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Kováčová M, Hlaváč V, Koževnikovová R, Rauš K, Gatěk J, Souček P. Artificial Intelligence-Driven Prediction Revealed CFTR Associated with Therapy Outcome of Breast Cancer: A Feasibility Study. Oncology 2024:1-12. [PMID: 39025053 DOI: 10.1159/000540395] [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: 01/12/2024] [Accepted: 07/09/2024] [Indexed: 07/20/2024]
Abstract
INTRODUCTION In silico tools capable of predicting the functional consequences of genomic differences between individuals, many of which are AI-driven, have been the most effective over the past two decades for non-synonymous single nucleotide variants (nsSNVs). When appropriately selected for the purpose of the study, a high predictive performance can be expected. In this feasibility study, we investigate the distribution of nsSNVs with an allele frequency below 5%. To classify the putative functional consequence, a tier-based filtration led by AI-driven predictors and scoring system was implemented to the overall decision-making process, resulting in a list of prioritised genes. METHODS The study has been conducted on breast cancer patients of homogeneous ethnicity. Germline rare variants have been sequenced in genes that influence pharmacokinetic parameters of anticancer drugs or molecular signalling pathways in cancer. After AI-driven functional pathogenicity classification and data mining in pharmacogenomic (PGx) databases, variants were collapsed to the gene level and ranked according to their putative deleterious role. RESULTS In breast cancer patients, seven of the twelve genes prioritised based on the predictions were found to be associated with response to oncotherapy, histological grade, and tumour subtype. Most importantly, we showed that the group of patients with at least one rare nsSNVs in cystic fibrosis transmembrane conductance regulator (CFTR) had significantly reduced disease-free (log rank, p = 0.002) and overall survival (log rank, p = 0.006). CONCLUSION AI-driven in silico analysis with PGx data mining provided an effective approach navigating for functional consequences across germline genetic background, which can be easily integrated into the overall decision-making process for future studies. The study revealed a statistically significant association with numerous clinicopathological parameters, including treatment response. Our study indicates that CFTR may be involved in the processes influencing the effectiveness of oncotherapy or in the malignant progression of the disease itself.
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Affiliation(s)
- Mária Kováčová
- Third Faculty of Medicine, Charles University, Prague, Czechia
| | - Viktor Hlaváč
- Laboratory of Pharmacogenomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czechia
- Toxicogenomics Unit, National Institute of Public Health, Prague, Czechia
| | | | - Karel Rauš
- Institute for the Care for Mother and Child, Prague, Czechia
| | - Jiří Gatěk
- Department of Surgery, EUC Hospital and University of Tomas Bata in Zlin, Zlin, Czechia
| | - Pavel Souček
- Laboratory of Pharmacogenomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czechia
- Toxicogenomics Unit, National Institute of Public Health, Prague, Czechia
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Perrone G, Rigacci L, Roviello G, Landini I, Fabbri A, Iovino L, Puccini B, Cencini E, Orciuolo E, Bocchia M, Bosi A, Mini E, Nobili S. Validation of single nucleotide polymorphisms potentially related to R-CHOP resistance in diffuse large B-cell lymphoma patients. CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2024; 7:21. [PMID: 38835350 PMCID: PMC11149109 DOI: 10.20517/cdr.2024.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 04/30/2024] [Accepted: 05/16/2024] [Indexed: 06/06/2024]
Abstract
Aim: Diffuse large B-cell lymphoma (DLBCL) is the most common B-cell non-Hodgkin lymphoma (NHL). Despite the availability of clinical and molecular algorithms applied for the prediction of prognosis, in up to 30%-40% of patients, intrinsic or acquired drug resistance occurs. Constitutional genetics may help to predict R-CHOP resistance. This study aimed to validate previously identified single nucleotide polymorphisms (SNPs) in the literature as potential predictors of R-CHOP resistance in DLBCL patients, SNPs. Methods: Twenty SNPs, involved in R-CHOP pharmacokinetics/pharmacodynamics or other pathobiological processes, were investigated in 185 stage I-IV DLBCL patients included in a multi-institution pharmacogenetic study to validate their previously identified correlations with resistance to R-CHOP. Results: Correlations between rs2010963 (VEGFA gene) and sex (P = 0.046), and rs1625895 (TP53 gene) and stage (P = 0.003) were shown. After multivariate analyses, a concordant effect (i.e., increased risk of disease progression and death) was observed for rs1883112 (NCF4 gene) and rs1800871 (IL10 gene). When patients were grouped according to the revised International Prognostic Index (R-IPI), both these SNPs further discriminated progression-free survival (PFS) and overall survival (OS) of the R-IPI-1-2 subgroup. Overall, patients harboring the rare allele showed shorter PFS and OS compared with wild-type patients. Conclusions: Two out of the 20 study SNPs were validated. Thus, these results support the role of previously identified rs1883112 and rs1800871 in predicting DLBCL resistance to R-CHOP and highlight their ability to further discriminate the prognosis of R-IPI-1-2 patients. These data point to the need to also focus on host genetics for a more comprehensive assessment of DLBCL patient outcomes in future prospective trials.
