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Smirnov A, Lena AM, Tosetti G, Yang X, Cappello A, Helmer Citterich M, Melino G, Candi E. Epigenetic priming of an epithelial enhancer by p63 and CTCF controls expression of a skin-restricted gene XP33. Cell Death Discov 2023; 9:446. [PMID: 38065940 PMCID: PMC10709559 DOI: 10.1038/s41420-023-01716-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/27/2023] [Accepted: 11/07/2023] [Indexed: 07/11/2024] Open
Abstract
The transcription factor p63 is a renowned master regulator of gene expression of stratified epithelia. While multiple proteins have been identified as p63 bona fide targets, little is known about non-coding RNAs (ncRNAs) whose transcription is controlled by p63. Here, we describe a skin-specific non-coding RNA XP33 as a novel target of p63. XP33 levels are increased during keratinocyte differentiation in vitro, while its depletion results in decreased expression of late cornified gene LCE2D. By using publicly available multi-omics data, we show that CTCF and p63 establish an epithelial enhancer to prime XP33 transcription in a tissue-restricted manner. XP33 promoter and enhancer form a chromatin loop exclusively in keratinocytes but not in other cell types. Moreover, the XP33 enhancer is occupied by differentiation-specific factors that control XP33 transcription. Altogether, we identify a tissue-specific non-coding RNA whose expression is epigenetically regulated by p63 and CTCF.
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Affiliation(s)
- Artem Smirnov
- Department of Experimental Medicine, Torvergata Oncoscience Research, University of Rome "Tor Vergata", via Montpellier 1, 00133, Rome, Italy
- Biochemistry Laboratory, Istituto Dermopatico Immacolata (IDI-IRCCS), 00166, Rome, Italy
| | - Anna Maria Lena
- Department of Experimental Medicine, Torvergata Oncoscience Research, University of Rome "Tor Vergata", via Montpellier 1, 00133, Rome, Italy
| | - Giulia Tosetti
- Department of Experimental Medicine, Torvergata Oncoscience Research, University of Rome "Tor Vergata", via Montpellier 1, 00133, Rome, Italy
| | - Xue Yang
- Department of Experimental Medicine, Torvergata Oncoscience Research, University of Rome "Tor Vergata", via Montpellier 1, 00133, Rome, Italy
- The Third Affiliated Hospital of Soochow University, Institutes for Translational Medicine, Soochow University, 215000, Suzhou, China
| | - Angela Cappello
- Department of Experimental Medicine, Torvergata Oncoscience Research, University of Rome "Tor Vergata", via Montpellier 1, 00133, Rome, Italy
- Interdisciplinary Department of Medicine University of Bari "Aldo Moro", 70124, Bari, Italy
| | - Manuela Helmer Citterich
- Biology Department, University of Rome "Tor Vergata", Via della Ricerca Scientifica, snc, 00133, Rome, Italy
| | - Gerry Melino
- Department of Experimental Medicine, Torvergata Oncoscience Research, University of Rome "Tor Vergata", via Montpellier 1, 00133, Rome, Italy
| | - Eleonora Candi
- Department of Experimental Medicine, Torvergata Oncoscience Research, University of Rome "Tor Vergata", via Montpellier 1, 00133, Rome, Italy.
- Biochemistry Laboratory, Istituto Dermopatico Immacolata (IDI-IRCCS), 00166, Rome, Italy.
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Xu X, Ju Y, Zhao X, Yang P, Zhu F, Fang B. SMG7-AS1 as a prognostic biomarker and predictor of immunotherapy responses for skin cutaneous melanoma. Genomics 2023; 115:110614. [PMID: 36931476 DOI: 10.1016/j.ygeno.2023.110614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 02/14/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2023]
Abstract
Skin cutaneous melanoma (SKCM) is the most life-threatening skin cancer and lacks early detection and effective treatment strategies. Many long noncoding RNAs are associated with the development of tumors and may serve as potential immunotherapeutic targets. In this study, microarray analysis was performed to screen for differentially expressed lncRNAs between SKCM and normal tissues, and SMG7-AS1 was identified as an upregulated lncRNA in SKCM. Subsequently, bioinformatic analysis revealed that dysregulation of SMG7-AS1 influences metastasis and immune infiltration. qRT-PCR of clinical samples demonstrated that the expression of SMG7-AS1 was higher in melanoma tissues. Flow cytometry showed that SMG7-AS1 plays a vital role in the cell cycle. Additionally, SMG7-AS1 was found to be associated with immunotherapy responses. To the best of our knowledge, this study is the first to report that SMG7-AS1 is associated with SKCM and may serve as a prognostic biomarker and predictor of immunotherapy responses in SKCM.
