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Mazzeo P, Ganster C, Wiedenhöft J, Shirneshan K, Rittscher K, Brzuszkiewicz EB, Steinemann D, Schieck M, Müller‐Thomas C, Treiber H, Braulke F, Germing U, Sockel K, Balaian E, Schanz J, Platzbecker U, Götze KS, Haase D. Comprehensive sequential genetic analysis delineating frequency, patterns, and prognostic impact of genomic dynamics in a real-world cohort of patients with lower-risk MDS. Hemasphere 2024; 8:e70014. [PMID: 39315323 PMCID: PMC11417473 DOI: 10.1002/hem3.70014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 07/13/2024] [Accepted: 08/05/2024] [Indexed: 09/25/2024] Open
Abstract
The acquisition of subsequent genetic lesions (clonal evolution, CE) and/or the expansion of existing clones (CEXP) contributes to clonal dynamics (CD) in myelodysplastic syndromes (MDS). Although CD plays an important role in high-risk patients in disease progression and transformation into acute myeloid leukemia (AML), knowledge about CD in lower-risk MDS (LR-MDS) patients is limited due to lack of robust longitudinal data considering the long clinically stable courses of the disease. In this retrospective analysis, we delineate the frequency and the prognostic impact of CD in an unselected real-world cohort of LR-MDS patients. We screened 68 patients with a median follow-up of 40.5 months and a median of 7.5 (range: 2-22) timepoints for CE and CEXP detected by chromosomal banding analysis, fluorescence in situ hybridization, sequencing, and molecular karyotyping. In 30/68 patients, 47 CE events and a CD rate of 1 event per 4 years were documented. Of note, patients with at least 1 CE event had an increased probability for subsequent treatment. Unexpectedly, CE did not correlate with inferior outcomes, which could be reasonably explained by CD detection triggering the subsequent start of a disease-modifying therapy.
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Affiliation(s)
- Paolo Mazzeo
- Department of Hematology and Medical Oncology, INDIGHO laboratoryUniversity Medical Center Göttingen (UMG)GöttingenGermany
| | - Christina Ganster
- Department of Hematology and Medical Oncology, INDIGHO laboratoryUniversity Medical Center Göttingen (UMG)GöttingenGermany
| | - John Wiedenhöft
- Department of Human GeneticsUniversity of Leipzig Medical CenterLeipzigGermany
| | - Katayoon Shirneshan
- Department of Hematology and Medical Oncology, INDIGHO laboratoryUniversity Medical Center Göttingen (UMG)GöttingenGermany
| | - Katharina Rittscher
- Department of Hematology and Medical Oncology, INDIGHO laboratoryUniversity Medical Center Göttingen (UMG)GöttingenGermany
| | - Elzbieta B. Brzuszkiewicz
- Department of Hematology and Medical Oncology, INDIGHO laboratoryUniversity Medical Center Göttingen (UMG)GöttingenGermany
| | - Doris Steinemann
- Department of Human GeneticsHannover Medical SchoolHannoverGermany
| | | | - Catharina Müller‐Thomas
- Department of Medicine IIITechnical University of Munich School of Medicine and HealthMunichGermany
| | - Hannes Treiber
- Department of Hematology and Medical Oncology, INDIGHO laboratoryUniversity Medical Center Göttingen (UMG)GöttingenGermany
| | - Friederike Braulke
- Department of Hematology and Medical Oncology, INDIGHO laboratoryUniversity Medical Center Göttingen (UMG)GöttingenGermany
- Comprehensive Cancer CenterUniversity Medical Center Göttingen (UMG)GöttingenGermany
| | - Ulrich Germing
- Department of Hematology, Oncology and Clinical ImmunologyHeinrich‐Heine‐UniversitätDüsseldorfGermany
| | - Katja Sockel
- Medical Clinic and Policlinic IUniversity Hospital Carl Gustav Carus DresdenDresdenGermany
| | - Ekaterina Balaian
- Medical Clinic and Policlinic IUniversity Hospital Carl Gustav Carus DresdenDresdenGermany
| | - Julie Schanz
- Department of Hematology and Medical Oncology, INDIGHO laboratoryUniversity Medical Center Göttingen (UMG)GöttingenGermany
| | - Uwe Platzbecker
