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Pei J, Peng Y, Ma K, Lan C, Zhang T, Li Y, Chen X, Gao H. Integrated analysis reveals FLI1 regulates the tumor immune microenvironment via its cell-type-specific expression and transcriptional regulation of distinct target genes of immune cells in breast cancer. BMC Genomics 2024; 25:250. [PMID: 38448802 PMCID: PMC10916124 DOI: 10.1186/s12864-024-10174-9] [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: 12/21/2023] [Accepted: 02/29/2024] [Indexed: 03/08/2024] Open
Abstract
BACKGROUND Immunotherapy is a practical therapeutic approach in breast cancer (BRCA), and the role of FLI1 in immune regulation has gradually been unveiled. However, the specific role of FLI1 in BRCA was conflicted; thus, additional convincing evidence is needed. METHODS We explored the upstream regulation of FLI1 expression via summary data-based Mendelian randomization (SMR) analysis and ncRNA network construction centering on FLI1 using BRCA genome-wide association study (GWAS) summary data with expression quantitative trait loci (eQTLs) and DNA methylation quantitative trait loci (mQTLs) from the blood and a series of in silico analyses, respectively. We illuminated the downstream function of FLI1 in immune regulation by integrating a series of analyses of single-cell RNA sequence data (scRNA-seq). RESULTS We verified a causal pathway from FLI1 methylation to FLI1 gene expression to BRCA onset and demonstrated that FLI1 was downregulated in BRCA. FLI1, a transcription factor, served as myeloid and T cells' communication regulator by targeting immune-related ligands and receptor transcription in BRCA tissues. We constructed a ceRNA network centering on FLI1 that consisted of three LncRNAs (CKMT2-AS1, PSMA3-AS1, and DIO3OS) and a miRNA (hsa-miR-324-5p), and the expression of FLI1 was positively related to a series of immune-related markers, including immune cell infiltration, biomarkers of immune cells, and immune checkpoints. CONCLUSION Low-methylation-induced or ncRNA-mediated downregulation of FLI1 is associated with poor prognosis, and FLI1 might regulate the tumor immune microenvironment via a cell-type-specific target genes manner in BRCA.
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Affiliation(s)
- Jianying Pei
- National Research Institute for Family Planning, Beijing, 100081, China
- Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China
- Institute of Clinical Medicine, Gansu Provincial Maternity and Child-care Hospital (Gansu Provincial Central Hospital), Lanzhou, 730000, China
| | - Ying Peng
- Department of General Surgery, Peking University Third Hospital, Beijing, 100191, China
| | - Kexin Ma
- National Research Institute for Family Planning, Beijing, 100081, China
- Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China
| | - Chunyan Lan
- National Research Institute for Family Planning, Beijing, 100081, China
- Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China
| | - Tingting Zhang
- Medical College of Northwest Minzu University, Lanzhou, 730030, China
| | - Yan Li
- Medical College of Northwest Minzu University, Lanzhou, 730030, China
| | - Xiaofang Chen
- School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China.
| | - Huafang Gao
- National Research Institute for Family Planning, Beijing, 100081, China.
- Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China.
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Landuzzi L, Ruzzi F, Pellegrini E, Lollini PL, Scotlandi K, Manara MC. IL-1 Family Members in Bone Sarcomas. Cells 2024; 13:233. [PMID: 38334625 PMCID: PMC10854900 DOI: 10.3390/cells13030233] [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: 12/30/2023] [Revised: 01/17/2024] [Accepted: 01/24/2024] [Indexed: 02/10/2024] Open
Abstract
IL-1 family members have multiple pleiotropic functions affecting various tissues and cells, including the regulation of the immune response, hematopoietic homeostasis, bone remodeling, neuronal physiology, and synaptic plasticity. Many of these activities are involved in various pathological processes and immunological disorders, including tumor initiation and progression. Indeed, IL-1 family members have been described to contribute to shaping the tumor microenvironment (TME), determining immune evasion and drug resistance, and to sustain tumor aggressiveness and metastasis. This review addresses the role of IL-1 family members in bone sarcomas, particularly the highly metastatic osteosarcoma (OS) and Ewing sarcoma (EWS), and discusses the IL-1-family-related mechanisms that play a role in bone metastasis development. We also consider the therapeutic implications of targeting IL-1 family members, which have been proposed as (i) relevant targets for anti-tumor and anti-metastatic drugs; (ii) immune checkpoints for immune suppression; and (iii) potential antigens for immunotherapy.
