Genetics and Pharmacogenetics in Primary Care

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Human Genomics and Genetic Diseases".

Deadline for manuscript submissions: closed (20 March 2024) | Viewed by 17758

Special Issue Editors


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Guest Editor
Department of Family Medicine, Mayo Clinic, Rochester, MN 55902, USA
Interests: genetics; pharmacogenetics; primary care; personalized medicine

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Co-Guest Editor
Department of Clinical Chemistry, Erasmus University Medical Center, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
Interests: pharmacogenetics; pharmacogenomics; personalized medicine; molecular biology; pharmacokinetics

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Co-Guest Editor
Department of Clinical Pharmacy and Toxicology, Leiden University Medical Centre, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands.
Interests: pharmacogenomics, phenoconversion, oncology, long-read sequencing
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Special Issue Information

Dear Colleagues,

Genetic and pharmacogenetic information has caused many of us to reflect on and discuss whether the creation of this information should be handled by the regular health system instead of a commercial market system (such as in direct to consumer testing). However, health care systems all over the world are increasingly working in a hybrid model and use eHealth and blended care integrated in daily medical practice. Of course, personalized health is of importance for the individual and society at large, but with a growing need for tailored care and prevention as well as cross-disciplinary approaches. However, there is great uncertainty in the future of (pharmaco)genetic and genomic service provision, and insight into perspectives of (non)genetic professionals on the topic is increasingly required. We are currently in the midst of a revolution in DNA sequencing that promises unprecedented access to genetic data. This new evidence is of utmost importance, since everybody knows by now that genetic information derived from DNA analysis can help address challenges in personalized medicine and prevention. Implementation of this knowledge is, however, only in the early stages, and further evaluation in addition to strategic planning and decision making are needed. Advances in DNA analysis technology, science, and international collaborations have shown us that genetic medicine is indeed changing, complicating implementation steps. Certainly, DNA analysis is increasingly being used in health care, but so far only in specialized settings and for a limited number of health problems and, thus, is still not capitalizing on its full potential.

Gene–disease relationships have been well described, thanks to decades of clinical genetic testing, which has led to the demonstrated prevention or early detection of diseases in cases where relatives are preventively tested after a relative patient carrier has been identified. The technology to screen for such predefined actionable genetic variants exists but is not currently used as preventive tool in the more general (patient) population. Additionally, genetic variants influencing the efficacy or occurrence of adverse events in drug prescription have been well described and even included in pharmacological guidelines, but widespread use to guide personalized treatment strategies and prevent adverse events is limited. Finally, polygenic risk scores (PRS) for many diseases have developed from the outcomes of genome-wide association studies (GWAS). Individualized genetic risk profiles (rare variants, pharmacogenetics, and PRS) are becoming increasingly affordable and available at any point in time, and they have a potential to be implemented at an unprecedented large scale in health care, both in clinics and for prevention. Yet, this is not fully exploited in medical practice because the logistic, technical, societal, ethical, legal, and educational requirements must still be determined while public engagement and governmental vision is lacking. 

Authors are encouraged to submit original manuscripts describing the current and potential utilization of genetics and pharmacogenetics in primary care and the hurdles still needed to be overcome in answering scientific questions on the differences in diversity and health systems, policies, education and financing, besides patient factors. Also encouraged are papers describing the application of new methods or (eHealth and Artificial Intelligence) instruments, as are reviews or comparisons as well as manuscripts dealing with bioinformatic methods of analysis facilitating the development of evidence-based strategies to urgently improve collaborative efforts to implement genomic medicine.

