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Auner S, Hillebrand C, Boehm PM, Boecker J, Koren D, Schwarz S, Kovacs Z, Murakoezy G, Fischer G, Aigner C, Hoetzenecker K, Jaksch P, Benazzo A. Impact of Transient and Persistent Donor-Specific Antibodies in Lung Transplantation. Transpl Int 2024; 37:12774. [PMID: 38779355 PMCID: PMC11110840 DOI: 10.3389/ti.2024.12774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 04/15/2024] [Indexed: 05/25/2024]
Abstract
Lung transplantation (LuTx) is an established treatment for patients with end-stage lung diseases, however, outcomes are limited by acute and chronic rejection. One aspect that has received increasing attention is the role of the host's humoral alloresponse, particularly the formation of de novo donor-specific antibodies (dnDSAs). The aim of this study was to investigate the clinical significance of transient and persistent dnDSAs and to understand their impact on outcomes after LuTx. A retrospective analysis was conducted using DSA screening data from LuTx recipients obtained at the Medical University of Vienna between February 2016 and March 2021. Of the 405 LuTx recipients analyzed, 205 patients developed dnDSA during the follow-up period. Among these, 167 (81%) had transient dnDSA and 38 (19%) persistent dnDSA. Persistent but not transient dnDSAs were associated with chronic lung allograft dysfunction (CLAD) and antibody-mediated rejection (AMR) (p < 0.001 and p = 0.006, respectively). CLAD-free survival rates for persistent dnDSAs at 1-, 3-, and 5-year post-transplantation were significantly lower than for transient dnDSAs (89%, 59%, 56% vs. 91%, 79%, 77%; p = 0.004). Temporal dynamics of dnDSAs after LuTx have a substantial effect on patient outcomes. This study underlines that the persistence of dnDSAs poses a significant risk to graft and patient survival.
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Affiliation(s)
- S. Auner
- Vienna Lung Transplant Program, Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria
| | - C. Hillebrand
- Vienna Lung Transplant Program, Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria
| | - P. M. Boehm
- Vienna Lung Transplant Program, Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria
| | - J. Boecker
- Vienna Lung Transplant Program, Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria
| | - D. Koren
- Department of Blood Group Serology and Transfusion Medicine, Medical University of Vienna, Vienna, Austria
| | - S. Schwarz
- Vienna Lung Transplant Program, Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria
| | - Z. Kovacs
- Vienna Lung Transplant Program, Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria
| | - G. Murakoezy
- Vienna Lung Transplant Program, Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria
| | - G. Fischer
- Department of Blood Group Serology and Transfusion Medicine, Medical University of Vienna, Vienna, Austria
| | - C. Aigner
- Vienna Lung Transplant Program, Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria
| | - K. Hoetzenecker
- Vienna Lung Transplant Program, Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria
| | - P. Jaksch
- Vienna Lung Transplant Program, Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria
| | - A. Benazzo
- Vienna Lung Transplant Program, Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria
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Hoetzenecker K, Benazzo A, Schwarz S, Keshavjee S, Cypel M. The Advent of Semi-Elective Lung Transplantation-Prolonged Static Cold Storage at 10°C. Transpl Int 2024; 37:12310. [PMID: 38317690 PMCID: PMC10839059 DOI: 10.3389/ti.2024.12310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 01/09/2024] [Indexed: 02/07/2024]
Abstract
Since the early days of clinical lung transplantation the preservation of donor organs has become a fairly standardized procedure and most centers do follow similar processes. This includes the use of low-potassium high dextran flush solutions and static cold storage (SCS) in a cooler filled with ice. Depending on the length of SCS, organs usually arrive at the recipient hospital at a temperature of 0°C-4°C. The question of the optimal storage temperature for donor lung preservation has been revisited as data from large animal experiments demonstrated that organs stored at 10°C experience less mitochondrial damage. Thus, prolonged cold ischemic times can be better tolerated at 10°C-even in pre-damaged organs. The clinical applicability of these findings was demonstrated in an international multi-center observational study including three high-volume lung transplant centers. Total clinical preservation times of up to 24 hrs have been successfully achieved in organs stored at 10°C without hampering primary organ function and short-term outcomes. Currently, a randomized-controlled trial (RCT) is recruiting patients with the aim to compare standard SCS on ice with prolonged SCS protocol at 10°C. If, as anticipated, this RCT confirms data from previous studies, lung transplantation could indeed become a semi-elective procedure.