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Affiliation(s)
- Lorena Landuzzi
- Experimental Oncology Laboratory, IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy; (E.P.); (K.S.); (M.C.M.)
| | - Francesca Ruzzi
- Laboratory of Immunology and Biology of Metastasis, Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy;
| | - Evelin Pellegrini
- Experimental Oncology Laboratory, IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy; (E.P.); (K.S.); (M.C.M.)
| | - Pier-Luigi Lollini
- Laboratory of Immunology and Biology of Metastasis, Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy;
| | - Katia Scotlandi
- Experimental Oncology Laboratory, IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy; (E.P.); (K.S.); (M.C.M.)
| | - Maria Cristina Manara
- Experimental Oncology Laboratory, IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy; (E.P.); (K.S.); (M.C.M.)
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Hassan M, Shahzadi S, Malik A, Din SU, Yasir M, Chun W, Kloczkowski A. Oncomeric Profiles of microRNAs as New Therapeutic Targets for Treatment of Ewing's Sarcoma: A Composite Review. Genes (Basel) 2023; 14:1849. [PMID: 37895198 PMCID: PMC10606885 DOI: 10.3390/genes14101849] [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: 06/30/2023] [Revised: 09/07/2023] [Accepted: 09/21/2023] [Indexed: 10/29/2023] Open
Abstract
Ewing's sarcoma is a rare type of cancer that forms in bones and soft tissues in the body, affecting mostly children and young adults. Current treatments for ES are limited to chemotherapy and/or radiation, followed by surgery. Recently, microRNAs have shown favourable results as latent diagnostic and prognostic biomarkers in various cancers. Furthermore, microRNAs have shown to be a good therapeutic agent due to their involvement in the dysregulation of various molecular pathways linked to tumour progression, invasion, angiogenesis, and metastasis. In this review, comprehensive data mining was employed to explore various microRNAs that might have therapeutic potential as target molecules in the treatment of ES.
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Affiliation(s)
- Mubashir Hassan
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children Hospital, Columbus, OH 43205, USA;
| | - Saba Shahzadi
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children Hospital, Columbus, OH 43205, USA;
| | - Amal Malik
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore 54590, Pakistan;
| | - Salah ud Din
- Department of Bioinformatics, University of Okara, Okara 56130, Pakistan;
| | - Muhammad Yasir
- Department of Pharmacology, College of Medicine, Kangwon National University, Chuncheon 24341, Republic of Korea; (M.Y.); (W.C.)
| | - Wanjoo Chun
- Department of Pharmacology, College of Medicine, Kangwon National University, Chuncheon 24341, Republic of Korea; (M.Y.); (W.C.)
