mexico
| | | | | | - Clementina Castro-Hernandez
- Unidad de Investigación Biomédica en Cáncer, Instituto de Investigaciones Biomédicas, UNAM-INCAN, Mexico City, Mexico
| | - Silvia Vidal-Millán
- Dirección de Investigación, Instituto Nacional de Cancerología, Mexico City, Mexico
| | | | - Lucia Taja-Chayeb
- Dirección de Investigación, Instituto Nacional de Cancerología, Mexico City, Mexico
| | - Olga Gutiérrez
- Dirección de Investigación, Instituto Nacional de Cancerología, Mexico City, Mexico
| | - Bernardo Cacho-Diaz
- Unidad de Neuro-oncologia, Instituto Nacional de Cancerologia, Mexico City, Mexico
| | | | - Juan Luis Gómez-Amador
- Departamento de Neurocirugía, Instituto Nacional de Neurología y Neurocirugía, "Manuel Velasco Suarez", Mexico City, Mexico
| | - Patricia Ostrosky-Wegman
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Teresa Corona
- Laboratorio Clínico de Enfermedades Neurodegenerativas, Instituto Nacional de Neurologia y Neurocirugia, "Manuel Velasco Suarez", Mexico City, Mexico
| | - Luis Alonso Herrera-Montalvo
- Dirección de Investigación, Instituto Nacional de Cancerología, Mexico City, Mexico
- Unidad de Investigación Biomédica en Cáncer, Instituto de Investigaciones Biomédicas, UNAM-INCAN, Mexico City, Mexico
| | - Talia Wegman-Ostrosky
- Dirección de Investigación, Instituto Nacional de Cancerología, Mexico City, Mexico
- * E-mail:
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Impact of Occupational Exposures and Genetic Polymorphisms on Recurrence and Progression of Non-Muscle-Invasive Bladder Cancer. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2018; 15:ijerph15081563. [PMID: 30042310 PMCID: PMC6121504 DOI: 10.3390/ijerph15081563] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 07/10/2018] [Accepted: 07/20/2018] [Indexed: 12/13/2022]
Abstract
Introduction: Additional or better markers are needed to guide the clinical monitoring of patients with non-muscle-invasive bladder cancer (NMIBC). Aim: To investigate the influence of occupational exposures and genetic polymorphisms on recurrence and progression of NMIBC. Methods: The study includes 160 NMIBC patients. We collected on questionnaire information on demographic variables, lifetime smoking history, lifetime history of occupational exposure to aromatic amines and polycyclic aromatic hydrocarbons. Genetic polymorphism (glutathione S-transferase M1; T1; P1 (GSTM1; GSTT1; GSTP1); N-acetyltransferase 1; 2 (NAT1; NAT2); cytochrome P450 1B1 (CYP1B1); sulfotransferase 1A1 (SULT1A1); myeloperoxidase (MPO); catechol-O-methyltransferase (COMT); manganese superoxide dismutase (MnSOD); NAD(P)H:quinone oxidoreductase (NQO1); X-ray repair cross-complementing group 1; 3 (XRCC1; XRCC3) and xeroderma pigmentosum complementation group (XPD)) was assessed in peripheral blood lymphocytes. DNA adducts were evaluated by 32P-postlabeling. Predictors of recurrence (histological confirmation of a newly found bladder tumor) and progression (transition of tumor from low-grade to high-grade and/or increase in TNM stage) were identified by multivariate Cox proportional hazard regression with stepwise backward selection of independent variables. Hazard ratios (HR) with 95% confidence interval (95%CI) and two-tail probability of error (p-value) were estimated. Results: The risk of BC progression decreased with the homozygous genotype “ValVal” of both COMT and MnSOD (HR = 0.195; 95%CI = 0.060 to 0.623; p = 0.006). The results on BC recurrence were of borderline significance. No occupational exposure influenced recurrence or progression. Conclusion: Our results are supported by experimental evidence of a plausible mechanism between cause (ValVal genotype of both MnSOD and COMT) and effect (decreased progression of tumor in NMIBC patients). The genetic polymorphisms associated with better prognosis may be used in clinic to guide selection of treatment for patients initially diagnosed with NMIBC. However, external validation studies are required.
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Li XP, Lan JY, Liu DQ, Zhou H, Qian MM, Wang WW, Yang M. OCA2 rs4778137 polymorphism predicts survival of breast cancer patients receiving neoadjuvant chemotherapy. Gene 2018; 651:161-165. [PMID: 29409738 DOI: 10.1016/j.gene.2018.01.100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 01/14/2018] [Accepted: 01/31/2018] [Indexed: 12/19/2022]
Abstract
BACKGROUND Genome-wide association study (GWAS) studies have showed that single nucleotide polymorphisms (SNPs) in OCA2 gene were associated with the survival of breast cancer patients treated with adjuvant chemotherapy. To further explain the association between OCA2 SNPs and breast cancer survival, we investigated the predictive value of rs4778137 located in OCA2 in local advanced breast cancer patients receiving neoadjuvant chemotherapy. PATIENTS AND METHODS A case-cohort with 150 breast cancer patients was performed to evaluate the effects of the OCA2 rs4778137 on breast cancer survival. The association between rs4778137 genotypes and pathological complete response (pCR, defined that the postoperative pathology indicating no residual invasive breast cancer in the breast or the axillary lymph node) were analyzed. Logistic regression analysis was performed to identify the independent predictors of pCR. Survival was assessed by Kaplan-Meier method and Cox regression analysis according to the rs4778137 genotypes. RESULTS The differences between pCR and the rs4778137 genotypes were statistically significant (p < 0.05). The patients with genotype GG harbored a better disease-free survival (HR: 2.358, p = 0.000) and overall survival (HR: 1.578, p = 0.008) than the patients with genotype CC in rs4778137. The further Univariate and Multivariate survival analysis revealed that SNP rs4778137 was an independent predictive factor of disease-free survival (p = 0.000/p = 0.001) and overall survival (p = 0.006/p = 0.045). CONCLUSION The OCA2 rs4778137 may be a predictor for the clinical response and survival in local advanced breast cancer patients who received neoadjuvant chemotherapy.
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Affiliation(s)
- Xiao-Ping Li
- Department of Laboratory Medicine, The Hospital Of Hangzhou Dianzi University, Hangzhou, Zhejiang, China
| | - Jian-Yun Lan
- Department of Pathology, The First People's Hospital of Yancheng City, Yancheng, Jiangsu, China
| | - Dong-Qin Liu
- Department of Pathology, Yancheng Maternity and Child Health Care Hospital, Affiliated of Yangzhou University Medical College, Yancheng, China
| | - Hang Zhou
- Department of General Surgery, The Hospital Of Hangzhou Dianzi University, Hangzhou, Zhejiang, China
| | - Miao-Miao Qian
- Department of Laboratory Medicine, The Hospital Of Hangzhou Dianzi University, Hangzhou, Zhejiang, China
| | - Wei-Wei Wang
- Department of Pathology, The First People's Hospital of Yancheng City, Yancheng, Jiangsu, China; Department of Pathology, The People's Hospital of Tinghu District, Yancheng, China.
| | - Man Yang
- Department of Laboratory Medicine, Yancheng TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Yancheng, Jiangsu, China.
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DMET™ (Drug Metabolism Enzymes and Transporters): a pharmacogenomic platform for precision medicine. Oncotarget 2018; 7:54028-54050. [PMID: 27304055 PMCID: PMC5288240 DOI: 10.18632/oncotarget.9927] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 05/29/2016] [Indexed: 02/07/2023] Open
Abstract
In the era of personalized medicine, high-throughput technologies have allowed the investigation of genetic variations underlying the inter-individual variability in drug pharmacokinetics/pharmacodynamics. Several studies have recently moved from a candidate gene-based pharmacogenetic approach to genome-wide pharmacogenomic analyses to identify biomarkers for selection of patient-tailored therapies. In this aim, the identification of genetic variants affecting the individual drug metabolism is relevant for the definition of more active and less toxic treatments. This review focuses on the potentiality, reliability and limitations of the DMET™ (Drug Metabolism Enzymes and Transporters) Plus as pharmacogenomic drug metabolism multi-gene panel platform for selecting biomarkers in the final aim to optimize drugs use and characterize the individual genetic background.
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Marcussen M, Skrubbeltrang C, Bødker JS, Christiansen I, Bøgsted M, Dybkær K, Bergmann OJ, Johnsen HE. A systematic review of molecular responses to cancer therapy in normal human mucosa. Oral Surg Oral Med Oral Pathol Oral Radiol 2017; 124:355-366. [PMID: 29042035 DOI: 10.1016/j.oooo.2017.08.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Revised: 07/24/2017] [Accepted: 08/01/2017] [Indexed: 01/19/2023]
Abstract
OBJECTIVE Cancer therapy-induced inflammation of oral and gastrointestinal mucosae affects patients nonuniformly. Preventive strategies are limited; no biomarker exists for pretreatment identification of patients likely to be severely affected. Animal models are preferred for studying molecular responses in mucosae during chemotherapy, but translation into clinical practice is difficult. We performed a systematic review to retrieve articles that described molecular changes in human mucosae during cancer therapy. STUDY DESIGN We searched MEDLINE and Ovid Embase searches for studies reported in the English language literature from January 1990 to November 2016 and studies referenced in selected articles, which analyzed mucosae from patients at risk of developing mucositis during cancer therapy. Two authors extracted data according to predefined data fields, including study quality indicators. RESULTS We identified 17 human studies on chemotherapy (n = 9) and radiotherapy (n = 8), but no studies on targeted therapy. Studies were heterogeneous with regard to patient cohorts, analysis methods, cancer treatments, biopsy timings, and correlations to clinical mucositis. Consequently, a meta-analysis was not feasible. CONCLUSIONS Few human studies described the molecular responses of the normal mucosa to cancer therapy. Studies were heterogeneous and had sparse correlations to clinical mucositis. We proposed a model for acquiring data on treatment- and disease-specific phenotypes and transcriptomes for predictive or preventive initiatives.
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Affiliation(s)
- Mette Marcussen
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark.
| | | | - Julie Støve Bødker
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark; Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
| | - Ilse Christiansen
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
| | - Martin Bøgsted
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark; Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark; Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
| | - Karen Dybkær
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark; Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark; Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
| | - Olav Jonas Bergmann
- School of Dentistry, Faculty of Health Science, Aarhus University; Aarhus, Denmark
| | - Hans Erik Johnsen
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark; Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark; Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
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11
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Dosing recommendations for pharmacogenetic interactions related to drug metabolism. Pharmacogenet Genomics 2017; 26:334-9. [PMID: 27058883 DOI: 10.1097/fpc.0000000000000220] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
OBJECTIVE Pharmacogenomic studies have established the important contribution of drug-metabolizing enzyme genotype toward drug toxicity and treatment failure; however, clinical implementation of pharmacogenomics has been slow. The aim of this study was to systematically review the information on drug-metabolizing enzyme pharmacogenomics available in the US drug labeling, practice guidelines, and recommendations. METHODS Drug-metabolizing enzyme genotype and phenotype information was assessed in US FDA drug labeling, clinical practice guidelines, and independent technology assessors to evaluate the consistency in information sources for healthcare providers. RESULTS Eighty four gene-drug pairs were identified as having drug-metabolizing enzyme genotype or phenotype information within the label. The manner in which pharmacogenomic information was presented was heterogeneous both within the label and between clinical practice recommendations. CONCLUSION For proper implementation of pharmacogenomics in clinical practice, information sources for healthcare providers should relay consistent and clear information for the appropriate use of biomarkers.