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Affiliation(s)
- Xuezheng Xu
- Department of Orthopaedics, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, People's Republic of China
| | - Yikun Ju
- Department of Plastic and Aesthetic (Burn) Surgery, The Second Xiangya Hospital, Central South University, Changsha 410011, People's Republic of China
| | - Xueheng Zhao
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Institute of Reproductive and Stem Cell Engineering, Central South University, Changsha 410078, People's Republic of China
| | - Pu Yang
- Department of Plastic and Aesthetic (Burn) Surgery, The Second Xiangya Hospital, Central South University, Changsha 410011, People's Republic of China
| | - Fang Zhu
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Institute of Reproductive and Stem Cell Engineering, Central South University, Changsha 410078, People's Republic of China
| | - Bairong Fang
- Department of Plastic and Aesthetic (Burn) Surgery, The Second Xiangya Hospital, Central South University, Changsha 410011, People's Republic of China.
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Ran Y, Yan Z, Huang M, Zhou S, Wu F, Wang M, Yang S, Zhang P, Huang X, Jiang B, Liang P. Severe Burn Injury Significantly Alters the Gene Expression and m6A Methylation Tagging of mRNAs and lncRNAs in Human Skin. J Pers Med 2023; 13:jpm13010150. [PMID: 36675811 PMCID: PMC9864918 DOI: 10.3390/jpm13010150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 01/02/2023] [Accepted: 01/05/2023] [Indexed: 01/15/2023] Open
Abstract
N6-methyladenosine (m6A) modulates RNA metabolism and functions in cell differentiation, tissue development, and immune response. After acute burns, skin wounds are highly susceptible to infection and poor healing. However, our understanding of the effect of burn injuries on m6A methylation and their potential mechanism is still limited. Human m6A-mRNA&lncRNA Epitranscriptomic microarray was used to obtain comprehensive mRNA and lncRNA transcriptome m6A profiling and gene expression patterns after burn injuries in human skin tissue. Bioinformatic and functional analyses were conducted to find molecular functions. Microarray profiling showed that 65 mRNAs and 39 lncRNAs were significantly hypermethylated; 5492 mRNAs and 754 lncRNAs were significantly hypomethylated. Notably, 3989 hypomethylated mRNAs were down-expressed and inhibited many wound healing biological processes and pathways including in the protein catabolic process and supramolecular fiber organization pathway; 39 hypermethylated mRNAs were up-expressed and influenced the cell surface receptor signaling pathway and inflammatory response. Moreover, we validated that m6A regulators (METTL14, METTL16, ALKBH5, FMR1, and HNRNPC) were significantly downregulated after burn injury which may be responsible for the alteration of m6A modification and gene expression. In summary, we found that homeostasis in the skin was disrupted and m6A modification may be a potential mechanism affecting trauma infection and wound healing.
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Affiliation(s)
- Yanqin Ran
- Department of Burns and Plastic Surgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Zhuoxian Yan
- Department of Burns and Plastic Surgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Mitao Huang
- Department of Burns and Plastic Surgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Situo Zhou
- Department of Burns and Plastic Surgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Fangqin Wu
- Department of Burns and Plastic Surgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Mengna Wang
- Department of Burns and Plastic Surgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Sifan Yang
- Department of Burns and Plastic Surgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Pihong Zhang
- Department of Burns and Plastic Surgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Xiaoyuan Huang
- Department of Burns and Plastic Surgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Bimei Jiang
- Department of Pathophysiology, Xiangya School of Medicine, Central South University, Changsha 410008, China
- Correspondence: (B.J.); (P.L.); Tel.: +86-0731-82355022 (B.J.); +86-13875858144 (P.L.)
| | - Pengfei Liang
- Department of Burns and Plastic Surgery, Xiangya Hospital, Central South University, Changsha 410008, China
- Correspondence: (B.J.); (P.L.); Tel.: +86-0731-82355022 (B.J.); +86-13875858144 (P.L.)