| | - Andrzej Kloczkowski
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children Hospital, Columbus, OH 43205, USA;
- Department of Pediatrics, The Ohio State University, Columbus, OH 43205, USA
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Apfelbaum AA, Wrenn ED, Lawlor ER. The importance of fusion protein activity in Ewing sarcoma and the cell intrinsic and extrinsic factors that regulate it: A review. Front Oncol 2022; 12:1044707. [PMID: 36505823 PMCID: PMC9727305 DOI: 10.3389/fonc.2022.1044707] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 10/27/2022] [Indexed: 11/24/2022] Open
Abstract
Accumulating evidence shows that despite clonal origins tumors eventually become complex communities comprised of phenotypically distinct cell subpopulations. This heterogeneity arises from both tumor cell intrinsic programs and signals from spatially and temporally dynamic microenvironments. While pediatric cancers usually lack the mutational burden of adult cancers, they still exhibit high levels of cellular heterogeneity that are largely mediated by epigenetic mechanisms. Ewing sarcomas are aggressive bone and soft tissue malignancies with peak incidence in adolescence and the prognosis for patients with relapsed and metastatic disease is dismal. Ewing sarcomas are driven by a single pathognomonic fusion between a FET protein and an ETS family transcription factor, the most common of which is EWS::FLI1. Despite sharing a single driver mutation, Ewing sarcoma cells demonstrate a high degree of transcriptional heterogeneity both between and within tumors. Recent studies have identified differential fusion protein activity as a key source of this heterogeneity which leads to profoundly different cellular phenotypes. Paradoxically, increased invasive and metastatic potential is associated with lower EWS::FLI1 activity. Here, we review what is currently understood about EWS::FLI1 activity, the cell autonomous and tumor microenvironmental factors that regulate it, and the downstream consequences of these activity states on tumor progression. We specifically highlight how transcription factor regulation, signaling pathway modulation, and the extracellular matrix intersect to create a complex network of tumor cell phenotypes. We propose that elucidation of the mechanisms by which these essential elements interact will enable the development of novel therapeutic approaches that are designed to target this complexity and ultimately improve patient outcomes.
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Kanojia D, Kirtonia A, Srujana NSV, Jeevanandan SP, Shyamsunder P, Sampath SS, Dakle P, Mayakonda A, Kaur H, Yanyi J, Koeffler HP, Garg M. Transcriptome analysis identifies TODL as a novel lncRNA associated with proliferation, differentiation, and tumorigenesis in liposarcoma through FOXM1 Running Title: TODL lncRNA as a potential therapeutic target for liposarcoma. Pharmacol Res 2022; 185:106462. [PMID: 36167276 DOI: 10.1016/j.phrs.2022.106462] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/14/2022] [Accepted: 09/19/2022] [Indexed: 11/15/2022]
Abstract
Liposarcoma, the most common soft tissue sarcoma, is a group of fat cell mesenchymal tumors with different histological subtypes. The dysregulation of long non-coding RNAs (lncRNAs) has been observed in human cancers including a few studies in sarcoma. However, the global transcriptome analysis and potential role of lncRNAs remain unexplored in liposarcoma. The present investigation uncovers the transcriptomic profile of liposarcoma by RNA sequencing to gain insight into the global transcriptional changes in liposarcoma. Our RNA sequencing analysis has identified that many oncogenic lncRNAs are differentially expressed in different subtypes of liposarcoma including MALAT1, PVT1, SNHG15, LINC00152, and MIR210HG. Importantly, we identified a highly overexpressed, unannotated, and novel lncRNA in dedifferentiated liposarcomas. We have named it TODL, transcript overexpressed in dedifferentiated liposarcoma. TODL lncRNA displayed significantly higher expression in dedifferentiated liposarcoma cell lines and patient samples. Interestingly, functional studies revealed that TODL lncRNA has an oncogenic function in liposarcoma cells by regulating proliferation, cell cycle, apoptosis, differentiation, and tumorigenesis in the murine model. Silencing of TODL lncRNA highlighted the enrichment of several key oncogenic signaling pathways including cell cycle, transcriptional misregulation, FOXM1 network, p53 signaling, PLK1 signaling, FoxO, and signaling Aurora signaling pathways. RNA pull-down assay revealed the binding of TODL lncRNA with FOXM1, an oncogenic transcription factor, and the key regulator of the cell cycle. Silencing of TODL lncRNA also induces adipogenesis in dedifferentiated liposarcomas. Altogether, our finding indicates that TODL could be utilized as a novel, specific diagnostic biomarker, and a pharmacological target for therapeutic development in controlling aggressive and metastatic dedifferentiated liposarcomas.
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Affiliation(s)
- Deepika Kanojia
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore.
| | - Anuradha Kirtonia
- Amity Institute of Molecular Medicine & Stem Cell Research (AIMMSCR), Amity University, Sector-125, Noida, Uttar Pradesh, 201313, India
| | | | | | - Pavithra Shyamsunder
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore
| | | | - Pushkar Dakle
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore
| | - Anand Mayakonda
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore; Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Harvinder Kaur
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore
| | - Jiang Yanyi
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore
| | - H Phillip Koeffler
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore; Division of Hematology/Oncology, Cedars-Sinai Medical Center, University of California, School of Medicine, Los Angeles, California, 90048, USA
| | - Manoj Garg
- Amity Institute of Molecular Medicine & Stem Cell Research (AIMMSCR), Amity University, Sector-125, Noida, Uttar Pradesh, 201313, India.