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12
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Molecular Biomarker Study in a Randomised Phase III Trial of Irinotecan Plus S-1 versus S-1 for Advanced Gastric Cancer (GC0301/TOP-002). Clin Oncol (R Coll Radiol) 2016; 28:e45-51. [DOI: 10.1016/j.clon.2016.04.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 02/29/2016] [Accepted: 03/03/2016] [Indexed: 11/22/2022]
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13
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Wang Y, Liu H, Ready NE, Su L, Wei Y, Christiani DC, Wei Q. Genetic variants in ABCG1 are associated with survival of nonsmall-cell lung cancer patients. Int J Cancer 2016; 138:2592-601. [PMID: 26757251 PMCID: PMC5294935 DOI: 10.1002/ijc.29991] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 12/14/2015] [Indexed: 01/01/2023]
Abstract
Cell membrane transporters and metabolic enzymes play a crucial role in the transportation of a wide variety of substrates that maintain homeostasis in biological processes. We explored associations between genetic variants in these genes and survival of nonsmall-cell lung cancer (NSCLC) patients by reanalyzing two datasets from published genome-wide association studies (GWASs). In the discovery by using the GWAS dataset of the Prostate, Lung, Colorectal and Ovarian (PLCO) Cancer Screening Trial, we evaluated associations of 1,245 single-nucleotide polymorphisms (SNPs) in genes of four transporter families and two metabolic enzyme families with survival of 1,185 NSCLC patients. We then performed a replication analysis in the Harvard University Lung Cancer study (LCS) with 984 NSCLC patients. Multivariate Cox proportional hazards regression and false discovery rate (FDR) corrections were performed to evaluate the associations. We identified that 21 genotyped SNPs in eight gene regions were significantly associated with survival with FDR ≤ 0.1 in the discovery dataset. Subsequently, we confirmed six SNPs, which were putative functional, in ABCG1 of the ATP-binding cassette transporter family in the replication dataset. In the pooled analysis, two tagging (at r(2) > 0.8 for linkage disequilibrium with other replicated SNPs)/functional SNPs were independently associated with survival: rs225388 G > A [adjusted hazards ratio (HR) = 1.12, 95% confidence interval (CI) = 1.03-1.20, Ptrend = 4.6 × 10(-3)] and rs225390 A > G (adjusted HR = 1.16, 95% CI = 1.07-1.25, Ptrend = 3.8 × 10(-4) ). Our results indicated that genetic variants of ABCG1 may be predictors of survival of NSCLC patients.
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Affiliation(s)
- Yanru Wang
- Duke Cancer Institute, Duke University Medical Center,
Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine,
Durham, NC 27710, USA
| | - Hongliang Liu
- Duke Cancer Institute, Duke University Medical Center,
Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine,
Durham, NC 27710, USA
| | - Neal E. Ready
- Duke Cancer Institute, Duke University Medical Center,
Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine,
Durham, NC 27710, USA
| | - Li Su
- Departments of Environmental Health and Department of
Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA
| | - Yongyue Wei
- Departments of Environmental Health and Department of
Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA
| | - David C. Christiani
- Departments of Environmental Health and Department of
Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA
- Department of Medicine, Massachusetts General Hospital,
Boston, MA 02114, USA
| | - Qingyi Wei
- Duke Cancer Institute, Duke University Medical Center,
Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine,
Durham, NC 27710, USA
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14
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Azad AK, Bairati I, Qiu X, Girgis H, Cheng L, Waggott D, Cheng D, Mirshams M, Ho J, Fortin A, Vigneault E, Huang SH, O'Sullivan B, Waldron J, Boutros PC, Goldstein D, Meyer F, Xu W, Liu G. A genome-wide association study of non-HPV-related head and neck squamous cell carcinoma identifies prognostic genetic sequence variants in the MAP-kinase and hormone pathways. Cancer Epidemiol 2016; 42:173-80. [PMID: 27173062 DOI: 10.1016/j.canep.2016.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 04/26/2016] [Accepted: 05/02/2016] [Indexed: 11/18/2022]
Abstract
BACKGROUND Carcinomas of the oral cavity, pharynx and larynx are referred to as head and neck cancers (HNC); together they account for 2-3% of all newly diagnosed cancers in North America. Between 40-50% of HNC are early diagnosed at stages I-II. The 5-year and 10-year relative survival rates are 61% and 50%, respectively. Germline genetic sequence variants (GSV) have become increasingly found to have prognostic implications in a variety of cancers. Identifying these variants may have important clinical and biological implications. METHODS We conducted a genome-wide association study (GWAS) in 531 Stage I-II radiation-treated HNC patients (originally recruited for α-tocopherol/β-carotene placebo-controlled secondary prevention study) and used a replication cohort of 566 HNC patients of all stages, of mostly non-HPV-related cancers. Survival rates were estimated by the Kaplan-Meier method. Cox proportional hazards models adjusted for potential clinical factors and principal components were used to test for associations between the GSV and overall survival (OS) in these tumors. RESULTS The median follow-up time for OS was 9.21 years (GWAS cohort) and 2.37 years (replication cohort). In both cohorts, CACNA2D1:rs2299187, ESRRG:rs946465 and ESRRG:rs1416612 were each individually significantly associated with survival. In silico analysis of ESRRG:rs946465 identifies that it produces a splice variant in ESRRG. Variant alleles of CACNA2D1:rs2299187 and ESRRG:rs946465 were associated with higher expression of the corresponding protein. CONCLUSIONS Putatively functional polymorphisms in the MAP-Kinase and estrogen pathways, identified through GWAS and replicated in an independent dataset were associated with the survival of HNC patients.
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Affiliation(s)
- Abul Kalam Azad
- Ontario Cancer Institute and Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Isabelle Bairati
- Laval University Cancer Research Center, Quebec City, QC, Canada
| | - Xin Qiu
- Ontario Cancer Institute and Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Hala Girgis
- Ontario Cancer Institute and Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Lu Cheng
- Ontario Cancer Institute and Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Daryl Waggott
- Informatics & Biocomputing Platform, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Dangxiao Cheng
- Ontario Cancer Institute and Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Maryam Mirshams
- Ontario Cancer Institute and Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - James Ho
- Ontario Cancer Institute and Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - André Fortin
- Laval University Cancer Research Center, Quebec City, QC, Canada
| | - Eric Vigneault
- Laval University Cancer Research Center, Quebec City, QC, Canada
| | - Shao-Hui Huang
- Ontario Cancer Institute and Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Brian O'Sullivan
- Ontario Cancer Institute and Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - John Waldron
- Ontario Cancer Institute and Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Paul C Boutros
- Informatics & Biocomputing Platform, Ontario Institute for Cancer Research, Toronto, ON, Canada,; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada,; Department of Pharmacology & Toxicology, University of Toronto, Toronto, ON, Canada
| | - David Goldstein
- Ontario Cancer Institute and Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Francois Meyer
- Laval University Cancer Research Center, Quebec City, QC, Canada
| | - Wei Xu
- Ontario Cancer Institute and Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Geoffrey Liu
- Ontario Cancer Institute and Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada,; Department of Environmental Health, Harvard School of Public Health, Boston, MA, USA.
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15
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Deenen MJ, Meulendijks D, Cats A, Sechterberger MK, Severens JL, Boot H, Smits PH, Rosing H, Mandigers CMPW, Soesan M, Beijnen JH, Schellens JHM. Upfront Genotyping of DPYD*2A to Individualize Fluoropyrimidine Therapy: A Safety and Cost Analysis. J Clin Oncol 2015; 34:227-34. [PMID: 26573078 DOI: 10.1200/jco.2015.63.1325] [Citation(s) in RCA: 233] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
PURPOSE Fluoropyrimidines are frequently prescribed anticancer drugs. A polymorphism in the fluoropyrimidine metabolizing enzyme dihydropyrimidine dehydrogenase (DPD; ie, DPYD*2A) is strongly associated with fluoropyrimidine-induced severe and life-threatening toxicity. This study determined the feasibility, safety, and cost of DPYD*2A genotype-guided dosing. PATIENTS AND METHODS Patients intended to be treated with fluoropyrimidine-based chemotherapy were prospectively genotyped for DPYD*2A before start of therapy. Variant allele carriers received an initial dose reduction of ≥ 50% followed by dose titration based on tolerance. Toxicity was the primary end point and was compared with historical controls (ie, DPYD*2A variant allele carriers receiving standard dose described in literature) and with DPYD*2A wild-type patients treated with the standard dose in this study. Secondary end points included a model-based cost analysis, as well as pharmacokinetic and DPD enzyme activity analyses. RESULTS A total of 2,038 patients were prospectively screened for DPYD*2A, of whom 22 (1.1%) were heterozygous polymorphic. DPYD*2A variant allele carriers were treated with a median dose-intensity of 48% (range, 17% to 91%). The risk of grade ≥ 3 toxicity was thereby significantly reduced from 73% (95% CI, 58% to 85%) in historical controls (n = 48) to 28% (95% CI, 10% to 53%) by genotype-guided dosing (P < .001); drug-induced death was reduced from 10% to 0%. Adequate treatment of genotype-guided dosing was further demonstrated by a similar incidence of grade ≥ 3 toxicity compared with wild-type patients receiving the standard dose (23%; P = .64) and by similar systemic fluorouracil (active drug) exposure. Furthermore, average total treatment cost per patient was lower for screening (€2,772 [$3,767]) than for nonscreening (€2,817 [$3,828]), outweighing screening costs. CONCLUSION DPYD*2A is strongly associated with fluoropyrimidine-induced severe and life-threatening toxicity. DPYD*2A genotype-guided dosing results in adequate systemic drug exposure and significantly improves safety of fluoropyrimidine therapy for the individual patient. On a population level, upfront genotyping seemed cost saving.