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Cui X, Huang X, Huang M, Zhou S, Guo L, Yu W, Duan M, Jiang B, Zeng J, Zhou J, Huang X, Liang P, Zhang P. miR-24-3p obstructs the proliferation and migration of HSFs after thermal injury by targeting PPAR-β and positively regulated by NF-κB. Exp Dermatol 2021; 31:841-853. [PMID: 34932851 DOI: 10.1111/exd.14517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 12/03/2021] [Accepted: 12/19/2021] [Indexed: 11/30/2022]
Abstract
Thermal injury repair is a complex process during which the maintenance of the proliferation and migration of human skin fibroblasts (HSFs) exert a crucial role. MicroRNAs have been proven to exert an essential function in repairing skin burns. This study delves into the regulatory effects of miR-24-3p on the migration and proliferation of HSFs that have sustained a thermal injury; thereby, providing deeper insight into thermal injury repair pathogenesis. The PPAR-β protein expression level progressively increased in a time-dependent manner on the 12th , 24th , and 48th hour following the thermal injury of the HSFs. The knockdown of PPAR-β markedly suppressed the proliferation of and migration of HSF. Following thermal injury, the knockdown also promoted the inflammatory cytokine IL-6, TNF-, PTGS-2, and P65 expression. PPAR-β contrastingly exhibited an opposite trend. A targeted relationship between PPAR-β and miR-24-3p was predicted and verified. miR-24-3p inhibited thermal injured-HSFs proliferation and migration and facilitated inflammatory cytokine expression through the regulation of PPAR-β. p65 directly targeted the transcriptional precursor of miR-24 and promoted miR-24 expression. A negative correlation between miR-24-3p expression level and PPAR-β expression level in rats burnt dermal tissues was observed. Our findings reveal that miR-24-3p is conducive to rehabilitating the denatured dermis, which may be beneficial in providing effective therapy of skin burns.
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Affiliation(s)
- Xu Cui
- Department of Burns and Plastic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P. R. China
| | - Xu Huang
- Department of Hyperbaric Oxygen, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P. R. China
| | - Mitao Huang
- Department of Burns and Plastic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P. R. China
| | - Situo Zhou
- Department of Burns and Plastic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P. R. China
| | - Le Guo
- Department of Burns and Plastic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P. R. China
| | - Wenchang Yu
- Department of Burns and Plastic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P. R. China
| | - Mengting Duan
- Department of Burns and Plastic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P. R. China
| | - Bimei Jiang
- Department of Pathophysiology, Xiangya School of Medicine, Central South University, Changsha, Hunan, 410008, P. R. China
| | - Jizhang Zeng
- Department of Burns and Plastic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P. R. China
| | - Jie Zhou
- Department of Burns and Plastic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P. R. China
| | - Xiaoyuan Huang
- Department of Burns and Plastic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P. R. China
| | - Pengfei Liang
- Department of Burns and Plastic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P. R. China
| | - Pihong Zhang
- Department of Burns and Plastic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P. R. China
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Luo J, You H, Zhan J, Guo G, Cheng X, Zheng G. Long non-coding RNA TPT1-AS1 alleviates cell injury and promotes the production of extracellular matrix by targeting the microRNA-324-5p/CDK16 axis in human dermal fibroblasts after thermal injury. Exp Ther Med 2021; 22:843. [PMID: 34149889 PMCID: PMC8210258 DOI: 10.3892/etm.2021.10275] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 04/30/2021] [Indexed: 12/14/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are associated with the healing of burn wounds in the dermis. The present study aimed to probe the role and regulatory network of the lncRNA TPT1 antisense RNA 1 (TPT1-AS1) in human dermal fibroblasts (HDFs) following thermal injury. A model of thermally injured cells was constructed with HDFs. The levels of TPT1-AS1, microRNA (miR)-324-5p and cyclin-dependent kinase (CDK)16 were determined through reverse transcription-quantitative PCR. Cell viability, cell cycle distribution, cell apoptosis rate and extracellular matrix (ECM) synthesis were assessed with a series of in vitro gain-of-function experiments and MTT, flow cytometry and western blot analyses. The binding ability of miR-324-5p and TPT1-AS1 (or the 3' untranslated region of CDK16) was identified via bioinformatics analysis and luciferase reporter assay. It was found that TPT1-AS1 and CDK16 were downregulated, but miR-324-5p was upregulated, in the HDFs after thermal injury. TPT1-AS1 elevation induced cell viability and ECM synthesis but attenuated cell cycle arrest at the G0/G1 stage and decreased the cell apoptosis rate of thermally injured HDFs. In addition, TPT1-AS1 sponged miR-324-5p to modulate CDK16 expression. Moreover, silencing CDK16 weakened the impacts of TPT1-AS1 upregulation on cell function and ECM synthesis in heat-treated HDFs. In summary, TPT1-AS1 relieved cell injury and induced ECM synthesis by sponging miR-324-5p and targeting CDK16 in the HDFs after thermal injury, implying a protective role for TPT1-AS1 in the burn wound healing process.
