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Guggemos J, Fuller SJ, Skarratt KK, Mayer B, Schneider EM. Loss-of-function/gain-of-function polymorphisms of the ATP sensitive P2X7R influence sepsis, septic shock, pneumonia, and survival outcomes. Front Immunol 2024; 15:1352789. [PMID: 38966639 PMCID: PMC11222724 DOI: 10.3389/fimmu.2024.1352789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 02/07/2024] [Indexed: 07/06/2024] Open
Abstract
Introduction Extracellular ATP (eATP) released from damaged cells activates the P2X7 receptor (P2X7R) ion channel on the surface of surrounding cells, resulting in calcium influx, potassium efflux and inflammasome activation. Inherited changes in the P2X7R gene (P2RX7) influence eATP induced responses. Single nucleotide polymorphisms (SNPs) of P2RX7 influence both function and signaling of the receptor, that in addition to ion flux includes pathogen control and immunity. Methods Subjects (n = 105) were admitted to the ICU at the University Hospital Ulm, Germany between June 2018 and August 2019. Of these, subjects with a diagnosis of sepsis (n = 75), were also diagnosed with septic shock (n = 24), and/or pneumonia (n = 42). Subjects with pneumonia (n = 43) included those without sepsis (n = 1), sepsis without shock (n = 29) and pneumonia with septic shock (n = 13). Out of the 75 sepsis/septic shock patients, 33 patients were not diagnosed with pneumonia. Controls (n = 30) were recruited to the study from trauma patients and surgical patients without sepsis, septic shock, or pneumonia. SNP frequencies were determined for 16 P2RX7 SNPs known to affect P2X7R function, and association studies were performed between frequencies of these SNPs in sepsis, septic shock, and pneumonia compared to controls. Results The loss-of-function (LOF) SNP rs17525809 (T253C) was found more frequently in patients with septic shock, and non-septic trauma patients when compared to sepsis. The LOF SNP rs2230911 (C1096G) was found to be more frequent in patients with sepsis and septic shock than in non-septic trauma patients. The frequencies of these SNPs were even higher in sepsis and septic patients with pneumonia. The current study also confirmed a previous study by our group that showed a five SNP combination that included the GOF SNPs rs208294 (C489T) and rs2230912 (Q460R) that was designated #21211 was associated with increased odds of survival in severe sepsis. Discussion The results found an association between expression of LOF P2RX7 SNPs and presentation to the ICU with sepsis, and septic shock compared to control ICU patients. Furthermore, frequencies of LOF SNPs were found to be higher in sepsis patients with pneumonia compared to those without pneumonia. In addition, a five SNP GOF combination was associated with increased odds of survival in severe sepsis. These results suggest that P2RX7 is required to control infection in pneumonia and that inheritance of LOF variants increases the risk of sepsis when associated with pneumonia. This study confirms that P2RX7 genotyping in pneumonia may identify patients at risk of developing sepsis. The study also identifies P2X7R as a target in sepsis associated with an excessive immune response in subjects with GOF SNP combinations.