- Medical Clinic and Policlinic 1, Hematology and Cellular TherapyLeipzig University HospitalLeipzigGermany
| | - Katharina S. Götze
- Department of Medicine IIITechnical University of Munich School of Medicine and HealthMunichGermany
| | - Detlef Haase
- Department of Hematology and Medical Oncology, INDIGHO laboratoryUniversity Medical Center Göttingen (UMG)GöttingenGermany
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Fletcher K, Michelmore R. Genome-Enabled Insights into Downy Mildew Biology and Evolution. ANNUAL REVIEW OF PHYTOPATHOLOGY 2023; 61:165-183. [PMID: 37268005 DOI: 10.1146/annurev-phyto-021622-103440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Oomycetes that cause downy mildew diseases are highly specialized, obligately biotrophic phytopathogens that can have major impacts on agriculture and natural ecosystems. Deciphering the genome sequence of these organisms provides foundational tools to study and deploy control strategies against downy mildew pathogens (DMPs). The recent telomere-to-telomere genome assembly of the DMP Peronospora effusa revealed high levels of synteny with distantly related DMPs, higher than expected repeat content, and previously undescribed architectures. This provides a road map for generating similar high-quality genome assemblies for other oomycetes. This review discusses biological insights made using this and other assemblies, including ancestral chromosome architecture, modes of sexual and asexual variation, the occurrence of heterokaryosis, candidate gene identification, functional validation, and population dynamics. We also discuss future avenues of research likely to be fruitful in studies of DMPs and highlight resources necessary for advancing our understanding and ability to forecast and control disease outbreaks.
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Affiliation(s)
- Kyle Fletcher
- The Genome Center, University of California, Davis, California, USA
| | - Richard Michelmore
- The Genome Center, University of California, Davis, California, USA
- Department of Plant Sciences; Department of Molecular and Cellular Biology; Department of Medical Microbiology and Immunology, University of California, Davis, California, USA;
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Qin Y, Zhang H, Feng L, Wei H, Wu Y, Jiang C, Xu Z, Zhu H, Liu T. Combining metaphase cytogenetics with single nucleotide polymorphism arrays can improve the diagnostic yield and identify prognosis more precisely in myelodysplastic syndromes. Ann Med 2022; 54:2627-2636. [PMID: 36148999 PMCID: PMC9518301 DOI: 10.1080/07853890.2022.2125173] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 08/24/2022] [Accepted: 09/11/2022] [Indexed: 11/05/2022] Open
Abstract
BACKGROUND Myelodysplastic syndromes (MDS) encompass a group of heterogeneous haematopoietic stem cell malignancies characterised by ineffective haematopoiesis, cytological aberrations, and a propensity for progression to acute myeloid leukaemia. Diagnosis and disease prognostic stratification are much based on genomic abnormalities. The traditional metaphase cytogenetics analysis (MC) can detect about 40-60% aberrations. Single-nucleotide polymorphism arrays (SNP-A) karyotyping can detect copy number variations with a higher resolution and has a unique advantage in detection of copy number neutral loss of heterozygosity (CN-LOH). Combining these two methods may improve the diagnostic efficiency and accuracy for MDS. METHODS We retrospectively analysed the data of 110 MDS patients diagnosed from January 2012 to December 2019 to compare the detection yield of chromosomal abnormalities by MC with by SNP-A, and the relationship between chromosomal abnormalities and prognosis. RESULTS Our results showed that SNP-A improved the detection yield of chromosomal aberrations compared with MC (74.5 vs. 55.5%, p < .001). In addition, the positive yield could be further improved by combining MC with SNP-A to 77.3%, compared with MC alone. Univariate analysis showed that age >65 