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Niba ETE, Nishio H, Wijaya YOS, Ar Rochmah M, Takarada T, Takeuchi A, Kimizu T, Okamoto K, Saito T, Awano H, Takeshima Y, Shinohara M. Stability and Oligomerization of Mutated SMN Protein Determine Clinical Severity of Spinal Muscular Atrophy. Genes (Basel) 2022; 13:genes13020205. [PMID: 35205250 PMCID: PMC8872419 DOI: 10.3390/genes13020205] [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] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/18/2022] [Accepted: 01/20/2022] [Indexed: 12/10/2022] Open
Abstract
Spinal muscular atrophy (SMA) is a common autosomal recessive neuromuscular disease characterized by defects of lower motor neurons. Approximately 95% of SMA patients are homozygous for survival motor neuron 1 (SMN1) gene deletion, while ~5% carry an intragenic SMN1 mutation. Here, we investigated the stability and oligomerization ability of mutated SMN1 proteins. Plasmids containing wild- and mutant-type SMN1 cDNA were constructed and transfected into HeLa cells. Reverse transcription-polymerase chain reaction (RT-PCR) demonstrated similar abundances of transcripts from the plasmids containing SMN cDNA, but Western blotting showed different expression levels of mutated SMN1 proteins, reflecting the degree of their instability. A mutated SMN1 protein with T274YfsX32 exhibited a much lower expression level than other mutated SMN1 proteins with E134K, Y276H, or Y277C. In immunoprecipitation analysis, the mutated SMN1 protein with T274YfsX32 did not bind to endogenous SMN1 protein in HeLa cells, suggesting that this mutation completely blocks the oligomerization with full-length SMN2 protein in the patient. The patient with T274YfsX32 showed a much more severe phenotype than the other patients with different mutations. In conclusion, the stability and oligomerization ability of mutated SMN1 protein may determine the protein stability and may be associated with the clinical severity of SMA caused by intragenic SMN1 mutation.
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Affiliation(s)
- Emma Tabe Eko Niba
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Hyogo, Japan; (E.T.E.N.); (Y.O.S.W.); (M.S.)
| | - Hisahide Nishio
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Hyogo, Japan; (E.T.E.N.); (Y.O.S.W.); (M.S.)
- Department of Occupational Therapy, Faculty of Rehabilitation, Kobe Gakuin University, 518 Arise, Ikawadani-cho, Nishi-ku, Kobe 651-2180, Hyogo, Japan
- Correspondence: ; Tel.: +81-789-745-073
| | - Yogik Onky Silvana Wijaya
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Hyogo, Japan; (E.T.E.N.); (Y.O.S.W.); (M.S.)
| | - Mawaddah Ar Rochmah
- Department of Neurology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Jalan Farmako, Sekip Utara, Yogyakarta 55281, Indonesia;
| | - Toru Takarada
- Laboratory of Functional Molecular Chemistry, Kobe Pharmaceutical University, 4-19-1 Motoyamakitamachi, Higashinada-ku, Kobe 658-8558, Hyogo, Japan;
| | - Atsuko Takeuchi
- Instrumental Analysis Center, Kobe Pharmaceutical University, 4-19-1 Motoyamakitamachi, Higashinada-ku, Kobe 658-8558, Hyogo, Japan;
| | - Tomokazu Kimizu
- Department of Pediatric Neurology, Osaka Women’s and Children’s Hospital, 840 Murodo-cho, Izumi 594-1101, Osaka, Japan;
| | - Kentaro Okamoto
- Department of Pediatrics, Ehime Prefectural Imabari Hospital, 4-5-5 Ishii-cho, Imabari 794-0006, Ehime, Japan;
| | - Toshio Saito
- Department of Neurology, National Hospital Organization Osaka Toneyama Medical Center, 5-1-1 Toneyama, Toyonaka 560-8552, Osaka, Japan;
| | - Hiroyuki Awano
- Department of Pediatrics, Kobe University Graduate School of Medicine, 7-5-2 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Hyogo, Japan;
| | - Yasuhiro Takeshima
- Department of Pediatrics, Hyogo College of Medicine, 1-1 Mukogawa-cho, Nishinomiya 663-8501, Hyogo, Japan;
| | - Masakazu Shinohara
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Hyogo, Japan; (E.T.E.N.); (Y.O.S.W.); (M.S.)