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Affiliation(s)
- Johanna Guggemos
- Clinic for Anesthesiology and Intensive Care Medicine, Ulm University Hospital, Ulm, Germany
| | - Stephen J. Fuller
- Nepean Clinical School, Faculty of Medicine and Health, The University of Sydney, Kingswood, NSW, Australia
- Department of Haematology, Nepean Hospital, Penrith, NSW, Australia
| | - Kristen K. Skarratt
- Nepean Clinical School, Faculty of Medicine and Health, The University of Sydney, Kingswood, NSW, Australia
- Department of Haematology, Nepean Hospital, Penrith, NSW, Australia
| | - Benjamin Mayer
- Institute for Epidemiology and Medical Biometry, Ulm University, Ulm, Germany
| | - E. Marion Schneider
- Clinic for Anesthesiology and Intensive Care Medicine, Ulm University Hospital, Ulm, Germany
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Lindo J, Nogueira C, Soares R, Cunha N, Almeida MR, Rodrigues L, Coelho P, Rodrigues F, Cunha RA, Gonçalves T. Genetic Polymorphisms of P2RX7 but Not of ADORA2A Are Associated with the Severity of SARS-CoV-2 Infection. Int J Mol Sci 2024; 25:6135. [PMID: 38892324 PMCID: PMC11173306 DOI: 10.3390/ijms25116135] [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: 04/26/2024] [Revised: 05/28/2024] [Accepted: 05/30/2024] [Indexed: 06/21/2024] Open
Abstract
SARS-CoV-2 infection ranges from mild to severe presentations, according to the intensity of the aberrant inflammatory response. Purinergic receptors dually control the inflammatory response: while adenosine A2A receptors (A2ARs) are anti-inflammatory, ATP P2X7 receptors (P2X7Rs) exert pro-inflammatory effects. The aim of this study was to assess if there were differences in allelic and genotypic frequencies of a loss-of-function SNP of ADORA2A (rs2298383) and a gain-of-function single nucleotide polymorphism (SNP) of P2RX7 (rs208294) in the severity of SARS-CoV-2-associated infection. Fifty-five individuals were enrolled and categorized according to the severity of the infection. Endpoint genotyping was performed in blood cells to screen for both SNPs. The TT genotype (vs. CT + CC) and the T allele (vs. C allele) of P2RX7 SNP were found to be associated with more severe forms of COVID-19, whereas the association between ADORA2A SNP and the severity of infection was not significantly different. The T allele of P2RX7 SNP was more frequent in people with more than one comorbidity and with cardiovascular conditions and was associated with colorectal cancer. Our findings suggest a more prominent role of P2X7R rather than of A2AR polymorphisms in SARS-CoV-2 infection, although larger population-based studies should be performed to validate our conclusions.
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Affiliation(s)
- Jorge Lindo
- FMUC—Faculty of Medicine, University Coimbra, 3004-504 Coimbra, Portugal; (J.L.); (C.N.); (R.S.); (M.R.A.)
- CNC-UC—Center for Neuroscience and Cell Biology, University Coimbra, 3004-504 Coimbra, Portugal;
- CIBB—Centre for Innovative Biomedicine and Biotechnology, University Coimbra, 3004-504 Coimbra, Portugal
| | - Célia Nogueira
- FMUC—Faculty of Medicine, University Coimbra, 3004-504 Coimbra, Portugal; (J.L.); (C.N.); (R.S.); (M.R.A.)
- CNC-UC—Center for Neuroscience and Cell Biology, University Coimbra, 3004-504 Coimbra, Portugal;
- CIBB—Centre for Innovative Biomedicine and Biotechnology, University Coimbra, 3004-504 Coimbra, Portugal
| | - Rui Soares
- FMUC—Faculty of Medicine, University Coimbra, 3004-504 Coimbra, Portugal; (J.L.); (C.N.); (R.S.); (M.R.A.)
- CNC-UC—Center for Neuroscience and Cell Biology, University Coimbra, 3004-504 Coimbra, Portugal;
- CIBB—Centre for Innovative Biomedicine and Biotechnology, University Coimbra, 3004-504 Coimbra, Portugal
- Clinical Pathology Service, Portuguese Oncology Institute of Coimbra, 3004-011 Coimbra, Portugal;
| | - Nuno Cunha
- Clinical Pathology Service, Portuguese Oncology Institute of Coimbra, 3004-011 Coimbra, Portugal;
| | - Maria Rosário Almeida
- FMUC—Faculty of Medicine, University Coimbra, 3004-504 Coimbra, Portugal; (J.L.); (C.N.); (R.S.); (M.R.A.)