Dr. Elisa J.F. Houwink
Prof. Dr. Ron van Schaik
Dr. Jesse J. Swen
Guest Editors

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Keywords

  • genetics
  • pharmacogenetics
  • primary care
  • prevention
  • early detection
  • bioinformatics
  • individualized medicine
  • genomic medicine
  • ethics
  • bioinformatics
  • personalized (pharmaco)genetic data
  • family history

Published Papers (9 papers)

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25 pages, 4592 KiB  
Article
G-Protein Signaling Modulator 2 as a Potential Biomarker in Colorectal Cancer: Integrative Analysis Using Genetic Profiling and Pan-Cancer Studies
by Doaa Jawad Kadhim, Hanieh Azari, Saeideh Khorshid Sokhangouy, Seyed Mahdi Hassanian, Hawraa Ibrahim Alshekarchi, Ladan Goshayeshi, Lena Goshayeshi, Mohammad Reza Abbaszadegan, Fatemeh Khojasteh-Leylakoohi, Majid Khazaei, Ibrahim Saeed Gataa, Godefridus J. Peters, Gordon A. Ferns, Jyotsna Batra, Alfred King-Yin Lam, Elisa Giovannetti and Amir Avan
Genes 2024, 15(4), 474; https://doi.org/10.3390/genes15040474 - 09 Apr 2024
Viewed by 429
Abstract
Colorectal cancer (CRC) imposes a significant healthcare burden globally, prompting the quest for innovative biomarkers to enhance diagnostic and therapeutic strategies. This study investigates the G-protein signaling modulator (GPSM) family across several cancers and presents a comprehensive pan-cancer analysis of the GPSM2 [...] Read more.
Colorectal cancer (CRC) imposes a significant healthcare burden globally, prompting the quest for innovative biomarkers to enhance diagnostic and therapeutic strategies. This study investigates the G-protein signaling modulator (GPSM) family across several cancers and presents a comprehensive pan-cancer analysis of the GPSM2 gene across several gastrointestinal (GI) cancers. Leveraging bioinformatics methodologies, we investigated GPSM2 expression patterns, protein interactions, functional enrichments, prognostic implications, genetic alterations, and immune infiltration associations. Furthermore, the expression of the GPSM2 gene was analyzed using real-time analysis. Our findings reveal a consistent upregulation of GPSM2 expression in all GI cancer datasets analyzed, suggesting its potential as a universal biomarker in GI cancers. Functional enrichment analysis underscores the involvement of GPSM2 in vital pathways, indicating its role in tumor progression. The prognostic assessment indicates that elevated GPSM2 expression correlates with adverse overall and disease-free survival outcomes across multiple GI cancer types. Genetic alteration analysis highlights the prevalence of mutations, particularly missense mutations, in GPSM2. Furthermore, significant correlations between GPSM2 expression and immune cell infiltration are observed, suggesting its involvement in tumor immune evasion mechanisms. Collectively, our study underscores the multifaceted role of GPSM2 in GI cancers, particularly in CRC, emphasizing its potential as a promising biomarker for prognosis and therapeutic targeting. Further functional investigations are warranted to elucidate its clinical utility and therapeutic implications in CRC management. Full article
(This article belongs to the Special Issue Genetics and Pharmacogenetics in Primary Care)
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12 pages, 1246 KiB  
Article
Implementation of Pharmacogenetics in First-Line Care: Evaluation of Its Use by General Practitioners
by Denise van der Drift, Mirjam Simoons, Birgit C. P. Koch, Gemma Brufau, Patrick Bindels, Maja Matic and Ron H. N. van Schaik
Genes 2023, 14(10), 1841; https://doi.org/10.3390/genes14101841 - 22 Sep 2023
Viewed by 1264
Abstract
Pharmacogenetics (PGx) can explain/predict drug therapy outcomes. There is, however, unclarity about the use and usefulness of PGx in primary care. In this study, we investigated PGx tests ordered by general practitioners (GPs) in 2021 at Dept. Clinical Chemistry, Erasmus MC, and analyzed [...] Read more.
