1
|
Siemens A, Anderson SJ, Rassekh SR, Ross CJD, Carleton BC. A Systematic Review of Polygenic Models for Predicting Drug Outcomes. J Pers Med 2022; 12:jpm12091394. [PMID: 36143179 PMCID: PMC9505711 DOI: 10.3390/jpm12091394] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/21/2022] [Accepted: 08/25/2022] [Indexed: 11/16/2022] Open
Abstract
Polygenic models have emerged as promising prediction tools for the prediction of complex traits. Currently, the majority of polygenic models are developed in the context of predicting disease risk, but polygenic models may also prove useful in predicting drug outcomes. This study sought to understand how polygenic models incorporating pharmacogenetic variants are being used in the prediction of drug outcomes. A systematic review was conducted with the aim of gaining insights into the methods used to construct polygenic models, as well as their performance in drug outcome prediction. The search uncovered 89 papers that incorporated pharmacogenetic variants in the development of polygenic models. It was found that the most common polygenic models were constructed for drug dosing predictions in anticoagulant therapies (n = 27). While nearly all studies found a significant association with their polygenic model and the investigated drug outcome (93.3%), less than half (47.2%) compared the performance of the polygenic model against clinical predictors, and even fewer (40.4%) sought to validate model predictions in an independent cohort. Additionally, the heterogeneity of reported performance measures makes the comparison of models across studies challenging. These findings highlight key considerations for future work in developing polygenic models in pharmacogenomic research.
Collapse
Affiliation(s)
- Angela Siemens
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC V6H 3N1, Canada
- BC Children’s Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada
| | - Spencer J. Anderson
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC V6H 3N1, Canada
- BC Children’s Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada
| | - S. Rod Rassekh
- Division of Translational Therapeutics, Department of Pediatrics, Faculty of Medicine, University of British Columbia, Vancouver, BC V6H 3V4, Canada
- Division of Oncology, Hematology and Bone Marrow Transplant, University of British Columbia, Vancouver, BC V6H 3V4, Canada
| | - Colin J. D. Ross
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC V6H 3N1, Canada
- BC Children’s Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada
- Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Bruce C. Carleton
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC V6H 3N1, Canada
- Division of Translational Therapeutics, Department of Pediatrics, Faculty of Medicine, University of British Columbia, Vancouver, BC V6H 3V4, Canada
- Pharmaceutical Outcomes Programme, British Columbia Children’s Hospital, Vancouver, BC V5Z 4H4, Canada
- Correspondence:
| |
Collapse
|
2
|
Virgili Manrique AC, Salazar J, Arranz MJ, Bagué S, Orellana R, López-Pousa A, Cerdà P, Gracia I, Majercakova K, Peiró A, Trullols L, Fernández M, Valverde S, Quintana MJ, Bell O, Artigas-Baleri A, Sebio A. Pharmacogenetic Profiling in High-Risk Soft Tissue Sarcomas Treated with Neoadjuvant Chemotherapy. J Pers Med 2022; 12:jpm12040618. [PMID: 35455734 PMCID: PMC9024670 DOI: 10.3390/jpm12040618] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 04/07/2022] [Indexed: 12/10/2022] Open
Abstract
Neoadjuvant chemotherapy based on anthracyclines and ifosfamide for high-risk soft tissue sarcomas (STS) of the extremities and trunk is a controversial treatment option. There are substantial interindividual differences in clinical outcomes in patients treated with neoadjuvant chemotherapy. The aim of this study was to evaluate, as biomarkers, polymorphisms in genes encoding drug-metabolizing enzymes, drug transporters, or drug targets and their association with toxicity and survival in STS patients treated with neoadjuvant chemotherapy. We analysed variants in genes involved in anthracycline metabolism (ABCB1, ABCC2, NQO1, CBR3, and SLC22A16) and in ifosfamide catabolism (ALDH1A1) in 79 treated patients. Two genes showed significant association after adjusted multivariate analysis: ABCC2 and ALDH1A1. In patients treated with anthracyclines, ABCC2 rs3740066 was associated with risk of febrile neutropenia (p = 0.031), and with decreased overall survival (OS) (p = 0.024). ABCC2 rs2273697 was associated with recurrence-free survival (RFS) (p = 0.024). In patients treated with ifosfamide, ALDH1A1 rs3764435 was associated with RFS (p = 0.046). Our pharmacogenetic study shows for the first time that variants in genes regulating the metabolism of neoadjuvant chemotherapy may be helpful to predict toxicity and survival benefit in high-risk STS treated with neoadjuvant chemotherapy. Further validation studies are needed to establish their clinical utility.
