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Giannitrapani L, Di Gaudio F, Cervello M, Scionti F, Ciliberto D, Staropoli N, Agapito G, Cannataro M, Tassone P, Tagliaferri P, Seidita A, Soresi M, Affronti M, Bertino G, Russello M, Ciriminna R, Lino C, Spinnato F, Verderame F, Augello G, Arbitrio M. Genetic Biomarkers of Sorafenib Response in Patients with Hepatocellular Carcinoma. Int J Mol Sci 2024; 25:2197. [PMID: 38396873 PMCID: PMC10888718 DOI: 10.3390/ijms25042197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 02/08/2024] [Accepted: 02/10/2024] [Indexed: 02/25/2024] Open
Abstract
The identification of biomarkers for predicting inter-individual sorafenib response variability could allow hepatocellular carcinoma (HCC) patient stratification. SNPs in angiogenesis- and drug absorption, distribution, metabolism, and excretion (ADME)-related genes were evaluated to identify new potential predictive biomarkers of sorafenib response in HCC patients. Five known SNPs in angiogenesis-related genes, including VEGF-A, VEGF-C, HIF-1a, ANGPT2, and NOS3, were investigated in 34 HCC patients (9 sorafenib responders and 25 non-responders). A subgroup of 23 patients was genotyped for SNPs in ADME genes. A machine learning classifier method was used to discover classification rules for our dataset. We found that only the VEGF-A (rs2010963) C allele and CC genotype were significantly associated with sorafenib response. ADME-related gene analysis identified 10 polymorphic variants in ADH1A (rs6811453), ADH6 (rs10008281), SULT1A2/CCDC101 (rs11401), CYP26A1 (rs7905939), DPYD (rs2297595 and rs1801265), FMO2 (rs2020863), and SLC22A14 (rs149738, rs171248, and rs183574) significantly associated with sorafenib response. We have identified a genetic signature of predictive response that could permit non-responder/responder patient stratification. Angiogenesis- and ADME-related genes correlation was confirmed by cumulative genetic risk score and network and pathway enrichment analysis. Our findings provide a proof of concept that needs further validation in follow-up studies for HCC patient stratification for sorafenib prescription.
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Affiliation(s)
- Lydia Giannitrapani
- Institute for Biomedical Research and Innovation, National Research Council (CNR), 90146 Palermo, Italy; (L.G.); (M.C.)
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, 90127 Palermo, Italy; (F.D.G.); (A.S.); (M.S.); (M.A.)
| | - Francesca Di Gaudio
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, 90127 Palermo, Italy; (F.D.G.); (A.S.); (M.S.); (M.A.)
| | - Melchiorre Cervello
- Institute for Biomedical Research and Innovation, National Research Council (CNR), 90146 Palermo, Italy; (L.G.); (M.C.)
| | - Francesca Scionti
- Department of Experimental and Clinical Medicine, Magna Graecia University, 88100 Catanzaro, Italy; (F.S.); (N.S.); (P.T.); (P.T.)
| | - Domenico Ciliberto
- Medical and Translational Oncology Unit, A.O.U. R. Dulbecco, 88100 Catanzaro, Italy;
| | - Nicoletta Staropoli
- Department of Experimental and Clinical Medicine, Magna Graecia University, 88100 Catanzaro, Italy; (F.S.); (N.S.); (P.T.); (P.T.)
- Medical and Translational Oncology Unit, A.O.U. R. Dulbecco, 88100 Catanzaro, Italy;
| | - Giuseppe Agapito
- Department of Legal, Economic and Social Sciences, Magna Graecia University, 88100 Catanzaro, Italy;
| | - Mario Cannataro
- Department of Medical and Surgical Sciences, University Magna Graecia of Catanzaro, 88100 Catanzaro, Italy;
| | - Pierfrancesco Tassone
- Department of Experimental and Clinical Medicine, Magna Graecia University, 88100 Catanzaro, Italy; (F.S.); (N.S.); (P.T.); (P.T.)
- Medical and Translational Oncology Unit, A.O.U. R. Dulbecco, 88100 Catanzaro, Italy;
- College of Science and Technology, Temple University, Philadelphia, PA 19122, USA
| | - Pierosandro Tagliaferri
- Department of Experimental and Clinical Medicine, Magna Graecia University, 88100 Catanzaro, Italy; (F.S.); (N.S.); (P.T.); (P.T.)
- Medical and Translational Oncology Unit, A.O.U. R. Dulbecco, 88100 Catanzaro, Italy;
| | - Aurelio Seidita
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, 90127 Palermo, Italy; (F.D.G.); (A.S.); (M.S.); (M.A.)