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Zooming in on Long Non-Coding RNAs in Ewing Sarcoma Pathogenesis. Cells 2022; 11:cells11081267. [PMID: 35455947 PMCID: PMC9032025 DOI: 10.3390/cells11081267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/29/2022] [Accepted: 04/06/2022] [Indexed: 11/16/2022] Open
Abstract
Ewing sarcoma (ES) is a rare aggressive cancer of bone and soft tissue that is mainly characterized by a reciprocal chromosomal translocation. As a result, about 90% of cases express the EWS-FLI1 fusion protein that has been shown to function as an aberrant transcription factor driving sarcomagenesis. ES is the second most common malignant bone tumor in children and young adults. Current treatment modalities include dose-intensified chemo- and radiotherapy, as well as surgery. Despite these strategies, patients who present with metastasis or relapse still have dismal prognosis, warranting a better understanding of treatment resistant-disease biology in order to generate better prognostic and therapeutic tools. Since the genomes of ES tumors are relatively quiet and stable, exploring the contributions of epigenetic mechanisms in the initiation and progression of the disease becomes inevitable. The search for novel biomarkers and potential therapeutic targets of cancer metastasis and chemotherapeutic drug resistance is increasingly focusing on long non-coding RNAs (lncRNAs). Recent advances in genome analysis by high throughput sequencing have immensely expanded and advanced our knowledge of lncRNAs. They are non-protein coding RNA species with multiple biological functions that have been shown to be dysregulated in many diseases and are emerging as crucial players in cancer development. Understanding the various roles of lncRNAs in tumorigenesis and metastasis would determine eclectic avenues to establish therapeutic and diagnostic targets. In ES, some lncRNAs have been implicated in cell proliferation, migration and invasion, features that make them suitable as relevant biomarkers and therapeutic targets. In this review, we comprehensively discuss known lncRNAs implicated in ES that could serve as potential biomarkers and therapeutic targets of the disease. Though some current reviews have discussed non-coding RNAs in ES, to our knowledge, this is the first review focusing exclusively on ES-associated lncRNAs.
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De Feo A, Pazzaglia L, Ciuffarin L, Mangiagli F, Pasello M, Simonetti E, Pellegrini E, Ferrari C, Bianchi G, Spazzoli B, Scotlandi K. miR-214-3p Is Commonly Downregulated by EWS-FLI1 and by CD99 and Its Restoration Limits Ewing Sarcoma Aggressiveness. Cancers (Basel) 2022; 14:cancers14071762. [PMID: 35406534 PMCID: PMC8997046 DOI: 10.3390/cancers14071762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/28/2022] [Accepted: 03/29/2022] [Indexed: 11/17/2022] Open
Abstract
Simple Summary Ewing’s sarcoma (EWS), the second most frequent primary tumor of bone in the pediatric population, is a very aggressive, undifferentiated mesenchymal malignancy with a high tendency to develop lung and/or bone metastasis. The prognosis of patients with metastasis remains dismal, and new strategies are needed to control the dissemination of EWS cells. EWS is driven by alterations induced by the EWS-FLI1 chimera which acts as an aberrant transcriptional factor that induces the complete reprograming of the gene expression. EWS cells are also characterized by high expression of CD99, a cell surface molecule that interacts with EWS-FLI1 to sustain EWS malignancy. This study shows that miR-214-3p is a common mediator of EWS-FLI1 and CD99, and we report that miR-214-3p acts as on oncosuppressor in EWS. MiR-214-3p is constitutively