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Affiliation(s)
- Gabriele Perrone
- Department of Health Sciences, University of Florence, Florence 50139, Italy
| | - Luigi Rigacci
- Research Unit of Hematology, Department of Medicine and Surgery, Campus Biomedico University, Rome 00128, Italy
| | | | - Ida Landini
- Department of Health Sciences, University of Florence, Florence 50139, Italy
| | - Alberto Fabbri
- Unit of Hematology, Azienda Ospedaliera Universitaria Senese, University of Siena, Siena 53100, Italy
| | - Lorenzo Iovino
- Unit of Hematology, Santa Chiara University Hospital, University of Pisa, Pisa 56126, Italy
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA 98109-4433, USA
| | - Benedetta Puccini
- Unit of Hematology, Careggi University-Hospital, Florence 50134, Italy
| | - Emanuele Cencini
- Unit of Hematology, Azienda Ospedaliera Universitaria Senese, University of Siena, Siena 53100, Italy
| | - Enrico Orciuolo
- Unit of Hematology, Santa Chiara University Hospital, University of Pisa, Pisa 56126, Italy
| | - Monica Bocchia
- Unit of Hematology, Azienda Ospedaliera Universitaria Senese, University of Siena, Siena 53100, Italy
| | - Alberto Bosi
- Department of Experimental and Clinical Medicine, University of Florence, Florence 50134, Italy
| | - Enrico Mini
- Department of Health Sciences, University of Florence, Florence 50139, Italy
- Authors contributed equally
| | - Stefania Nobili
- Department of Neuroscience, Psychology, Drug Research and Child Health, University of Florence, Florence 50139, Italy
- Authors contributed equally
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Zeng S, Qing Q, Xu W, Yu S, Zheng M, Tan H, Peng J, Huang J. Personalized anesthesia and precision medicine: a comprehensive review of genetic factors, artificial intelligence, and patient-specific factors. Front Med (Lausanne) 2024; 11:1365524. [PMID: 38784235 PMCID: PMC11111965 DOI: 10.3389/fmed.2024.1365524] [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: 01/04/2024] [Accepted: 04/22/2024] [Indexed: 05/25/2024] Open
Abstract
Precision medicine, characterized by the personalized integration of a patient's genetic blueprint and clinical history, represents a dynamic paradigm in healthcare evolution. The emerging field of personalized anesthesia is at the intersection of genetics and anesthesiology, where anesthetic care will be tailored to an individual's genetic make-up, comorbidities and patient-specific factors. Genomics and biomarkers can provide more accurate anesthetic protocols, while artificial intelligence can simplify anesthetic procedures and reduce anesthetic risks, and real-time monitoring tools can improve perioperative safety and efficacy. The aim of this paper is to present and summarize the applications of these related fields in anesthesiology by reviewing them, exploring the potential of advanced technologies in the implementation and development of personalized anesthesia, realizing the future integration of new technologies into clinical practice, and promoting multidisciplinary collaboration between anesthesiology and disciplines such as genomics and artificial intelligence.
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Affiliation(s)
- Shiyue Zeng
- Zhuzhou Clinical College, Jishou University, Jishou, China
| | - Qi Qing
- Zhuzhou Clinical College, Jishou University, Jishou, China
| | - Wei Xu
- Department of Anesthesiology, Zhuzhou Central Hospital, Zhuzhou, China
| | - Simeng Yu
- Zhuzhou Clinical College, Jishou University, Jishou, China
| | - Mingzhi Zheng
- Department of Anesthesiology, Zhuzhou Central Hospital, Zhuzhou, China
| | - Hongpei Tan
- Department of Radiology, Third Xiangya Hospital, Central South University, Changsha, China
| | - Junmin Peng
- Department of Anesthesiology, Zhuzhou Central Hospital, Zhuzhou, China
| | - Jing Huang
- Department of Anesthesiology, Zhuzhou Central Hospital, Zhuzhou, China
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Bouhniz OE, Kenani A. Potential role of genetic polymorphisms in neoadjuvant chemotherapy response in breast cancer. J Chemother 2024:1-15. [PMID: 38511398 DOI: 10.1080/1120009x.2024.2330241] [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: 10/27/2023] [Accepted: 03/11/2024] [Indexed: 03/22/2024]
Abstract
Chemoresistance leads to treatment failure, which can arise through different mechanisms including patients' characteristics. Searching for genetic profiles as a predictor for drug response and toxicity has been extensively studied in pharmacogenomics, thus contributing to personalized medicine and providing alternative treatments. Numerous studies have demonstrated significant evidence of association between genetic polymorphisms and response to neoadjuvant chemotherapy (NAC) in breast cancer. In this review, we explored the potential impact of genetic polymorphisms in NAC primary resistance through selecting a specific clinical profile. The genetic variability within pharmacokinetics, pharmacodynamics, DNA synthesis and repair, and oncogenic signaling pathways genes could be predictive or prognostic markers for NAC resistance. The clinical implication of these results can help provide individualized treatment plans in the early stages of breast cancer treatment. Further studies are needed to determine the genetic hosts of primary chemoresistance mechanisms in order to further emphasize the implementation of genotypic approaches in personalized medicine.