Pharmacogenetics (PGx) can explain/predict drug therapy outcomes. There is, however, unclarity about the use and usefulness of PGx in primary care. In this study, we investigated PGx tests ordered by general practitioners (GPs) in 2021 at Dept. Clinical Chemistry, Erasmus MC, and analyzed the gene tests ordered, drugs/drug groups, reasons for testing and single-gene versus panel testing. Additionally, a survey was sent to 90 GPs asking about their experiences and barriers to implementing PGx. In total, 1206 patients and 6300 PGx tests were requested by GPs. CYP2C19 was requested most frequently (17%), and clopidogrel was the most commonly indicated drug (23%). Regarding drug groups, antidepressants (51%) were the main driver for requesting PGx, followed by antihypertensives (26%). Side effects (79%) and non-response (27%) were the main indicators. Panel testing was preferred over single-gene testing. The survey revealed knowledge on when and how to use PGx as one of the main barriers. In conclusion, PGx is currently used by GPs in clinical practice in the Netherlands. Side effects are the main reason for testing, which mostly involves antidepressants. Lack of knowledge is indicated as a major barrier, indicating the need for more education on PGx for GPs. Full article
(This article belongs to the Special Issue Genetics and Pharmacogenetics in Primary Care)
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35 pages, 1306 KiB  
Article
Personal Genomes in Practice: Exploring Citizen and Healthcare Professionals’ Perspectives on Personalized Genomic Medicine and Personal Health Data Spaces Using a Mixed-Methods Design
by Judith Tommel, Daan Kenis, Nathalie Lambrechts, Richard M. Brohet, Jordy Swysen, Lotte Mollen, Marie-José F. Hoefmans, Murih Pusparum, Andrea W. M. Evers, Gökhan Ertaylan, Marco Roos, Kristien Hens and Elisa J. F. Houwink
Genes 2023, 14(4), 786; https://doi.org/10.3390/genes14040786 - 24 Mar 2023
Cited by 1 | Viewed by 2547
Abstract
Ongoing health challenges, such as the increased global burden of chronic disease, are increasingly answered by calls for personalized approaches to healthcare. Genomic medicine, a vital component of these personalization strategies, is applied in risk assessment, prevention, prognostication, and therapeutic targeting. However, several [...] Read more.
Ongoing health challenges, such as the increased global burden of chronic disease, are increasingly answered by calls for personalized approaches to healthcare. Genomic medicine, a vital component of these personalization strategies, is applied in risk assessment, prevention, prognostication, and therapeutic targeting. However, several practical, ethical, and technological challenges remain. Across Europe, Personal Health Data Space (PHDS) projects are under development aiming to establish patient-centered, interoperable data ecosystems balancing data access, control, and use for individual citizens to complement the research and commercial focus of the European Health Data Space provisions. The current study explores healthcare users’ and health care professionals’ perspectives on personalized genomic medicine and PHDS solutions, in casu the Personal Genetic Locker (PGL). A mixed-methods design was used, including surveys, interviews, and focus groups. Several meta-themes were generated from the data: (i) participants were interested in genomic information; (ii) participants valued data control, robust infrastructure, and sharing data with non-commercial stakeholders; (iii) autonomy was a central concern for all participants; (iv) institutional and interpersonal trust were highly significant for genomic medicine; and (v) participants encouraged the implementation of PHDSs since PHDSs were thought to promote the use of genomic data and enhance patients’ control over their data. To conclude, we formulated several facilitators to implement genomic medicine in healthcare based on the perspectives of a diverse set of stakeholders. Full article
(This article belongs to the Special Issue Genetics and Pharmacogenetics in Primary Care)
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18 pages, 1739 KiB  
Article
Feasibility of Community Pharmacist-Initiated and Point-of-Care CYP2C19 Genotype-Guided De-Escalation of Oral P2Y12 Inhibitors
by Amar D. Levens, Melina C. den Haan, J. Wouter Jukema, Mette Heringa, Wilbert B. van den Hout, Dirk Jan A. R. Moes and Jesse J. Swen
Genes 2023, 14(3), 578; https://doi.org/10.3390/genes14030578 - 25 Feb 2023
Cited by 1 | Viewed by 1934
Abstract
Tailoring antiplatelet therapy based on CYP2C19 pharmacogenetic (PGx) testing can improve cardiovascular outcomes and potentially reduce healthcare costs in patients on a P2Y12-inhibitor regime with prasugrel or ticagrelor. However, ubiquitous adoption—particularly in an outpatient setting—remains limited. We conducted a proof-of-concept study [...] Read more.
