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Fanara S, Schloesser M, Joris M, De Franco S, Vandevenne M, Kerff F, Hanikenne M, Motte P. The Arabidopsis SR45 splicing factor bridges the splicing machinery and the exon-exon junction complex. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2280-2298. [PMID: 38180875 DOI: 10.1093/jxb/erae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 01/04/2024] [Indexed: 01/07/2024]
Abstract
The Arabidopsis splicing factor serine/arginine-rich 45 (SR45) contributes to several biological processes. The sr45-1 loss-of-function mutant exhibits delayed root development, late flowering, unusual numbers of floral organs, shorter siliques with decreased seed sets, narrower leaves and petals, and altered metal distribution. SR45 bears a unique RNA recognition motif (RRM) flanked by one serine/arginine-rich (RS) domain on both sides. Here, we studied the function of each SR45 domains by examining their involvement in: (i) the spatial distribution of SR45; (ii) the establishment of a protein-protein interaction network including spliceosomal and exon-exon junction complex (EJC) components; and (iii) the RNA binding specificity. We report that the endogenous SR45 promoter is active during vegetative and reproductive growth, and that the SR45 protein localizes in the nucleus. We demonstrate that the C-terminal arginine/serine-rich domain is a determinant of nuclear localization. We show that the SR45 RRM domain specifically binds purine-rich RNA motifs via three residues (H101, H141, and Y143), and is also involved in protein-protein interactions. We further show that SR45 bridges both mRNA splicing and surveillance machineries as a partner of EJC core components and peripheral factors, which requires phosphoresidues probably phosphorylated by kinases from both the CLK and SRPK families. Our findings provide insights into the contribution of each SR45 domain to both spliceosome and EJC assemblies.
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Affiliation(s)
- Steven Fanara
- InBioS-PhytoSystems, Functional Genomics and Plant Molecular Imaging, University of Liège, 4000, Liège, Belgium
| | - Marie Schloesser
- InBioS-PhytoSystems, Functional Genomics and Plant Molecular Imaging, University of Liège, 4000, Liège, Belgium
| | - Marine Joris
- InBioS-PhytoSystems, Functional Genomics and Plant Molecular Imaging, University of Liège, 4000, Liège, Belgium
| | - Simona De Franco
- InBioS-Center for Protein Engineering, Laboratory of Biological Macromolecules, University of Liège, 4000, Liège, Belgium
| | - Marylène Vandevenne
- InBioS-Center for Protein Engineering, Laboratory of Biological Macromolecules, University of Liège, 4000, Liège, Belgium
| | - Frédéric Kerff
- InBioS-Center for Protein Engineering, Laboratory of Crystallography, University of Liège, 4000, Liège, Belgium
| | - Marc Hanikenne
- InBioS-PhytoSystems, Translational Plant Biology, University of Liège, 4000, Liège, Belgium
| | - Patrick Motte
- InBioS-PhytoSystems, Functional Genomics and Plant Molecular Imaging, University of Liège, 4000, Liège, Belgium
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Kornienko J, Rodríguez-Martínez M, Fenzl K, Hinze F, Schraivogel D, Grosch M, Tunaj B, Lindenhofer D, Schraft L, Kueblbeck M, Smith E, Mao C, Brown E, Owens A, Saguner AM, Meder B, Parikh V, Gotthardt M, Steinmetz LM. Mislocalization of pathogenic RBM20 variants in dilated cardiomyopathy is caused by loss-of-interaction with Transportin-3. Nat Commun 2023; 14:4312. [PMID: 37463913 DOI: 10.1038/s41467-023-39965-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 07/05/2023] [Indexed: 07/20/2023] Open
Abstract
Severe forms of dilated cardiomyopathy (DCM) are associated with point mutations in the alternative splicing regulator RBM20 that are frequently located in the arginine/serine-rich domain (RS-domain). Such mutations can cause defective splicing and cytoplasmic mislocalization, which leads to the formation of detrimental cytoplasmic granules. Successful development of personalized therapies requires identifying the direct mechanisms of pathogenic RBM20 variants. Here, we decipher the molecular mechanism of RBM20 mislocalization and its specific role in DCM pathogenesis. We demonstrate that mislocalized RBM20 RS-domain variants retain their splice regulatory activity, which reveals that aberrant cellular localization is the main driver of their pathological phenotype. A genome-wide CRISPR knockout screen combined with image-enabled cell sorting identified Transportin-3 (TNPO3) as the main nuclear importer of RBM20. We show that the direct RBM20-TNPO3 interaction involves the RS-domain, and is disrupted by pathogenic variants. Relocalization of pathogenic RBM20 variants to the nucleus restores alternative splicing and dissolves cytoplasmic granules in cell culture and animal models. These findings provide proof-of-principle for developing therapeutic strategies to restore RBM20's nuclear localization in RBM20-DCM patients.