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Affiliation(s)
- Om Elez Bouhniz
- Research Laboratory "Environment, Inflammation, Signaling and Pathologies" (LR18ES40), Faculty of Medicine of Monastir, University of Monastir, Monastir, Tunisia
| | - Abderraouf Kenani
- Research Laboratory "Environment, Inflammation, Signaling and Pathologies" (LR18ES40), Faculty of Medicine of Monastir, University of Monastir, Monastir, Tunisia
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Cătană A, Trifa AP, Achimas-Cadariu PA, Bolba-Morar G, Lisencu C, Kutasi E, Chelaru VF, Muntean M, Martin DL, Antone NZ, Fetica B, Pop F, Militaru MS. Hereditary Breast Cancer in Romania-Molecular Particularities and Genetic Counseling Challenges in an Eastern European Country. Biomedicines 2023; 11:biomedicines11051386. [PMID: 37239058 DOI: 10.3390/biomedicines11051386] [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: 02/27/2023] [Revised: 04/24/2023] [Accepted: 04/28/2023] [Indexed: 05/28/2023] Open
Abstract
In Romania, breast cancer (BC) is the most common malignancy in women. However, there is limited data on the prevalence of predisposing germline mutations in the population in the era of precision medicine, where molecular testing has become an indispensable tool in cancer diagnosis, prognosis, and therapeutics. Therefore, we conducted a retrospective study to determine the prevalence, mutational spectrum, and histopathological prediction factors for hereditary breast cancer (HBC) in Romania. A cohort of 411 women diagnosed with BC selected upon NCCN v.1.2020 guidelines underwent an 84-gene NGS-based panel testing for breast cancer risk assessment during 2018-2022 in the Department of Oncogenetics of the Oncological Institute of Cluj-Napoca, Romania. A total of 135 (33%) patients presented pathogenic mutations in 19 genes. The prevalence of genetic variants was determined, and demographic and clinicopathological characteristics were analyzed. We observed differences among BRCA and non-BRCA carriers regarding family history of cancer, age of onset, and histopathological subtypes. Triple-negative (TN) tumors were more often BRCA1 positive, unlike BRCA2 positive tumors, which were more often the Luminal B subtype. The most frequent non-BRCA mutations were found in CHEK2, ATM, and PALB2, and several recurrent variants were identified for each gene. Unlike other European countries, germline testing for HBC is still limited due to the high costs and is not covered by the National Health System (NSH), thus leading to significant discrepancies related to the screening and prophylaxis of cancer.
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Affiliation(s)
- Andreea Cătană
- Department of Molecular Sciences, Discipline of Medical Genetics, University of Medicine and Pharmacy Iuliu Hațieganu, Victor Babeș 8, 400347 Cluj-Napoca, Romania
- Breast Cancer Tumour Center, Institute of Oncology I. Chiricuță, Republicii Nr. 34-36, 400015 Cluj-Napoca, Romania
| | - Adrian P Trifa
- Breast Cancer Tumour Center, Institute of Oncology I. Chiricuță, Republicii Nr. 34-36, 400015 Cluj-Napoca, Romania
- Discipline of Medical Genetics, University of Medicine and Pharmacy Victor Babeș, Eftimie Murgu 2, 300041 Timișoara, Romania
| | - Patriciu A Achimas-Cadariu
- Breast Cancer Tumour Center, Institute of Oncology I. Chiricuță, Republicii Nr. 34-36, 400015 Cluj-Napoca, Romania
- Department of Oncology, Discipline of Surgery and Gynecological Oncology, University of Medicine and Pharmacy Iuliu Hațieganu, Republicii Nr. 34-36, 400015 Cluj-Napoca, Romania
| | - Gabriela Bolba-Morar
- Breast Cancer Tumour Center, Institute of Oncology I. Chiricuță, Republicii Nr. 34-36, 400015 Cluj-Napoca, Romania
| | - Carmen Lisencu
- Breast Cancer Tumour Center, Institute of Oncology I. Chiricuță, Republicii Nr. 34-36, 400015 Cluj-Napoca, Romania
| | - Eniko Kutasi
- Department of Molecular Sciences, Discipline of Medical Genetics, University of Medicine and Pharmacy Iuliu Hațieganu, Victor Babeș 8, 400347 Cluj-Napoca, Romania
| | - Vlad F Chelaru