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Affiliation(s)
- Maarten J Deenen
- Maarten J. Deenen, Didier Meulendijks, Annemieke Cats, Marjolein K. Sechterberger, Henk Boot, Hilde Rosing, Jos H. Beijnen, and Jan H.M. Schellens, Netherlands Cancer Institute; Paul H. Smits and Marcel Soesan, Slotervaart Hospital, Amsterdam; Johan L. Severens, Erasmus University Medical Center, Rotterdam; Caroline M.P.W. Mandigers, Canisius Wilhelmina Hospital, Nijmegen; and Jos H. Beijnen and Jan H.M. Schellens, Utrecht University, Utrecht, the Netherlands
| | - Didier Meulendijks
- Maarten J. Deenen, Didier Meulendijks, Annemieke Cats, Marjolein K. Sechterberger, Henk Boot, Hilde Rosing, Jos H. Beijnen, and Jan H.M. Schellens, Netherlands Cancer Institute; Paul H. Smits and Marcel Soesan, Slotervaart Hospital, Amsterdam; Johan L. Severens, Erasmus University Medical Center, Rotterdam; Caroline M.P.W. Mandigers, Canisius Wilhelmina Hospital, Nijmegen; and Jos H. Beijnen and Jan H.M. Schellens, Utrecht University, Utrecht, the Netherlands
| | - Annemieke Cats
- Maarten J. Deenen, Didier Meulendijks, Annemieke Cats, Marjolein K. Sechterberger, Henk Boot, Hilde Rosing, Jos H. Beijnen, and Jan H.M. Schellens, Netherlands Cancer Institute; Paul H. Smits and Marcel Soesan, Slotervaart Hospital, Amsterdam; Johan L. Severens, Erasmus University Medical Center, Rotterdam; Caroline M.P.W. Mandigers, Canisius Wilhelmina Hospital, Nijmegen; and Jos H. Beijnen and Jan H.M. Schellens, Utrecht University, Utrecht, the Netherlands
| | - Marjolein K Sechterberger
- Maarten J. Deenen, Didier Meulendijks, Annemieke Cats, Marjolein K. Sechterberger, Henk Boot, Hilde Rosing, Jos H. Beijnen, and Jan H.M. Schellens, Netherlands Cancer Institute; Paul H. Smits and Marcel Soesan, Slotervaart Hospital, Amsterdam; Johan L. Severens, Erasmus University Medical Center, Rotterdam; Caroline M.P.W. Mandigers, Canisius Wilhelmina Hospital, Nijmegen; and Jos H. Beijnen and Jan H.M. Schellens, Utrecht University, Utrecht, the Netherlands
| | - Johan L Severens
- Maarten J. Deenen, Didier Meulendijks, Annemieke Cats, Marjolein K. Sechterberger, Henk Boot, Hilde Rosing, Jos H. Beijnen, and Jan H.M. Schellens, Netherlands Cancer Institute; Paul H. Smits and Marcel Soesan, Slotervaart Hospital, Amsterdam; Johan L. Severens, Erasmus University Medical Center, Rotterdam; Caroline M.P.W. Mandigers, Canisius Wilhelmina Hospital, Nijmegen; and Jos H. Beijnen and Jan H.M. Schellens, Utrecht University, Utrecht, the Netherlands
| | - Henk Boot
- Maarten J. Deenen, Didier Meulendijks, Annemieke Cats, Marjolein K. Sechterberger, Henk Boot, Hilde Rosing, Jos H. Beijnen, and Jan H.M. Schellens, Netherlands Cancer Institute; Paul H. Smits and Marcel Soesan, Slotervaart Hospital, Amsterdam; Johan L. Severens, Erasmus University Medical Center, Rotterdam; Caroline M.P.W. Mandigers, Canisius Wilhelmina Hospital, Nijmegen; and Jos H. Beijnen and Jan H.M. Schellens, Utrecht University, Utrecht, the Netherlands
| | - Paul H Smits
- Maarten J. Deenen, Didier Meulendijks, Annemieke Cats, Marjolein K. Sechterberger, Henk Boot, Hilde Rosing, Jos H. Beijnen, and Jan H.M. Schellens, Netherlands Cancer Institute; Paul H. Smits and Marcel Soesan, Slotervaart Hospital, Amsterdam; Johan L. Severens, Erasmus University Medical Center, Rotterdam; Caroline M.P.W. Mandigers, Canisius Wilhelmina Hospital, Nijmegen; and Jos H. Beijnen and Jan H.M. Schellens, Utrecht University, Utrecht, the Netherlands
| | - Hilde Rosing
- Maarten J. Deenen, Didier Meulendijks, Annemieke Cats, Marjolein K. Sechterberger, Henk Boot, Hilde Rosing, Jos H. Beijnen, and Jan H.M. Schellens, Netherlands Cancer Institute; Paul H. Smits and Marcel Soesan, Slotervaart Hospital, Amsterdam; Johan L. Severens, Erasmus University Medical Center, Rotterdam; Caroline M.P.W. Mandigers, Canisius Wilhelmina Hospital, Nijmegen; and Jos H. Beijnen and Jan H.M. Schellens, Utrecht University, Utrecht, the Netherlands
| | - Caroline M P W Mandigers
- Maarten J. Deenen, Didier Meulendijks, Annemieke Cats, Marjolein K. Sechterberger, Henk Boot, Hilde Rosing, Jos H. Beijnen, and Jan H.M. Schellens, Netherlands Cancer Institute; Paul H. Smits and Marcel Soesan, Slotervaart Hospital, Amsterdam; Johan L. Severens, Erasmus University Medical Center, Rotterdam; Caroline M.P.W. Mandigers, Canisius Wilhelmina Hospital, Nijmegen; and Jos H. Beijnen and Jan H.M. Schellens, Utrecht University, Utrecht, the Netherlands
| | - Marcel Soesan
- Maarten J. Deenen, Didier Meulendijks, Annemieke Cats, Marjolein K. Sechterberger, Henk Boot, Hilde Rosing, Jos H. Beijnen, and Jan H.M. Schellens, Netherlands Cancer Institute; Paul H. Smits and Marcel Soesan, Slotervaart Hospital, Amsterdam; Johan L. Severens, Erasmus University Medical Center, Rotterdam; Caroline M.P.W. Mandigers, Canisius Wilhelmina Hospital, Nijmegen; and Jos H. Beijnen and Jan H.M. Schellens, Utrecht University, Utrecht, the Netherlands
| | - Jos H Beijnen
- Maarten J. Deenen, Didier Meulendijks, Annemieke Cats, Marjolein K. Sechterberger, Henk Boot, Hilde Rosing, Jos H. Beijnen, and Jan H.M. Schellens, Netherlands Cancer Institute; Paul H. Smits and Marcel Soesan, Slotervaart Hospital, Amsterdam; Johan L. Severens, Erasmus University Medical Center, Rotterdam; Caroline M.P.W. Mandigers, Canisius Wilhelmina Hospital, Nijmegen; and Jos H. Beijnen and Jan H.M. Schellens, Utrecht University, Utrecht, the Netherlands
| | - Jan H M Schellens
- Maarten J. Deenen, Didier Meulendijks, Annemieke Cats, Marjolein K. Sechterberger, Henk Boot, Hilde Rosing, Jos H. Beijnen, and Jan H.M. Schellens, Netherlands Cancer Institute; Paul H. Smits and Marcel Soesan, Slotervaart Hospital, Amsterdam; Johan L. Severens, Erasmus University Medical Center, Rotterdam; Caroline M.P.W. Mandigers, Canisius Wilhelmina Hospital, Nijmegen; and Jos H. Beijnen and Jan H.M. Schellens, Utrecht University, Utrecht, the Netherlands.
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Snowsill T, Huxley N, Hoyle M, Jones-Hughes T, Coelho H, Cooper C, Frayling I, Hyde C. A systematic review and economic evaluation of diagnostic strategies for Lynch syndrome. Health Technol Assess 2015; 18:1-406. [PMID: 25244061 DOI: 10.3310/hta18580] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Lynch syndrome (LS) is an inherited autosomal dominant disorder characterised by an increased risk of colorectal cancer (CRC) and other cancers, and caused by mutations in the deoxyribonucleic acid (DNA) mismatch repair genes. OBJECTIVE To evaluate the accuracy and cost-effectiveness of strategies to identify LS in newly diagnosed early-onset CRC patients (aged < 50 years). Cascade testing of relatives is employed in all strategies for individuals in whom LS is identified. DATA SOURCES AND METHODS Systematic reviews were conducted of the test accuracy of microsatellite instability (MSI) testing or immunohistochemistry (IHC) in individuals with CRC at risk of LS, and of economic evidence relating to diagnostic strategies for LS. Reviews were carried out in April 2012 (test accuracy); and in February 2012, repeated in February 2013 (economic evaluations). Databases searched included MEDLINE (1946 to April week 3, 2012), EMBASE (1980 to week 17, 2012) and Web of Science (inception to 30 April 2012), and risk of bias for test accuracy was assessed using the Quality Assessment of Diagnostic Accuracy Studies-2 (QUADAS-2) quality appraisal tool. A de novo economic model of diagnostic strategies for LS was developed. RESULTS Inconsistencies in study designs precluded pooling of diagnostic test accuracy results from a previous systematic review and nine subsequent primary studies. These were of mixed quality, with significant methodological concerns identified for most. IHC and MSI can both play a part in diagnosing LS but neither is gold standard. No UK studies evaluated the cost-effectiveness of diagnosing and managing LS, although studies from other countries generally found some strategies to be cost-effective compared with no testing. The de novo model demonstrated that all strategies were cost-effective compared with no testing at a threshold of £20,000 per quality-adjusted life-year (QALY), with the most cost-effective strategy utilising MSI and BRAF testing [incremental cost-effectiveness ratio (ICER) = £5491 per QALY]. The maximum health benefit to the population of interest would be obtained using universal germline testing, but this would not be a cost-effective use of NHS resources compared with the next best strategy. When the age limit was raised from 50 to 60 and 70 years, the ICERs compared with no testing increased but remained below £20,000 per QALY (except for universal germline testing with an age limit of 70 years). The total net health benefit increased with the age limit as more individuals with LS were identified. Uncertainty was evaluated through univariate sensitivity analyses, which suggested that the parameters substantially affecting cost-effectiveness: were the risk of CRC for individuals with LS; the average number of relatives identified per index patient; the effectiveness of colonoscopy in preventing metachronous CRC; the cost of colonoscopy; the duration of the psychological impact of genetic testing on health-related quality of life (HRQoL); and the impact of prophylactic hysterectomy and bilateral salpingo-oophorectomy on HRQoL (this had the potential to make all testing strategies more expensive and less effective than no testing). LIMITATIONS The absence of high-quality data for the impact of prophylactic gynaecological surgery and the psychological impact of genetic testing on HRQoL is an acknowledged limitation. CONCLUSIONS Results suggest that reflex testing for LS in newly diagnosed CRC patients aged < 50 years is cost-effective. Such testing may also be cost-effective in newly diagnosed CRC patients aged < 60 or < 70 years. Results are subject to uncertainty due to a number of parameters, for some of which good estimates were not identified. We recommend future research to estimate the cost-effectiveness of testing for LS in individuals with newly diagnosed endometrial or ovarian cancer, and the inclusion of aspirin chemoprevention. Further research is required to accurately estimate the impact of interventions on HRQoL. STUDY REGISTRATION This study is registered as PROSPERO CRD42012002436. FUNDING The National Institute for Health Research Health Technology Assessment programme.
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Affiliation(s)
- Tristan Snowsill
- Peninsula Technology Assessment Group (PenTAG), University of Exeter Medical School, Exeter, UK
| | - Nicola Huxley
- Peninsula Technology Assessment Group (PenTAG), University of Exeter Medical School, Exeter, UK
| | - Martin Hoyle
- Peninsula Technology Assessment Group (PenTAG), University of Exeter Medical School, Exeter, UK
| | - Tracey Jones-Hughes
- Peninsula Technology Assessment Group (PenTAG), University of Exeter Medical School, Exeter, UK
| | - Helen Coelho
- Peninsula Technology Assessment Group (PenTAG), University of Exeter Medical School, Exeter, UK
| | - Chris Cooper
- Peninsula Technology Assessment Group (PenTAG), University of Exeter Medical School, Exeter, UK
| | - Ian Frayling
- Institute of Medical Genetics, Cardiff University, Cardiff, UK
| | - Chris Hyde
- Peninsula Technology Assessment Group (PenTAG), University of Exeter Medical School, Exeter, UK
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17
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Genetic polymorphisms in cytochrome P450 and clinical outcomes of FOLFIRI chemotherapy in patients with metastatic colorectal cancer. Tumour Biol 2015; 36:7691-8. [DOI: 10.1007/s13277-015-3492-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 04/23/2015] [Indexed: 12/18/2022] Open
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Clinical validity of new genetic biomarkers of irinotecan neutropenia: an independent replication study. THE PHARMACOGENOMICS JOURNAL 2015; 16:54-9. [PMID: 25869015 DOI: 10.1038/tpj.2015.23] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 12/04/2014] [Accepted: 01/28/2015] [Indexed: 01/26/2023]
Abstract
The overall goal of this study was to provide evidence for the clinical validity of nine genetic variants in five genes previously associated with irinotecan neutropenia and pharmacokinetics. Variants associated with absolute neutrophil count (ANC) nadir and/or irinotecan pharmacokinetics in a discovery cohort of cancer patients were genotyped in an independent replication cohort of 108 cancer patients. Patients received single-agent irinotecan every 3 weeks. For ANC nadir, we replicated UGT1A1*28, UGT1A1*93 and SLCO1B1*1b in univariate analyses. For irinotecan area under the concentration-time curve (AUC0-24), we replicated ABCC2 -24C>T; however, ABCC2 -24C>T only predicted a small fraction of the variance. For SN-38 AUC0-24 and the glucuronidation ratio, we replicated UGT1A1*28 and UGT1A1*93. In addition to UGT1A1*28, this study independently validated UGT1A1*93 and SLCO1B1*1b as new predictors of irinotecan neutropenia. Further demonstration of their clinical utility will optimize irinotecan therapy in cancer patients.