Collapse
Affiliation(s)
- Anna C. Virgili Manrique
- Department of Medical Oncology, Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain; (A.C.V.M.); (A.L.-P.); (P.C.)
- Department of Medicine, Universitat Autònoma de Barcelona, 08035 Barcelona, Spain
| | - Juliana Salazar
- Medical Translational Oncology Laboratory, IIB-Sant Pau, Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain;
- Correspondence: (J.S.); (A.S.)
| | | | - Silvia Bagué
- Department of Pathology, Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain; (S.B.); (R.O.)
| | - Ruth Orellana
- Department of Pathology, Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain; (S.B.); (R.O.)
| | - Antonio López-Pousa
- Department of Medical Oncology, Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain; (A.C.V.M.); (A.L.-P.); (P.C.)
| | - Paula Cerdà
- Department of Medical Oncology, Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain; (A.C.V.M.); (A.L.-P.); (P.C.)
| | - Isidre Gracia
- Orthopaedics and Trauma Surgery, Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain; (I.G.); (A.P.); (L.T.)
| | - Katarina Majercakova
- Radiation Oncology, Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain;
| | - Ana Peiró
- Orthopaedics and Trauma Surgery, Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain; (I.G.); (A.P.); (L.T.)
| | - Laura Trullols
- Orthopaedics and Trauma Surgery, Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain; (I.G.); (A.P.); (L.T.)
| | - Manuel Fernández
- Plastic and Reconstructive Surgery, Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain;
| | - Sandra Valverde
- Radiology Department, Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain;
| | - María Jesús Quintana
- Epidemiology Department, Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain;
| | - Olga Bell
- Medical Translational Oncology Laboratory, IIB-Sant Pau, Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain;
| | - Alícia Artigas-Baleri
- Genetics Department, IIB-Sant Pau, Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain;
| | - Ana Sebio
- Department of Medical Oncology, Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain; (A.C.V.M.); (A.L.-P.); (P.C.)
- Correspondence: (J.S.); (A.S.)
| |
Collapse
|
3
|
刘 坤, 顾 湘, 陈 南, 游 玮, 魏 健, 马 林, 张 欣. [Clinical significance of tumor chemosensitivity assay in patients with head and neck cancer]. LIN CHUANG ER BI YAN HOU TOU JING WAI KE ZA ZHI = JOURNAL OF CLINICAL OTORHINOLARYNGOLOGY, HEAD, AND NECK SURGERY 2022; 36:205-211. [PMID: 35193343 PMCID: PMC10128289 DOI: 10.13201/j.issn.2096-7993.2022.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Indexed: 06/14/2023]
Abstract
Objective:To evaluate the clinical significance of OncoDrug-Seq™ tumor gene detection in patients with head and neck malignancies. Methods:A retrospective analysis of 338 patients with locally advanced or unresectable head and neck malignancies admitted to the Department of Otorhinolaryngology Head and Neck Surgery, Chinese PLA General Hospital from April 2011 to February 2021. Among them, 301 patients were pathologically diagnosed as squamous cell carcinoma, 37 cases were non-squamous cell carcinoma. All patients underwent OncoDrug-Seq™ gene detection, combined with the test results and the treatment response after induction chemotherapy to evaluate whether to change the chemotherapy regimen, and to calculate the accuracy of the gene detection and the survival rate of the patient. Results:Among 301 patients with head and neck squamous cell carcinoma, the results of the drug sensitivity test were compared with the actual clinical response, the true positive rate(TP), true negative rate(TN), positive predictive value(PPV), negative predictive value(NPV) and total predictive accuracy rates were 85.37%, 65.45%, 91.70%, 50.00% and 81.73%, respectively. For patients who changed chemotherapy regimen(TN+FP) and did not change(TP+FN), the 5-year progression-free survival(PFS) was 63.45% and 80.58%(P<0.05), respectively, the 5-year overall survival(OS) was 54.18% and 84.74%(P<0.05). Among 37 patients with non-squamous cell carcinoma, the TP, TN, PPV, NPV and total predictive accuracy rates were 88.46%, 72.73%, 88.46%, 72.73%, and 83.78%, respectively. The 5-year PFS of the patients who changed(TN+FP) and did not change the