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Wijaya YOS, Ar Rohmah M, Niba ETE, Morisada N, Noguchi Y, Hidaka Y, Ozasa S, Inoue T, Shimazu T, Takahashi Y, Tozawa T, Chiyonobu T, Inoue T, Shiroshita T, Yokoyama A, Okamoto K, Awano H, Takeshima Y, Saito T, Saito K, Nishio H, Shinohara M. Phenotypes of SMA patients retaining SMN1 with intragenic mutation. Brain Dev 2021; 43:745-758. [PMID: 33892995 DOI: 10.1016/j.braindev.2021.03.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 03/17/2021] [Accepted: 03/21/2021] [Indexed: 01/09/2023]
Abstract
BACKGROUND Spinal muscular atrophy (SMA) is an autosomal recessive neuromuscular disorder caused by homozygous deletion or intragenic mutation of the SMN1 gene. It is well-known that high copy number of its homologous gene, SMN2, modifies the phenotype of SMN1-deleted patients. However, in the patients with intragenic SMN1 mutation, the relationship between phenotype and SMN2 copy number remains unclear. METHODS We have analyzed a total of 515 Japanese patients with SMA-like symptoms (delayed developmental milestones, respiratory failures, muscle weakness etc.) from 1996 to 2019. SMN1 and SMN2 copy numbers were determined by quantitative polymerase chain reaction (PCR) method and/or multiplex ligation-dependent probe amplification (MLPA) method. Intragenic SMN1 mutations were identified through DNA and RNA analysis of the fresh blood samples. RESULTS A total of 241 patients were diagnosed as having SMA. The majority of SMA patients showed complete loss of SMN1 (n = 228, 95%), but some patients retained SMN1 and carried an intragenic mutation in the retaining SMN1 (n = 13, 5%). Ten different mutations were identified in these 13 patients, consisting of missense, nonsense, frameshift and splicing defect-causing mutations. The ten mutations were c.275G > C (p.Trp92Ser), c.819_820insT (p.Thr274Tyrfs*32), c.830A > G (p.Tyr277Cys), c.5C > T (p.Ala2Val), c.826 T > C (p.Tyr276His), c.79C > T (p.Gln27*), c.188C > A (p.Ser63*), c.422 T > C (p.Leu141Pro), c.835-2A > G (exon 7 skipping) and c.835-3C > A (exon 7 skipping). It should be noted here that some patients with milder phenotype carried only a single SMN2 copy (n = 3), while other patients with severe phenotype carried 3 SMN2 copies (n = 4). CONCLUSION Intragenic mutations in SMN1 may contribute more significantly to clinical severity than SMN2 copy numbers.
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Affiliation(s)
- Yogik Onky Silvana Wijaya
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe, Japan.
| | - Mawaddah Ar Rohmah
- Department of Neurology, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia.
| | - Emma Tabe Eko Niba
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe, Japan.
| | - Naoya Morisada
- Department of Clinical Genetics, Hyogo Prefectural Kobe Children's Hospital, Kobe, Japan.
| | - Yoriko Noguchi
- Department of Clinical Laboratory, Kobe University Hospital, Kobe, Japan.
| | - Yasufumi Hidaka
- Department of Pediatrics, Kitakyushu Municipal Medical Center, Kitakyushu, Japan.
| | - Shiro Ozasa
- Department of Pediatrics, Kumamoto University, Kumamoto, Japan.
| | - Takeshi Inoue
- Department of Neonatology, Kumamoto City Hospital, Kumamoto, Japan.
| | - Tomoyuki Shimazu
- Department of Pediatrics, National Hospital Organization Kumamoto Saishunso Hospital, Kumamoto, Japan.
| | - Yuya Takahashi
- Department of Pediatrics, Nagaoka Red Cross Hospital, Nagaoka, Japan.
| | - Takenori Tozawa
- Department of Pediatrics, Kyoto Prefectural University of Medicine, Kyoto, Japan.
| | - Tomohiro Chiyonobu
- Department of Pediatrics, Kyoto Prefectural University of Medicine, Kyoto, Japan.
| | - Takushi Inoue
- Department of Pediatrics, National Hospital Organization Okayama Medical Center, Okayama, Japan.
| | | | - Atsushi Yokoyama
- Department of Pediatrics, Kyoto University Graduate School of Medicine, Kyoto, Japan.
| | - Kentaro Okamoto
- Department of Pediatrics, Ehime Prefectural Imabari Hospital, Imabari, Japan.
| | - Hiroyuki Awano
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan.
| | - Yasuhiro Takeshima
- Department of Pediatrics, Hyogo College of Medicine, Nishinomiya, Japan.
| | - Toshio Saito
- Division of Child Neurology, Department of Neurology, National Hospital Organization Osaka Toneyama Medical Center, Toyonaka, Japan.
| | - Kayoko Saito
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan.
| | - Hisahide Nishio
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe, Japan; Faculty of Medical Rehabilitation, Kobe Gakuin University, Kobe, Japan.
| | - Masakazu Shinohara
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe, Japan.