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Pezzolo E, Modena Y, Corso B, Giusti P, Gusella M. Germ line polymorphisms as predictive markers for pre-surgical radiochemotherapy in locally advanced rectal cancer: a 5-year literature update and critical review. Eur J Clin Pharmacol 2015; 71:529-39. [PMID: 25740678 DOI: 10.1007/s00228-015-1824-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 02/11/2015] [Indexed: 12/19/2022]
Abstract
PURPOSE Locally advanced rectal cancer is currently treated with pre-surgical radiotherapy and chemotherapy. Approximately one-half of patients obtain a relevant shrinkage/disappearance of tumour, with major clinical advantages. The remaining patients, in contrast, show no benefit and possibly need alternative treatment. To provide the best therapeutic option for each individual patient, predictive markers have been widely researched. This review was undertaken to evaluate recent progress made in this field. METHODS A systematic literature search was performed using PubMed and Scopus database, focused on germ line gene polymorphisms as biomarkers and response and toxicity as outcomes. Because an exhaustive previous review was available describing findings up to 2008, we restricted our analysis to the last 5 years. RESULTS Ten original research articles were found, reporting promising results for some candidate genes in drug metabolism (TYMS, MTHFR), DNA repair (XRCC1, OGG1, CCND1) and inflammation (SOD2, TGFB1)/immunity (IL13) pathways, but with no firm conclusion. All the studies had small sample size and were defined as exploratory. This review highlights pivotal molecular, clinical, genetic and statistical issues in the investigation of genetic polymorphisms as outcome predictors for rectal cancer and offers suggestions for future development. CONCLUSIONS What emerges is a clear need for new proposals, especially in view of the increasing evidence for tumour-host and gene-gene interactions during anticancer treatment, together with stronger adherence to proper methodological requirements.
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Affiliation(s)
- Elisa Pezzolo
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Largo Meneghetti, 2, 35131, Padua, Italy,
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LGR5 rs17109924 is a predictive genetic biomarker for time to recurrence in patients with colon cancer treated with 5-fluorouracil-based adjuvant chemotherapy. THE PHARMACOGENOMICS JOURNAL 2015; 15:391-6. [PMID: 25665511 PMCID: PMC4762902 DOI: 10.1038/tpj.2015.2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 10/13/2014] [Accepted: 12/02/2014] [Indexed: 01/03/2023]
Abstract
We recently found variants in cancer stem cell genes (CD44, ALCAM and LGR5) significantly associated with increased time to recurrence (TTR) in patients with stage III and high-risk stage II colon cancer treated with 5-fluorouracil (5-FU)-based chemotherapy. In this study, we validated these genetic biomarkers in a large and independent patient cohort (n=599). Patients who received 5-FU-based adjuvant chemotherapy (n=391) carrying at least one C allele in LGR5 rs17109924 had a significantly increased TTR compared with patients carrying the homozygous T/T variant (HR 0.38, 95%CI 0.19–0.79; P=0.006). In patients treated with surgery alone (n=208), no association between LGR rs17109924 and TTR was found (P=0.728). In the multivariate Cox-analysis, LGR5 rs17109924 remained statistically significant (HR 0.38, 95%CI 0.18–0.78; P=0.008) for patients who received adjuvant chemotherapy. We confirmed in a large and independent study cohort that LGR5 rs17109924 is a predictive genetic biomarker for TTR in patients with colon cancer treated with 5-FU-based adjuvant chemotherapy.
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Ceppi F, Cazzaniga G, Colombini A, Biondi A, Conter V. Risk factors for relapse in childhood acute lymphoblastic leukemia: prediction and prevention. Expert Rev Hematol 2014; 8:57-70. [PMID: 25367188 DOI: 10.1586/17474086.2015.978281] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
With current treatment regimens, survival rates for acute lymphoblastic leukemia (ALL) have improved dramatically since the 1980s, with current 5-year overall survival rates estimated at greater than 85%. This success was achieved, in part, through the implementation of risk-stratified therapy. Nevertheless, for a subgroup of patients (15-20%) with newly diagnosed ALL who will ultimately relapse, traditional risk assessment remains inadequate. The risk of relapse may be estimated on the basis of diagnostic features or early treatment response findings. Further progress in this field may thus come from refinement of predictive factors for relapse and treatment adaptation and from the identification of biological subsets of ALL patients who could benefit from specific target therapies. This article summarizes the aspects associated with the identification of predictive factors for relapse in childhood ALL and options available for prevention of disease recurrence.
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Affiliation(s)
- Francesco Ceppi
- Division of Haematology/Oncology, The Hospital for Sick Children and University of Toronto, Toronto, Ontario, Canada
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22
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Multi-agent chemotherapy overcomes glucocorticoid resistance conferred by a BIM deletion polymorphism in pediatric acute lymphoblastic leukemia. PLoS One 2014; 9:e103435. [PMID: 25090024 PMCID: PMC4121131 DOI: 10.1371/journal.pone.0103435] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 06/29/2014] [Indexed: 12/03/2022] Open
Abstract
A broad range of anti-cancer agents, including glucocorticoids (GCs) and tyrosine kinase inhibitors (TKIs), kill cells by upregulating the pro-apoptotic BCL2 family member, BIM. A common germline deletion in the BIM gene was recently shown to favor the production of non-apoptotic BIM isoforms, and to predict inferior responses in TKI-treated chronic myeloid leukemia (CML) and EGFR-driven lung cancer patients. Given that both in vitro and in vivo GC resistance are predictive of adverse outcomes in acute lymphoblastic leukemia (ALL), we hypothesized that this polymorphism would mediate GC resistance, and serve as a biomarker of poor response in ALL. Accordingly, we used zinc finger nucleases to generate ALL cell lines with the BIM deletion, and confirmed the ability of the deletion to mediate GC resistance in vitro. In contrast to CML and lung cancer, the BIM deletion did not predict for poorer clinical outcome in a retrospective analysis of 411 pediatric ALL patients who were uniformly treated with GCs and chemotherapy. Underlying the lack of prognostic significance, we found that the chemotherapy agents used in our cohort (vincristine, L-asparaginase, and methotrexate) were each able to induce ALL cell death in a BIM-independent fashion, and resensitize BIM deletion-containing cells to GCs. Together, our work demonstrates how effective therapy can overcome intrinsic resistance in ALL patients, and suggests the potential of using combinations of drugs that work via divergent mechanisms of cell killing to surmount BIM deletion-mediated drug resistance in other cancers.
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Ng CKY, Weigelt B, A’Hern R, Bidard FC, Lemetre C, Swanton C, Shen R, Reis-Filho JS. Predictive performance of microarray gene signatures: impact of tumor heterogeneity and multiple mechanisms of drug resistance. Cancer Res 2014; 74:2946-2961. [PMID: 24706696 PMCID: PMC4040235 DOI: 10.1158/0008-5472.can-13-3375] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Gene signatures have failed to predict responses to breast cancer therapy in patients to date. In this study, we used bioinformatic methods to explore the hypothesis that the existence of multiple drug resistance mechanisms in different patients may limit the power of gene signatures to predict responses to therapy. In addition, we explored whether substratification of resistant cases could improve performance. Gene expression profiles from 1,550 breast cancers analyzed with the same microarray platform were retrieved from publicly available sources. Gene expression changes were introduced in cases defined as sensitive or resistant to a hypothetical therapy. In the resistant group, up to five different mechanisms of drug resistance causing distinct or overlapping gene expression changes were generated bioinformatically, and their impact on sensitivity, specificity, and predictive values of the signatures was investigated. We found that increasing the number of resistance mechanisms corresponding to different gene expression changes weakened the performance of the predictive signatures generated, even if the resistance-induced changes in gene expression were sufficiently strong and informative. Performance was also affected by cohort composition and the proportion of sensitive versus resistant cases or resistant cases that were mechanistically distinct. It was possible to improve response prediction by substratifying chemotherapy-resistant cases from actual datasets (non-bioinformatically perturbed datasets) and by using outliers to model multiple resistance mechanisms. Our work supports the hypothesis that the presence of multiple resistance mechanisms in a given therapy in patients limits the ability of gene signatures to make clinically useful predictions.
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Affiliation(s)
- Charlotte K. Y. Ng
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Roger A’Hern
- Cancer Research UK Clinical Trials Unit, The Institute of Cancer Research, Sutton, SM2 5NG, UK
| | | | - Christophe Lemetre
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Charles Swanton
- Cancer Research UK London Research Institute, London, WC2A 3LY, UK
- University College London Cancer Institute, London, WC1E 6BT, UK
| | - Ronglai Shen
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jorge S. Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
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Eng L, Liu G. VEGF pathway polymorphisms as prognostic and pharmacogenetic factors in cancer: a 2013 update. Pharmacogenomics 2014; 14:1659-67. [PMID: 24088136 DOI: 10.2217/pgs.13.165] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
With the recent advances in genomic medicine and the development of targeted antiangiogenic therapy for cancer patients, there has been an increased interest in the role of predictive and prognostic markers for antiangiogenic therapy. Here, we provide a summary of the angiogenesis pathway, the role of predictive and prognostic markers in cancer and a summary of the current literature and studies on predictive and prognostic markers for antiangiogenic therapy. Our aim is to summarize those studies that are currently in the literature with an emphasis on the future directions of the field from 2013 and beyond. We conclude by providing our perspective on the future directions of this growing field, as well as possible challenges and pitfalls along the way.
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Affiliation(s)
- Lawson Eng
- Division of Medical Oncology & Hematology, Department of Medicine, Princess Margaret Hospital/University of Toronto, Toronto, ON, Canada
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25
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Bodian DL, McCutcheon JN, Kothiyal P, Huddleston KC, Iyer RK, Vockley JG, Niederhuber JE. Germline variation in cancer-susceptibility genes in a healthy, ancestrally diverse cohort: implications for individual genome sequencing. PLoS One 2014; 9:e94554. [PMID: 24728327 PMCID: PMC3984285 DOI: 10.1371/journal.pone.0094554] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 02/17/2014] [Indexed: 01/05/2023] Open
Abstract
Technological advances coupled with decreasing costs are bringing whole genome and whole exome sequencing closer to routine clinical use. One of the hurdles to clinical implementation is the high number of variants of unknown significance. For cancer-susceptibility genes, the difficulty in interpreting the clinical relevance of the genomic variants is compounded by the fact that most of what is known about these variants comes from the study of highly selected populations, such as cancer patients or individuals with a family history of cancer. The genetic variation in known cancer-susceptibility genes in the general population has not been well characterized to date. To address this gap, we profiled the nonsynonymous genomic variation in 158 genes causally implicated in carcinogenesis using high-quality whole genome sequences from an ancestrally diverse cohort of 681 healthy individuals. We found that all individuals carry multiple variants that may impact cancer susceptibility, with an average of 68 variants per individual. Of the 2,688 allelic variants identified within the cohort, most are very rare, with 75% found in only 1 or 2 individuals in our population. Allele frequencies vary between ancestral groups, and there are 21 variants for which the minor allele in one population is the major allele in another. Detailed analysis of a selected subset of 5 clinically important cancer genes, BRCA1, BRCA2, KRAS, TP53, and PTEN, highlights differences between germline variants and reported somatic mutations. The dataset can serve a resource of genetic variation in cancer-susceptibility genes in 6 ancestry groups, an important foundation for the interpretation of cancer risk from personal genome sequences.