treatment regimen(TP+FN) were 68.57% and 56.00%, and the 5-year OS was 69.26% and 48.72%, the difference was not statistically significant. Conclusion:OncoDrug-Seq™ testing has certain significance in guiding clinicians to formulate personalized chemotherapy regimens. Timely replacement of the treatment plan can enable the patient to obtain a more ideal curative effect. Compared with patients with squamous cell carcinoma, patients with non-squamous cell carcinoma can obtain greater survival benefit from this testing. However, there are still some deviations in the accuracy of the test results compared with the actual clinical situation. Therefore, the decision should be made based on the test results in combination with the clinical reality.
Collapse
Affiliation(s)
- 坤 刘
- 解放军总医院耳鼻咽喉头颈外科医学部 国家耳鼻咽喉疾病临床医学研究中心(北京,100853)College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, National Clinical Research Center for Otolaryngologic Diseases, Beijing, 100853, China
| | - 湘 顾
- 解放军总医院耳鼻咽喉头颈外科医学部 国家耳鼻咽喉疾病临床医学研究中心(北京,100853)College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, National Clinical Research Center for Otolaryngologic Diseases, Beijing, 100853, China
| | - 南翔 陈
- 解放军总医院耳鼻咽喉头颈外科医学部 国家耳鼻咽喉疾病临床医学研究中心(北京,100853)College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, National Clinical Research Center for Otolaryngologic Diseases, Beijing, 100853, China
| | - 玮 游
- 解放军总医院耳鼻咽喉头颈外科医学部 国家耳鼻咽喉疾病临床医学研究中心(北京,100853)College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, National Clinical Research Center for Otolaryngologic Diseases, Beijing, 100853, China
| | - 健 魏
- 解放军总医院耳鼻咽喉头颈外科医学部 国家耳鼻咽喉疾病临床医学研究中心(北京,100853)College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, National Clinical Research Center for Otolaryngologic Diseases, Beijing, 100853, China
| | - 林 马
- 解放军总医院放射治疗科Department of Radiotherapy, Chinese PLA General Hospital
| | - 欣欣 张
- 解放军总医院耳鼻咽喉头颈外科医学部 国家耳鼻咽喉疾病临床医学研究中心(北京,100853)College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, National Clinical Research Center for Otolaryngologic Diseases, Beijing, 100853, China
| |
Collapse
|
4
|
Vivoda Tomšič M, Korošec P, Kovač V, Bisdas S, Šurlan Popovič K. Dynamic contrast-enhanced MRI in malignant pleural mesothelioma: prediction of outcome based on DCE-MRI measurements in patients undergoing cytotoxic chemotherapy. BMC Cancer 2022; 22:191. [PMID: 35184730 PMCID: PMC8859879 DOI: 10.1186/s12885-022-09277-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 02/09/2022] [Indexed: 11/22/2022] Open
Abstract
Background The malignant pleural mesothelioma (MPM) response rate to chemotherapy is low. The identification of imaging biomarkers that could help guide the most effective therapy approach for individual patients is highly desirable. Our aim was to investigate the dynamic contrast-enhanced (DCE) MR parameters as predictors for progression-free (PFS) and overall survival (OS) in patients with MPM treated with cisplatin-based chemotherapy. Methods Thirty-two consecutive patients with MPM were enrolled in this prospective study. Pretreatment and intratreatment DCE-MRI were scheduled in each patient. The DCE parameters were analyzed using the extended Tofts (ET) and the adiabatic approximation tissue homogeneity (AATH) model. Comparison analysis, logistic regression and ROC analysis were used to identify the predictors for the patient’s outcome. Results Patients with higher pretreatment ET and AATH-calculated Ktrans and ve values had longer OS (P≤.006). Patients with a more prominent reduction in ET-calculated Ktrans and kep values during the early phase of chemotherapy had longer PFS (P =.008). No parameter was identified to predict PFS. Pre-treatment ET-calculated Ktrans was found to be an independent predictive marker for longer OS (P=.02) demonstrating the most favourable discrimination performance compared to other DCE parameters with an estimated sensitivity of 89% and specificity of 78% (AUC 0.9, 95% CI 0.74-0.98, cut off > 0.08 min-1). Conclusions In the present study, higher pre-treatment ET-calculated Ktrans values were associated with longer OS. The results suggest that DCE-MRI might provide additional information for identifying MPM patients that may respond to chemotherapy. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-09277-x.