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Harahap NIF, Niba ETE, Ar Rochmah M, Wijaya YOS, Saito T, Saito K, Awano H, Morioka I, Iijima K, Lai PS, Matsuo M, Nishio H, Shinohara M. Intron-retained transcripts of the spinal muscular atrophy genes, SMN1 and SMN2. Brain Dev 2018; 40:670-677. [PMID: 29580671 DOI: 10.1016/j.braindev.2018.03.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 03/02/2018] [Accepted: 03/04/2018] [Indexed: 11/24/2022]
Abstract
BACKGROUND The SMN genes, SMN1 and SMN2, are highly homologous genes which are related to the development or clinical severity of spinal muscular atrophy. Some alternative splicing patterns of the SMN genes have been well documented. In 2007, an SMN1 transcript with a full sequence of intron 3 was reported as the first intron-retained SMN transcript. METHODS Intron-retained SMN transcripts in various cells and tissues were studied using reverse transcription (RT)-PCR. HeLa cells were used for subcellular localization of the transcripts and protein expression analysis with Western blotting. RESULTS Two intron-retained SMN transcripts were detected, which contain full sequences of intron 2b or intron 3. These transcripts were produced from SMN1 and SMN2, and ubiquitously expressed in human cells and tissues. Western blotting analysis showed no proteins derived from the intron-retained transcripts. Fractionation analysis showed that these intron-retained transcripts were localized mainly in the nucleus. Contrary to our expectation, the intron-retained transcript levels decreased during the treatment of cycloheximide, an inhibitor of nonsense-mediated decay (NMD), suggesting that they were not targets of NMD. CONCLUSION Intron 2b-retained SMN transcript and intron3-retained SMN transcript were ubiquitously expressed in human cells and tissues. The intron-retained transcripts were mainly localized in the nucleus and decreased through non-NMD pathway.
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Affiliation(s)
- Nur Imma Fatimah Harahap
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan; Department of Clinical Pathology, Faculty of Medicine, Universitas Gadjah Mada, Radiopoetro Building 5th Floor, Jl. Farmako, Sekip Utara, Yogyakarta 55281, Indonesia
| | - Emma Tabe Eko Niba
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan
| | - Mawaddah Ar Rochmah
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan; Department of Neurology, Faculty of Medicine, Universitas Gadjah Mada, Jl. Kesehatan No.1, Sekip, Yogyakarta 55281, Indonesia
| | - Yogik Onky Silvana Wijaya
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan
| | - Toshio Saito
- Department of Neurology, National Hospital Organization Toneyama National Hospital, Toneyama 5-1-1, Toyonaka, Osaka 560-8552, Japan
| | - Kayoko Saito
- Institute of Medical Genetics, School of Medicine, Tokyo Women's Medical University, 8-1 Kawadacho, Shinjuku-ku, Tokyo 162-8666, Japan
| | - Hiroyuki Awano
- Department of Pediatrics, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan
| | - Ichiro Morioka
- Department of Pediatrics, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan
| | - Kazumoto Iijima
- Department of Pediatrics, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan
| | - Poh San Lai
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Road, NUHS Tower Block, Level 12, 119228, Singapore
| | - Masafumi Matsuo
- Department of Physical Therapy, Faculty of Rehabilitation, Kobe Gakuin University, 518 Arise, Ikawadani, Nishi, Kobe 6512180, Japan
| | - Hisahide Nishio
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan.
| | - Masakazu Shinohara
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan
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Takarada T, Ar Rochmah M, Harahap NIF, Shinohara M, Saito T, Saito K, Lai PS, Bouike Y, Takeshima Y, Awano H, Morioka I, Iijima K, Nishio H, Takeuchi A. SMA mutations in SMN Tudor and C-terminal domains destabilize the protein. Brain Dev 2017; 39:606-612. [PMID: 28366534 DOI: 10.1016/j.braindev.2017.03.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 02/27/2017] [Accepted: 03/03/2017] [Indexed: 10/19/2022]
Abstract
BACKGROUND AND PURPOSE Most spinal muscular atrophy (SMA) patients are homozygous for survival of motor neuron 1 gene (SMN1) deletion. However, some SMA patients carry an intragenic SMN1 mutation. Such patients provide a clue to understanding the function of the SMN protein and the role of each domain of the protein. We previously identified mutations in the Tudor domain and C-terminal region of the SMN protein in three Japanese SMA patients. To clarify the effect of these mutations on protein stability, we conducted expression assays of SMN with mutated domains. PATIENTS AND METHODS Patients A and B carried a mutation in SMN1 exon 3, which encodes a Tudor domain, c.275G>C (p.Trp92Ser). Patient C carried a mutation in SMN1 exon 6, which encodes a YG-box; c.819_820insT (p.Thr274Tyrfs). We constructed plasmid expression vectors containing wild-type and mutant SMN1 cDNAs. After transfection of HeLa cells with the expression plasmids, RNA and protein were isolated and analyzed by reverse-transcription PCR and western blot analysis. RESULTS The abundance of wild-type and mutant SMN1 transcripts in HeLa cells was almost the same. However, western blot analysis showed lower levels of mutant SMN proteins compared with wild-type SMN. In mutant SMN proteins, it is noteworthy that the level of the p.Thr274Tyrfs mutant was much reduced compared with that of the p.Trp92Ser mutant. CONCLUSIONS SMN mutations may affect the stability and levels of the protein.
