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Rahmati S, Bagherzadeh K, Arab SS, Torkashvand F, Amanlou M, Vaziri B. Computational designing of the ligands of Protein L affinity chromatography based on molecular docking and molecular dynamics simulations. J Biomol Struct Dyn 2023:1-11. [PMID: 37855377 DOI: 10.1080/07391102.2023.2268219] [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: 02/27/2023] [Accepted: 09/29/2023] [Indexed: 10/20/2023]
Abstract
Protein L is a multidomain protein from Peptostreptococcus magnus with binding affinity to kappa light chain of human immunoglobulin (Ig) which is used for the purification of antibody fragments by affinity chromatography. The advances in protein engineering and computational biology approaches lead to the development of engineered affinity ligands with improved properties including binding affinity. In this study, molecular dynamics simulations (MDs) and Osprey software were used to design single B domains of the Protein L with higher affinity to antibody fragments. The modified B domains were then polymerized to ligand with six B domains by homology modeling methods. The results showed that single B domain mutants of MB1 (Thr865Trp) and MB2 (Thr847Met-Thr865Trp) had higher binding affinity to Fab compared to the wild single B domain. Also, MDs and molecular docking results showed that the polymerized Proteins L including the wild and mutated six B domains (6B0, 6B1, and 6B2) were stable during MDs and the two mutants of 6B1 and 6B2 showed higher binding affinity to Fab relative to the wild type.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Saman Rahmati
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Kowsar Bagherzadeh
- Stem Cell and Regenerative Medicine Research Center, Iran University of Medical Sciences, Tehran, Iran
- Eye Research Center, The Five Senses Health Institute, Rassoul Akram Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Seyed Shahriar Arab
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | | | - Massoud Amanlou
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Behrouz Vaziri
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
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2
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Kumada Y, Rakotondravao HM, Hasegawa Y, Iwashita Y, Okura H, Uchimura S, Horiuchi JI. Strategies for selection and identification of rabbit single-chain Fv antibodies as ligand in affinity chromatography. J Biosci Bioeng 2022; 134:233-239. [DOI: 10.1016/j.jbiosc.2022.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 10/17/2022]
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3
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Rahmati S, Torkashvand F, Amanlou M, Bagherzadeh K, Fard Esfahani P, Aghamirza Moghim Aliabadi H, Vaziri B. Computational Engineering of Protein L to Achieve an Optimal Affinity Chromatography Resin for Purification of Antibody Fragments. Anal Chem 2021; 93:15253-15261. [PMID: 34747593 DOI: 10.1021/acs.analchem.1c01871] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Protein L affinity chromatography is a useful method for the purification of antibody fragments containing kappa light chains. In affinity chromatography, increasing the binding affinity leads to increased product purity, recovery, and dynamic binding capacity (DBC). In this study, molecular docking and molecular dynamics simulation techniques were used to design the engineered Protein L with higher affinity to the kappa light chain. Each engineered ligand was produced as a recombinant protein and coupled to a solid matrix. The purity, recovery, and DBC of the engineered resins were evaluated and then compared to those of a commercially available resin. The results showed important parameters for engineering more efficient Protein L ligands for affinity chromatography.
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Affiliation(s)
- Saman Rahmati
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran 1316943551, Iran
| | - Fatemeh Torkashvand
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran 1316943551, Iran
| | - Massoud Amanlou
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran 1417614411, Iran
| | - Kowsar Bagherzadeh
- Eye Research Center, The Five Senses Institute Rassoul Akram Hospital, Iran University of Medical Sciences, Tehran 1445613131, Iran.,Stem Cell and Regenerative Medicine Research Center, Iran University of Medical Sciences, Tehran 1449614535, Iran
| | | | | | - Behrouz Vaziri
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran 1316943551, Iran
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4
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Sakhnini LI, Pedersen AK, Dainiak MB, Bülow L. Multimeric fusion single-chain variable fragments as potential novel high-capacity ligands. FEBS Open Bio 2020; 10:507-514. [PMID: 31950675 PMCID: PMC7137789 DOI: 10.1002/2211-5463.12789] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 12/24/2019] [Accepted: 01/10/2020] [Indexed: 12/17/2022] Open
Abstract
In basic and applied biotechnology, design of affinity ligands has become essential for high-capacity applications such as affinity-based downstream processes for therapeutic molecules. Here, we established a proof-of-concept for the use of multimeric fusion single-chain variable fragment (scFvs) as high-capacity ligands in affinity adsorbents. Mono- and di/tri-scFvs separated by Pro-rich negatively charged linkers were designed, produced, and immobilized to 6% cross-linked agarose beads. Frontal binding experiments with a target protein of 50 kDa resulted in up to 20 mg·mL-1 and 82% in dynamic binding capacity and utilization yield, respectively, at 100% breakthrough. The utilization of the binding sites was impacted by the ligand format and ligand density, rather than limitation in pore size of adsorbent as previously suggested. Overall, we demonstrated that multimeric fusion scFvs can successfully be developed and used as high-capacity ligands in affinity adsorbents, enabling lean process design and alignment with process specifications.