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Affiliation(s)
- Dale L. Bodian
- Inova Translational Medicine Institute, Inova Health System, Falls Church, Virginia, United States of America
| | - Justine N. McCutcheon
- Inova Translational Medicine Institute, Inova Health System, Falls Church, Virginia, United States of America
| | - Prachi Kothiyal
- Inova Translational Medicine Institute, Inova Health System, Falls Church, Virginia, United States of America
| | - Kathi C. Huddleston
- Inova Translational Medicine Institute, Inova Health System, Falls Church, Virginia, United States of America
| | - Ramaswamy K. Iyer
- Inova Translational Medicine Institute, Inova Health System, Falls Church, Virginia, United States of America
| | - Joseph G. Vockley
- Inova Translational Medicine Institute, Inova Health System, Falls Church, Virginia, United States of America
- * E-mail:
| | - John E. Niederhuber
- Inova Translational Medicine Institute, Inova Health System, Falls Church, Virginia, United States of America
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Gillis NK, Patel JN, Innocenti F. Clinical implementation of germ line cancer pharmacogenetic variants during the next-generation sequencing era. Clin Pharmacol Ther 2014; 95:269-80. [PMID: 24136381 PMCID: PMC4128332 DOI: 10.1038/clpt.2013.214] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 10/12/2013] [Indexed: 01/13/2023]
Abstract
More than 100 medications approved by the US Food and Drug Administration include pharmacogenetic biomarkers in the drug label, many with cancer indications referencing germ line DNA variations. With the advent of next-generation sequencing (NGS) and its rapidly increasing uptake into cancer research and clinical practice, an enormous amount of data to inform documented gene-drug associations will be collected that must be exploited to optimize patient benefit. This review focuses on the implementation of germ line cancer pharmacogenetics in clinical practice. Specifically, it discusses the importance of germ line variation in cancer and the role of NGS in pharmacogenetic discovery and implementation. In the context of a scenario in which massive amounts of NGS-based genetic information will be increasingly available to health stakeholders, this review explores the ongoing debate regarding the threshold of evidence necessary for implementation, provides an overview of recommendations in cancer by professional organizations and regulatory bodies, and discusses limitations of current guidelines and strategies to improve third-party coverage.
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Affiliation(s)
- Nancy K. Gillis
- Eshelman School of Pharmacy, Institute for Pharmacogenomics and Individualized Therapy, University of North Carolina, Chapel Hill, NC
| | - Jai N. Patel
- Eshelman School of Pharmacy, Institute for Pharmacogenomics and Individualized Therapy, University of North Carolina, Chapel Hill, NC
- Levine Cancer Institute, Carolinas HealthCare System, Charlotte, NC
| | - Federico Innocenti
- Eshelman School of Pharmacy, Institute for Pharmacogenomics and Individualized Therapy, University of North Carolina, Chapel Hill, NC
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina, Chapel Hill, NC
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27
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Grotenhuis AJ, Dudek AM, Verhaegh GW, Witjes JA, Aben KK, van der Marel SL, Vermeulen SH, Kiemeney LA. Prognostic relevance of urinary bladder cancer susceptibility loci. PLoS One 2014; 9:e89164. [PMID: 24586564 PMCID: PMC3934869 DOI: 10.1371/journal.pone.0089164] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 01/16/2014] [Indexed: 12/13/2022] Open
Abstract
In the last few years, susceptibility loci have been identified for urinary bladder cancer (UBC) through candidate-gene and genome-wide association studies. Prognostic relevance of most of these loci is yet unknown. In this study, we used data of the Nijmegen Bladder Cancer Study (NBCS) to perform a comprehensive evaluation of the prognostic relevance of all confirmed UBC susceptibility loci. Detailed clinical data concerning diagnosis, stage, treatment, and disease course of a population-based series of 1,602 UBC patients were collected retrospectively based on a medical file survey. Kaplan-Meier survival analyses and Cox proportional hazard regression were performed, and log-rank tests calculated, to evaluate the association between 12 confirmed UBC susceptibility variants and recurrence and progression in non-muscle invasive bladder cancer (NMIBC) patients. Among muscle-invasive or metastatic bladder cancer (MIBC) patients, association of these variants with overall survival was tested. Subgroup analyses by tumor aggressiveness and smoking status were performed in NMIBC patients. In the overall NMIBC group (n = 1,269), a statistically significant association between rs9642880 at 8q24 and risk of progression was observed (GT vs. TT: HR = 1.08 (95% CI: 0.76-1.54), GG vs. TT: HR = 1.81 (95% CI: 1.23-2.66), P for trend = 2.6 × 10(-3)). In subgroup analyses, several other variants showed suggestive, though non-significant, prognostic relevance for recurrence and progression in NMIBC and survival in MIBC. This study provides suggestive evidence that genetic loci involved in UBC etiology may influence disease prognosis. Elucidation of the causal variant(s) could further our understanding of the mechanism of disease, could point to new therapeutic targets, and might aid in improvement of prognostic tools.
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Affiliation(s)
- Anne J. Grotenhuis
- Department for Health Evidence, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Aleksandra M. Dudek
- Department of Urology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Gerald W. Verhaegh
- Department of Urology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - J. Alfred Witjes
- Department of Urology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Katja K. Aben
- Department for Health Evidence, Radboud University Medical Center, Nijmegen, The Netherlands
- Comprehensive Cancer Center The Netherlands, Utrecht, The Netherlands
| | | | - Sita H. Vermeulen
- Department for Health Evidence, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lambertus A. Kiemeney
- Department for Health Evidence, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Urology, Radboud University Medical Center, Nijmegen, The Netherlands
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Szkandera J, Pichler M, Absenger G, Stotz M, Weissmueller M, Samonigg H, Asslaber M, Lax S, Leitner G, Winder T, Renner W, Gerger A. A functional germline variant in GLI1 implicates hedgehog signaling in clinical outcome of stage II and III colon carcinoma patients. Clin Cancer Res 2014; 20:1687-97. [PMID: 24470513 DOI: 10.1158/1078-0432.ccr-13-1517] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Cumulating evidence indicates that germline variants in the Wnt, Notch, and Hedgehog pathways are involved in colon carcinoma progression and metastasis. We investigated germline polymorphisms in a comprehensive panel of Wnt, Notch, and Hedgehog pathway genes to predict time to recurrence (TTR) and overall survival in patients with stage II and III colon carcinoma. EXPERIMENTAL DESIGN A total of 742 consecutively collected patients with stage II and III colon carcinoma were included in this retrospective study. Genomic DNA was analyzed for 18 germline polymorphisms in Wnt, Notch, and Hedgehog pathway genes (SFRP, DKK 2 and 3, AXIN2, APC, MYC, TCF7L2, NOTCH2, and GLI1) by TaqMan 5'-exonuclease assays. RESULTS In univariate analysis, the homozygous mutant variant of GLI1 rs2228226 G>C was significantly associated with decreased TTR in a recessive genetic model after adjustment for multiple testing [HR = 2.35; confidence interval (95% CI), 1.48-3.74; P < 0.001] and remained significant in multivariate analysis including clinical stage, lymphovascular-, vascular-, and perineural-invasion (HR = 2.43; CI 95%, 1.52-3.87; P < 0.001). In subanalyses, the association was limited to patients with surgery alone (HR = 3.21; CI 95%, 1.59-6.49; P = 0.001), in contrast with patients with adjuvant chemotherapy (HR = 0.82; CI 95%, 0.35-1.95; P = 0.657). When the subgroup of patients with "high-risk" GLI1 rs2228226 C/C genotype was analyzed, no benefit of adjuvant 5-fluorouracil-based chemotherapy could be found. CONCLUSION This is the first study identifying GLI1 rs2228226 G>C as an independent prognostic marker in patients with stage II and III colon carcinoma. Prospective studies are warranted to validate our findings.
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Affiliation(s)
- Joanna Szkandera
- Authors' Affiliations: Division of Clinical Oncology, Department of Medicine; Research Unit: Genetic Epidemiology and Pharmacogenetics, Division of Clinical Oncology; Institute of Pathology; Clinical Institute of Medical and Laboratory Diagnostics, Medical University of Graz; Department of Pathology, General Hospital Graz West, Graz; Department of Pathology, General Hospital of Leoben, Leoben, Austria; and Department of Medical Oncology, University Hospital Zuerich, Zuerich, Switzerland
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Zardavas D, Pugliano L, Piccart M. Personalized therapy for breast cancer: a dream or a reality? Future Oncol 2013; 9:1105-19. [PMID: 23902243 DOI: 10.2217/fon.13.57] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Breast cancer oncology represents one of the disciplines where personalized cancer medicine has been most actively pursued. The class-discovery studies conceptually advanced the field, underlining the molecular heterogeneity governing this common disease. The advent of high-throughput molecular profiling technologies holds great promise for the advance of all aspects of personalized cancer medicine, namely accurate prognostication, prediction of response to common systemic therapies and individualized monitoring of the disease. Moreover, an ever-expanding arsenal of targeted therapeutic compounds under clinical development, coupled with emerging powerful tools for comprehensive molecular and functional characterization, pose significant promise for improved clinical outcomes for breast cancer patients. Interrogation of the germline genetic variation offers further promise towards tailoring of breast cancer management. Well-conducted prospective validation studies are needed if breast cancer personalized therapy is to transform from a dream into a reality.
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Affiliation(s)
- Dimitrios Zardavas
- Institut Jules Bordet, Boulevard de Waterloo, 125, 1000 Brussels, Belgium
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Lee SY, Kang HG, Yoo SS, Kang YR, Choi YY, Lee WK, Choi JE, Jeon HS, Shin KM, Oh IJ, Kim KS, Lee J, Cha SI, Kim CH, Kim YC, Park JY. Polymorphisms in DNA repair and apoptosis-related genes and clinical outcomes of patients with non-small cell lung cancer treated with first-line paclitaxel-cisplatin chemotherapy. Lung Cancer 2013; 82:330-9. [PMID: 23973201 DOI: 10.1016/j.lungcan.2013.07.024] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2013] [Revised: 07/19/2013] [Accepted: 07/26/2013] [Indexed: 10/26/2022]
Abstract
This study was conducted to analyze a comprehensive panel of single nucleotide polymorphisms (SNPs) in genes in DNA repair and apoptosis pathways and determine the relationship between polymorphisms and treatment outcomes of patients with non-small cell lung cancer (NSCLC) treated with first-line paclitaxel-cisplatin chemotherapy. Three hundred eighty two patients with NSCLC were enrolled. Seventy-four SNPs in 48 genes (42 SNPs in 27 DNA repair pathway genes and 32 SNPs in 21 apoptotic pathway genes) were genotyped and their associations with chemotherapy response and overall survival (OS) were analyzed. Among SNPs in DNA repair genes, BRCA1 rs799917 was significantly associated with both chemotherapy response and OS. XRCC1 rs25487 exhibited a significant association with chemotherapy response and ERCC2 rs1052555 with OS. Four SNPs in apoptotic genes (TNFRSF1B rs1061624, BCL2 rs2279115, BIRC5 rs9904341, and CASP8 rs3769818) were significantly associated with OS, but not with response to chemotherapy. When the six SNPs which were associated with OS in individual analysis were combined, OS decreased as the number of bad genotypes increased (P(trend) = 2 × 10(-6)). Patients with 3, and 4-6 bad genotypes had significantly worse OS compared with those carrying 0-2 bad genotypes (adjusted hazard ratio [aHR] = 1.54, 95% CI = 1.14-2.08, P = 0.005; aHR = 2.10, 95% CI = 1.55-2.85, P = 2 × 10(-6), respectively). In conclusion, these findings suggest that the six SNPs identified, particularly their combined genotypes, could be used as biomarkers predicting chemotherapy response and survival of NSCLC patients treated with first-line paclitaxel-cisplatin chemotherapy.