Tailoring antiplatelet therapy based on CYP2C19 pharmacogenetic (PGx) testing can improve cardiovascular outcomes and potentially reduce healthcare costs in patients on a P2Y12-inhibitor regime with prasugrel or ticagrelor. However, ubiquitous adoption—particularly in an outpatient setting—remains limited. We conducted a proof-of-concept study to evaluate the feasibility of CYP2C19-guided de-escalation of prasugrel/ticagrelor to clopidogrel through point-of-care (POC) PGx testing in the community pharmacy. Multiple feasibility outcomes were assessed. Overall, 144 patients underwent CYP2C19 PGx testing in 27 community pharmacies. Successful test results were obtained in 142 patients (98.6%). De-escalation to clopidogrel occurred in 19 patients (20%) out of 95 (67%) eligible for therapy de-escalation, which was mainly due to PGx testing not being included in cardiology guidelines. Out of the 119 patients (84%) and 14 pharmacists (100%) surveyed, 109 patients (92%) found the community pharmacy a suitable location for PGx testing, and the majority of pharmacists (86%) thought it has added value. Net costs due to PGx testing were estimated at €43 per patient, which could be reduced by earlier testing and could turn into savings if de-escalation would double to 40%. Although the observed de-escalation rate was low, POC CYP2C19-guided de-escalation to clopidogrel appears feasible in a community pharmacy setting. Full article
(This article belongs to the Special Issue Genetics and Pharmacogenetics in Primary Care)
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11 pages, 471 KiB  
Article
Influence of the Osteogenomic Profile in Response to Alendronate Therapy in Postmenopausal Women with Osteoporosis: A Retrospective Cohort Study
by Alejandra Villagómez Vega, Jorge Iván Gámez Nava, Francisco Ruiz González, Misael Pérez Romero, Walter Ángel Trujillo Rangel and Ismael Nuño Arana
Genes 2023, 14(2), 524; https://doi.org/10.3390/genes14020524 - 19 Feb 2023
Cited by 2 | Viewed by 1504
Abstract
Background: Postmenopausal osteoporosis is a multifactorial disease. Genetic factors play an essential role in contributing to bone mineral density (BMD) variability, which ranges from 60 to 85%. Alendronate is used as the first line of pharmacological treatment for osteoporosis; however, some patients do [...] Read more.
Background: Postmenopausal osteoporosis is a multifactorial disease. Genetic factors play an essential role in contributing to bone mineral density (BMD) variability, which ranges from 60 to 85%. Alendronate is used as the first line of pharmacological treatment for osteoporosis; however, some patients do not respond adequately to therapy with alendronate. Aim: The aim of this work was to investigate the influence of combinations of potential risk alleles (genetic profiles) associated with response to anti-osteoporotic treatment in postmenopausal women with primary osteoporosis. Methods: A total of 82 postmenopausal women with primary osteoporosis receiving alendronate (70 mg administered orally per week) for one year were observed. The bone mineral density (BMD; g/cm2) of the femoral neck and lumbar spine was measured. According to BMD change, patients were divided into two groups: responders and non-responders to alendronate therapy. Polymorphic variants in CYP19, ESR1, IL-6, PTHR1, TGFβ, OPG and RANKL genes were determined and profiles were generated from the combination of risk alleles. Results: A total of 56 subjects were responders to alendronate and 26 subjects were non-responders. Carriers of the G-C-G-C profile (constructed from rs700518, rs1800795, rs2073618 and rs3102735) were predisposed to response to alendronate treatment (p = 0.001). Conclusions: Our findings highlight the importance of the identified profiles for the pharmacogenetics of alendronate therapy in osteoporosis. Full article
(This article belongs to the Special Issue Genetics and Pharmacogenetics in Primary Care)
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10 pages, 554 KiB  
Article
Predictive Value of SLCO1B1 c.521T>C Polymorphism on Observed Changes in the Treatment of 1136 Statin-Users
by Marleen E. Jansen, Tessel Rigter, Thom M. C. Fleur, Patrick C. Souverein, W. M. Monique Verschuren, Susanne J. Vijverberg, Jesse J. Swen, Wendy Rodenburg and Martina C. Cornel
Genes 2023, 14(2), 456; https://doi.org/10.3390/genes14020456 - 10 Feb 2023
Cited by 3 | Viewed by 1237
Abstract