- Department of Molecular Sciences, Discipline of Medical Genetics, University of Medicine and Pharmacy Iuliu Hațieganu, Victor Babeș 8, 400347 Cluj-Napoca, Romania
| | - Maximilian Muntean
- Breast Cancer Tumour Center, Institute of Oncology I. Chiricuță, Republicii Nr. 34-36, 400015 Cluj-Napoca, Romania
- Department of Oncology, Discipline of Surgery and Gynecological Oncology, University of Medicine and Pharmacy Iuliu Hațieganu, Republicii Nr. 34-36, 400015 Cluj-Napoca, Romania
| | - Daniela L Martin
- Breast Cancer Tumour Center, Institute of Oncology I. Chiricuță, Republicii Nr. 34-36, 400015 Cluj-Napoca, Romania
| | - Nicoleta Z Antone
- Breast Cancer Tumour Center, Institute of Oncology I. Chiricuță, Republicii Nr. 34-36, 400015 Cluj-Napoca, Romania
| | - Bogdan Fetica
- Breast Cancer Tumour Center, Institute of Oncology I. Chiricuță, Republicii Nr. 34-36, 400015 Cluj-Napoca, Romania
| | - Florina Pop
- Breast Cancer Tumour Center, Institute of Oncology I. Chiricuță, Republicii Nr. 34-36, 400015 Cluj-Napoca, Romania
| | - Mariela S Militaru
- Department of Molecular Sciences, Discipline of Medical Genetics, University of Medicine and Pharmacy Iuliu Hațieganu, Victor Babeș 8, 400347 Cluj-Napoca, Romania
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DNA Copy Number Aberrations and Expression of ABC Transporter Genes in Breast Tumour: Correlation with the Effect of Neoadjuvant Chemotherapy and Prognosis of the Disease. Pharmaceutics 2022; 14:pharmaceutics14050948. [PMID: 35631534 PMCID: PMC9146568 DOI: 10.3390/pharmaceutics14050948] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/21/2022] [Accepted: 04/26/2022] [Indexed: 11/17/2022] Open
Abstract
One of the important reasons for the ineffectiveness of chemotherapy in breast cancer (BC) is considered to be the formation of a multidrug resistance phenotype in tumour cells, which is caused by the expression of energy-dependent ABC transporters. The aim of this work was to assess chromosomal aberrations and the level of transcripts of all 49 known ABC transporter genes in breast tumours. Materials and Methods. The study included 129 patients with breast cancer. A microarray study of all tumour samples was carried out on microchips. Results. This study established that the presence of a deletion in genes ABCB1, ABCB4, ABCB8, ABCC7, ABCC11, ABCC12, ABCF2, and ABCG4 is associated with an objective response to treatment (p ≤ 0.05). A decrease in the expression of genes was associated with a good response to chemotherapy, whereas an increase in expression caused the progression and stabilization of the tumour. Analysis of metastatic-free survival rates showed that the presence of ABCB1/4 and ABCC1/6 deletions was associated with 100% survival (log-rank test p = 0.01 and p = 0.03). Conclusions. The study showed that the aberrant state of ABC transporter genes, as well as a decrease in the expression of these genes, is a predictor of the effectiveness of therapeutic treatment and a potential prognostic marker of metastatic survival.
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Kulbay M, Paimboeuf A, Ozdemir D, Bernier J. Review of cancer cell resistance mechanisms to apoptosis and actual targeted therapies. J Cell Biochem 2021; 123:1736-1761. [PMID: 34791699 DOI: 10.1002/jcb.30173] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 10/04/2021] [Accepted: 10/22/2021] [Indexed: 11/11/2022]
Abstract
The apoptosis pathway is a programmed cell death mechanism that is crucial for cellular and tissue homeostasis and organ development. There are three major caspase-dependent pathways of apoptosis that ultimately lead to DNA fragmentation. Cancerous cells are known to highly regulate the apoptotic pathway and its role in cancer hallmark acquisition has been discussed over the past decades. Numerous mutations in cancer cell types have been reported to be implicated in chemoresistance and treatment outcome. In this review, we summarize the mutations of the caspase-dependant apoptotic pathways that are the source of cancer development and the targeted therapies currently available or in trial.