- Villa Sofia-Cervello Hospital, C.O.U. Medical Oncology, 90146 Palermo, Italy; (F.S.); (F.V.)
| | - Maurizio Soresi
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, 90127 Palermo, Italy; (F.D.G.); (A.S.); (M.S.); (M.A.)
| | - Marco Affronti
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, 90127 Palermo, Italy; (F.D.G.); (A.S.); (M.S.); (M.A.)
| | - Gaetano Bertino
- Hepatology Unit, A.O.U. Policlinico-San Marco, Department of Clinical and Experimental Medicine, University of Catania, 95123 Catania, Italy;
| | | | - Rosaria Ciriminna
- Institute of Nanostructured Materials, National Research Council (CNR), 90146 Palermo, Italy; (R.C.); (C.L.)
| | - Claudia Lino
- Institute of Nanostructured Materials, National Research Council (CNR), 90146 Palermo, Italy; (R.C.); (C.L.)
| | - Francesca Spinnato
- Villa Sofia-Cervello Hospital, C.O.U. Medical Oncology, 90146 Palermo, Italy; (F.S.); (F.V.)
| | - Francesco Verderame
- Villa Sofia-Cervello Hospital, C.O.U. Medical Oncology, 90146 Palermo, Italy; (F.S.); (F.V.)
| | - Giuseppa Augello
- Institute for Biomedical Research and Innovation, National Research Council (CNR), 90146 Palermo, Italy; (L.G.); (M.C.)
| | - Mariamena Arbitrio
- Institute for Biomedical Research and Innovation, National Research Council (CNR), 88100 Catanzaro, Italy
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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.
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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:
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Forouzandeh A, Rutar A, Kalmady SV, Greiner R. Analyzing biomarker discovery: Estimating the reproducibility of biomarker sets. PLoS One 2022; 17:e0252697. [PMID: 35901020 PMCID: PMC9333302 DOI: 10.1371/journal.pone.0252697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 06/29/2022] [Indexed: 11/19/2022] Open
Abstract
Many researchers try to understand a biological condition by identifying biomarkers. This is typically done using univariate hypothesis testing over a labeled dataset, declaring a feature to be a biomarker if there is a significant statistical difference between its values for the subjects with different outcomes. However, such sets of proposed biomarkers are often not reproducible – subsequent studies often fail to identify the same sets. Indeed, there is often only a very small overlap between the biomarkers proposed in pairs of related studies that explore the same phenotypes over the same distribution of subjects. This paper first defines the Reproducibility Score for a labeled dataset as a measure (taking values between 0 and 1) of the reproducibility of the results produced by a specified fixed biomarker discovery process for a given distribution of subjects. We then provide ways to reliably estimate this score by defining algorithms that produce an over-bound and an under-bound for this score for a given dataset and biomarker discovery process, for the case of univariate hypothesis testing on dichotomous groups. We confirm that these approximations are meaningful by providing empirical results on a large number of datasets and show that these predictions match known reproducibility results. To encourage others to apply this technique to analyze their biomarker sets, we have also created a publicly available website, https://biomarker.shinyapps.io/BiomarkerReprod/, that produces these Reproducibility Score approximations for any given dataset (with continuous or discrete features and binary class labels).
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Affiliation(s)
- Amir Forouzandeh
- Department of Computing Science, University of Alberta, Edmonton, Canada
- * E-mail:
| | - Alex Rutar
- Department of Pure Math, University of Waterloo, Waterloo, ON, Canada
| | - Sunil V. Kalmady
- Department of Computing Science, University of Alberta, Edmonton, Canada
- Canadian VIGOUR Centre, University of Alberta, Edmonton, Canada
| | - Russell Greiner
- Department of Computing Science, University of Alberta, Edmonton, Canada
- Alberta Machine Intelligence Institute, Edmonton, Canada
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Insights on the interaction mechanism of exemestane to three digestive enzymes by multi-spectroscopy and molecular docking. Int J Biol Macromol 2021; 187:54-65. [PMID: 34274402 DOI: 10.1016/j.ijbiomac.2021.07.079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 07/06/2021] [Accepted: 07/12/2021] [Indexed: 01/27/2023]
Abstract
Exemestane is an irreversible steroidal aromatase inhibitor, typically used to treat breast cancer. As an anti-tumor drug, exemestane has more obvious side effects on the gastrointestinal tract. The purpose of this work is to investigate the combination of exemestane with three important digestive enzymes including pepsin (Pep), trypsin (Try) and α-Chymotrypsin (α-ChT) so as to analyze the mechanism of the gastrointestinal adverse effects causing by exemestane binding. Enzyme activity experiment showed that the enzyme activity of Pep was decreased in the presence of exemestane. Fluorescence spectra revealed that exemestane formed stable complexes with digestive enzymes, and the quenching mechanism of drug-digestive enzymes interaction were all static quenching. The binding constants of Pep, Try and α-ChT at 298 K were 2.34 × 105, 1.45 × 105, and 2.05 × 105 M-1, respectively. Synchronous fluorescence and 3D fluorescence spectroscopy showed that the conformation of exemestane was slightly changed after combining with digestive enzymes, and non-radiative energy transfer occurred. Circular dichroism results indicated that exemestane could change the secondary structure of digestive enzymes via increase the α-helix content and decrease in the β-sheet content. Thermodynamic parameters (ΔH0, ΔS0, and ΔG0) revealed that exemestane interacted with α-ChT through electrostatic force, and the binding force with Pep and Try was van der Waals interactions and hydrogen, which was basically consistent with the molecular docking results.