Pharmacogenomic testing is a method to prevent adverse drug reactions. Pharmacogenomics could be relevant to optimize statin treatment, by identifying patients at high risk for adverse drug reactions. We aim to investigate the clinical validity and utility of pre-emptive pharmacogenomics screening in primary [...] Read more.
Pharmacogenomic testing is a method to prevent adverse drug reactions. Pharmacogenomics could be relevant to optimize statin treatment, by identifying patients at high risk for adverse drug reactions. We aim to investigate the clinical validity and utility of pre-emptive pharmacogenomics screening in primary care, with SLCO1B1 c.521T>C as a risk factor for statin-induced adverse drug reactions. The focus was on changes in therapy as a proxy for adverse drug reactions observed in statin-users in a population-based Dutch cohort. In total, 1136 statin users were retrospectively genotyped for the SLCO1B1 c.521T>C polymorphism (rs4149056) and information on their statin dispensing was evaluated as cross-sectional research. Approximately half of the included participants discontinued or switched their statin treatment within three years. In our analyses, we could not confirm an association between the SLCO1B1 c.521T>C genotype and any change in statin therapy or arriving at a stable dose sooner in primary care. To be able to evaluate the predictive values of SLCO1B1 c.521T>C genotype on adverse drug reactions from statins, prospective data collection of actual adverse drug reactions and reasons to change statin treatment should be facilitated. Full article
(This article belongs to the Special Issue Genetics and Pharmacogenetics in Primary Care)
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18 pages, 8751 KiB  
Article
Significance of Identifying Key Genes Involved in HBV-Related Hepatocellular Carcinoma for Primary Care Surveillance of Patients with Cirrhosis
by Yaqun Li, Jianhua Li, Tianye He, Yun Song, Jian Wu and Bin Wang
Genes 2022, 13(12), 2331; https://doi.org/10.3390/genes13122331 - 10 Dec 2022
Cited by 4 | Viewed by 2193
Abstract
Cirrhosis is frequently the final stage of disease preceding the development of hepatocellular carcinoma (HCC) and is one of the risk factors for HCC. Preventive surveillance for early HCC in patients with cirrhosis is advantageous for achieving early HCC prevention and diagnosis, thereby [...] Read more.
Cirrhosis is frequently the final stage of disease preceding the development of hepatocellular carcinoma (HCC) and is one of the risk factors for HCC. Preventive surveillance for early HCC in patients with cirrhosis is advantageous for achieving early HCC prevention and diagnosis, thereby enhancing patient prognosis and reducing mortality. However, there is no highly sensitive diagnostic marker for the clinical surveillance of HCC in patients with cirrhosis, which significantly restricts its use in primary care for HCC. To increase the accuracy of illness diagnosis, the study of the effective and sensitive genetic biomarkers involved in HCC incidence is crucial. In this study, a set of 120 significantly differentially expressed genes (DEGs) was identified in the GSE121248 dataset. A protein–protein interaction (PPI) network was constructed among the DEGs, and Cytoscape was used to extract hub genes from the network. In TCGA database, the expression levels, correlation analysis, and predictive performance of hub genes were validated. In total, 15 hub genes showed increased expression, and their positive correlation ranged from 0.80 to 0.90, suggesting they may be involved in the same signaling pathway governing HBV-related HCC. The GSE10143, GSE25097, GSE54236, and GSE17548 datasets were used to investigate the expression pattern of these hub genes in the progression from cirrhosis to HCC. Using Cox regression analysis, a prediction model was then developed. The ROC curves, DCA, and calibration analysis demonstrated the superior disease prediction accuracy of this model. In addition, using proteomic analysis, we investigated whether these key hub genes interact with the HBV-encoded oncogene X protein (HBx), the oncogenic protein in HCC. We constructed stable HBx-expressing LO2-HBx and Huh-7-HBx cell lines. Co-immunoprecipitation coupled with mass spectrometry (Co-IP/MS) results demonstrated that CDK1, RRM2, ANLN, and HMMR interacted specifically with HBx in both cell models. Importantly, we investigated 15 potential key genes (CCNB1, CDK1, BUB1B, ECT2, RACGAP1, ANLN, PBK, TOP2A, ASPM, RRM2, NEK2, PRC1, SPP1, HMMR, and DTL) participating in the transformation process of HBV infection to HCC, of which 4 hub genes (CDK1, RRM2, ANLN, and HMMR) probably serve as potential oncogenic HBx downstream target molecules. All these findings of our study provided valuable research direction for the diagnostic gene detection of HBV-related HCC in primary care surveillance for HCC in patients with cirrhosis. Full article