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Affiliation(s)
- Merve Kulbay
- INRS - Centre Armand-Frappier Santé Biotechnologie, Laval, Quebec, Canada.,Department of Medicine, Université de Montréal, Montréal, Quebec, Canada
| | - Adeline Paimboeuf
- INRS - Centre Armand-Frappier Santé Biotechnologie, Laval, Quebec, Canada
| | - Derman Ozdemir
- Department of Medicine, One Brooklyn Health-Brookdale Hospital Medical Center, Brooklyn, New York, USA
| | - Jacques Bernier
- INRS - Centre Armand-Frappier Santé Biotechnologie, Laval, Quebec, Canada
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García-Alfonso P, Saiz-Rodríguez M, Mondéjar R, Salazar J, Páez D, Borobia AM, Safont MJ, García-García I, Colomer R, García-González X, Herrero MJ, López-Fernández LA, Abad-Santos F. Consensus of experts from the Spanish Pharmacogenetics and Pharmacogenomics Society and the Spanish Society of Medical Oncology for the genotyping of DPYD in cancer patients who are candidates for treatment with fluoropyrimidines. Clin Transl Oncol 2021; 24:483-494. [PMID: 34773566 PMCID: PMC8885558 DOI: 10.1007/s12094-021-02708-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/11/2021] [Indexed: 11/29/2022]
Abstract
5-Fluorouracil (5-FU) and oral fluoropyrimidines, such as capecitabine, are widely used in the treatment of cancer, especially gastrointestinal tumors and breast cancer, but their administration can produce serious and even lethal toxicity. This toxicity is often related to the partial or complete deficiency of the dihydropyrimidine dehydrogenase (DPD) enzyme, which causes a reduction in clearance and a longer half-life of 5-FU. It is advisable to determine if a DPD deficiency exists before administering these drugs by genotyping DPYD gene polymorphisms. The objective of this consensus of experts, in which representatives from the Spanish Pharmacogenetics and Pharmacogenomics Society and the Spanish Society of Medical Oncology participated, is to establish clear recommendations for the implementation of genotype and/or phenotype testing for DPD deficiency in patients who are candidates to receive fluoropyrimidines. The genotyping of DPYD previous to treatment classifies individuals as normal, intermediate, or poor metabolizers. Normal metabolizers do not require changes in the initial dose, intermediate metabolizers should start treatment with fluoropyrimidines at doses reduced to 50%, and poor metabolizers are contraindicated for fluoropyrimidines.
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Affiliation(s)
- P García-Alfonso
- Medical Oncology Department, Hospital General Universitario Gregorio Marañón, Sociedad Española de Oncología Médica (SEOM), C/Doctor Esquerdo, 46, 28007, Madrid, Spain.
| | - M Saiz-Rodríguez
- Research Unit, Fundación Burgos por la Investigación de la Salud (FBIS), Hospital Universitario de Burgos, Sociedad Española de Farmacogenética y Farmacogenómica (SEFF), Burgos, Spain
| | - R Mondéjar
- Medical Oncology Service, Hospital Universitario de la Princesa, Sociedad Española de Oncología Médica (SEOM), Madrid, Spain
| | - J Salazar
- Research Institute of Hospital de la Santa Creu I Sant Pau, Sociedad Española de Farmacogenética y Farmacogenómica (SEFF), Barcelona, Spain
| | - D Páez
- Medical Oncology Department, Hospital de la Santa Creu I Sant Pau, Sociedad Española de Oncología Médica (SEOM), Barcelona, España
| | - A M Borobia
- Clinical Pharmacology Service, Hospital Universitario La Paz, Sociedad Española de Farmacogenética y Farmacogenómica (SEFF), Madrid, Spain
| | - M J Safont
- Medical Oncology Service, Consorcio Hospital General Universitario de Valencia, Universidad de Valencia, CIBERONC, Sociedad Española de Oncología Médica (SEOM), Valencia, Spain
| | - I García-García
- Clinical Pharmacology Service, Hospital Universitario La Paz, Sociedad Española de Farmacogenética y Farmacogenómica (SEFF), Madrid, Spain
| | - R Colomer
- Medical Oncology Service, Hospital Universitario de La Princesa y Cátedra de Medicina Personalizada de Precisión de la Universidad Autónoma de Madrid (UAM), Sociedad Española de Oncología Médica (SEOM), Madrid, Spain
| | - X García-González
- Hospital Pharmacy Service, Hospital General Universitario Gregorio Marañón, Sociedad Española de Farmacogenética y Farmacogenómica (SEFF), Madrid, Spain
| | - M J Herrero
- Pharmacogenetics Platform, IIS La Fe-Hospital La Fe and Pharmacology Department, Universidad de Valencia, Sociedad Española de Farmacogenética y Farmacogenómica (SEFF), Valencia, Spain
| | - L A López-Fernández
- Hospital Pharmacy Service, Hospital General Universitario Gregorio Marañón, Sociedad Española de Farmacogenética y Farmacogenómica (SEFF), Madrid, Spain
| | - F Abad-Santos
- Clinical Pharmacology Service, Hospital Universitario de La Princesa, Universidad Autónoma de Madrid, Sociedad Española de Farmacogenética y Farmacogenómica (SEFF), C/Diego de León, 62., 28006, Madrid, Spain.