Collapse
|
5
|
Goričar K, Holcar M, Mavec N, Kovač V, Lenassi M, Dolžan V. Extracellular Vesicle Enriched miR-625-3p Is Associated with Survival of Malignant Mesothelioma Patients. J Pers Med 2021; 11:jpm11101014. [PMID: 34683154 PMCID: PMC8538530 DOI: 10.3390/jpm11101014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 10/03/2021] [Accepted: 10/07/2021] [Indexed: 12/29/2022] Open
Abstract
Malignant mesothelioma (MM) is characterized by poor prognosis and short survival. Extracellular vesicles (EVs) are membrane-bound particles released from cells into various body fluids, and their molecular composition reflects the characteristics of the origin cell. Blood EVs or their miRNA cargo might serve as new minimally invasive biomarkers that would enable earlier detection of MM or treatment outcome prediction. Our aim was to evaluate miRNAs enriched in serum EVs as potential prognostic biomarkers in MM patients in a pilot longitudinal study. EVs were isolated from serum samples obtained before and after treatment using ultracentrifugation on 20% sucrose cushion. Serum EV-enriched miR-103-3p, miR-126-3p and miR-625-3p were quantified using qPCR. After treatment, expression of miR-625-3p and miR-126-3p significantly increased in MM patients with poor treatment outcome (p = 0.012 and p = 0.036, respectively). A relative increase in miR-625-3p expression after treatment for more than 3.2% was associated with shorter progression-free survival (7.5 vs. 19.4 months, HR = 3.92, 95% CI = 1.20-12.80, p = 0.024) and overall survival (12.5 vs. 49.1 months, HR = 5.45, 95% CI = 1.06-28.11, p = 0.043) of MM patients. Bioinformatic analysis showed enrichment of 33 miR-625-3p targets in eight biological pathways. Serum EV-enriched miR-625-3p could therefore serve as a prognostic biomarker in MM and could contribute to a more personalized treatment.
Collapse
Affiliation(s)
- Katja Goričar
- Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia; (K.G.); (M.H.); (N.M.); (M.L.)
| | - Marija Holcar
- Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia; (K.G.); (M.H.); (N.M.); (M.L.)
| | - Nina Mavec
- Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia; (K.G.); (M.H.); (N.M.); (M.L.)
| | - Viljem Kovač
- Institute of Oncology Ljubljana, Zaloška 2, 1000 Ljubljana, Slovenia;
- Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia
| | - Metka Lenassi
- Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia; (K.G.); (M.H.); (N.M.); (M.L.)
| | - Vita Dolžan
- Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia; (K.G.); (M.H.); (N.M.); (M.L.)
