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Xiao W, Lai Y, Yang H, Que H. Predictive Role of a Novel Ferroptosis-Related lncRNA Pairs Model in the Prognosis of Papillary Thyroid Carcinoma. Biochem Genet 2024; 62:775-797. [PMID: 37436560 DOI: 10.1007/s10528-023-10447-0] [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: 02/27/2023] [Accepted: 06/29/2023] [Indexed: 07/13/2023]
Abstract
This study aimed to evaluate the potential prognostic value of ferroptosis-related long non-coding RNAs (lncRNAs) in papillary thyroid carcinoma (PTC). Based on The TCGA database, lncRNAs and ferroptosis-related genes with differential expression levels in PTC tumors vs. normal tissues were screened. After the co-expression network construction, ferroptosis-related lncRNAs (FRLs) were screened. Kaplan-Meier analysis was conducted to compare the survival performance of patients with PTC in the high- and low-risk groups. Furthermore, a nomogram was created to enhance PTC prognosis. CIBERSORT was used to investigate the infiltration of various immune cells in high- and low-risk groups. In total, 10 lncRNA pairs with differential expression levels were obtained. There were significant differences in the histological subtype and pathological stage between the high- and low-risk groups, and age (P = 7.39E-13) and FRLM model status (P = 1.09E-04) were identified as independent prognostic factors. Subsequently, the nomogram survival model showed that the predicted one-, three-, and five-year survival rates were similar to the actual one- (c-index = 0.8475), three- (c-index = 0.7964), and five-year (c-index = 0.7555) survival rates. Subjects in the low-risk group had significantly more CD4 + memory T cells and resting myeloid dendritic cells, and subjects in the high-risk group had more plasma B cells and monocytes. The risk assessment model constructed using FRLs showed good predictive value for the prognosis of patients with PTC.
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Affiliation(s)
- Wen Xiao
- Department of Traditional Chinese Surgery, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200032, China
| | - Yi Lai
- Department of Head and Neck Surgery, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, 200127, China
| | - Haojie Yang
- Department of Coloproctology, Yueyang Hospital of Integrated Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, No.1200, Cailun Road, Shanghai, 200032, China.
| | - Huafa Que
- Department of Traditional Chinese Surgery, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200032, China.
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Hadiatullah H, He Z, Yuchi Z. Structural Insight Into Ryanodine Receptor Channelopathies. Front Pharmacol 2022; 13:897494. [PMID: 35677449 PMCID: PMC9168041 DOI: 10.3389/fphar.2022.897494] [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: 03/16/2022] [Accepted: 05/09/2022] [Indexed: 11/28/2022] Open
Abstract
The ryanodine receptors (RyRs) are large cation-selective ligand-gated channels that are expressed in the sarcoplasmic reticulum (SR) membrane. They mediate the controlled release of Ca2+ from SR and play an important role in many cellular processes. The mutations in RyRs are associated with several skeletal muscle and cardiac conditions, including malignant hyperthermia (MH), central core disease (CCD), catecholaminergic polymorphic ventricular tachycardia (CPVT), and arrhythmogenic right ventricular dysplasia (ARVD). Recent breakthroughs in structural biology including cryo-electron microscopy (EM) and X-ray crystallography allowed the determination of a number of near-atomic structures of RyRs, including wildtype and mutant structures as well as the structures in complex with different modulating molecules. This allows us to comprehend the physiological gating and regulatory mechanisms of RyRs and the underlying pathological mechanisms of the disease-causing mutations. In this review, based on the insights gained from the available high-resolution structures of RyRs, we address several questions: 1) what are the gating mechanisms of different RyR isoforms; 2) how RyRs are regulated by multiple channel modulators, including ions, small molecules, and regulatory proteins; 3) how do disease-causing mutations affect the structure and function of RyRs; 4) how can these structural information aid in the diagnosis of the related diseases and the development of pharmacological therapies.