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Role of Genetic Variation in Cytochromes P450 in Breast Cancer Prognosis and Therapy Response. Int J Mol Sci 2021; 22:ijms22062826. [PMID: 33802237 PMCID: PMC8001203 DOI: 10.3390/ijms22062826] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/05/2021] [Accepted: 03/08/2021] [Indexed: 12/16/2022] Open
Abstract
Breast cancer is the most frequent cancer in the female population worldwide. The role of germline genetic variability in cytochromes P450 (CYP) in breast cancer prognosis and individualized therapy awaits detailed elucidation. In the present study, we used the next-generation sequencing to assess associations of germline variants in the coding and regulatory sequences of all human CYP genes with response of the patients to the neoadjuvant cytotoxic chemotherapy and disease-free survival (n = 105). A total of 22 prioritized variants associating with a response or survival in the above evaluation phase were then analyzed by allelic discrimination in the large confirmation set (n = 802). Associations of variants in CYP1B1, CYP4F12, CYP4X1, and TBXAS1 with the response to the neoadjuvant cytotoxic chemotherapy were replicated by the confirmation phase. However, just association of variant rs17102977 in CYP4X1 passed the correction for multiple testing and can be considered clinically and statistically validated. Replicated associations for variants in CYP4X1, CYP24A1, and CYP26B1 with disease-free survival of all patients or patients stratified to subgroups according to therapy type have not passed a false discovery rate test. Although statistically not confirmed by the present study, the role of CYP genes in breast cancer prognosis should not be ruled out. In conclusion, the present study brings replicated association of variant rs17102977 in CYP4X1 with the response of patients to the neoadjuvant cytotoxic chemotherapy and warrants further research of genetic variation CYPs in breast cancer.
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SLC46A1 Haplotype with Predicted Functional Impact has Prognostic Value in Breast Carcinoma. Mol Diagn Ther 2021; 25:99-110. [PMID: 33387348 DOI: 10.1007/s40291-020-00506-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/05/2020] [Indexed: 12/24/2022]
Abstract
BACKGROUND AND OBJECTIVE Membrane solute carrier transporters play an important role in the transport of a wide spectrum of substrates including anticancer drugs and cancer-related physiological substrates. This study aimed to assess the prognostic relevance of gene expression and genetic variability of selected solute carrier transporters in breast cancer. METHODS Gene expression was determined by quantitative real-time polymerase chain reaction. All SLC46A1 and SLCO1A2 exons and surrounding non-coding sequences in DNA extracted from the blood of patients with breast cancer (exploratory phase) were analyzed by next-generation sequencing technology. Common variants (minor allele frequency ≥ 5%) with in silico-predicted functional relevance were further analyzed in a large cohort of patients with breast cancer (n = 815) and their prognostic and predictive potential was estimated (validation phase). RESULTS A gene expression and bioinformatics analysis suggested SLC46A1 and SLCO1A2 to play a putative role in the prognosis of patients with breast cancer. In total, 135 genetic variants (20 novel) were identified in both genes in the exploratory phase. Of these variants, 130 were non-coding, three missense, and two synonymous. One common variant in SLCO1A2 and four variants in SLC46A1 were predicted to be pathogenic by in silico programs and subsequently validated. A SLC46A1 haplotype block composed of rs2239911-rs2239910-rs8079943 was significantly associated with ERBB2/HER2 status and disease-free survival of hormonally treated patients. CONCLUSIONS This study revealed the prognostic value of a SLC46A1 haplotype block for breast cancer that should be further studied.
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Hlaváč V, Václavíková R, Brynychová V, Koževnikovová R, Kopečková K, Vrána D, Gatěk J, Souček P. Role of Genetic Variation in ABC Transporters in Breast Cancer Prognosis and Therapy Response. Int J Mol Sci 2020; 21:ijms21249556. [PMID: 33334016 PMCID: PMC7765380 DOI: 10.3390/ijms21249556] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/10/2020] [Accepted: 12/11/2020] [Indexed: 12/25/2022] Open
Abstract
Breast cancer is the most common cancer in women in the world. The role of germline genetic variability in ATP-binding cassette (ABC) transporters in cancer chemoresistance and prognosis still needs to be elucidated. We used next-generation sequencing to assess associations of germline variants in coding and regulatory sequences of all human ABC genes with response of the patients to the neoadjuvant cytotoxic chemotherapy and disease-free survival (n = 105). A total of 43 prioritized variants associating with response or survival in the above testing phase were then analyzed by allelic discrimination in the large validation set (n = 802). Variants in ABCA4, ABCA9, ABCA12, ABCB5, ABCC5, ABCC8, ABCC11, and ABCD4 associated with response and variants in ABCA7, ABCA13, ABCC4, and ABCG8 with survival of the patients. No association passed a false discovery rate test, however, the rs17822931 (Gly180Arg) in ABCC11, associating with response, and the synonymous rs17548783 in ABCA13 (survival) have a strong support in the literature and are, thus, interesting for further research. Although replicated associations have not reached robust statistical significance, the role of ABC transporters in breast cancer should not be ruled out. Future research and careful validation of findings will be essential for assessment of genetic variation which was not in the focus of this study, e.g., non-coding sequences, copy numbers, and structural variations together with somatic mutations.