- CNC-UC—Center for Neuroscience and Cell Biology, University Coimbra, 3004-504 Coimbra, Portugal;
- CIBB—Centre for Innovative Biomedicine and Biotechnology, University Coimbra, 3004-504 Coimbra, Portugal
| | - Lisa Rodrigues
- CNC-UC—Center for Neuroscience and Cell Biology, University Coimbra, 3004-504 Coimbra, Portugal;
- CIBB—Centre for Innovative Biomedicine and Biotechnology, University Coimbra, 3004-504 Coimbra, Portugal
| | - Patrícia Coelho
- IPCB/ESALD—Instituto Politécnico de Castelo Branco, Escola Superior de Saúde Dr. Lopes Dias, SPRINT-IPCB—Sport Physical Activity and Health Research & Innovation Center, 6000-767 Castelo Branco, Portugal; (P.C.); (F.R.)
| | - Francisco Rodrigues
- IPCB/ESALD—Instituto Politécnico de Castelo Branco, Escola Superior de Saúde Dr. Lopes Dias, SPRINT-IPCB—Sport Physical Activity and Health Research & Innovation Center, 6000-767 Castelo Branco, Portugal; (P.C.); (F.R.)
| | - Rodrigo A. Cunha
- FMUC—Faculty of Medicine, University Coimbra, 3004-504 Coimbra, Portugal; (J.L.); (C.N.); (R.S.); (M.R.A.)
- CNC-UC—Center for Neuroscience and Cell Biology, University Coimbra, 3004-504 Coimbra, Portugal;
- CIBB—Centre for Innovative Biomedicine and Biotechnology, University Coimbra, 3004-504 Coimbra, Portugal
| | - Teresa Gonçalves
- FMUC—Faculty of Medicine, University Coimbra, 3004-504 Coimbra, Portugal; (J.L.); (C.N.); (R.S.); (M.R.A.)
- CNC-UC—Center for Neuroscience and Cell Biology, University Coimbra, 3004-504 Coimbra, Portugal;
- CIBB—Centre for Innovative Biomedicine and Biotechnology, University Coimbra, 3004-504 Coimbra, Portugal
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Rajpurohit YS, Sharma DK, Lal M, Soni I. A perspective on tumor radiation resistance following high-LET radiation treatment. J Cancer Res Clin Oncol 2024; 150:226. [PMID: 38696003 PMCID: PMC11065934 DOI: 10.1007/s00432-024-05757-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 04/22/2024] [Indexed: 05/05/2024]
Abstract
High-linear energy transfer (LET) radiation is a promising alternative to conventional low-LET radiation for therapeutic gain against cancer owing to its ability to induce complex and clustered DNA lesions. However, the development of radiation resistance poses a significant barrier. The potential molecular mechanisms that could confer resistance development are translesion synthesis (TLS), replication gap suppression (RGS) mechanisms, autophagy, epithelial-mesenchymal transition (EMT) activation, release of exosomes, and epigenetic changes. This article will discuss various types of complex clustered DNA damage, their repair mechanisms, mutagenic potential, and the development of radiation resistance strategies. Furthermore, it highlights the importance of careful consideration and patient selection when employing high-LET radiotherapy in clinical settings.
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Affiliation(s)
- Yogendra Singh Rajpurohit
- Molecular Biology Division, Bhabha Atomic Research Centre, 2-46-S, Modular Lab, A-Block, Mumbai, 400085, India.
- Homi Bhabha National Institute, DAE- Deemed University, Mumbai, 400094, India.
| | - Dhirendra Kumar Sharma
- Molecular Biology Division, Bhabha Atomic Research Centre, 2-46-S, Modular Lab, A-Block, Mumbai, 400085, India
| | - Mitu Lal
- Molecular Biology Division, Bhabha Atomic Research Centre, 2-46-S, Modular Lab, A-Block, Mumbai, 400085, India
| | - Ishu Soni
- Homi Bhabha National Institute, DAE- Deemed University, Mumbai, 400094, India
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Norris AC, Mansueto AJ, Jimenez M, Yazlovitskaya EM, Jain BK, Graham TR. Flipping the script: Advances in understanding how and why P4-ATPases flip lipid across membranes. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119700. [PMID: 38382846 DOI: 10.1016/j.bbamcr.2024.119700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 11/15/2023] [Accepted: 02/16/2024] [Indexed: 02/23/2024]
Abstract
Type IV P-type ATPases (P4-ATPases) are a family of transmembrane enzymes that translocate lipid substrates from the outer to the inner leaflet of biological membranes and thus create an asymmetrical distribution of lipids within membranes. On the cellular level, this asymmetry is essential for maintaining the integrity and functionality of biological membranes, creating platforms for signaling events and facilitating vesicular trafficking. On the organismal level, this asymmetry has been shown to be important in maintaining blood homeostasis, liver metabolism, neural development, and the immune response. Indeed, dysregulation of P4-ATPases has been linked to several diseases; including anemia, cholestasis, neurological disease, and several cancers. This review will discuss the evolutionary transition of P4-ATPases from cation pumps to lipid flippases, the new lipid substrates that have been discovered, the significant advances that have been achieved in recent years regarding the structural mechanisms underlying the recognition and flipping of specific lipids across biological membranes, and the consequences of P4-ATPase dysfunction on cellular and physiological functions. Additionally, we emphasize the requirement for additional research to comprehensively understand the involvement of flippases in cellular physiology and disease and to explore their potential as targets for therapeutics in treating a variety of illnesses. The discussion in this review will primarily focus on the budding yeast, C. elegans, and mammalian P4-ATPases.