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Affiliation(s)
- K. Hoetzenecker
- Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria
| | - A. Benazzo
- Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria
| | - S. Schwarz
- Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria
| | - S. Keshavjee
- Toronto Lung Transplant Program, Division of Thoracic Surgery, University Health Network, University of Toronto, Toronto, ON, Canada
| | - M. Cypel
- Toronto Lung Transplant Program, Division of Thoracic Surgery, University Health Network, University of Toronto, Toronto, ON, Canada
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Boehm P, Frick A, Schwarz S, Auner S, Benazzo A, Kovacs Z, Murakoezy G, Jaksch P, Hoetzenecker K. Lung Transplantation for Patients with a High-Risk Profile. J Heart Lung Transplant 2023. [DOI: 10.1016/j.healun.2023.02.1618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
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Benazzo A, Auner S, Boehm P, Schwarz S, Bagnera C, Ius F, Hoetzenecker K, Meloni F, Jaksch P, Greer M. A Multicenter Experience with Extracorporeal Photopheresis as Treatment of Clad. J Heart Lung Transplant 2023. [DOI: 10.1016/j.healun.2023.02.1603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
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Benazzo A, Jaksch P, Cho A, Wekerle T, Worel N, Hoetzenecker K, Muraközy G, Knobler R. Prophylactic Use of Extracorporeal Photopheresis (ecp) - A Prospective Randomized Single Center Trial. J Heart Lung Transplant 2023. [DOI: 10.1016/j.healun.2023.02.130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
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Oya BH, Auner S, Boehm P, Schwarz S, Nasrollahi S, Jaksch P, Hoetzenecker K, Benazzo A. Eight Micro-Rnas Show Differential Expression Twelve Months after Lung Transplantation: Preliminary Data from a High Throughput Technology. J Heart Lung Transplant 2023. [DOI: 10.1016/j.healun.2023.02.1484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
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Auner S, Boehm P, Schwarz S, Schweiger T, Frick A, Murakoezy G, Kovacs Z, Lang G, Taghavi S, Jaksch P, Hoetzenecker K, Benazzo A. Effect of Clad Phenotypes on the Outcome after Lung Retransplantation - A Retrospective Single Center Data Analysis. J Heart Lung Transplant 2023. [DOI: 10.1016/j.healun.2023.02.126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
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Begic M, Schwarz S, Boehm P, Benazzo A, Kovac Z, Murakoezy G, Jaksch P, Hoetzenecker K. Lung Transplant in Patients with Suspicious Lung Nodules: A Single-Center Retrospective Data Analysis. J Heart Lung Transplant 2023. [DOI: 10.1016/j.healun.2023.02.1615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
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Jaksch P, Muraközy G, Benazzo A, Kovacs Z, Hoetzenecker K, Fischer G. Donor Derived Cell Free Dna after Lung Transplantation: Marker for Acute and Chronic Lung Allograft Injury? J Heart Lung Transplant 2023. [DOI: 10.1016/j.healun.2023.02.1397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
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Schwarz S, Fruhmann N, Benazzo A, Koren D, Fischer G, Jaksch P, Hoetzenecker K. Unlike the US-LAS, the Eurotransplant-LAS is Not a Risk Factor for De-Novo Donor Specific Antibodies. J Heart Lung Transplant 2023. [DOI: 10.1016/j.healun.2023.02.1413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
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Benazzo A, Bozzini S, Auner S, Berezhinskiy HO, Watzenboeck ML, Schwarz S, Schweiger T, Klepetko W, Wekerle T, Hoetzenecker K, Meloni F, Jaksch P. Differential expression of circulating miRNAs after alemtuzumab induction therapy in lung transplantation. Sci Rep 2022; 12:7072. [PMID: 35490174 PMCID: PMC9056512 DOI: 10.1038/s41598-022-10866-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 04/13/2022] [Indexed: 11/17/2022] Open