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Affiliation(s)
- Julia Kornienko
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Heidelberg, Germany
| | | | - Kai Fenzl
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Heidelberg, Germany
| | - Florian Hinze
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany
- Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Daniel Schraivogel
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Markus Grosch
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Heidelberg, Germany
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Brigit Tunaj
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Dominik Lindenhofer
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Laura Schraft
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Moritz Kueblbeck
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Eric Smith
- University of Michigan, Ann Arbor, MI, USA
| | - Chad Mao
- Children's Healthcare of Atlanta & Emory University, Atlanta, GA, USA
| | | | - Anjali Owens
- University of Pennsylvania, Philadelphia, PA, USA
| | - Ardan M Saguner
- Department of Cardiology, University Heart Center Zurich, University Hospital Zurich, Zurich, Switzerland
| | - Benjamin Meder
- Cardiogenetics Center Heidelberg, Department of Cardiology, Angiology and Pulmology, University Hospital Heidelberg, Heidelberg, Germany
| | - Victoria Parikh
- Stanford Center for Inherited Cardiovascular Disease, Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael Gotthardt
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany
- Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Lars M Steinmetz
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
- DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Heidelberg, Germany.
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
- Stanford Genome Technology Center, Palo Alto, CA, USA.
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Sandoval-Castellanos AM, Bhargava A, Zhao M, Xu J, Ning K. Serine and arginine rich splicing factor 1: a potential target for neuroprotection and other diseases. Neural Regen Res 2023; 18:1411-1416. [PMID: 36571335 PMCID: PMC10075106 DOI: 10.4103/1673-5374.360243] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Alternative splicing is the process of producing variably spliced mRNAs by choosing distinct combinations of splice sites within a messenger RNA precursor. This splicing enables mRNA from a single gene to synthesize different proteins, which have different cellular properties and functions and yet arise from the same single gene. A family of splicing factors, Serine-arginine rich proteins, are needed to initiate the assembly and activation of the spliceosome. Serine and arginine rich splicing factor 1, part of the arginine/serine-rich splicing factor protein family, can either activate or inhibit the splicing of mRNAs, depending on the phosphorylation status of the protein and its interaction partners. Considering that serine and arginine rich splicing factor 1 is either an activator or an inhibitor, this protein has been studied widely to identify its various roles in different diseases. Research has found that serine and arginine rich splicing factor 1 is a key target for neuroprotection, showing its promising potential use in therapeutics for neurodegenerative disorders. Furthermore, serine and arginine rich splicing factor 1 might be used to regulate cancer development and autoimmune diseases. In this review, we highlight how serine and arginine rich splicing factor 1 has been studied concerning neuroprotection. In addition, we draw attention to how serine and arginine rich splicing factor 1 is being studied in cancer and immunological disorders, as well as how serine and arginine rich splicing factor 1 acts outside the central or peripheral nervous system.