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Affiliation(s)
- Shin Yup Lee
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, South Korea
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Absenger G, Benhaim L, Szkandera J, Zhang W, Yang D, Labonte MJ, Pichler M, Stotz M, Samonigg H, Renner W, Gerger A, Lenz HJ. The cyclin D1 (CCND1) rs9344 G>A polymorphism predicts clinical outcome in colon cancer patients treated with adjuvant 5-FU-based chemotherapy. THE PHARMACOGENOMICS JOURNAL 2013; 14:130-4. [PMID: 23567490 DOI: 10.1038/tpj.2013.15] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Revised: 02/04/2013] [Accepted: 02/19/2013] [Indexed: 11/09/2022]
Abstract
Recent evidence indicates a potential prognostic and predictive value for germline polymorphisms in genes involved in cell cycle control. We investigated the effect of cyclin D1 (CCND1) rs9344 G>A in stage II/III colon cancer patients and validated the findings in an independent study cohort. For evaluation and validation set, a total of 264 and 234 patients were included. Patients treated with 5-fluorouracil-based chemotherapy, carrying the CCND1 rs9344 A/A genotype had significantly decreased time-to-tumor recurrence (TTR) in univariate analysis and multivariate analysis (hazard ratio (HR) 2.47; 95% confidence interval (CI) 1.16-5.29; P=0.019). There was no significant association between CCND1 rs9344 G>A and TTR in patients with curative surgery alone. In the validation set, the A allele of CCND1 rs9344 G>A remained significantly associated with decreased TTR in univariate and multivariate analyses (HR 1.94; 95% CI 1.05-3.58; P=0.035). CCND1 rs9344 G>A may be a predictive and/or prognostic biomarker in stage II/III colon cancer patients, however, prospective trials are warranted to confirm our findings.
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Affiliation(s)
- G Absenger
- 1] Division of Clinical Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria [2] Research Unit Genetic Epidemiology and Pharmacogenetics, Medical University of Graz, Graz, Austria
| | - L Benhaim
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - J Szkandera
- 1] Division of Clinical Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria [2] Research Unit Genetic Epidemiology and Pharmacogenetics, Medical University of Graz, Graz, Austria
| | - W Zhang
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - D Yang
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - M J Labonte
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - M Pichler
- Division of Clinical Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - M Stotz
- 1] Division of Clinical Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria [2] Research Unit Genetic Epidemiology and Pharmacogenetics, Medical University of Graz, Graz, Austria
| | - H Samonigg
- Division of Clinical Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - W Renner
- 1] Research Unit Genetic Epidemiology and Pharmacogenetics, Medical University of Graz, Graz, Austria [2] Clinical Institute of Medical and Laboratory Diagnostics, Medical University of Graz, Graz, Austria
| | - A Gerger
- 1] Division of Clinical Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria [2] Research Unit Genetic Epidemiology and Pharmacogenetics, Medical University of Graz, Graz, Austria
| | - H-J Lenz
- 1] Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA [2] USC Center for Molecular Pathways and Drug Discovery, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
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Schoenfeld JD, Margalit DN, Kasperzyk JL, Shui IM, Rider JR, Epstein MM, Meisner A, Kenfield SA, Martin NE, Nguyen PL, Kantoff PW, Giovannucci EL, Stampfer MJ, Mucci LA. A single nucleotide polymorphism in inflammatory gene RNASEL predicts outcome after radiation therapy for localized prostate cancer. Clin Cancer Res 2013; 19:1612-9. [PMID: 23382116 PMCID: PMC3602407 DOI: 10.1158/1078-0432.ccr-12-2718] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
PURPOSE To study associations between single nucleotide polymorphisms (SNP) in Ribonuclease L (RNASEL), a gene implicated in inflammation and prostate cancer risk, and outcomes after radiation therapy. EXPERIMENTAL DESIGN We followed participants in the prospective US Health Professionals Follow-Up Study treated with radiation therapy for early-stage prostate cancer. Three SNPs were genotyped based on previously determined functional and biological significance. We used multivariable Cox proportional hazards models to assess per-allele associations with the primary outcome defined as time to a composite endpoint including development of lethal prostate cancer or biochemical recurrence. RESULTS We followed 434 patients treated with radiation therapy for a median of 9 years. On multivariate analysis, the rs12757998 variant allele was associated with significantly decreased risk of the composite endpoint [HR: 0.65; 95% confidence interval (CI), 0.45-0.94%; P = 0.02] driven by decreased biochemical recurrence (HR: 0.60; 95% CI, 0.40-0.89%; P = 0.01) and men treated with external beam (HR: 0.58; 95% CI, 0.36-0.93%; P = 0.02). In contrast, in 516 men from the same cohort treated with radical prostatectomy, we found no significant impact of this variant on outcome. Furthermore, the rs12757998 variant allele significantly modified the association between androgen deprivation therapy and outcomes after radiation therapy (p-interaction = 0.02). CONCLUSION We show an association between RNASEL SNP rs12757998 and outcome after radiation therapy for prostate cancer. This SNP is associated with increased circulating C-reactive protein and interleukin-6, suggesting a potential role for inflammation in the response to radiation. If validated, genetic predictors of outcome may help inform prostate cancer management.
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Schutz FAB, Pomerantz MM, Gray KP, Atkins MB, Rosenberg JE, Hirsch MS, McDermott DF, Lampron ME, Lee GSM, Signoretti S, Kantoff PW, Freedman ML, Choueiri TK. Single nucleotide polymorphisms and risk of recurrence of renal-cell carcinoma: a cohort study. Lancet Oncol 2012; 14:81-7. [PMID: 23219378 DOI: 10.1016/s1470-2045(12)70517-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND Germline genetic polymorphisms might affect the risk of recurrence in patients with localised renal-cell carcinoma. We investigated the association between genetic polymorphisms and recurrence of renal-cell carcinoma. METHODS We analysed germline DNA samples extracted from patients with localised renal-cell carcinoma treated at the Dana-Farber/Harvard Cancer Center (Boston, MA, USA). We selected a discovery cohort from a prospective database at the Dana-Farber/Harvard Cancer Center and selected a validation cohort from department records at the Brigham and Women's Hospital (Boston, MA, USA). We validated the findings from the discovery cohort in the validation cohort. We genotyped 70 genes involved in the pathogenesis of renal-cell carcinoma (including the VHL/HIF/VEGF and PI3K/AKT/mTOR pathways, and genes involved in immune regulation and metabolism) for single nucleotide polymorphisms. We assessed the association between genotype and recurrence-free survival, adjusted for baseline characteristics, with the Cox proportional hazards model, the Kaplan-Meier method, and the log-rank test. We used a false discovery rate q value to adjust for multiple comparisons. FINDINGS We included 554 patients (403 in the discovery cohort and 151 in the validation cohort). We successfully genotyped 290 single nucleotide polymorphisms in the discovery cohort, but excluded five because they did not have a variant group for comparison. The polymorphism rs11762213, which causes a synonymous aminoacid change in MET (144G→A, located in exon 2), was associated with recurrence-free survival. Patients with one or two copies of the minor (risk) allele had an increased risk of recurrence or death (hazard ratio [HR] 1·86, 95% CI 1·17-2·95; p=0·0084) in multivariate analysis. Median recurrence-free survival for carriers of the risk allele was 19 months (95% CI 9-not reached) versus 50 months (95% CI 37-75) for patients without the risk allele. In the validation cohort the HR was 2·45 (95% CI 1·01-5·95; p=0·048). INTERPRETATION Patients with localised renal-cell carcinoma and the MET polymorphism rs11762213 might have an increased risk of recurrence after nephrectomy. If these results are further validated in a similar population, they could be incorporated into future prognostic instruments, potentially aiding the design of adjuvant clinical trials of MET inhibitors and management of renal-cell carcinoma. FUNDING Conquer Cancer Foundation and American Society of Clinical Oncology (Career Development Award); The Trust Family Research Fund for Kidney Cancer; US National Institutes of Health, National Cancer Institute Kidney Cancer Specialized Program of Research Excellence.
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Crona D, Innocenti F. Can knowledge of germline markers of toxicity optimize dosing and efficacy of cancer therapy? Biomark Med 2012; 6:349-62. [PMID: 22731909 DOI: 10.2217/bmm.12.19] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The systemic treatment of cancer with traditional cytotoxic chemotherapeutic agents and more targeted agents is often complicated by the onset of adverse drug reactions. Pharmacogenetic prediction of adverse drug reactions might have consequences for dosing and efficacy. This review discusses relevant examples where the germline variant-toxicity relationship has been validated as an initial step in developing clinically useful pharmacogenetic markers and provides examples where germline variants have influenced dosing strategies and/or survival or other outcomes of efficacy. This review will also provide insight into the reasons why more pharmacogenetic markers have not been routinely integrated into clinical practice.
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Affiliation(s)
- Daniel Crona
- Institute for Pharmacogenomics and Individualized Therapy, University of North Carolina, Chapel Hill, USA
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Phenotyping drug disposition in oncology. Cancer Treat Rev 2012; 38:715-25. [DOI: 10.1016/j.ctrv.2011.12.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2011] [Revised: 12/05/2011] [Accepted: 12/08/2011] [Indexed: 12/11/2022]
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Naidoo N, Pawitan Y, Soong R, Cooper DN, Ku CS. Human genetics and genomics a decade after the release of the draft sequence of the human genome. Hum Genomics 2012; 5:577-622. [PMID: 22155605 PMCID: PMC3525251 DOI: 10.1186/1479-7364-5-6-577] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Substantial progress has been made in human genetics and genomics research over the past ten years since the publication of the draft sequence of the human genome in 2001. Findings emanating directly from the Human Genome Project, together with those from follow-on studies, have had an enormous impact on our understanding of the architecture and function of the human genome. Major developments have been made in cataloguing genetic variation, the International HapMap Project, and with respect to advances in genotyping technologies. These developments are vital for the emergence of genome-wide association studies in the investigation of complex diseases and traits. In parallel, the advent of high-throughput sequencing technologies has ushered in the 'personal genome sequencing' era for both normal and cancer genomes, and made possible large-scale genome sequencing studies such as the 1000 Genomes Project and the International Cancer Genome Consortium. The high-throughput sequencing and sequence-capture technologies are also providing new opportunities to study Mendelian disorders through exome sequencing and whole-genome sequencing. This paper reviews these major developments in human genetics and genomics over the past decade.