Abstract
Alemtuzumab is a monoclonal antibody targeting CD52, used as induction therapy after lung transplantation (LTx). Its engagement produces a long-lasting immunodepletion; however, the mechanisms driving cell reconstitution are poorly defined. We hypothesized that miRNAs are involved in this process. The expression of a set of miRNAs, cytokines and co-signaling molecules was measured with RT-qPCR and flow cytometry in prospectively collected serum samples of LTx recipients, after alemtuzumab or no induction therapy. Twenty-six LTx recipients who received alemtuzumab and twenty-seven matched LTx recipients without induction therapy were included in the analysis. One year after transplantation four miRNAs were differentially regulated: miR-23b (p = 0.05) miR-146 (p = 0.04), miR-155 (p < 0.001) and miR-486 (p < 0.001). Expression of 3 miRNAs changed within the alemtuzumab group: miR-146 (p < 0.001), miR-155 (p < 0.001) and miR-31 (p < 0.001). Levels of IL-13, IL-4, IFN-γ, BAFF, IL-5, IL-9, IL-17F, IL-17A and IL-22 were different one year after transplantation compared to baseline. In no-induction group, concentration of sCD27, sB7.2 and sPD-L1 increased overtime. Expression of miR-23b, miR-146, miR-486, miR-155 and miR-31 was different in LTx recipients who received alemtuzumab compared to recipients without induction therapy. The observed cytokine pattern suggested proliferation of specific B cell subsets in alemtuzumab group and co-stimulation of T-cells in no-induction group.
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Affiliation(s)
- A Benazzo
- Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria.
- Department of Thoracic Surgery, Lung Transplantation Research Lab, Medical University of Vienna, Vienna, Austria.
- Division of Thoracic Surgery, Medical University of Vienna, Währinger Guertel 18-20, 1090, Vienna, Austria.
| | - S Bozzini
- Department of Internal Medicine, Unit of Respiratory Diseases, Laboratory of Cell Biology and Immunology, University of Pavia and IRCCS Policlinico San Matteo Foundation, Pavia, Italy
| | - S Auner
- Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria
- Department of Thoracic Surgery, Lung Transplantation Research Lab, Medical University of Vienna, Vienna, Austria
| | - H Oya Berezhinskiy
- Department of Thoracic Surgery, Lung Transplantation Research Lab, Medical University of Vienna, Vienna, Austria
| | - M L Watzenboeck
- Department of Biomedical Imaging and Image-Guided Therapy, Medical University of Vienna, Vienna, Austria
| | - S Schwarz
- Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria
| | - T Schweiger
- Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria
| | - W Klepetko
- Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria
| | - T Wekerle
- Section of Transplantation Immunology, Division of Transplantation, Department of General Surgery, Medical University of Vienna, Vienna, Austria
| | - K Hoetzenecker
- Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria
| | - F Meloni
- Department of Internal Medicine, Unit of Respiratory Diseases, Laboratory of Cell Biology and Immunology, University of Pavia and IRCCS Policlinico San Matteo Foundation, Pavia, Italy
| | - P Jaksch
- Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria
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Auner S, Cho A, Berezhinskiy H, Murakozy G, Lang G, Taghavi S, Klepetko W, Wekerle T, Hoetzenecker K, Jaksch P, Benazzo A. Short-Time Effect of Alemtuzumab Induction Therapy on B- and T-cell Subsets After Lung Transplantation. J Heart Lung Transplant 2022. [DOI: 10.1016/j.healun.2022.01.759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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13