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Affiliation(s)
- Ana M Sandoval-Castellanos
- Sheffield Institute of Translational Neuroscience, SITraN, The University of Sheffield, Sheffield, UK; Department of Ophthalmology & Vision Science, and Department of Dermatology, Institute for Regenerative Cures, University of California at Davis, School of Medicine, Sacramento, CA, USA
| | - Anushka Bhargava
- Sheffield Institute of Translational Neuroscience, SITraN, The University of Sheffield, Sheffield, UK
| | - Min Zhao
- Department of Ophthalmology & Vision Science, and Department of Dermatology, Institute for Regenerative Cures, University of California at Davis, School of Medicine, Sacramento, CA, USA
| | - Jun Xu
- East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Ke Ning
- Sheffield Institute of Translational Neuroscience, SITraN, The University of Sheffield, Sheffield, UK; East Hospital, Tongji University School of Medicine, Shanghai, China
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CRISPR-Cas9 editing of a TNPO3 mutation in a muscle cell model of limb-girdle muscular dystrophy type D2. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 31:324-338. [PMID: 36789274 PMCID: PMC9898580 DOI: 10.1016/j.omtn.2023.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 01/06/2023] [Indexed: 01/13/2023]
Abstract
A single-nucleotide deletion in the stop codon of the nuclear import receptor transportin-3 (TNPO3), also involved in human immunodeficiency virus type 1 (HIV-1) infection, causes the ultrarare autosomal dominant disease limb-girdle muscular dystrophy D2 (LGMDD2) by extending the wild-type protein. Here, we generated a patient-derived in vitro model of LGMDD2 as an immortalized myoblast cell line carrying the TNP O 3 mutation. The cell model reproduced critical molecular alterations seen in patients, such as TNP O 3 overexpression, defects in terminal muscle markers, and autophagy overactivation. Correction of the TNP O 3 mutation via CRISPR-Cas9 editing caused a significant reversion of the pathological phenotypes in edited cells, including a complete absence of the mutant TNPO3 protein, as detected with a polyclonal antibody specific against the abnormal 15-aa peptide. Transcriptomic analyses found that 15% of the transcriptome was differentially expressed in model myotubes. CRISPR-Cas9-corrected cells showed that 44% of the alterations were rescued toward normal levels. MicroRNAs (miRNAs) analyses showed that around 50% of miRNAs with impaired expression because of the disease were recovered on the mutation edition. In summary, this work provides proof of concept of the potential of CRISPR-Cas9-mediated gene editing of TNP O 3 as a therapeutic approach and describes critical reagents in LGMDD2 research.
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Hobson CM, Aaron JS. Combining multiple fluorescence imaging techniques in biology: when one microscope is not enough. Mol Biol Cell 2022; 33:tp1. [PMID: 35549314 PMCID: PMC9265156 DOI: 10.1091/mbc.e21-10-0506] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
While fluorescence microscopy has proven to be an exceedingly useful tool in bioscience, it is difficult to offer simultaneous high resolution, fast speed, large volume, and good biocompatibility in a single imaging technique. Thus, when determining the image data required to quantitatively test a complex biological hypothesis, it often becomes evident that multiple imaging techniques are necessary. Recent years have seen an explosion in development of novel fluorescence microscopy techniques, each of which features a unique suite of capabilities. In this Technical Perspective, we highlight recent studies to illustrate the benefits, and often the necessity, of combining multiple fluorescence microscopy modalities. We provide guidance in choosing optimal technique combinations to effectively address a biological question. Ultimately, we aim to promote a more well-rounded approach in designing fluorescence microscopy experiments, leading to more robust quantitative insight.