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Affiliation(s)
- Hadiatullah Hadiatullah
- Tianjin Key Laboratory for Modern Drug Delivery and High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
- Department of Molecular Pharmacology, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Zhao He
- Tianjin Key Laboratory for Modern Drug Delivery and High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
- Department of Molecular Pharmacology, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Zhiguang Yuchi
- Tianjin Key Laboratory for Modern Drug Delivery and High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
- Department of Molecular Pharmacology, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
- *Correspondence: Zhiguang Yuchi,
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Xu Z, Xiang L, Wang R, Xiong Y, Zhou H, Gu H, Wang J, Peng L. Bioinformatic Analysis of Immune Significance of RYR2 Mutation in Breast Cancer. BIOMED RESEARCH INTERNATIONAL 2021; 2021:8072796. [PMID: 34888385 PMCID: PMC8651385 DOI: 10.1155/2021/8072796] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 10/04/2021] [Indexed: 12/24/2022]
Abstract
BACKGROUND Currently, immunotherapy is widely used for breast cancer (BC) patients, and tumor mutation burden (TMB) is regarded as a valuable independent predictor of response to immunotherapy. However, specific gene mutations and their relationship with TMB and tumor-infiltrating immune cells in BC are not fully understood. METHODS Comprehensive bioinformatic analyses were performed using data from The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) datasets. Survival curves were analyzed via Kaplan-Meier analysis. Univariate and multivariate Cox regression analyses were used for prognosis analysis. Gene set enrichment analysis (GSEA) was performed to explore regulatory mechanisms and functions. The CIBERSORT algorithm was used to calculate the tumor-infiltrating immune cell fractions. RESULTS We analyzed somatic mutation data of BC from TCGA and ICGC datasets and found that 19 frequently mutated genes were reported in both cohorts, namely, SPTA1, TTN, MUC17, MAP3K1, CDH1, FAT3, SYNE1, FLG, HMCN1, RYR2 (ryanodine receptor 2), GATA3, MUC4, PIK3CA, KMT2C, TP53, PTEN, ZFHX4, MUC16, and USH2A. Among them, we observed that RYR2 mutation was significantly associated with higher TMB and better clinical prognosis. Moreover, GSEA revealed that RYR2 mutation-enriched signaling pathways were related to immune-associated pathways. Furthermore, based on the CIBERSORT algorithm, we found that RYR2 mutation enhanced the antitumor immune response by enriching CD8+ T cells, activated memory CD4+ T cells, and M1 macrophages. CONCLUSION RYR2 is frequently mutated in BC, and its mutation is related to increased TMB and promotes antitumor immunity; thus, RYR2 may serve as a valuable biomarker to predict the immune response.
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Affiliation(s)
- Zhiquan Xu
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China
| | - Ling Xiang
- Department of Clinical Nutrition, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China
| | - Rong Wang
- Department of Oncology, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai 519000, China
| | - Yongfu Xiong
- Department of Hepatobiliary Surgery, The Affiliated Hospital of North Sichuan Medical College, Sichuan 637000, China
| | - He Zhou
- Department of Gastrointestinal Surgery, The Affiliated Hospital of North Sichuan Medical College, Sichuan 637000, China
| | - Haitao Gu
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China
| | - Jijian Wang
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China
| | - Linglong Peng
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China
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Sharma A, Ramena GT, Elble RC. Advances in Intracellular Calcium Signaling Reveal Untapped Targets for Cancer Therapy. Biomedicines 2021; 9:1077. [PMID: 34572262 PMCID: PMC8466575 DOI: 10.3390/biomedicines9091077] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/15/2021] [Accepted: 07/18/2021] [Indexed: 02/07/2023] Open
Abstract
Intracellular Ca2+ distribution is a tightly regulated process. Numerous Ca2+ chelating, storage, and transport mechanisms are required to maintain normal cellular physiology. Ca2+-binding proteins, mainly calmodulin and calbindins, sequester free intracellular Ca2+ ions and apportion or transport them to signaling hubs needing the cations. Ca2+ channels, ATP-driven pumps, and exchangers assist the binding proteins in transferring the ions to and from appropriate cellular compartments. Some, such as the endoplasmic reticulum, mitochondria, and lysosomes, act as Ca2+ repositories. Cellular Ca2+ homeostasis is inefficient without the active contribution of these organelles. Moreover, certain key cellular processes also rely on inter-organellar Ca2+ signaling. This review attempts to encapsulate the structure, function, and regulation of major intracellular Ca2+ buffers, sensors, channels, and signaling molecules before highlighting how cancer cells manipulate them to survive and thrive. The spotlight is then shifted to the slow pace of translating such research findings into anticancer therapeutics. We use the PubMed database to highlight current clinical studies that target intracellular Ca2+ signaling. Drug repurposing and improving the delivery of small molecule therapeutics are further discussed as promising strategies for speeding therapeutic development in this area.