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Benazzo A, Schwarz S, Frommlet F, Sinn K, Schweiger T, Klikovits T, Hoda A, Moser B, Matilla J, Renyi Vamos F, Lang G, Jaksch P, Di Nardo M, Del Sorbo L, Taghavi S, Keshavjee S, Klepetko W, Cypel M, Hoetzenecker K. Donor Ventilation Parameters as Predictors for Length of Mechanical Ventilation after Lung Transplantation: Results of a Prospective Multicenter Study. J Heart Lung Transplant 2021. [DOI: 10.1016/j.healun.2021.01.911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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14
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Benazzo A, Schwarz S, Schweiger T, Frick A, Moser B, Matilla J, Lang G, Taghavi S, Jaksch P, Klepetko W, Hoetzenecker K. Respiratory Failure Treated by ECLS in Previously Unscreened Patients - Is Lung Transplantation Feasible? J Heart Lung Transplant 2020. [DOI: 10.1016/j.healun.2020.01.458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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15
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Benazzo A, Schwarz S, Schweiger T, Frick A, Muraközy G, Lambers C, Moser B, Matilla J, Lang G, Taghavi S, Klepetko W, Hoetzenecker K, Jaksch P. Outcome of Extracorporeal Photopheresis as Add-On Therapy in Patients for Antibody-Mediated Rejection after Lung Transplantation. J Heart Lung Transplant 2020. [DOI: 10.1016/j.healun.2020.01.1303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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16
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Jaksch P, Benazzo A, Schwarz S, Gabriella M, Hielle-Wittmann E, Lambers C, Hötzenecker K, Klepetko W, Görzer I, Puchhammer-Stöckl E. Torque Teno Virus (TTV) Kinetics Can Predict Complications after Lung Transplantation. J Heart Lung Transplant 2020. [DOI: 10.1016/j.healun.2020.01.724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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17
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Frick A, Kifjak D, Taghavi S, Lang G, Moser B, Schwarz S, Benazzo A, Klepetko W, Jaksch P, Hoetzenecker K. Lung Transplantation for Acute Respiratory Distress Syndrome Patients: A Single Center Experience. J Heart Lung Transplant 2020. [DOI: 10.1016/j.healun.2020.01.338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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18
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Benazzo A, Schwarz S, Geleff S, Weber D, Murakozy G, Lambers C, Moser B, Matilla J, Lang G, Taghavi S, Klepetko W, Hoetzenecker K, Jaksch P. Donor-Specific Antibodies and Antibody-Mediated Rejection after Alemtuzumab Induction Therapy: A Retrospective Analysis of a High-Volume Lung Transplant Center. J Heart Lung Transplant 2019. [DOI: 10.1016/j.healun.2019.01.399] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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19
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Miyahara N, Benazzo A, Oberndorfer F, Jaksch P, Klepetko W, Hoetzenecker K. Impact of mir21 Expression in Chronic Lung Allograft Dysfunction after Lung Transplantation. J Heart Lung Transplant 2019. [DOI: 10.1016/j.healun.2019.01.393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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20