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Affiliation(s)
- Chad M Hobson
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147
| | - Jesse S Aaron
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147
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Costa R, Rodia MT, Pacilio S, Angelini C, Cenacchi G. LGMD D2 TNPO3-Related: From Clinical Spectrum to Pathogenetic Mechanism. Front Neurol 2022; 13:840683. [PMID: 35309568 PMCID: PMC8931187 DOI: 10.3389/fneur.2022.840683] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 01/31/2022] [Indexed: 11/13/2022] Open
Abstract
Limb-girdle muscular dystrophies (LGMDs) are clinically and genetically heterogeneous diseases presenting with a wide clinical spectrum. Autosomal dominant LGMDs represent about 10–15% of LGMDs and include disorders due to defects of DNAJB6, transportin-3 (TNPO3), HNRNPDL, Calpain-3 (CAPN3), and Bethlem myopathy. This review article aims to describe the clinical spectrum of LGMD D2 TNPO3-related, a rare disease due to heterozygous mutation in the TNPO3 gene. TNPO3 encodes for transportin-3, which belongs to the importin beta family and transports into the nucleus serine/arginine-rich (SR) proteins, such as splicing factors, and HIV-1 proteins, thus contributing to viral infection. The purpose of this review is to present and compare the clinical features and the genetic and histopathological findings described in LGMD D2, performing a comparative analytical description of all the families and sporadic cases identified. Even if the causative gene and mutations of this disease have been identified, the pathogenic mechanisms are still an open issue; therefore, we will present an overview of the hypotheses that explain the pathology of LGMD D2 TNPO3-related.
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Affiliation(s)
- Roberta Costa
- Department of Biomedical and Neuromotor Sciences–DIBINEM, Alma Mater Studiorum University of Bologna, Bologna, Italy
- Applied Biomedical Research Center–CRBA, IRCCS St. Orsola Hospital, Alma Mater Studiorum University of Bologna, Bologna, Italy
| | - Maria Teresa Rodia
- Department of Biomedical and Neuromotor Sciences–DIBINEM, Alma Mater Studiorum University of Bologna, Bologna, Italy
- Applied Biomedical Research Center–CRBA, IRCCS St. Orsola Hospital, Alma Mater Studiorum University of Bologna, Bologna, Italy
| | - Serafina Pacilio
- Department of Biomedical and Neuromotor Sciences–DIBINEM, Alma Mater Studiorum University of Bologna, Bologna, Italy
- Applied Biomedical Research Center–CRBA, IRCCS St. Orsola Hospital, Alma Mater Studiorum University of Bologna, Bologna, Italy
| | - Corrado Angelini
- Laboratory for Neuromuscular Diseases, Campus Pietro d'Abano, University of Padova, Padova, Italy
| | - Giovanna Cenacchi
- Department of Biomedical and Neuromotor Sciences–DIBINEM, Alma Mater Studiorum University of Bologna, Bologna, Italy
- Applied Biomedical Research Center–CRBA, IRCCS St. Orsola Hospital, Alma Mater Studiorum University of Bologna, Bologna, Italy
- *Correspondence: Giovanna Cenacchi
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Blázquez-Bernal Á, Fernandez-Costa JM, Bargiela A, Artero R. Inhibition of autophagy rescues muscle atrophy in a LGMDD2 Drosophila model. FASEB J 2021; 35:e21914. [PMID: 34547132 DOI: 10.1096/fj.202100539rr] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 08/23/2021] [Accepted: 08/25/2021] [Indexed: 01/18/2023]
Abstract
Limb-girdle muscular dystrophy D2 (LGMDD2) is an ultrarare autosomal dominant myopathy caused by mutation of the normal stop codon of the TNPO3 nuclear importin. The mutant protein carries a 15 amino acid C-terminal extension associated with pathogenicity. Here we report the first animal model of the disease by expressing the human mutant TNPO3 gene in Drosophila musculature or motor neurons and concomitantly silencing the endogenous expression of the fly protein ortholog. A similar genotype expressing wildtype TNPO3 served as a control. Phenotypes characterization revealed that mutant TNPO3 expression targeted at muscles or motor neurons caused LGMDD2-like phenotypes such as muscle degeneration and atrophy, and reduced locomotor ability. Notably, LGMDD2 mutation increase TNPO3 at the transcript and protein level in the Drosophila model Upregulated muscle autophagy observed in LGMDD2 patients was also confirmed in the fly model, in which the anti-autophagic drug chloroquine was able to rescue histologic and functional phenotypes. Overall, we provide a proof of concept of autophagy as a target to treat disease phenotypes and propose a neurogenic component to explain mutant TNPO3 pathogenicity in diseased muscles.