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Affiliation(s)
- Aarushi Sharma
- Department of Pharmacology and Simmons Cancer Institute, Southern Illinois University School of Medicine, Springfield, IL 62702, USA;
| | - Grace T. Ramena
- Department of Aquaculture, University of Arkansas, Pine Bluff, AR 71601, USA;
| | - Randolph C. Elble
- Department of Pharmacology and Simmons Cancer Institute, Southern Illinois University School of Medicine, Springfield, IL 62702, USA;
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Cui C, Zhang Y, Liu G, Zhang S, Zhang J, Wang X. Advances in the study of cancer metastasis and calcium signaling as potential therapeutic targets. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2021; 2:266-291. [PMID: 36046433 PMCID: PMC9400724 DOI: 10.37349/etat.2021.00046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 04/21/2021] [Indexed: 11/19/2022] Open
Abstract
Metastasis is still the primary cause of cancer-related mortality. However, the underlying mechanisms of cancer metastasis are not yet fully understood. Currently, the epithelial-mesenchymal transition, metabolic remodeling, cancer cell intercommunication and the tumor microenvironment including diverse stromal cells, are reported to affect the metastatic process of cancer cells. Calcium ions (Ca2+) are ubiquitous second messengers that manipulate cancer metastasis by affecting signaling pathways. Diverse transporter/pump/channel-mediated Ca2+ currents form Ca2+ oscillations that can be decoded by Ca2+-binding proteins, which are promising prognostic biomarkers and therapeutic targets of cancer metastasis. This paper presents a review of the advances in research on the mechanisms underlying cancer metastasis and the roles of Ca2+-related signals in these events.
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Affiliation(s)
- Chaochu Cui
- Henan Key Laboratory of Medical Tissue Regeneration, College of Basic Medical Sciences, Xinxiang Medical University, Xinxiang 453003, Henan, China
| | - Yongxi Zhang
- Department of Oncology, The Third Affiliated Hospital of Xinxiang Medical University, Xinxiang 453003, Henan, China
| | - Gang Liu
- Henan Key Laboratory of Medical Tissue Regeneration, College of Basic Medical Sciences, Xinxiang Medical University, Xinxiang 453003, Henan, China
| | - Shuhong Zhang
- Henan Key Laboratory of Medical Tissue Regeneration, College of Basic Medical Sciences, Xinxiang Medical University, Xinxiang 453003, Henan, China
| | - Jinghang Zhang
- Department of Pathology, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang 453003, Henan, China
| | - Xianwei Wang
- Henan Key Laboratory of Medical Tissue Regeneration, College of Basic Medical Sciences, Xinxiang Medical University, Xinxiang 453003, Henan, China
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Yu P, Cai X, Liang Y, Wang M, Yang W. Roles of NAD + and Its Metabolites Regulated Calcium Channels in Cancer. Molecules 2020; 25:molecules25204826. [PMID: 33092205 PMCID: PMC7587972 DOI: 10.3390/molecules25204826] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/11/2020] [Accepted: 10/16/2020] [Indexed: 02/08/2023] Open
Abstract
Nicotinamide adenine dinucleotide (NAD+) is an essential cofactor for redox enzymes, but also moonlights as a regulator for ion channels, the same as its metabolites. Ca2+ homeostasis is dysregulated in cancer cells and affects processes such as tumorigenesis, angiogenesis, autophagy, progression, and metastasis. Herein, we summarize the regulation of the most common calcium channels (TRPM2, TPCs, RyRs, and TRPML1) by NAD+ and its metabolites, with a particular focus on their roles in cancers. Although the mechanisms of NAD+ metabolites in these pathological processes are yet to be clearly elucidated, these ion channels are emerging as potential candidates of alternative targets for anticancer therapy.