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Schwarz S, Rahimi N, Muckenhuber M, Benazzo A, Moser B, Matilla J, Lang G, Taghavi S, Jaksch P, Klepetko W, Hoetzenecker K. The Use of Polytrauma Donor Organs Does Not Impair Long-Term Outcome after Lung Transplantation. J Heart Lung Transplant 2019. [DOI: 10.1016/j.healun.2019.01.859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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Benazzo A, Schwarz S, Weber D, Murakozy G, Lambers C, Moser B, Matilla J, Lang G, Taghavi S, Klepetko W, Hoetzenecker K, Jaksch P. Ten-Year-Experience with Alemtuzumab as Induction Therapy: A Single-Center Analysis of More Than 500 Patients. J Heart Lung Transplant 2019. [DOI: 10.1016/j.healun.2019.01.286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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Schwarz S, Muckenhuber M, Rahimi N, Benazzo A, Moser B, Matilla J, Lang G, Taghavi S, Jaksch P, Klepetko W, Hoetzenecker K. Outcome of Lung Transplantation Using Organ Donors with Evidence of Aspiration. J Heart Lung Transplant 2019. [DOI: 10.1016/j.healun.2019.01.862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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Hoetzenecker K, Benazzo A, Stork T, Sinn K, Schwarz S, Baron D, Hager H, Faybik P, Bacher A, Krenn C, Prosch H, Klepetko. W. BLTX on Intraoperative ECMO Sets the New Benchmark for Postoperative Graft Function: Results of a Prospective Trial. J Heart Lung Transplant 2018. [DOI: 10.1016/j.healun.2018.01.407] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Schwarz S, Muckenhuber M, Benazzo A, Beer L, Gittler F, Bata O, Prosch H, Matilla J, Moser B, Lang G, Taghavi S, Klepetko W, Hoetzenecker K. Is the Current PGD Grading Still Valid in Modern Lung Transplantation? - A Retrospective Analysis of a High-Volume Center. J Heart Lung Transplant 2018. [DOI: 10.1016/j.healun.2018.01.485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Murakoezy G, Benazzo A, Schwarz S, Obermair-Ramp S, Stork T, Klepetko W, Jaksch P. Conversion from Advagraf/Prograf to Envarsus in Stable Lung Transplant Patients. J Heart Lung Transplant 2018. [DOI: 10.1016/j.healun.2018.01.785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
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Fuselli S, Baptista RP, Panziera A, Magi A, Guglielmi S, Tonin R, Benazzo A, Bauzer LG, Mazzoni CJ, Bertorelle G. A new hybrid approach for MHC genotyping: high-throughput NGS and long read MinION nanopore sequencing, with application to the non-model vertebrate Alpine chamois (Rupicapra rupicapra). Heredity (Edinb) 2018; 121:293-303. [PMID: 29572469 PMCID: PMC6133961 DOI: 10.1038/s41437-018-0070-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 01/24/2018] [Accepted: 02/25/2018] [Indexed: 12/13/2022] Open
Abstract
The major histocompatibility complex (MHC) acts as an interface between the immune system and infectious diseases. Accurate characterization and genotyping of the extremely variable MHC loci are challenging especially without a reference sequence. We designed a combination of long-range PCR, Illumina short-reads, and Oxford Nanopore MinION long-reads approaches to capture the genetic variation of the MHC II DRB locus in an Italian population of the Alpine chamois (Rupicapra rupicapra). We utilized long-range PCR to generate a 9 Kb fragment of the DRB locus. Amplicons from six different individuals were fragmented, tagged, and simultaneously sequenced with Illumina MiSeq. One of these amplicons was sequenced with the MinION device, which produced long reads covering the entire amplified fragment. A pipeline that combines short and long reads resolved several short tandem repeats and homopolymers and produced a de novo reference, which was then used to map and genotype the short reads from all individuals. The assembled DRB locus showed a high level of polymorphism and the presence of a recombination breakpoint. Our results suggest that an amplicon-based NGS approach coupled with single-molecule MinION nanopore sequencing can efficiently achieve both the assembly and the genotyping of complex genomic regions in multiple individuals in the absence of a reference sequence.
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Affiliation(s)
- S Fuselli
- Department of Life Sciences and Biotechnology, University of Ferrara, Via L. Borsari 46, Ferrara, 44121, Italy.