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Affiliation(s)
- Viktor Hlaváč
- Toxicogenomics Unit, National Institute of Public Health, 100 42 Prague, Czech Republic; (V.H.); (R.V.); (V.B.)
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, 323 00 Pilsen, Czech Republic
| | - Radka Václavíková
- Toxicogenomics Unit, National Institute of Public Health, 100 42 Prague, Czech Republic; (V.H.); (R.V.); (V.B.)
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, 323 00 Pilsen, Czech Republic
| | - Veronika Brynychová
- Toxicogenomics Unit, National Institute of Public Health, 100 42 Prague, Czech Republic; (V.H.); (R.V.); (V.B.)
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, 323 00 Pilsen, Czech Republic
| | | | - Katerina Kopečková
- Department of Oncology, Second Faculty of Medicine, Charles University and Motol University Hospital, 150 06 Prague, Czech Republic;
| | - David Vrána
- Department of Oncology, Medical School and Teaching Hospital, Palacky University, 779 00 Olomouc, Czech Republic;
| | - Jiří Gatěk
- Department of Surgery, EUC Hospital and University of Tomas Bata in Zlin, 760 01 Zlin, Czech Republic;
| | - Pavel Souček
- Toxicogenomics Unit, National Institute of Public Health, 100 42 Prague, Czech Republic; (V.H.); (R.V.); (V.B.)
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, 323 00 Pilsen, Czech Republic
- Correspondence: ; Tel.: +420-267-082-711
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Hlavac V, Mohelnikova-Duchonova B, Lovecek M, Ehrmann J, Brynychova V, Kolarova K, Soucek P. Targeted Sequencing of Pancreatic Adenocarcinomas from Patients with Metachronous Pulmonary Metastases. Genes (Basel) 2020; 11:E1391. [PMID: 33255265 PMCID: PMC7760784 DOI: 10.3390/genes11121391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/20/2020] [Accepted: 11/22/2020] [Indexed: 12/24/2022] Open
Abstract
Mutation spectra of 250 cancer driver, druggable, and actionable genes were analyzed in surgically resected pancreatic ductal adenocarcinoma (PDAC) patients who developed metachronous pulmonary metastases. Targeted sequencing was performed in DNA from blood and archival samples of 15 primary tumors and three paired metastases. Results were complemented with the determination of G12V mutation in KRAS by droplet digital PCR. The median number of protein-changing mutations was 52 per patient. KRAS and TP53 were significantly enriched in fractions of mutations in hotspots. Individual gene mutation frequencies or mutational loads accounting separately for drivers, druggable, or clinically actionable genes, did not significantly associate with patients' survival. LRP1B was markedly mutated in primaries of patients who generalized (71%) compared to those developing solitary pulmonary metastases (0%). FLG2 was mutated exclusively in primary tumors compared to paired metastases. In conclusion, signatures of prognostically differing subgroups of PDAC patients were generated for further utilization in precision medicine.
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Affiliation(s)
- Viktor Hlavac
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, 306 05 Pilsen, Czech Republic; (V.B.); (P.S.)
- Toxicogenomics Unit, National Institute of Public Health, 100 42 Prague, Czech Republic
| | - Beatrice Mohelnikova-Duchonova
- Department of Oncology, Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, 779 00 Olomouc, Czech Republic; (B.M.-D.); (K.K.)
| | - Martin Lovecek
- Department of Surgery I, University Hospital Olomouc and Faculty of Medicine and Dentistry, Palacky University, 779 00 Olomouc, Czech Republic;
| | - Jiri Ehrmann
- Department of Clinical and Molecular Pathology, University Hospital Olomouc and Faculty of Medicine and Dentistry, Palacky University, 779 00 Olomouc, Czech Republic;
| | - Veronika Brynychova
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, 306 05 Pilsen, Czech Republic; (V.B.); (P.S.)
- Toxicogenomics Unit, National Institute of Public Health, 100 42 Prague, Czech Republic
| | - Katerina Kolarova
- Department of Oncology, Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, 779 00 Olomouc, Czech Republic; (B.M.-D.); (K.K.)
| | - Pavel Soucek
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, 306 05 Pilsen, Czech Republic; (V.B.); (P.S.)