years, bone marrow blasts ≥5%, with acquired CN-LOH, new aberrations detected by SNP-A, TGA value > the median (81.435 Mb), higher risk by IPSS-R-MC, higher risk by IPSS-R-SNP-A all had poorer prognosis. More critically, multivariable analysis showed that age >65 years and higher risk by IPSS-R-SNP-A were independent predictors of inferior OS in MDS patients. CONCLUSION The combination of MC and SNP-A based karyotyping can further improve the diagnostic yield and provide more precise prognostic stratification in MDS patients. However, SNP-A may not completely replace MC because of its inability to detect balanced translocation and to detect different clones. From a practical point of view, we recommend the concurrent use of SNP-A and MC in the initial karyotypic evaluation for MDS patients on diagnosis and prognosis stratification.KEY MESSAGESSNP-A based karyotyping can further improve the MDS diagnostic yield and provide more precise prognostic stratification in MDS patients.Acquired CN-LOH is a characteristic chromosomal aberration of MDS, which should be integrated to the diagnostic project of MDS.The concurrent use of SNP-A and MC in the initial karyotypic evaluation for MDS patients can be recommended.
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Affiliation(s)
- Yao Qin
- Department of Hematology, Institute of Hematology, West China Hospital, Sichuan University, Chengdu, P. R. China
| | - Hang Zhang
- Department of Hematology, Institute of Hematology, West China Hospital, Sichuan University, Chengdu, P. R. China
| | - Lin Feng
- Department of Hematology, Institute of Hematology, West China Hospital, Sichuan University, Chengdu, P. R. China
| | - Haichen Wei
- Department of Hematology, Institute of Hematology, West China Hospital, Sichuan University, Chengdu, P. R. China
| | - Yuling Wu
- Department of Hematology, Institute of Hematology, West China Hospital, Sichuan University, Chengdu, P. R. China
| | - Chaoran Jiang
- Sichuan Hua Xi Kindstar Medical Diagnostic Centre, Chengdu, Sichuan, P. R. China
| | - Zhihong Xu
- Sichuan Hua Xi Kindstar Medical Diagnostic Centre, Chengdu, Sichuan, P. R. China
| | - Huanling Zhu
- Department of Hematology, Institute of Hematology, West China Hospital, Sichuan University, Chengdu, P. R. China
| | - Ting Liu
- Department of Hematology, Institute of Hematology, West China Hospital, Sichuan University, Chengdu, P. R. China
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Ciani Y, Fedrizzi T, Prandi D, Lorenzin F, Locallo A, Gasperini P, Franceschini GM, Benelli M, Elemento O, Fava LL, Inga A, Demichelis F. Allele-specific genomic data elucidate the role of somatic gain and copy-number neutral loss of heterozygosity in cancer. Cell Syst 2021; 13:183-193.e7. [PMID: 34731645 PMCID: PMC8856743 DOI: 10.1016/j.cels.2021.10.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 07/23/2021] [Accepted: 10/08/2021] [Indexed: 12/12/2022]
Abstract
Pan-cancer studies sketched the genomic landscape of the tumor types spectrum. We delineated the purity- and ploidy-adjusted allele-specific profiles of 4,950 patients across 27 tumor types from the Cancer Genome Atlas (TCGA). Leveraging allele-specific data, we reclassified as loss of heterozygosity (LOH) 9% and 7% of apparent copy-number wild-type and gain calls, respectively, and overall observed more than 18 million allelic imbalance somatic events at the gene level. Reclassification of copy-number events revealed associations between driver mutations and LOH, pointing out the timings between the occurrence of point mutations and copy-number events. Integrating allele-specific genomics and matched transcriptomics, we observed that allele-specific gene status is relevant in the regulation of TP53 and its targets. Further, we disclosed the role of copy-neutral LOH in the impairment of tumor suppressor genes and in disease progression. Our results highlight the role of LOH in cancer and contribute to the understanding of tumor progression.