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Affiliation(s)
- Jinhua Luo
- Department of Burns, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Haoyuan You
- Department of Burns, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Jianhua Zhan
- Department of Burns, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Guanghua Guo
- Department of Burns, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Xing Cheng
- Department of Burns, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Guoyu Zheng
- Department of Burns, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
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Sahlén P, Spalinskas R, Asad S, Mahapatra KD, Höjer P, Anil A, Eisfeldt J, Srivastava A, Nikamo P, Mukherjee A, Kim KH, Bergman O, Ståhle M, Sonkoly E, Pivarcsi A, Wahlgren CF, Nordenskjöld M, Taylan F, Bradley M, Tapia-Páez I. Chromatin interactions in differentiating keratinocytes reveal novel atopic dermatitis- and psoriasis-associated genes. J Allergy Clin Immunol 2020; 147:1742-1752. [PMID: 33069716 DOI: 10.1016/j.jaci.2020.09.035] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 08/14/2020] [Accepted: 09/17/2020] [Indexed: 12/30/2022]
Abstract
BACKGROUND Hundreds of variants associated with atopic dermatitis (AD) and psoriasis, 2 common inflammatory skin disorders, have previously been discovered through genome-wide association studies (GWASs). The majority of these variants are in noncoding regions, and their target genes remain largely unclear. OBJECTIVE We sought to understand the effects of these noncoding variants on the development of AD and psoriasis by linking them to the genes that they regulate. METHODS We constructed genomic 3-dimensional maps of human keratinocytes during differentiation by using targeted chromosome conformation capture (Capture Hi-C) targeting more than 20,000 promoters and 214 GWAS variants and combined these data with transcriptome and epigenomic data sets. We validated our results with reporter assays, clustered regularly interspaced short palindromic repeats activation, and examination of patient gene expression from previous studies. RESULTS We identified 118 target genes of 82 AD and psoriasis GWAS variants. Differential expression of 58 of the 118 target genes (49%) occurred in either AD or psoriatic lesions, many of which were not previously linked to any skin disease. We highlighted the genes AFG1L, CLINT1, ADO, LINC00302, and RP1-140J1.1 and provided further evidence for their potential roles in AD and psoriasis. CONCLUSIONS Our work focused on skin barrier pathology through investigation of the interaction profile of GWAS variants during keratinocyte differentiation. We have provided a catalogue of candidate genes that could modulate the risk of AD and psoriasis. Given that only 35% of the target genes are the gene nearest to the known GWAS variants, we expect that our work will contribute to the discovery of novel pathways involved in AD and psoriasis.
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Affiliation(s)
- Pelin Sahlén
- KTH Royal Institute of Technology, School of Chemistry, Biotechnology and Health, Science for Life Laboratory, Stockholm, Sweden.
| | - Rapolas Spalinskas
- KTH Royal Institute of Technology, School of Chemistry, Biotechnology and Health, Science for Life Laboratory, Stockholm, Sweden
| | - Samina Asad
- Dermatology and Venereology Division, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Kunal Das Mahapatra
- Dermatology and Venereology Division, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Pontus Höjer
- KTH Royal Institute of Technology, School of Chemistry, Biotechnology and Health, Science for Life Laboratory, Stockholm, Sweden
| | - Anandashankar Anil
- KTH Royal Institute of Technology, School of Chemistry, Biotechnology and Health, Science for Life Laboratory, Stockholm, Sweden
| | - Jesper Eisfeldt
- Department of Molecular Medicine and Surgery Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Ankit Srivastava
- Dermatology and Venereology Division, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Pernilla Nikamo
- Dermatology and Venereology Division, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Anaya Mukherjee
- Dermatology and Venereology Division, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Kyu-Han Kim
- Basic Research and Innovation Division, Research and Development Unit, AmorePacific Corporation, Yongin-si, Korea
| | - Otto Bergman
- Division of Cardiovascular Medicine, Center for Molecular Medicine, Department of Medicine Solna, Karolinska Institutet, Stockholm, Karolinska University Hospital, Solna, Sweden
| | - Mona Ståhle
- Dermatology and Venereology Division, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Enikö Sonkoly
- Dermatology and Venereology Division, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden; Dermatology Unit, Karolinska University Hospital, Stockholm, Sweden; Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Andor Pivarcsi
- Dermatology and Venereology Division, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden; Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden; Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Carl-Fredrik Wahlgren
- Dermatology and Venereology Division, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Magnus Nordenskjöld
- Department of Molecular Medicine and Surgery Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Fulya Taylan
- Department of Molecular Medicine and Surgery Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Maria Bradley
- Dermatology and Venereology Division, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden; Dermatology Unit, Karolinska University Hospital, Stockholm, Sweden
| | - Isabel Tapia-Páez
- Dermatology and Venereology Division, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
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