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Affiliation(s)
- Águeda Blázquez-Bernal
- Translational Genomics Group, University Institute for Biotechnology and Biomedicine (BIOTECMED), University of Valencia, Valencia, Spain.,Area of Metabolism and Organic Failure, Incliva Health Research Institute, Valencia, Spain.,Incliva-CIPF Joint Unit, Valencia, Spain
| | - Juan M Fernandez-Costa
- Translational Genomics Group, University Institute for Biotechnology and Biomedicine (BIOTECMED), University of Valencia, Valencia, Spain.,Area of Metabolism and Organic Failure, Incliva Health Research Institute, Valencia, Spain.,Incliva-CIPF Joint Unit, Valencia, Spain
| | - Ariadna Bargiela
- Translational Genomics Group, University Institute for Biotechnology and Biomedicine (BIOTECMED), University of Valencia, Valencia, Spain.,Area of Metabolism and Organic Failure, Incliva Health Research Institute, Valencia, Spain.,Incliva-CIPF Joint Unit, Valencia, Spain
| | - Ruben Artero
- Translational Genomics Group, University Institute for Biotechnology and Biomedicine (BIOTECMED), University of Valencia, Valencia, Spain.,Area of Metabolism and Organic Failure, Incliva Health Research Institute, Valencia, Spain.,Incliva-CIPF Joint Unit, Valencia, Spain
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Liu H, Gong Z, Li K, Zhang Q, Xu Z, Xu Y. SRPK1/2 and PP1α exert opposite functions by modulating SRSF1-guided MKNK2 alternative splicing in colon adenocarcinoma. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:75. [PMID: 33602301 PMCID: PMC7893936 DOI: 10.1186/s13046-021-01877-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 02/11/2021] [Indexed: 12/11/2022]
Abstract
BACKGROUND The Mnk2 kinase, encoded by MKNK2 gene, plays critical roles in MAPK signaling and was involved in oncogenesis. Human MKNK2 pre-mRNA can be alternatively spliced into two splicing isoforms, the MKNK2a and MKNK2b, thus yielding Mnk2a and Mnk2b proteins with different domains. The involvement of Mnk2 alternative splicing in colon cancer has been implicated based on RNA-sequencing data from TCGA database. This study aimed at investigating the upstream modulators and clinical relevance of Mnk2 alternative splicing in colon adenocarcinoma (CAC). METHODS PCR, western blotting and immunohistochemistry (IHC) were performed to assess the expression of Mnk2 and upstream proteins in CAC. The function of Mnk2 and its regulators were demonstrated in different CAC cell lines as well as in xenograft models. Two independent cohorts of CAC patients were used to reveal the clinical significance of MKNK2 alternative splicing. RESULTS Comparing with adjacent nontumorous tissue, CAC specimen showed a decreased MKNK2a level and an increased MKNK2b level, which were correlated with KRAS mutation and tumor size. The SRSF1 (serine/arginine-rich splicing factor 1) was further confirmed to be the major splicing factor targeting MKNK2 in CAC cells. Higher expression of SRPK1/2 or decreased activity of PP1α were responsible for enhancing SRSF1 phosphorylation and nucleus translocation, subsequently resulted in a switch of MKNK2 alternative splicing. CONCLUSIONS Our data showed that phosphorylation and subcellular localization of SRSF1 were balanced by SRPK1/2 and PP1α in CAC cells. High nucleus SRSF1 promoted MKNK2 splicing into MKNK2b instead of MNK2a, consequently enhanced tumor proliferation.
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Affiliation(s)
- Hongda Liu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China
| | - Zheng Gong
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA
| | - Kangshuai Li
- Department of General Surgery, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Qun Zhang
- Department of Respiratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Zekuan Xu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China.
| | - Yunfei Xu
- Department of General Surgery, Qilu Hospital of Shandong University, Jinan, 250012, China.
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