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Affiliation(s)
- Yari Ciani
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Tarcisio Fedrizzi
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Davide Prandi
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Francesca Lorenzin
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Alessio Locallo
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Paola Gasperini
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Gian Marco Franceschini
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Matteo Benelli
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy; Bioinformatics Unit, Hospital of Prato, 59100 Prato, Italy
| | - Olivier Elemento
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10021, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10021, USA; The Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Luca L Fava
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Alberto Inga
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Francesca Demichelis
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy; Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10021, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10021, USA; The Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA.
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Genetics of Myelodysplastic Syndromes. Cancers (Basel) 2021; 13:cancers13143380. [PMID: 34298596 PMCID: PMC8304604 DOI: 10.3390/cancers13143380] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 06/30/2021] [Accepted: 07/01/2021] [Indexed: 12/15/2022] Open
Abstract
Myelodysplastic syndrome (MDS) describes a heterogeneous group of bone marrow diseases, now understood to reflect numerous germline and somatic drivers, characterized by recurrent cytogenetic abnormalities and gene mutations. Precursor conditions including clonal hematopoiesis of indeterminate potential and clonal cytopenia of undetermined significance confer risk for MDS as well as other hematopoietic malignancies and cardiovascular complications. The future is likely to bring an understanding of those individuals who are at the highest risk of progression to MDS and preventive strategies to prevent malignant transformation.
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Genomic variations in patients with myelodysplastic syndrome and karyotypes without numerical or structural changes. Sci Rep 2021; 11:2783. [PMID: 33531543 PMCID: PMC7854738 DOI: 10.1038/s41598-021-81467-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 12/23/2020] [Indexed: 01/30/2023] Open
Abstract
Myelodysplastic syndrome (MDS) is an onco-hematologic disease with distinct levels of peripheral blood cytopenias, dysplasias in cell differentiation and various forms of chromosomal and cytogenomic alterations. In this study, the Chromosomal Microarray Analysis (CMA) was performed in patients with primary MDS without numerical and/or structural chromosomal alterations in karyotypes. A total of 17 patients was evaluated by GTG banding and eight patients showed no numerical and/or structural alterations. Then, the CMA was carried out and identified gains and losses CNVs and long continuous stretches of homozygosity (LCSHs). They were mapped on chromosomes 1, 2, 3, 4, 5, 6, 7, 9, 10, 12, 14, 16, 17, 18, 19, 20, 21, X, and Y. Ninety-one genes that have already been implicated in molecular pathways important for cell viability were selected and in-silico expression analyses demonstrated 28 genes differentially expressed in mesenchymal stromal cells of patients. Alterations in these genes may be related to the inactivation of suppressor genes or the activation of oncogenes contributing to the evolution and malignization of MDS. CMA provided additional information in patients without visible changes in the karyotype and our findings could contribute with additional information to improve the prognostic and personalized stratification for patients.
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Ronaghy A, Yang RK, Khoury JD, Kanagal-Shamanna R. Clinical Applications of Chromosomal Microarray Testing in Myeloid Malignancies. Curr Hematol Malig Rep 2020; 15:194-202. [PMID: 32382988 DOI: 10.1007/s11899-020-00578-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
PURPOSE OF REVIEW Knowledge of both somatic mutations and copy number aberrations are important for the understanding of cancer pathogenesis and management of myeloid neoplasms. The currently available standard of care technologies for copy number assessment such as conventional karyotype and FISH are either limited by low resolution or restriction to targeted assessment. RECENT FINDINGS Chromosomal microarray (CMA) is effective in characterization of chromosomal and gene aberrations of diagnostic, prognostic, and therapeutic significance at a higher resolution than conventional karyotyping. These results are complementary to NGS mutation studies. Copy-neutral loss of heterozygosity (CN-LOH), which is prognostic in AML, is currently only identified by CMA. Yet, despite the widespread availability, CMA testing is not routinely performed in diagnostic laboratories due to lack of knowledge on best-testing practices for clinical work-up of myeloid neoplasms. In this review, we provide an overview of the clinical significance of CMA in acute myeloid leukemia (AML), myelodysplastic syndromes (MDS), and myelodysplastic/myeloproliferative neoplasms (MDS/MPN). We will also elaborate the specific clinical scenarios where CMA can provide additional information essential for management and could potentially alter treatment. Chromosomal microarray (CMA) is an effective technology for characterizing chromosomal copy number changes and copy-neutral loss of heterozygosity of diagnostic, prognostic, and therapeutic significance at a high resolution in myeloid malignancies.