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Affiliation(s)
- Nasheen Naidoo
- Centre for Molecular Epidemiology, Department of Epidemiology and Public Health, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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Germline pharmacogenomics in oncology: decoding the patient for targeting therapy. Mol Oncol 2012; 6:251-9. [PMID: 22321460 DOI: 10.1016/j.molonc.2012.01.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Revised: 12/14/2011] [Accepted: 01/13/2012] [Indexed: 11/24/2022] Open
Abstract
Pharmacogenomics is the study of genetic factors determining drug response or toxicity. The use of pharmacogenomics is especially desirable in oncology because the therapeutic index of oncology drugs is often narrow, the need for favorable drug response is often acute, and the consequences of drug toxicity can be life-threatening. In this review, we examine the state of pharmacogenomics in oncology, focusing only on germline pharmacogenomic variants. We consider several critical points when assessing the quality of pharmacogenomic findings and their relevance to clinical use, and discuss potential confounding factors limiting interpretation and implementation. Several of the most extensively studied drug-gene pairs (irinotecan and UGT1A1; tamoxifen and CYP2D6; 5-fluorouracil and DPYD) are inspected in depth as illustrations of both the state of advancement-and the current limitations of-present knowledge. We argue that there will likely soon be a critical mass of important germline pharmacogenomic biomarkers in oncology which deserve clinical implementation to provide optimal, personalized oncologic care. We conclude with a vision of how routine clinical testing of such germline markers could one day change the paradigm for cancer care.
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Fung C, Vaughn DJ, Mitra N, Ciosek SL, Vardhanabhuti S, Nathanson KL, Kanetsky PA. Chemotherapy refractory testicular germ cell tumor is associated with a variant in Armadillo Repeat gene deleted in Velco-Cardio-Facial syndrome (ARVCF). Front Endocrinol (Lausanne) 2012; 3:163. [PMID: 23248619 PMCID: PMC3521241 DOI: 10.3389/fendo.2012.00163] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 11/28/2012] [Indexed: 11/27/2022] Open
Abstract
INTRODUCTION There is evidence that inherited genetic variation affects both testicular germ cell tumor (TGCT) treatment outcome and risks of late-complications arising from cisplatin-based chemotherapy. Using a candidate gene approach, we examined associations of three genes involved in the cisplatin metabolism pathway, GSTP1, COMT, and TPMT, with TGCT outcome and cisplatin-induced neurotoxicity. MATERIALS AND METHODS Our study population includes a subset of patients (n = 137) from a genome-wide association study at the University of Pennsylvania that evaluates inherited genetic susceptibility to TGCT. All patients in our study had at least one course of cisplatin-based chemotherapy with at least 1 year of follow-up. A total of 90 markers in GSTP1, COMT, and TPMT and their adjacent genomic regions (±20 kb) were analyzed for associations with refractory TGCT after first course of chemotherapy, progression-free survival (PFS), overall survival (OS), peripheral neuropathy, and ototoxicity. RESULTS After adjustment for multiple comparisons, one Single nucleotide polymorphism (SNP), rs2073743, in the flanking region (±20 kb) of COMT was associated with refractory TGCT after initial chemotherapy. This SNP lies within the intron region of the Armadillo Repeat gene deleted in Velco-Cardio-Facial syndrome (ARVCF). The G allele of rs2073743 predisposed patients to refractory disease with a relative risk of 2.6 (95% CI 1.1, 6.3; P = 0.03). Assuming recessive inheritance, patients with the GG genotype had 22.7 times higher risk (95% CI 3.3, 155.8; P = 0.04) of developing refractory disease when compared to those with the GC or CC genotypes. We found no association of our candidate genes with peripheral neuropathy, ototoxicity, PFS and OS. DISCUSSION This is the first study to suggest that germline genetic variants of ARVCF may affect TGCT outcome. The result of this study is hypothesis generating and should be validated in future studies.
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Affiliation(s)
- Chunkit Fung
- Department of Hematology and Oncology, Wilmot Cancer Center, University of Rochester Medical CenterRochester, NY, USA
- *Correspondence: Chunkit Fung, Department of Hematology and Oncology, Wilmot Cancer Center, University of Rochester Medical Center, 601 Elmwood Avenue, Box 704, Rochester, NY 14642, USA. e-mail:
| | - David J. Vaughn
- Department of Hematology and Oncology, Abramson Cancer Center, University of PennsylvaniaPhiladelphia, PA, USA
| | - Nandita Mitra
- Department of Biostatistics and Epidemiology, Perelman School of Medicine, University of PennsylvaniaPhiladelphia, PA, USA
| | - Stephanie L. Ciosek
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of PennsylvaniaPhiladelphia, PA, USA
| | - Saran Vardhanabhuti
- Center for Biostatistics in AIDS research, Harvard School of Public HealthBoston, MA, USA
| | - Katherine L. Nathanson
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of PennsylvaniaPhiladelphia, PA, USA
| | - Peter A. Kanetsky
- Department of Biostatistics and Epidemiology, Perelman School of Medicine, University of PennsylvaniaPhiladelphia, PA, USA
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Dahan L, Norguet E, Etienne-Grimaldi MC, Formento JL, Gasmi M, Nanni I, Gaudart J, Garcia S, Ouafik L, Seitz JF, Milano G. Pharmacogenetic profiling and cetuximab outcome in patients with advanced colorectal cancer. BMC Cancer 2011; 11:496. [PMID: 22117530 PMCID: PMC3235081 DOI: 10.1186/1471-2407-11-496] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Accepted: 11/25/2011] [Indexed: 02/01/2023] Open
Abstract
Background We analyzed the influence of 8 germinal polymorphisms of candidate genes potentially related to EGFR signalling (EGFR, EGF, CCND1) or antibody-directed cell cytotoxicity (FCGR2A and FCGR3A) on outcome of colorectal cancer (CRC) patients receiving cetuximab-based therapy. Methods Fifty-eight advanced CRC patients treated with cetuximab-irinotecan salvage therapy between 2001 and 2007 were analyzed (mean age 60; 50 PS 0-1). The following polymorphisms were analyzed on blood DNA: EGFR (CA repeats in intron 1, -216 G > T, -191C > A, R497K), EGF (A61G), CCND1 (A870G), FCGR2A (R131H), FCGR3A (F158V). Statistical analyses were conducted on the total population and on patients with wt KRas tumors. All SNPs were considered as ternary variables (wt/wt vs wt/mut vs mut/mut), with the exception of -191C > A EGFR polymorphism (AA patient merged with CA patients). Results Analysis of skin toxicity as a function of EGFR intron 1 polymorphism showed a tendency for higher toxicity in patients with a low number of CA-repeats (p = 0.058). CCND1 A870G polymorphism was significantly related to clinical response, both in the entire population and in KRas wt patients, with the G allele being associated with a lack of response. In wt KRas patients, time to progression (TTP) was significantly related to EGFR -191C > A polymorphism with a longer TTP in CC patients as compared to others, and to CCND1 A870G polymorphism with the G allele being associated with a shorter TTP; a multivariate analysis including these two polymorphisms only retained CCND1 polymorphism. Overall survival was significantly related to CCND1 polymorphism with a shorter survival in patients bearing the G allele, and to FCGR3A F158V polymorphism with a shorter survival in VV patients (in the entire population and in KRas wt patients). FCGR3A F158V and CCND1 A870G polymorphisms were significant independent predictors of overall survival. Conclusions Present original data obtained in wt KRas patients corresponding to the current cetuximab-treated population clearly suggest that CCND1 A870G polymorphism may be used as an additional marker for predicting cetuximab efficacy, TTP and overall survival. In addition, FCGR3A F158V polymorphism was a significant independent predictor of overall survival.
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Affiliation(s)
- Laetitia Dahan
- Assistance Publique-Hôpitaux de Marseille, Hôpital Timone, Université de la Méditerranée, Marseille, France.
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Nichol AM, Yerushalmi R, Tyldesley S, Lesperance M, Bajdik CD, Speers C, Gelmon KA, Olivotto IA. A case-match study comparing unilateral with synchronous bilateral breast cancer outcomes. J Clin Oncol 2011; 29:4763-8. [PMID: 22105824 DOI: 10.1200/jco.2011.35.0165] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PURPOSE There is controversy about whether patients with synchronous bilateral breast cancer (SBBC) have similar or worse outcomes compared with patients with unilateral breast cancer. The purpose of this study was to determine whether survival outcomes for patients with SBBC can be estimated from the characteristics of their individual cancers. PATIENTS AND METHODS Patients had invasive breast cancer, without metastases or inflammatory disease, diagnosed in British Columbia between 1989 and 2000. There were 207 cases with SBBC (diagnosed ≤ 2 months apart) and 15,497 with unilateral breast cancer. By using 10-year breast cancer-specific survival (BCSS) estimates, the higher-risk cancer of each SBBC case was determined and matched with three breast cancers from the unilateral cohort to select 621 high-risk matches. The priority sequence of matching the prognostic and predictive variables was positive lymph node number, primary tumor size, age, grade, lymphovascular invasion, estrogen receptor status, local therapy used, margin status, treating clinic, diagnosis year, and type of systemic therapy used. RESULTS With a median follow-up of 10.2 years, the overall 10-year BCSS was significantly higher for the unilateral cohort (81%; 95% CI, 81% to 82%) than for the SBBC cases (71%; 95% CI, 63% to 77%). The SBBC cases had significantly higher mean age and stage at presentation. The 10-year BCSS was 74% (95% CI, 69% to 77%) for the high-risk matches. CONCLUSION BCSS was not significantly different between the SBBC cases and their high-risk matches.
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Affiliation(s)
- Alan M Nichol
- British Columbia Cancer Agency-Vancouver Centre, Vancouver, BC, Canada.
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Azad AK, Bairati I, Samson E, Cheng D, Mirshams M, Qiu X, Savas S, Waldron J, Wang C, Goldstein D, Xu W, Meyer F, Liu G. Validation of genetic sequence variants as prognostic factors in early-stage head and neck squamous cell cancer survival. Clin Cancer Res 2011; 18:196-206. [PMID: 22076708 DOI: 10.1158/1078-0432.ccr-11-1759] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE From the published literature, we identified 23 germ line sequence variants in 17 genes from hypothesis-generating studies that were associated with prognosis of head and neck cancer, including sequence variants of DNA repair (ERCC1, ERCC4, ERCC5, MSH2, XPA, ERCC2, XRCC1, XRCC3), DNA methylation (DNMT3B), cell cycle and proliferation (CCND1, TP53), xenobiotic metabolism (GSTM1, GSTT1, CYP2D6), metastatic -potential (MMP3), immunologic (CTLA4), and growth factor pathways (FGFR4). The purpose of this study was to validate the role of these 23 sequence variants for overall (OS) and disease-free survival (DFS) in a large, comprehensive, well-annotated data set of patients with head and neck cancer. EXPERIMENTAL DESIGN We genotyped these sequence variants in 531 patients with stage I and II radiation-treated head and neck cancer (originally recruited for an alpha-tocopherol/beta-carotene placebo-controlled secondary prevention study), and analyzed using Cox proportional hazards models, stratified by treatment arm, adjusting for clinical prognostic factors. RESULTS Two OS associations were statistically significant for each variant allele when compared with the wild-type: CTLA4: A49G [rs231775; adjusted HR (aHR), 1.32 (1.1-1.6); P = 0.01] and XRCC1: Arg339Gln [rs25487; aHR, 1.28 (1.05-1.57); P = 0.02]. Both of these sequence variants had significant results in the opposite direction as prior published literature. Two DFS associations were of borderline significance in the same direction as prior literature: ERCC2: Lys751Gln [rs13181; aHR, 0.80 (0.6-1.0); P = 0.05] and TP53: Arg72Pro [rs1042522; aHR, 1.28 (1.0-1.6); P = 0.03], comparing number of variant alleles with reference of zero variants. CONCLUSIONS None of the prognostic sequence variants previously published was validated for OS in our patients with early-stage radiation-treated head and neck cancer, though rs1381and rs1042522 had borderline significant association with DFS.