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Affiliation(s)
- Adriana C Norris
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | | | - Mariana Jimenez
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | | | - Bhawik K Jain
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Todd R Graham
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.
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Yazlovitskaya EM, Graham TR. Type IV P-Type ATPases: Recent Updates in Cancer Development, Progression, and Treatment. Cancers (Basel) 2023; 15:4327. [PMID: 37686603 PMCID: PMC10486736 DOI: 10.3390/cancers15174327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/15/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023] Open
Abstract
Adaptations of cancer cells for survival are remarkable. One of the most significant properties of cancer cells to prevent the immune system response and resist chemotherapy is the altered lipid metabolism and resulting irregular cell membrane composition. The phospholipid distribution in the plasma membrane of normal animal cells is distinctly asymmetric. Lipid flippases are a family of enzymes regulating membrane asymmetry, and the main class of flippases are type IV P-type ATPases (P4-ATPases). Alteration in the function of flippases results in changes to membrane organization. For some lipids, such as phosphatidylserine, the changes are so drastic that they are considered cancer biomarkers. This review will analyze and discuss recent publications highlighting the role that P4-ATPases play in the development and progression of various cancer types, as well as prospects of targeting P4-ATPases for anti-cancer treatment.
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Affiliation(s)
| | - Todd R. Graham
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
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Learning high-order interactions for polygenic risk prediction. PLoS One 2023; 18:e0281618. [PMID: 36763605 PMCID: PMC9916647 DOI: 10.1371/journal.pone.0281618] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 01/27/2023] [Indexed: 02/11/2023] Open
Abstract
Within the framework of precision medicine, the stratification of individual genetic susceptibility based on inherited DNA variation has paramount relevance. However, one of the most relevant pitfalls of traditional Polygenic Risk Scores (PRS) approaches is their inability to model complex high-order non-linear SNP-SNP interactions and their effect on the phenotype (e.g. epistasis). Indeed, they incur in a computational challenge as the number of possible interactions grows exponentially with the number of SNPs considered, affecting the statistical reliability of the model parameters as well. In this work, we address this issue by proposing a novel PRS approach, called High-order Interactions-aware Polygenic Risk Score (hiPRS), that incorporates high-order interactions in modeling polygenic risk. The latter combines an interaction search routine based on frequent itemsets mining and a novel interaction selection algorithm based on Mutual Information, to construct a simple and interpretable weighted model of user-specified dimensionality that can predict a given binary phenotype. Compared to traditional PRSs methods, hiPRS does not rely on GWAS summary statistics nor any external information. Moreover, hiPRS differs from Machine Learning-based approaches that can include complex interactions in that it provides a readable and interpretable model and it is able to control overfitting, even on small samples. In the present work we demonstrate through a comprehensive simulation study the superior performance of hiPRS w.r.t. state of the art methods, both in terms of scoring performance and interpretability of the resulting model. We also test hiPRS against small sample size, class imbalance and the presence of noise, showcasing its robustness to extreme experimental settings. Finally, we apply hiPRS to a case study on real data from DACHS cohort, defining an interaction-aware scoring model to predict mortality of stage II-III Colon-Rectal Cancer patients treated with oxaliplatin.