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Affiliation(s)
- Peilin Yu
- Department of Toxicology, and Department of Medical Oncology of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, Zhejiang, China; (P.Y.); (Y.L.)
| | - Xiaobo Cai
- Department of Biophysics, and Department of Neurosurgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, Zhejiang, China;
| | - Yan Liang
- Department of Toxicology, and Department of Medical Oncology of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, Zhejiang, China; (P.Y.); (Y.L.)
| | - Mingxiang Wang
- BrioPryme Biologics, Inc., Hangzhou 310058, Zhejiang, China;
| | - Wei Yang
- Department of Biophysics, and Department of Neurosurgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, Zhejiang, China;
- Correspondence: ; Tel.: +86-571-8820-8713
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Zhai X, Sterea AM, El Hiani Y. Lessons from the Endoplasmic Reticulum Ca 2+ Transporters-A Cancer Connection. Cells 2020; 9:E1536. [PMID: 32599788 PMCID: PMC7349521 DOI: 10.3390/cells9061536] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 06/21/2020] [Accepted: 06/22/2020] [Indexed: 02/06/2023] Open
Abstract
Ca2+ is an integral mediator of intracellular signaling, impacting almost every aspect of cellular life. The Ca2+-conducting transporters located on the endoplasmic reticulum (ER) membrane shoulder the responsibility of constructing the global Ca2+ signaling landscape. These transporters gate the ER Ca2+ release and uptake, sculpt signaling duration and intensity, and compose the Ca2+ signaling rhythm to accommodate a plethora of biological activities. In this review, we explore the mechanisms of activation and functional regulation of ER Ca2+ transporters in the establishment of Ca2+ homeostasis. We also contextualize the aberrant alterations of these transporters in carcinogenesis, presenting Ca2+-based therapeutic interventions as a means to tackle malignancies.
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Affiliation(s)
- Xingjian Zhai
- Department of Physiology and Biophysics, Faculty of Medicine, Dalhousie University, Halifax, NS B3H 4R2, Canada;
| | | | - Yassine El Hiani
- Department of Physiology and Biophysics, Faculty of Medicine, Dalhousie University, Halifax, NS B3H 4R2, Canada;
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Chava S, Gupta R. Identification of the Mutational Landscape of Gynecological Malignancies. J Cancer 2020; 11:4870-4883. [PMID: 32626534 PMCID: PMC7330690 DOI: 10.7150/jca.46174] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 05/30/2020] [Indexed: 12/15/2022] Open
Abstract
Background: Cancer is a complex disease that arises from the accumulation of multiple genetic and non-genetic changes. Advances in sequencing technologies have allowed unbiased and global analysis of patient-derived tumor samples and the discovery of genetic and transcriptional changes in key genes and oncogenic pathways. That in turn has facilitated a better understanding of the underlying causes of cancer initiation and progression, resulting in new therapeutic targets. Methods: In our study, we have analyzed the mutational landscape of gynecological malignancies using datasets from The Cancer Genome Atlas (TCGA). We have also analyzed Oncomine datasets to establish the impact of their alteration on disease recurrence and survival of patients. Results: In this study, we analyzed a series of different gynecological malignancies for commonly occurring genetic and non-genetic alterations. These studies show that white women have higher incidence of gynecological malignancies. Furthermore, our study identified 16 genes that are altered at a frequency >10% among all of the gynecological malignancies and tumor suppressor TP53 is the most altered gene in these malignancies (>50% of the cases). The top 16 genes fall into the categories of either tumor suppressor or oncogenes and a subset of these genes are associated with poor prognosis, some affecting recurrence and survival of ovarian cancer patients. Conclusion: In sum, our study identified 16 major genes that are broadly mutated in a large majority of gynecological malignancies and in some cases predict survival and recurrence in patients with gynecological malignancies. We predict that the functional studies will determine their relative role in the initiation and progression of gynecological malignancies and also establish if some of them represents drug targets for anti-cancer therapy.