repressed in cell lines and clinical samples but is re-expressed after the silencing of EWS-FLI1 and/or CD99. The restoration of miR-214-3p limits EWS cell growth and migration and represses the expression of its target HMGA1, supporting the potential role of this miRNA as a marker of tumor aggressiveness. Abstract Ewing’s sarcoma (EWS), an aggressive pediatric bone and soft-tissue sarcoma, has a very stable genome with very few genetic alterations. Unlike in most cancers, the progression of EWS appears to depend on epigenetic alterations. EWS–FLI1 and CD99, the two hallmarks of EWS, are reported to severely impact the malignancy of EWS cells, at least partly by regulating the expression of several types of non-coding RNAs. Here, we identify miR-214-3p as a common mediator of either EWS-FLI1 or CD99 by in silico analysis. MiR-214-3p expression was lower in EWS cells and in clinical samples than in bone marrow mesenchymal stem cells, and this miRNA was barely expressed in metastatic lesions. Silencing of EWS-FLI1 or CD99 restored the expression of miR-214-3p, leading to a reduced cell growth and migration. Mechanistically, miR-214-3p restoration inhibits the expression of the high-mobility group AT-hook 1 (HMGA1) protein, a validated target of miR-214-3p and a major regulator of the transcriptional machinery. The decrease in HMGA1 expression reduced the growth and the migration of EWS cells. Taken together, our results support that the miR-214-3p is constitutively repressed by both EWS-FLI1 and CD99 because it acts as an oncosuppressor limiting the dissemination of EWS cells.
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Affiliation(s)
- Alessandra De Feo
- SSD Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano 1/10, 40136 Bologna, Italy; (L.P.); (L.C.); (F.M.); (M.P.); (E.S.); (E.P.); (C.F.)
- Correspondence: (A.D.F.); (K.S.); Tel.: +39-051-6366760 (K.S.); +39-051-6366937 (A.D.F.); Fax: +39-051-6366763 (A.D.F. & K.S.)
| | - Laura Pazzaglia
- SSD Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano 1/10, 40136 Bologna, Italy; (L.P.); (L.C.); (F.M.); (M.P.); (E.S.); (E.P.); (C.F.)
| | - Lisa Ciuffarin
- SSD Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano 1/10, 40136 Bologna, Italy; (L.P.); (L.C.); (F.M.); (M.P.); (E.S.); (E.P.); (C.F.)
| | - Fabio Mangiagli
- SSD Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano 1/10, 40136 Bologna, Italy; (L.P.); (L.C.); (F.M.); (M.P.); (E.S.); (E.P.); (C.F.)
| | - Michela Pasello
- SSD Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano 1/10, 40136 Bologna, Italy; (L.P.); (L.C.); (F.M.); (M.P.); (E.S.); (E.P.); (C.F.)
| | - Elisa Simonetti
- SSD Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano 1/10, 40136 Bologna, Italy; (L.P.); (L.C.); (F.M.); (M.P.); (E.S.); (E.P.); (C.F.)
| | - Evelin Pellegrini
- SSD Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano 1/10, 40136 Bologna, Italy; (L.P.); (L.C.); (F.M.); (M.P.); (E.S.); (E.P.); (C.F.)
| | - Cristina Ferrari
- SSD Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano 1/10, 40136 Bologna, Italy; (L.P.); (L.C.); (F.M.); (M.P.); (E.S.); (E.P.); (C.F.)
| | - Giuseppe Bianchi
- IRCCS Istituto Ortopedico Rizzoli, Third Orthopaedic Clinic and Traumatology, 40136 Bologna, Italy; (G.B.); (B.S.)
| | - Benedetta Spazzoli
- IRCCS Istituto Ortopedico Rizzoli, Third Orthopaedic Clinic and Traumatology, 40136 Bologna, Italy; (G.B.); (B.S.)
| | - Katia Scotlandi
- SSD Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano 1/10, 40136 Bologna, Italy; (L.P.); (L.C.); (F.M.); (M.P.); (E.S.); (E.P.); (C.F.)
- Correspondence: (A.D.F.); (K.S.); Tel.: +39-051-6366760 (K.S.); +39-051-6366937 (A.D.F.); Fax: +39-051-6366763 (A.D.F. & K.S.)
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