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Affiliation(s)
- Toru Takarada
- Analytical Laboratory, Kobe Pharmaceutical University, Kobe, Japan
| | - Mawaddah Ar Rochmah
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Nur Imma Fatimah Harahap
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Masakazu Shinohara
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Toshio Saito
- Department of Neurology, Toneyama National Hospital, Osaka, Japan
| | - Kayoko Saito
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan
| | - Poh San Lai
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | | | - Hiroyuki Awano
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Ichiro Morioka
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Kazumoto Iijima
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Hisahide Nishio
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe, Japan; Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan.
| | - Atsuko Takeuchi
- Analytical Laboratory, Kobe Pharmaceutical University, Kobe, Japan
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Locatelli D, Terao M, Kurosaki M, Zanellati MC, Pletto DR, Finardi A, Colciaghi F, Garattini E, Battaglia GS. Different Stability and Proteasome-Mediated Degradation Rate of SMN Protein Isoforms. PLoS One 2015. [PMID: 26214005 PMCID: PMC4516248 DOI: 10.1371/journal.pone.0134163] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The key pathogenic steps leading to spinal muscular atrophy (SMA), a genetic disease characterized by selective motor neuron degeneration, are not fully clarified. The full-length SMN protein (FL-SMN), the main protein product of the disease gene SMN1, plays an established role in the cytoplasm in snRNP biogenesis ultimately leading to mRNA splicing within the nucleus. It is also involved in the mRNA axonal transport. However, to what extent the impairment of these two SMN functions contributes to SMA pathogenesis remains unknown. A shorter SMN isoform, axonal-SMN or a-SMN, with more specific axonal localization, has been discovered, but whether it might act in concert with FL-SMN in SMA pathogenesis is not known. As a first step in defining common or divergent intracellular roles of FL-SMN vs a-SMN proteins, we here characterized the turn-over of both proteins and investigated which pathway contributed to a-SMN degradation. We performed real time western blot and confocal immunofluorescence analysis in easily controllable in vitro settings. We analyzed co-transfected NSC34 and HeLa cells and cell clones stably expressing both a-SMN and FL-SMN proteins after specific blocking of transcript or protein synthesis and inhibition of known intracellular degradation pathways. Our data indicated that whereas the stability of both FL-SMN and a-SMN transcripts was comparable, the a-SMN protein was characterized by a much shorter half-life than FL-SMN. In addition, as already demonstrated for FL-SMN, the Ub/proteasome pathway played a major role in the a-SMN protein degradation. We hypothesize that the faster degradation rate of a-SMN vs FL-SMN is related to the protection provided by the protein complex in which FL-SMN is assembled. The diverse a-SMN vs FL-SMN C-terminus may dictate different protein interactions and complex formation explaining the different localization and role in the neuronal compartment, and the lower expression and stability of a-SMN.
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Affiliation(s)
- Denise Locatelli
- Molecular Neuroanatomy and Pathogenesis Unit, IRCCS Neurological Institute “C. Besta”, Milano, Italy
- * E-mail:
| | - Mineko Terao
- Laboratory of Molecular Biology, IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", Milano, Italy
| | - Mami Kurosaki
- Laboratory of Molecular Biology, IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", Milano, Italy
| | - Maria Clara Zanellati
- Molecular Neuroanatomy and Pathogenesis Unit, IRCCS Neurological Institute “C. Besta”, Milano, Italy
| | - Daniela Rita Pletto
- Molecular Neuroanatomy and Pathogenesis Unit, IRCCS Neurological Institute “C. Besta”, Milano, Italy
| | - Adele Finardi
- Molecular Neuroanatomy and Pathogenesis Unit, IRCCS Neurological Institute “C. Besta”, Milano, Italy
| | - Francesca Colciaghi
- Molecular Neuroanatomy and Pathogenesis Unit, IRCCS Neurological Institute “C. Besta”, Milano, Italy
| | - Enrico Garattini
- Laboratory of Molecular Biology, IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", Milano, Italy
| | - Giorgio Stefano Battaglia
- Molecular Neuroanatomy and Pathogenesis Unit, IRCCS Neurological Institute “C. Besta”, Milano, Italy
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