| | - R P Baptista
- Center for Tropical & Emerging Global Diseases, University of Georgia, 107 Paul D. Coverdell Center, 500 D. W. Brooks Drive, Athens, GA, 30602-7394, USA
| | - A Panziera
- Department of Life Sciences and Biotechnology, University of Ferrara, Via L. Borsari 46, Ferrara, 44121, Italy.,Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via Edmund Mach 1, San Michele all'Adige, I-38010, Italy
| | - A Magi
- Department of Experimental and Clinical Medicine, University of Florence, Largo Brambilla, Florence, 3-50134, Italy
| | - S Guglielmi
- Department of Life Sciences and Biotechnology, University of Ferrara, Via L. Borsari 46, Ferrara, 44121, Italy
| | - R Tonin
- Department of Life Sciences and Biotechnology, University of Ferrara, Via L. Borsari 46, Ferrara, 44121, Italy.,Faculty of Science and Technology, Free University of Bozen-Bolzano, Piazza Università 5, Bolzano, Italy
| | - A Benazzo
- Department of Life Sciences and Biotechnology, University of Ferrara, Via L. Borsari 46, Ferrara, 44121, Italy
| | - L G Bauzer
- Laboratório de Fisiologia e Controle de Artrópodes Vetores, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil.,Berlin Center for Genomics in Biodiversity Research, Königin-Luise-Str. 6-8, Berlin, 14195, Germany
| | - C J Mazzoni
- Berlin Center for Genomics in Biodiversity Research, Königin-Luise-Str. 6-8, Berlin, 14195, Germany
| | - G Bertorelle
- Department of Life Sciences and Biotechnology, University of Ferrara, Via L. Borsari 46, Ferrara, 44121, Italy
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Schweiger T, Schwarz S, Benazzo A, Augustin F, Lang G, Klepetko W. P-187SUCCESSFUL PERIOPERATIVE MANAGEMENT OF DONOR-ACQUIRED FAT EMBOLISM AFTER DOUBLE LUNG TRANSPLANTATION. Interact Cardiovasc Thorac Surg 2017. [DOI: 10.1093/icvts/ivx280.187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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28
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Benazzo A, Tukora G, Schwarz S, Hoetzenecker K, Moser B, Matilla Sigueenza J, Taghavi S, Jaksch P, Klepetko W, Lang G. ECLS Bridge to Lung Transplantation: A Review of Our Institutional Experience. J Heart Lung Transplant 2017. [DOI: 10.1016/j.healun.2017.01.178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Waseda R, Hoda M, Benazzo A, Jaksch P, Klikovits T, Lang G, Taghavi S, Klepetko W. De Novo Solid Organ Malignancies After Lung Transplantation: A 25-Year Single Center Experience. J Heart Lung Transplant 2017. [DOI: 10.1016/j.healun.2017.01.241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Schwarz S, Schweiger T, Benazzo A, Rösner I, Denk-Linnert DM, Hötzenecker K, Klepetko W. Segmentale Trachealresektion bei einer Patientin mit Chondrodysplasie und früher Posttracheostoma-Trachealstenose. Zentralbl Chir 2016. [DOI: 10.1055/s-0036-1587566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Waseda R, Jaksch P, Muraközy G, Gruber S, Lambers C, Benazzo A, Szepfalusi Z, Nachbaur E, Klepetko W. Pediatric Lung Transplantation - 25 Years of Experience. J Heart Lung Transplant 2016. [DOI: 10.1016/j.healun.2016.01.095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Benazzo A, Ghirotto S, Vilaça ST, Hoban S. Using ABC and microsatellite data to detect multiple introductions of invasive species from a single source. Heredity (Edinb) 2015; 115:262-72. [PMID: 25920671 DOI: 10.1038/hdy.2015.38] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 03/12/2015] [Accepted: 03/14/2015] [Indexed: 11/09/2022] Open
Abstract
The introduction of invasive species to new locations (that is, biological invasions) can have major impact on biodiversity, agriculture and public health. As such, determining the routes and modality of introductions with genetic data has become a fundamental goal in molecular ecology. To assist with this goal, new statistical methods and frameworks have been developed, such as approximate Bayesian computation (ABC) for inferring invasion history. Here, we present a model of invasion accounting for multiple introductions from a single source (MISS), a heretofore largely unexplored model. We simulate microsatellite data to evaluate the power of ABC to distinguish between single and multiple introductions from the same source, under a range of demographic parameters. We also apply ABC to microsatellite data from three invasions of bumblebee in New Zealand. In addition, we assess the performance of several methods of summary statistics selection. Our simulated results suggested good ability to distinguish between one- and two-wave models over much but not all of the parameter space tested, independent of summary statistics used. Globally, parameter estimation was good except for bottleneck timing. For one of the bumblebee species, we clearly rejected the MISS model, while for the other two we found inconclusive results. Since a second wave may provide genetic reinforcement to initial colonists, help relieve inbreeding among founders, or increase the hazard of the invasion, its detection may be crucial for managing invasions; we suggest that the MISS model could be considered as a potential model in future theoretical and empirical studies of invasions.