- Correspondence: ; Tel.: +386-1-543-76
| |
Collapse
|
6
|
Howlader NR, Rahman MM, Hossain MA, Sultana R, Hossain SM, Mazid MA, Rahman MM. Genetic polymorphisms in DNA repair genes XRCC1 and 3 are associated with increased risk of breast cancer in Bangladeshi population. Breast Cancer Res Treat 2020; 182:739-750. [PMID: 32562117 DOI: 10.1007/s10549-020-05738-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 06/09/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND Genetic polymorphisms in DNA repair genes, XRCC1 (Arg399Gln) and XRCC3 (Thr241Met), may affect their DNA repair capacity leading to individual variation in breast cancer susceptibility among Bangladeshi females. METHODS The case-control study comprised 121 breast cancer patients and 133 healthy controls. Genomic DNA isolated from peripheral blood was genotyped for target SNPs using PCR-RFLP method. RESULTS For XRCC1, heterozygous Arg/Gln and homozygous Gln/Gln genotypes showed 1.78-fold (95% CI 1.0084 to 3.1442, p = 0.0467) and 2.41-fold (95% CI 1.0354 to 5.5914, p = 0.0413) increased risk of breast cancer, respectively, when compared with Arg/Arg genotype. The presence of any XRCC1 Gln showed association with 1.93-fold increased risk. The variant Gln allele was associated with increased risk of breast cancer (95% CI 1.1885 to 2.6805, p = 0.0052). For XRCC3, Thr/Met heterozygous and combined Thr/Met + Met/Met genotypes were associated with 1.85-fold (95% CI 1.0815 to 3.1834, p = 0.0248) and 1.89-fold (95% CI 1.1199 to 3.1908, p = 0.0171) higher risk, respectively, compared to Thr/Thr genotypes. The variant Met allele showed significant association with increased breast cancer susceptibility. Among cases genotype frequencies were significantly different in patients with age 55 or above, and with menopause and diabetes. CONCLUSION XRCC1 (Arg399Gln) and XRCC3 (Thr241Met) polymorphisms may be associated with increased breast cancer risk in Bangladeshi females.
Collapse
Affiliation(s)
- Nupur Rani Howlader
- Pharmacy Discipline, Life Science School, Khulna University, Khulna, 9208, Bangladesh
| | - Md Mostafizur Rahman
- Pharmacy Discipline, Life Science School, Khulna University, Khulna, 9208, Bangladesh
| | - Md Amir Hossain
- Department of Pharmacy, ASA University Bangladesh, Dhaka, Bangladesh
| | | | | | - Md Abdul Mazid
- Department of Pharmaceutical Chemistry, University of Dhaka, Dhaka, Bangladesh
| | - Md Mustafizur Rahman
- Pharmacy Discipline, Life Science School, Khulna University, Khulna, 9208, Bangladesh.
| |
Collapse
|
7
|
Wu HY, Shendre A, Zhang S, Zhang P, Wang L, Zeruesenay D, Rocha LM, Shatkay H, Quinney SK, Ning X, Li L. Translational Knowledge Discovery Between Drug Interactions and Pharmacogenetics. Clin Pharmacol Ther 2020; 107:886-902. [PMID: 31863452 DOI: 10.1002/cpt.1745] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 11/25/2019] [Indexed: 12/12/2022]
Abstract
Clinical translation of drug-drug interaction (DDI) studies is limited, and knowledge gaps across different types of DDI evidence make it difficult to consolidate and link them to clinical consequences. Consequently, we developed information retrieval (IR) models to retrieve DDI and drug-gene interaction (DGI) evidence from 25 million PubMed abstracts and distinguish DDI evidence into in vitro pharmacokinetic (PK), clinical PK, and clinical pharmacodynamic (PD) studies for US Food and Drug Administration (FDA) approved and withdrawn drugs. Additionally, information extraction models were developed to extract DDI-pairs and DGI-pairs from the IR-retrieved abstracts. An overlapping analysis identified 986 unique DDI-pairs between all 3 types of evidence. Another 2,157 and 13,012 DDI-pairs and 3,173 DGI-pairs were identified from known clinical PK/PD DDI, clinical PD DDI, and DGI evidence, respectively. By integrating DDI and DGI evidence, we discovered 119 and 18 new pharmacogenetic hypotheses associated with CYP3A and CYP2D6, respectively. Some of these DGI evidence can also aid us in understanding DDI mechanisms.