(This article belongs to the Special Issue Genetics and Pharmacogenetics in Primary Care)
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10 pages, 564 KiB  
Article
FHH Quick App Review: How Can a Quality Review Process Assist Primary Care Providers in Choosing a Family Health History App for Patient Care?
by Grant M. Wood, Sander van Boom, Kasper Recourt and Elisa J. F. Houwink
Genes 2022, 13(8), 1407; https://doi.org/10.3390/genes13081407 - 08 Aug 2022
Viewed by 3266
Abstract
Family health history (FHH) is a data type serving risk assessment, diagnosis, research, and preventive health. Despite technological leaps in genomic variant detection, FHH remains the most accessible, least expensive, and most practical assessment tool for assessing risks attributable to genetic inheritance. The [...] Read more.
Family health history (FHH) is a data type serving risk assessment, diagnosis, research, and preventive health. Despite technological leaps in genomic variant detection, FHH remains the most accessible, least expensive, and most practical assessment tool for assessing risks attributable to genetic inheritance. The purpose of this manuscript is to outline a process to assist primary care professionals in choosing FHH digital tools for patient care based on the new ISO/TS 82304-2 Technical Specification (TS), which is a recently developed method to determine eHealth app quality. With a focus on eHealth in primary care, we applied the quality label concept to FHH, and how a primary care physician can quickly review the quality and reliability of an FHH app. Based on our review of the ISO TS’s 81 questions, we compiled a list of 25 questions that are recommended to be more succinct as an initial review. We call this process the FHH Quick App Review. Our ‘informative-only’ 25 questions do not produce a quality score, but a guide to complete an initial review of FHH apps. Most of the questions are straight from the ISO TS, some are modified or de novo. We believe the 25 questions are not only relevant to FHH app reviews but could also serve to aid app development and clinical implementation. Full article
(This article belongs to the Special Issue Genetics and Pharmacogenetics in Primary Care)
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19 pages, 888 KiB  
Hypothesis
Targeted Anti-Mitochondrial Therapy: The Future of Oncology
by Farzad Taghizadeh-Hesary, Hassan Akbari, Moslem Bahadori and Babak Behnam
Genes 2022, 13(10), 1728; https://doi.org/10.3390/genes13101728 - 26 Sep 2022
Cited by 25 | Viewed by 2152
Abstract
Like living organisms, cancer cells require energy to survive and interact with their environment. Mitochondria are the main organelles for energy production and cellular metabolism. Recently, investigators demonstrated that cancer cells can hijack mitochondria from immune cells. This behavior sheds light on a [...] Read more.
Like living organisms, cancer cells require energy to survive and interact with their environment. Mitochondria are the main organelles for energy production and cellular metabolism. Recently, investigators demonstrated that cancer cells can hijack mitochondria from immune cells. This behavior sheds light on a pivotal piece in the cancer puzzle, the dependence on the normal cells. This article illustrates the benefits of new functional mitochondria for cancer cells that urge them to hijack mitochondria. It describes how functional mitochondria help cancer cells’ survival in the harsh tumor microenvironment, immune evasion, progression, and treatment resistance. Recent evidence has put forward the pivotal role of mitochondria in the metabolism of cancer stem cells (CSCs), the tumor components responsible for cancer recurrence and metastasis. This theory highlights the mitochondria in cancer biology and explains how targeting mitochondria may improve oncological outcomes. Full article
(This article belongs to the Special Issue Genetics and Pharmacogenetics in Primary Care)
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