- Toxicogenomics Unit, National Institute of Public Health, 100 42 Prague, Czech Republic
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13
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Dvorak P, Hlavac V, Soucek P. 5' Untranslated Region Elements Show High Abundance and Great Variability in Homologous ABCA Subfamily Genes. Int J Mol Sci 2020; 21:ijms21228878. [PMID: 33238634 PMCID: PMC7700387 DOI: 10.3390/ijms21228878] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/16/2020] [Accepted: 11/20/2020] [Indexed: 11/16/2022] Open
Abstract
The 12 members of the ABCA subfamily in humans are known for their ability to transport cholesterol and its derivatives, vitamins, and xenobiotics across biomembranes. Several ABCA genes are causatively linked to inborn diseases, and the role in cancer progression and metastasis is studied intensively. The regulation of translation initiation is implicated as the major mechanism in the processes of post-transcriptional modifications determining final protein levels. In the current bioinformatics study, we mapped the features of the 5' untranslated regions (5'UTR) known to have the potential to regulate translation, such as the length of 5'UTRs, upstream ATG codons, upstream open-reading frames, introns, RNA G-quadruplex-forming sequences, stem loops, and Kozak consensus motifs, in the DNA sequences of all members of the subfamily. Subsequently, the conservation of the features, correlations among them, ribosome profiling data as well as protein levels in normal human tissues were examined. The 5'UTRs of ABCA genes contain above-average numbers of upstream ATGs, open-reading frames and introns, as well as conserved ones, and these elements probably play important biological roles in this subfamily, unlike RG4s. Although we found significant correlations among the features, we did not find any correlation between the numbers of 5'UTR features and protein tissue distribution and expression scores. We showed the existence of single nucleotide variants in relation to the 5'UTR features experimentally in a cohort of 105 breast cancer patients. 5'UTR features presumably prepare a complex playground, in which the other elements such as RNA binding proteins and non-coding RNAs play the major role in the fine-tuning of protein expression.
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Affiliation(s)
- Pavel Dvorak
- Department of Biology, Faculty of Medicine in Pilsen, Charles University, 32300 Pilsen, Czech Republic
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, 32300 Pilsen, Czech Republic; (V.H.); (P.S.)
- Correspondence: ; Tel.: +420-377593263
| | - Viktor Hlavac
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, 32300 Pilsen, Czech Republic; (V.H.); (P.S.)
- Toxicogenomics Unit, National Institute of Public Health, 100 42 Prague, Czech Republic
| | - Pavel Soucek
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, 32300 Pilsen, Czech Republic; (V.H.); (P.S.)
- Toxicogenomics Unit, National Institute of Public Health, 100 42 Prague, Czech Republic
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14
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Al-Mahayri ZN, Patrinos GP, Ali BR. Toxicity and Pharmacogenomic Biomarkers in Breast Cancer Chemotherapy. Front Pharmacol 2020; 11:445. [PMID: 32351390 PMCID: PMC7174767 DOI: 10.3389/fphar.2020.00445] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 03/20/2020] [Indexed: 02/05/2023] Open
Abstract
Breast cancer (BC) is one of the most prevalent types of cancer worldwide with high morbidity and mortality rates. Treatment modalities include systemic therapy, in which chemotherapy is a major component in many cases. Several chemotherapeutic agents are used in combinations or as single agents with many adverse events occurring in variable frequencies. These events can be a significant barrier in completing the treatment regimens. Germline genomic variants are thought of as potential determinants in chemotherapy response and the development of side effects. Some pharmacogenomic studies were designed to explore germline variants that can be used as biomarkers for predicting developing toxicity or adverse events during chemotherapy in BC. In this review, we reassess and summarize the major findings of pharmacogenomic studies of chemotherapy toxicity during BC management. In addition, deficiencies hampering utilizing these findings and the potential targets of future research are emphasized. Main insufficiencies in toxicity pharmacogenomics studies originate from study design, sample limitations, heterogeneity of selected genes, variants, and toxicity definitions. With the advent of high throughput genotyping techniques, researchers are expected to explore the identified as well as the potential genetic biomarkers of toxicity and efficacy to improve BC management. However, to achieve this, the limitations of previous work should be evaluated and avoided to reach more conclusive and translatable evidence for personalizing BC chemotherapy.
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Affiliation(s)
- Zeina N Al-Mahayri
- Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - George P Patrinos
- Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates.,Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece.,Zayed Center for Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Bassam R Ali
- Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates.,Zayed Center for Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates.,Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
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15
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Andrei L, Kasas S, Ochoa Garrido I, Stanković T, Suárez Korsnes M, Vaclavikova R, Assaraf YG, Pešić M. Advanced technological tools to study multidrug resistance in cancer. Drug Resist Updat 2020; 48:100658. [DOI: 10.1016/j.drup.2019.100658] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/26/2019] [Accepted: 09/27/2019] [Indexed: 02/06/2023]
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