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Park HA, Edelmann D, Canzian F, Harrison TA, Hua X, Shi Q, Silverman A, Schneider M, Goldberg RM, Alberts SR, Hoffmeister M, Brenner H, Chan AT, Peters U, Newcomb PA, Chang-Claude J. Predictive Polygenic Score for Outcome after First-Line Oxaliplatin-Based Chemotherapy in Colorectal Cancer Patients Using Supervised Principal Component Analysis. Cancer Epidemiol Biomarkers Prev 2022; 31:2087-2091. [PMID: 35984985 PMCID: PMC9627260 DOI: 10.1158/1055-9965.epi-22-0320] [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: 04/07/2022] [Revised: 06/23/2022] [Accepted: 08/17/2022] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Associations between candidate germline genetic variants and treatment outcome of oxaliplatin, a drug commonly used for patients with colorectal cancer, have been reported but not robustly established. This study aimed to construct polygenic hazard scores (PHSs) as predictive markers for oxaliplatin treatment outcome by using a supervised principal component approach (PCA). METHODS Genome-wide association analysis for overall survival, including interaction terms (SNP*treatment type) was carried out using two phase III trials, 3,098 resected stage III colon cancer (rCC) patients of NCCTG N0147 and 506 metastatic colorectal cancer (mCRC) patients of NCCTG N9741, separately. SNPs showing interaction with genome-wide significance (P < 5 × 10-8) were selected for PCA to derive a PHS. PHS interaction with treatment was included in Cox regression models to predict outcome. Replication of prediction models was performed in an independent cohort, DACHS. RESULTS The two PHSs based on the first two principal components of selected SNPs (15SNPs for rCC and 13SNPs for mCRC) were used to construct interaction terms with treatment type and included in models adjusted for clinical covariables. However, in the DACHS study, the addition of the two PHS terms to clinical models did not improve the prediction error in either patients with rCC or mCRC. PHS interaction was also not replicated. CONCLUSIONS The PHSs derived using principal components efficiently combined multiple predictive SNPs for estimating likelihood of benefit from oxaliplatin versus other treatment but could not be replicated. IMPACT These results highlight the potential but also challenges in generating evidence for a predictive polygenic score for oxaliplatin efficacy.
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Affiliation(s)
- Hanla A. Park
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Medical Faculty, University of Heidelberg, Heidelberg, Germany
| | - Dominic Edelmann
- Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Tabitha A. Harrison
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Xinwei Hua
- Department of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, Massachusetts
- Department of Cardiology, Peking University Third Hospital, Peking University, Beijing, China
| | - Qian Shi
- Department of Quantitative Science, Mayo Clinic, Rochester, Minnesota
| | - Allison Silverman
- Epidemiology Program, Fred Hutchinson Research Cancer Research Center, Seattle, Washington
| | - Martin Schneider
- Department of General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | | | | | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andrew T. Chan
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
- School of Public Health, University of Washington, Seattle, Washington
| | - Polly A. Newcomb
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
- School of Public Health, University of Washington, Seattle, Washington
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Cancer Epidemiology Group, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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Nobili S, Mini E. Special Issue: “Gastrointestinal Cancers and Personalized Medicine”. J Pers Med 2022; 12:jpm12030338. [PMID: 35330338 PMCID: PMC8953463 DOI: 10.3390/jpm12030338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 02/22/2022] [Indexed: 02/01/2023] Open
Affiliation(s)
- Stefania Nobili
- Department of Neurosciences, Imaging and Clinical Sciences, “G. d’Annunzio” University of Chieti-Pescara, 66100 Chieti, Italy
- Center for Advanced Studies and Technology (CAST), “G. d’Annunzio” University of Chieti-Pescara, 66100 Chieti, Italy
- Correspondence:
| | - Enrico Mini
- Department of Health Sciences, University of Florence, 50139 Florence, Italy;
- DENOTHE Excellence Center, University of Florence, 50139 Florence, Italy
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