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Affiliation(s)
| | - Romi Gupta
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
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Danese A, Marchi S, Vitto VAM, Modesti L, Leo S, Wieckowski MR, Giorgi C, Pinton P. Cancer-Related Increases and Decreases in Calcium Signaling at the Endoplasmic Reticulum-Mitochondria Interface (MAMs). Rev Physiol Biochem Pharmacol 2020; 185:153-193. [PMID: 32789789 DOI: 10.1007/112_2020_43] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Endoplasmic reticulum (ER)-mitochondria regions are specialized subdomains called also mitochondria-associated membranes (MAMs). MAMs allow regulation of lipid synthesis and represent hubs for ion and metabolite signaling. As these two organelles can module both the amplitude and the spatiotemporal patterns of calcium (Ca2+) signals, this particular interaction controls several Ca2+-dependent pathways well known for their contribution to tumorigenesis, such as metabolism, survival, sensitivity to cell death, and metastasis. Mitochondria-mediated apoptosis arises from mitochondrial Ca2+ overload, permeabilization of the mitochondrial outer membrane, and the release of mitochondrial apoptotic factors into the cytosol. Decreases in Ca2+ signaling at the ER-mitochondria interface are being studied in depth as failure of apoptotic-dependent cell death is one of the predominant characteristics of cancer cells. However, some recent papers that linked MAMs Ca2+ crosstalk-related upregulation to tumor onset and progression have aroused the interest of the scientific community.In this review, we will describe how different MAMs-localized proteins modulate the effectiveness of Ca2+-dependent apoptotic stimuli by causing both increases and decreases in the ER-mitochondria interplay and, specifically, by modulating Ca2+ signaling.
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Affiliation(s)
- Alberto Danese
- Department of Medical Sciences, Laboratory for Technologies of Advanced Therapies (LTTA), University of Ferrara, Ferrara, Italy
| | - Saverio Marchi
- Department of Clinical and Molecular Sciences, Marche Polytechnic University, Ancona, Italy
| | - Veronica Angela Maria Vitto
- Department of Medical Sciences, Laboratory for Technologies of Advanced Therapies (LTTA), University of Ferrara, Ferrara, Italy
| | - Lorenzo Modesti
- Department of Medical Sciences, Laboratory for Technologies of Advanced Therapies (LTTA), University of Ferrara, Ferrara, Italy
| | - Sara Leo
- Department of Medical Sciences, Laboratory for Technologies of Advanced Therapies (LTTA), University of Ferrara, Ferrara, Italy
| | - Mariusz R Wieckowski
- Laboratory of Mitochondrial Biology and Metabolism, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Carlotta Giorgi
- Department of Medical Sciences, Laboratory for Technologies of Advanced Therapies (LTTA), University of Ferrara, Ferrara, Italy
| | - Paolo Pinton
- Department of Medical Sciences, Laboratory for Technologies of Advanced Therapies (LTTA), University of Ferrara, Ferrara, Italy.
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