Collapse
Affiliation(s)
- Heng-Yi Wu
- Genentech Inc., San Francisco, California, USA
| | - Aditi Shendre
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Shijun Zhang
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Pengyue Zhang
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Lei Wang
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Desta Zeruesenay
- Division of Clinical Pharmacology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Luis M Rocha
- School of Informatics, Computing & Engineering, Indiana University, Bloomington, Indiana, USA.,Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Hagit Shatkay
- Department of Computer and Information Sciences, University of Delaware, Newark, Delaware, USA
| | - Sara K Quinney
- Division of Clinical Pharmacology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA.,Department of Obstetrics and Gynecology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Xia Ning
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, Ohio, USA.,Department of Computer Science and Engineering, The Ohio State University, Columbus, Ohio, USA
| | - Lang Li
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, Ohio, USA
| |
Collapse
|
8
|
Assaraf YG, Brozovic A, Gonçalves AC, Jurkovicova D, Linē A, Machuqueiro M, Saponara S, Sarmento-Ribeiro AB, Xavier CP, Vasconcelos MH. The multi-factorial nature of clinical multidrug resistance in cancer. Drug Resist Updat 2019; 46:100645. [DOI: 10.1016/j.drup.2019.100645] [Citation(s) in RCA: 196] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 09/05/2019] [Accepted: 09/14/2019] [Indexed: 12/16/2022]
|
9
|
Hearing Protection, Restoration, and Regeneration: An Overview of Emerging Therapeutics for Inner Ear and Central Hearing Disorders. Otol Neurotol 2019; 40:559-570. [DOI: 10.1097/mao.0000000000002194] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
10
|
Senk B, Goricar K, Kovac V, Dolzan V, Franko A. Genetic polymorphisms in aquaporin 1 as risk factors for malignant mesothelioma and biomarkers of response to cisplatin treatment. Radiol Oncol 2019; 53:96-104. [PMID: 30840592 PMCID: PMC6411020 DOI: 10.2478/raon-2019-0009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 01/25/2019] [Indexed: 12/26/2022] Open
Abstract
Background Malignant mesothelioma (MM) is an asbestos related aggressive tumor with poor prognosis. The aim of this study was to investigate if aquaporin 1 (AQP1) genetic polymorphisms influence the risk of MM and the response to cisplatin based MM treatment. Patients and methods The case-control study included 231 patients with MM and a control group of 316 healthy blood donors. All subjects were genotyped for three AQP1polymorphisms (rs1049305, rs1476597 and rs28362731). Logistic and Cox regression were used in statistical analysis. Results AQP1 rs1049305 polymorphism was significantly associated with MM risk in dominant model adjusted for gender and age (OR = 0.60, 95% CI = 0.37-0.96, Padj = 0.033). This polymorphism was also significantly associated with cisplatin based treatment related anaemia (unadjusted: OR = 0.49, 95% CI = 0.27-0.90, P = 0.021; adjusted: for CRP: OR = 0.52, 95% CI = 0.27-0.99, P = 0.046), with leukopenia (OR = 2.09, 95% CI = 1.00-4.35, P = 0.049) in dominant model and with thrombocytopenia (OR = 3.06, 95% CI = 1.01-9.28, P = 0.048) and alopecia (OR = 2.92, 95% CI = 1.00-8.46, P = 0.049) in additive model. AQP1 rs28362731 was significantly associated with thrombocytopenia (unadjusted: OR = 3.73, 95% CI = 1.00-13.84, P = 0.049; adjusted for pain: OR = 4.63, 95% CI = 1.13-19.05, P = 0.034) in additive model. Conclusions AQP1 may play a role in the risk of MM. Furthermore, AQP1 genotype information could improve the prediction of MM patients at increased risk for cisplatin toxicity.