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Affiliation(s)
- Abul Kalam Azad
- Applied Molecular Oncology, Ontario Cancer Institute, Princess Margaret Hospital, University Health Network, University of Toronto, Toronto, Ontario, Canada
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Association of Keap1 and Nrf2 Genetic Mutations and Polymorphisms With Endometrioid Endometrial Adenocarcinoma Survival. Int J Gynecol Cancer 2011; 21:1428-35. [DOI: 10.1097/igc.0b013e31822d0eb2] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
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Gerger A, Zhang W, Yang D, Bohanes P, Ning Y, Winder T, LaBonte MJ, Wilson PM, Benhaim L, Paez D, El-Khoueiry R, El-Khoueiry A, Kahn M, Lenz HJ. Common cancer stem cell gene variants predict colon cancer recurrence. Clin Cancer Res 2011; 17:6934-43. [PMID: 21918173 DOI: 10.1158/1078-0432.ccr-11-1180] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Recent evidence suggests that cancer stem cells (CSC) are responsible for key elements of colon cancer progression and recurrence. Germline variants in CSC genes may result in altered gene function and/or activity, thereby causing interindividual differences in a patient's tumor recurrence capacity and chemoresistance. We investigated germline polymorphisms in a comprehensive panel of CSC genes to predict time to tumor recurrence (TTR) in patients with stage III and high-risk stage II colon cancer. EXPERIMENTAL DESIGN A total of 234 patients treated with 5-fluorouracil-based chemotherapy at the University of Southern California were included in this study. Whole blood samples were analyzed for germline polymorphisms in genes that have been previously associated with colon CSC (CD44, Prominin-1, DPP4, EpCAM, ALCAM, Msi-1, ITGB1, CD24, LGR5, and ALDH1A1) by PCR-RFLP or direct DNA-sequencing. RESULTS The minor alleles of CD44 rs8193 C>T, ALCAM rs1157 G>A, and LGR5 rs17109924 T>C were significantly associated with increased TTR (9.4 vs. 5.4 years; HR, 0.51; 95% CI: 0.35-0.93; P = 0.022; 11.3 vs. 5.7 years; HR, 0.56; 95% CI: 0.33-0.94; P = 0.024, and 10.7 vs. 5.7 years; HR, 0.33; 95% CI: 0.12-0.90; P = 0.023, respectively) and remained significant in the multivariate analysis stratified by ethnicity. In recursive partitioning, a specific gene variant profile including LGR5 rs17109924, CD44 rs8193, and ALDH1A1 rs1342024 represented a high-risk subgroup with a median TTR of 1.7 years (HR, 6.71, 95% CI: 2.71-16.63, P < 0.001). CONCLUSION This is the first study identifying common germline variants in colon CSC genes as independent prognostic markers for stage III and high-risk stage II colon cancer patients.
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Affiliation(s)
- Armin Gerger
- Division of Medical Oncology, Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA
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Barbolosi D, Verga F, You B, Benabdallah A, Hubert F, Mercier C, Ciccolini J, Faivre C. Modélisation du risque d’évolution métastatique chez les patients supposés avoir une maladie localisée. ONCOLOGIE 2011. [DOI: 10.1007/s10269-011-2028-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Parmar S, Stingl JC, Huber-Wechselberger A, Kainz A, Renner W, Langsenlehner U, Krippl P, Brockmöller J, Haschke-Becher E. Impact of UGT2B7 His268Tyr polymorphism on the outcome of adjuvant epirubicin treatment in breast cancer. Breast Cancer Res 2011; 13:R57. [PMID: 21658222 PMCID: PMC3218946 DOI: 10.1186/bcr2894] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Revised: 04/15/2011] [Accepted: 06/09/2011] [Indexed: 01/18/2023] Open
Abstract
INTRODUCTION Epirubicin is a common adjuvant treatment for breast cancer. It is mainly eliminated after glucuronidation through uridine diphosphate-glucuronosyltransferase 2B7 (UGT2B7). The present study aimed to describe the impact of the UGT2B7(His268Tyr) polymorphism on invasive disease-free survival in breast cancer patients after epirubicin treatment. METHODS This is a pharmacogenetic study based on samples collected from 745 breast cancer patients of the Austrian Tumor of breast tissue: Incidence, Genetics, and Environmental Risk factors (TIGER) cohort who did not present metastases at baseline. This cohort included 205 women with epirubicin-based combination chemotherapy, 113 patients having received chemotherapy without epirubicin and 427 patients having received no chemotherapy at all. Of the epirubicin-treated subgroup, 120 were subsequently treated with tamoxifen. For all women UGT2B7(His268Tyr) was genotyped. Invasive disease-free survival was assessed using Kaplan-Meier and Cox's proportional hazard regression analysis. RESULTS Among the 205 epirubicin-treated patients, carriers of two UGT2B7(268Tyr) alleles had a mean invasive disease-free survival of 8.6 (95% confidence interval (CI) 7.9 to 9.3) years as compared to 7.5 (95% CI 6.9 to 8.0) years in carriers of at least one UGT2B7(268His) allele (adjusted hazard ratio (HR) = 2.64 (95% CI 1.22 to 5.71); P = 0.014). In addition, the impact of the UGT2B7(His268Tyr) polymorphism became even more pronounced in patients subsequently treated with tamoxifen (adjusted HR = 5.22 (95% CI 1.67 to 26.04); P = 0.015) whereas no such difference in invasive disease-free survival was observed in patients not receiving epirubicin. CONCLUSIONS Breast cancer patients carrying the UGT2B7(268Tyr/Tyr) genotype may benefit most from adjuvant epirubicin-based chemotherapy. These results warrant confirmation in further studies.
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Affiliation(s)
- Sumit Parmar
- Institute of Pharmacology of Natural Products and Clinical Pharmacology, University Ulm, Helmholtzstrasse 20, Ulm, 89081, Germany
| | - Julia Carolin Stingl
- Institute of Pharmacology of Natural Products and Clinical Pharmacology, University Ulm, Helmholtzstrasse 20, Ulm, 89081, Germany
| | - Ariana Huber-Wechselberger
- Institute of Medical and Laboratory Diagnostics, Elisabethinen Hospital Linz, Fadingerstrasse 1, Linz, 4020, Austria
| | - Alexander Kainz
- Department of Nephrology and Dialysis, Medical University Vienna, Währingergürtel 18-20, Vienna, 1090, Austria
| | - Wilfried Renner
- Clinical Institute of Medical and Laboratory Diagnostics, Medical University Graz, Auenbruggerplatz 15, Graz, 8036, Austria
| | - Uwe Langsenlehner
- Department of Internal Medicine, Hospital of Fürstenfeld, Krankenhausgasse 1, Fürstenfeld, 8280, Austria
| | - Peter Krippl
- Department of Internal Medicine, Hospital of Fürstenfeld, Krankenhausgasse 1, Fürstenfeld, 8280, Austria
| | - Jürgen Brockmöller
- Department of Clinical Pharmacology, University Göttingen, Robert-Koch-Strasse 40, Göttingen, 37075, Germany
| | - Elisabeth Haschke-Becher
- Institute of Medical and Laboratory Diagnostics, Elisabethinen Hospital Linz, Fadingerstrasse 1, Linz, 4020, Austria
- Christian Doppler Clinic, Private Paracelsus Medical University Salzburg, Ignaz Harrerstrasse 79, Salzburg, 5020, Austria
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Donzella V, Crea F. Optical biosensors to analyze novel biomarkers in oncology. JOURNAL OF BIOPHOTONICS 2011; 4:442-452. [PMID: 21567973 DOI: 10.1002/jbio.201000123] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2010] [Revised: 04/18/2011] [Accepted: 04/25/2011] [Indexed: 05/28/2023]
Abstract
Many cancer types are characterized by poor survival and unpredictable therapy response. Easy-to-perform molecular analyses may help patient stratification and treatment tailoring. Several integrated devices have been proposed to overcome current analysis equipment limitations. They offer improved sensitivity and easy availability of parallel detection. Particularly, unlabelled optical biosensors combine the manifold advantages of integrated sensors (e.g. easy handling, portability and low-volume requirement) with detection of target molecules in their original form. Here, we review integrated optical biosensor current features, and discuss their possible application to the detection of protein variants from body fluids, with particular regard to histone modifications. Indeed, histone post-translational modifications are a set of epigenetic markers frequently deregulated in cancer. Available technology does not allow a comprehensive analysis of all histone modifications in a single patient. Thus, label-free optical biosensors may pave the way to the discovery and detection of a novel class of biomarkers in oncology.
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Affiliation(s)
- Valentina Donzella
- Scuola Superiore Sant'Anna, Piazza Martiri della Liberta' 33, 56100 Pisa, Italy.
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Abstract
The field of pharmacogenomics is focused on the characterization of genetic factors contributing to the response of patients to pharmacological interventions. Drug response and toxicity are complex traits; therefore the effects are likely influenced by multiple genes. The investigation of the genetic basis of drug response has evolved from a focus on single genes to relevant pathways to the entire genome. Preclinical (cell-based models) and clinical genome-wide association studies (GWAS) in oncology provide an unprecedented opportunity for a comprehensive and unbiased assessment of the heritable factors associated with drug response. The primary challenge with attempting to identify pharmacogenomic markers from clinical studies is that they require a homogeneous population of patients treated with the same dosage regimen and minimal confounding variables. Therefore, the development of cell-based models for pharmacogenomic marker identification has utility for the field since performing these types of studies in humans is difficult and costly. This review intends to provide a current report on the status of genomic studies in oncology, the methods for discovery, and implications for patient care. We present a perspective and summary of the challenges and opportunities in translating heritable genomic discoveries to patients.
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Affiliation(s)
- Federico Innocenti
- Department of Medicine, Comprehensive Cancer Center, The University of Chicago, Chicago, IL 60637, USA
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Kitahara H, Masumoto J, Parker AL, Maruta F, Kubo N, Shimizu A, Akita N, Miwa S, Kobayashi N, Nakayama J, Miyagawa S. COP35, a Cholangiocarcinoma-Binding Oligopeptide, Interacts with the Clathrin Heavy Chain Accompanied by GRP78. Mol Cancer Res 2011; 9:688-701. [DOI: 10.1158/1541-7786.mcr-10-0470] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Information Overload in Oncology Practice and its Potential Negative Impact on the Delivery of Optimal Patient Care. Curr Oncol Rep 2011; 13:249-51. [DOI: 10.1007/s11912-011-0179-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Possible association between a genetic polymorphism at 8q24 and risk of upper gastrointestinal cancer. Eur J Cancer Prev 2011; 20:54-7. [PMID: 21102338 DOI: 10.1097/cej.0b013e328341e320] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Over recent years, genome-wide association studies have contributed to our understanding of genetic susceptibility to sporadic cancer. In this study, we assessed the association between upper gastrointestinal cancer risk and four genome-wide association studies-identified single nucleotide polymorphisms (SNPs), implicated earlier in prostate and colorectal cancer susceptibility. Genotyping for each SNP was performed in two independent Caucasian population-based case-control studies. The first study comprised 290 gastric cancer cases and 374 controls. The second study included 185 noncardia gastric cancers, 123 cardia cancers, 158 oesophageal cancers and 209 controls. Odds ratios (ORs) were computed from logistic models and adjusted for potential confounding variables. An inverse association was observed between the SNP rs1447295, located at 8q24, and gastric cancer risk in the first study population (OR=0.63; 95% confidence interval: 0.41-0.97). A positive association was observed for the same SNP and oesophageal squamous cell carcinoma in the second study population (OR=7.43; 95% confidence interval: 1.37-49.98). No significant associations were detected in either study for the three remaining SNPs (rs6983297, rs10505477 and rs719725). Our data represent novel findings on heritable susceptibility to gastric and oesophageal cancer and warrant validation in additional populations.
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