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MESH Headings
- Chromosome Aberrations
- Chromosomes, Human
- Comparative Genomic Hybridization
- DNA Copy Number Variations
- Genetic Predisposition to Disease
- High-Throughput Nucleotide Sequencing
- Humans
- Leukemia, Myeloid, Acute/diagnosis
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myelomonocytic, Chronic/diagnosis
- Leukemia, Myelomonocytic, Chronic/genetics
- Loss of Heterozygosity
- Microarray Analysis
- Myelodysplastic Syndromes/diagnosis
- Myelodysplastic Syndromes/genetics
- Polymorphism, Single Nucleotide
- Predictive Value of Tests
- Prognosis
- Reproducibility of Results
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Affiliation(s)
- Arash Ronaghy
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd. Unit 072, Houston, TX, 77030, USA
| | - Richard K Yang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd. Unit 072, Houston, TX, 77030, USA
| | - Joseph D Khoury
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd. Unit 072, Houston, TX, 77030, USA
| | - Rashmi Kanagal-Shamanna
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd. Unit 072, Houston, TX, 77030, USA.
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Gallo Cantafio ME, Grillone K, Caracciolo D, Scionti F, Arbitrio M, Barbieri V, Pensabene L, Guzzi PH, Di Martino MT. From Single Level Analysis to Multi-Omics Integrative Approaches: A Powerful Strategy towards the Precision Oncology. High Throughput 2018; 7:ht7040033. [PMID: 30373182 PMCID: PMC6306876 DOI: 10.3390/ht7040033] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 10/09/2018] [Accepted: 10/22/2018] [Indexed: 02/06/2023] Open
Abstract
Integration of multi-omics data from different molecular levels with clinical data, as well as epidemiologic risk factors, represents an accurate and promising methodology to understand the complexity of biological systems of human diseases, including cancer. By the extensive use of novel technologic platforms, a large number of multidimensional data can be derived from analysis of health and disease systems. Comprehensive analysis of multi-omics data in an integrated framework, which includes cumulative effects in the context of biological pathways, is therefore eagerly awaited. This strategy could allow the identification of pathway-addiction of cancer cells that may be amenable to therapeutic intervention. However, translation into clinical settings requires an optimized integration of omics data with clinical vision to fully exploit precision cancer medicine. We will discuss the available technical approach and more recent developments in the specific field.
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Affiliation(s)
- Maria Eugenia Gallo Cantafio
- Department of Experimental and Clinical Medicine, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy.
| | - Katia Grillone
- Department of Experimental and Clinical Medicine, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy.
| | - Daniele Caracciolo
- Department of Experimental and Clinical Medicine, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy.
| | - Francesca Scionti
- Department of Experimental and Clinical Medicine, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy.
| | | | - Vito Barbieri
- Medical Oncology Unit, Mater Domini Hospital, Salvatore Venuta University Campus, 88100 Catanzaro, Italy.
| | - Licia Pensabene
- Department of Medical and Surgical Sciences Pediatric Unit, Magna Graecia University, 88100 Catanzaro, Italy.
| | - Pietro Hiram Guzzi
- Department of Medical and Surgical Sciences, Magna Graecia University, 88100 Catanzaro, Italy.
| | - Maria Teresa Di Martino
- Department of Experimental and Clinical Medicine, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy.
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