Collapse
Affiliation(s)
- Barbara Senk
- Pharmacogenetics Laboratory, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Katja Goricar
- Pharmacogenetics Laboratory, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Viljem Kovac
- Institute of Oncology Ljubljana, Ljubljana, Slovenia
| | - Vita Dolzan
- Pharmacogenetics Laboratory, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Alenka Franko
- Clinical Institute of Occupational Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| |
Collapse
|
11
|
Rossini M, Rizzo P, Bononi I, Clementz A, Ferrari R, Martini F, Tognon MG. New Perspectives on Diagnosis and Therapy of Malignant Pleural Mesothelioma. Front Oncol 2018; 8:91. [PMID: 29666782 PMCID: PMC5891579 DOI: 10.3389/fonc.2018.00091] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 03/15/2018] [Indexed: 12/24/2022] Open
Abstract
Malignant pleural mesothelioma (MPM) is a rare, but severe form of cancer, with an incidence that varies significantly within and among different countries around the world. It develops in about one to two persons per million of the general population, leading to thousands of deaths every year worldwide. To date, the MPM is mostly associated with occupational asbestos exposure. Asbestos represents the predominant etiological factor, with approximately 70% of cases of MPM with well-documented occupational exposure to asbestos, with the exposure time, on average greater than 40 years. Environmental exposure to asbestos is increasingly becoming recognized as a cause of mesothelioma, together with gene mutations. The possible roles of other cofactors, such as viral infection and radiation exposure, are still debated. MPM is a fatal tumor. This cancer arises during its early phase without clinical signs. Consequently, its diagnosis occurs at advanced stages. Standard clinical therapeutic approaches include surgery, chemo- and radiotherapies. Preclinical and clinical researches are making great strides in the field of this deadly disease, identifying new biomarkers and innovative therapeutic approaches. Among the newly identified markers and potential therapeutic targets, circulating microRNAs and the Notch pathway represent promising avenues that could result in the early detection of the tumor and novel therapeutic approaches.
Collapse
Affiliation(s)
- Marika Rossini
- Department of Morphology, Surgery and Experimental Medicine, Section of Pathology, Oncology and Experimental Biology, School of Medicine, University of Ferrara, Ferrara, Italy
| | - Paola Rizzo
- Department of Morphology, Surgery and Experimental Medicine, Section of Pathology, Oncology and Experimental Biology, School of Medicine, University of Ferrara, Ferrara, Italy
| | - Ilaria Bononi
- Department of Morphology, Surgery and Experimental Medicine, Section of Pathology, Oncology and Experimental Biology, School of Medicine, University of Ferrara, Ferrara, Italy
| | - Anthony Clementz
- Department of Natural Sciences and Geography, Concordia University Chicago, River Forest, IL, United States
| | - Roberto Ferrari
- Department of Medical Sciences, Section of Internal Medicine and Cardiorespiratory, School of Medicine, University of Ferrara, Ferrara, Italy.,E.S. Health Science Foundation, GVM Care & Research, Maria Cecilia Hospital, Cotignola, Italy
| | - Fernanda Martini
- Department of Morphology, Surgery and Experimental Medicine, Section of Pathology, Oncology and Experimental Biology, School of Medicine, University of Ferrara, Ferrara, Italy
| | - Mauro G Tognon
- Department of Morphology, Surgery and Experimental Medicine, Section of Pathology, Oncology and Experimental Biology, School of Medicine, University of Ferrara, Ferrara, Italy
| |
Collapse
|
12
|
Devi KR, Ahmed J, Narain K, Mukherjee K, Majumdar G, Chenkual S, Zonunmawia JC. DNA Repair Mechanism Gene, XRCC1A ( Arg194Trp) but not XRCC3 ( Thr241Met) Polymorphism Increased the Risk of Breast Cancer in Premenopausal Females: A Case-Control Study in Northeastern Region of India. Technol Cancer Res Treat 2017; 16:1150-1159. [PMID: 29332455 PMCID: PMC5762082 DOI: 10.1177/1533034617736162] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