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Alimardani M, Moghbeli M, Rastgar-Moghadam A, Shandiz FH, Abbaszadegan MR. Single nucleotide polymorphisms as the efficient prognostic markers in breast cancer. Curr Cancer Drug Targets 2021; 21:768-793. [PMID: 34036920 DOI: 10.2174/1568009621666210525151846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 03/15/2021] [Accepted: 04/19/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Breast cancer (BC) is known as the most common malignancy in women. Environmental and genetic factors are associated with BC progression. Genetic polymorphisms have been reported as important risk factors of BC prognosis and drug response. Main body: Therefore, in the present review, we have summarized all single nucleotide polymorphisms (SNPs) which have been significantly associated with drug response in BC patients around the world. We have also categorized the reported SNPs based on their related genes functions to clarify the molecular biology of drug responses in BC. CONCLUSION The majority of SNPs were reported in detoxifying enzymes, which introduced such genes as the main genetic risk factors during BC drug responses. This review paves the way for introducing a prognostic panel of SNPs for the BC patients in the world.
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Affiliation(s)
- Maliheh Alimardani
- Medical Genetics Research Center, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Meysam Moghbeli
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Azam Rastgar-Moghadam
- Medical Genetics Research Center, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Fatemeh Homaei Shandiz
- Department of Radiotherapy/Oncology, Omid Hospital, Mashhad University of Medical Science, Mashhad, Iran
| | - Mohammad Reza Abbaszadegan
- Medical Genetics Research Center, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
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Alkasaby MK, Abd El-Fattah AI, Ibrahim IH, Abd El-Samie HS. Polymorphism of XRCC3 in Egyptian Breast Cancer Patients. PHARMACOGENOMICS & PERSONALIZED MEDICINE 2020; 13:273-282. [PMID: 32821150 PMCID: PMC7418173 DOI: 10.2147/pgpm.s260682] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 07/20/2020] [Indexed: 12/20/2022]
Abstract
Purpose Polymorphisms of DNA repair genes may contribute to variations in DNA repair capacity and subsequent genetic susceptibility to different cancers. In Egypt, breast cancer is the most common cancer among women, representing 18.9% of the total cancer cases. The present study assesses the correlation between X-ray repair cross-complementing group 3 (XRCC3) polymorphism with breast cancer and treatment response in Egyptian female breast cancer patients. Patients and Methods This pilot case–control study was conducted on 66 female breast cancer patients and 20 apparently healthy females as a control group. Tumor grading, immunohistostaining of hormone (progesterone and estrogen) receptors and human epidermal growth factor receptor 2 (HER2), and RFLP-PCR for XRCC3 (rs861539) polymorphism were performed. All breast cancer patients received a treatment protocol (after surgery) which was either chemotherapy (anthracyclines followed by paclitaxel or anthracyclines + fluorouracil) or radiotherapy, or both. Disease-free survival (DFS) and overall survival (OS) were recorded. Results The number of patients with a heterozygous allele (GA) was significantly higher in cases of tumor size >20 mm. The A allele was correlated with younger age at diagnosis in both chemotherapy and radiotherapy groups. Poor treatment response and higher mortality rates were significantly associated with AA and GA compared with GG alleles (normal allele). In the chemotherapy group, out of eight patients with the A allele, six showed a poor response to treatment containing fluorouracil. Conclusion XRCC3 rs861539 polymorphism could be associated with lower DFS and OS and poor treatment response. So, we recommend carrying out XRCC3 genotyping before starting treatment to choose the most effective treatment strategy according to XRCC3 polymorphism. ![]()
Point your SmartPhone at the code above. If you have a QR code reader the video abstract will appear. Or use: https://youtu.be/_MRawBP1Tmg
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Affiliation(s)
- Mona Khyri Alkasaby
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy (Girls), Al-Azhar University, Nasr City, Cairo, Egypt
| | - Abeer Ibrahim Abd El-Fattah
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy (Girls), Al-Azhar University, Nasr City, Cairo, Egypt
| | - Iman Hassan Ibrahim
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy (Girls), Al-Azhar University, Nasr City, Cairo, Egypt
| | - Hesham Samir Abd El-Samie
- Department of Clinical Pathology, Faculty of Medicine (New Damietta), Al-Azhar University, New Damietta, Damietta, Egypt
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