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Affiliation(s)
- A Benazzo
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - S Ghirotto
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - S T Vilaça
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - S Hoban
- 1] Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy [2] National Institute for Mathematical and Biological Synthesis (NIMBioS), University of Tennessee, Knoxville, TN, USA
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Marino IAM, Benazzo A, Agostini C, Mezzavilla M, Hoban SM, Patarnello T, Zane L, Bertorelle G. Evidence for past and present hybridization in three Antarctic icefish species provides new perspectives on an evolutionary radiation. Mol Ecol 2013; 22:5148-61. [DOI: 10.1111/mec.12458] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Revised: 07/17/2013] [Accepted: 07/18/2013] [Indexed: 11/27/2022]
Affiliation(s)
- I. A. M. Marino
- Department of Biology; University of Padova; via U. Bassi 58/b 35121 Padova Italy
| | - A. Benazzo
- Department of Life Sciences and Biotechnology; University of Ferrara; via L. Borsari 46 44100 Ferrara Italy
| | - C. Agostini
- Department of Biology; University of Padova; via U. Bassi 58/b 35121 Padova Italy
| | - M. Mezzavilla
- Institute for Maternal and Child Health - IRCCS Burlo Garofolo and University of Trieste; Via dell'Istria, 65/1 34137 Trieste Italy
| | - S. M. Hoban
- Department of Life Sciences and Biotechnology; University of Ferrara; via L. Borsari 46 44100 Ferrara Italy
| | - T. Patarnello
- Department of Comparative Biomedicine and Food Science; University of Padova; viale dell'Università 16 35020 Agripolis Legnaro Padova Italy
| | - L. Zane
- Department of Biology; University of Padova; via U. Bassi 58/b 35121 Padova Italy
| | - G. Bertorelle
- Department of Life Sciences and Biotechnology; University of Ferrara; via L. Borsari 46 44100 Ferrara Italy
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Abstract
The analysis of genetic variation to estimate demographic and historical parameters and to quantitatively compare alternative scenarios recently gained a powerful and flexible approach: the Approximate Bayesian Computation (ABC). The likelihood functions does not need to be theoretically specified, but posterior distributions can be approximated by simulation even assuming very complex population models including both natural and human-induced processes. Prior information can be easily incorporated and the quality of the results can be analysed with rather limited additional effort. ABC is not a statistical analysis per se, but rather a statistical framework and any specific application is a sort of hybrid between a simulation and a data-analysis study. Complete software packages performing the necessary steps under a set of models and for specific genetic markers are already available, but the flexibility of the method is better exploited combining different programs. Many questions relevant in ecology can be addressed using ABC, but adequate amount of time should be dedicated to decide among alternative options and to evaluate the results. In this paper we will describe and critically comment on the different steps of an ABC analysis, analyse some of the published applications of ABC and provide user guidelines.
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Affiliation(s)
- G Bertorelle
- Department of Biology and Evolution, University of Ferrara, Via Borsari 46, 44100 Ferrara, Italy.
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Ghirotto S, Mona S, Benazzo A, Paparazzo F, Caramelli D, Barbujani G. Inferring Genealogical Processes from Patterns of Bronze-Age and Modern DNA Variation in Sardinia. Mol Biol Evol 2009; 27:875-86. [DOI: 10.1093/molbev/msp292] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
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Guimaraes S, Ghirotto S, Benazzo A, Milani L, Lari M, Pilli E, Pecchioli E, Mallegni F, Lippi B, Bertoldi F, Gelichi S, Casoli A, Belle EM, Caramelli D, Barbujani G. Genealogical Discontinuities among Etruscan, Medieval, and Contemporary Tuscans. Mol Biol Evol 2009; 26:2157-66. [DOI: 10.1093/molbev/msp126] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
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