X-ray repair cross complementary group gene is one of the most studied candidate gene involved in different types of cancers. Studies have shown that X-ray repair cross complementary genes are significantly associated with increased risk of breast cancer in females. Moreover, studies have revealed that X-ray repair cross complementary gene polymorphism significantly varies between and within different ethnic groups globally. The present case–control study was aimed to investigate the association of X-ray repair cross complementary 1A (Arg194Trp) and X-ray repair cross complementary 3 (Thr241Met) polymorphism with the risk of breast cancer in females from northeastern region of India. The present case–control study includes histopathologically confirmed and newly diagnosed 464 cases with breast cancer and 534 apparently healthy neighborhood community controls. Information on sociodemographic factors and putative risk factors were collected from each study participant by conducting face-to-face interviews. Genotyping of X-ray repair cross complementary 1A (Arg194Trp) and X-ray repair cross complementary 3 (Thr241Met) was carried out by polymerase chain reaction-restriction fragment length polymorphism. For statistical analysis, both univariate and multivariate logistic regression analyses were performed. We also performed stratified analysis to find out the association of X-ray repair cross complementary genes with the risk of breast cancer stratified based on menstrual status. This study revealed that tryptophan allele (R/W-W/W genotype) in X-ray repair cross complementary 1A (Arg194Trp) gene significantly increased the risk of breast cancer (adjusted odds ratio = 1.44, 95% confidence interval = 1.06-1.97, P < .05 for R/W-W/W genotype). Moreover, it was found that tryptophan allele (W/W genotype) at codon 194 of X-ray repair cross complementary 1A (Arg194Trp) gene significantly increased the risk of breast cancer in premenopausal females (crude odds ratio = 1.66, 95% confidence interval = 1.11-2.46, P < .05 for R/W-W/W genotype). The present study did not reveal any significant association of X-ray repair cross complementary 3 (Thr241Met) polymorphism with the risk of breast cancer. The present study has explored that X-ray repair cross complementary 1A (Arg194Trp) gene polymorphism is significantly associated with the increased risk of breast cancer in premenopausal females from northeastern region of India which may be beneficial for prognostic purposes.
Collapse
Affiliation(s)
- K Rekha Devi
- 1 Regional Medical Research Centre, NE Region, Indian Council of Medical Research, Dibrugarh, Assam, India
| | - Jishan Ahmed
- 2 Assam Medical College and Hospital, Dibrugarh, Assam, India
| | - Kanwar Narain
- 1 Regional Medical Research Centre, NE Region, Indian Council of Medical Research, Dibrugarh, Assam, India
| | - Kaustab Mukherjee
- 1 Regional Medical Research Centre, NE Region, Indian Council of Medical Research, Dibrugarh, Assam, India
| | | | | | | |
Collapse
|
13
|
Matrix Metalloproteinases Polymorphisms as Prognostic Biomarkers in Malignant Pleural Mesothelioma. DISEASE MARKERS 2017; 2017:8069529. [PMID: 29138529 PMCID: PMC5613362 DOI: 10.1155/2017/8069529] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 07/28/2017] [Accepted: 08/13/2017] [Indexed: 12/15/2022]
Abstract
Background Malignant pleural mesothelioma (MPM) is a rare disease with a relatively short overall survival (OS). Metalloproteinases (MMPs) have a vast biological effect on tumor progression, invasion, metastasis formation, and apoptosis. MMP expression was previously associated with survival in MPM. Our aim was to evaluate if genetic variability of MMP genes could also serve as a prognostic biomarker in MPM. Methods We genotyped 199 MPM patients for ten polymorphisms: rs243865, rs243849 and rs7201, in MMP2; rs17576, rs17577, rs20544, and rs2250889 in MMP9; and rs1042703, rs1042704, and rs743257 in MMP14. We determined the influence on survival using Cox regression. Results Carriers of polymorphic MMP9 rs2250889 allele had shorter time to progression (TTP) (6.07 versus 10.03 months, HR = 2.45, 95% CI = 1.45–4.14, p = 0.001) and OS (9.23 versus 19.2 months, HR = 2.39, 95% CI = 1.37–4.18, p = 0.002). In contrast, carriers of at least one polymorphic MMP9 rs20544 allele had longer TTP (10.93 versus 9.40 months, HR = 0.57, 95% CI = 0.38–0.86 p = 0.007) and OS (20.67 versus 13.50 months, HR = 0.56, 95% CI = 0.37–0.85, p = 0.007). MMP14 rs1042703 was associated with nominally shorter TTP (8.7 versus 9.27 months, HR = 2.09, 95% CI = 1.06–4.12, p = 0.032). Conclusions Selected MMP SNPs were associated with survival and could be used as potential genetic biomarkers in MPM.
Collapse
|