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Affiliation(s)
- Laila I. Sakhnini
- Global Research TechnologiesNovo Nordisk A/SCopenhagenDenmark
- Division of Pure and Applied BiochemistryLund UniversityLundSweden
| | - Anja K. Pedersen
- Chemistry, Manufacturing and ControlNovo Nordisk A/SCopenhagenDenmark
| | | | - Leif Bülow
- Division of Pure and Applied BiochemistryLund UniversityLundSweden
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5
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Xu L, Wen Y, Pandit S, Mokkapati VRSS, Mijakovic I, Li Y, Ding M, Ren S, Li W, Liu G. Graphene-based biosensors for the detection of prostate cancer protein biomarkers: a review. BMC Chem 2019; 13:112. [PMID: 31508598 PMCID: PMC6720397 DOI: 10.1186/s13065-019-0611-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 07/15/2019] [Indexed: 02/07/2023] Open
Abstract
Prostate cancer (PC) is the sixth most common cancer type in the world, which causes approximately 10% of total cancer fatalities. The detection of protein biomarkers in body fluids is the key topic for the diagnosis and prognosis of PC. Highly sensitive screening of PC is the most effective approach for reducing mortality. Thus, there are a growing number of literature that recognizes the importance of new technologies for early diagnosis of PC. Graphene is playing an important role in the biosensor field with remarkable physical, optical, electrochemical and magnetic properties. Many recent studies demonstrated the potential of graphene materials for sensitive detection of protein biomarkers. In this review, the graphene-based biosensors toward PC analysis are mainly discussed in two groups: Firstly, novel biosensor interfaces were constructed through the modification of graphene materials onto sensor surfaces. Secondly, ingenious signal amplification strategies were developed using graphene materials as catalysts or carriers. Graphene-based biosensors have exhibited remarkable performance with high sensitivities, wide detection ranges, and long-term stabilities.
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Affiliation(s)
- Li Xu
- 1Laboratory of Biometrory, Division of Chemistry and Ionizing Radiation Measurement Technology, Shanghai Institute of Measurement and Testing Technology, Shanghai, 201203 People's Republic of China.,2Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, 41126 Gothenburg, Sweden
| | - Yanli Wen
- 1Laboratory of Biometrory, Division of Chemistry and Ionizing Radiation Measurement Technology, Shanghai Institute of Measurement and Testing Technology, Shanghai, 201203 People's Republic of China
| | - Santosh Pandit
- 2Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, 41126 Gothenburg, Sweden
| | - Venkata R S S Mokkapati
- 2Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, 41126 Gothenburg, Sweden
| | - Ivan Mijakovic
- 2Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, 41126 Gothenburg, Sweden.,3The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Yan Li
- 1Laboratory of Biometrory, Division of Chemistry and Ionizing Radiation Measurement Technology, Shanghai Institute of Measurement and Testing Technology, Shanghai, 201203 People's Republic of China
| | - Min Ding
- 1Laboratory of Biometrory, Division of Chemistry and Ionizing Radiation Measurement Technology, Shanghai Institute of Measurement and Testing Technology, Shanghai, 201203 People's Republic of China
| | - Shuzhen Ren
- 1Laboratory of Biometrory, Division of Chemistry and Ionizing Radiation Measurement Technology, Shanghai Institute of Measurement and Testing Technology, Shanghai, 201203 People's Republic of China
| | - Wen Li
- 1Laboratory of Biometrory, Division of Chemistry and Ionizing Radiation Measurement Technology, Shanghai Institute of Measurement and Testing Technology, Shanghai, 201203 People's Republic of China
| | - Gang Liu
- 1Laboratory of Biometrory, Division of Chemistry and Ionizing Radiation Measurement Technology, Shanghai Institute of Measurement and Testing Technology, Shanghai, 201203 People's Republic of China
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6
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Sakhnini LI, Greisen PJ, Wiberg C, Bozoky Z, Lund S, Wolf Perez AM, Karkov HS, Huus K, Hansen JJ, Bülow L, Lorenzen N, Dainiak MB, Pedersen AK. Improving the Developability of an Antigen Binding Fragment by Aspartate Substitutions. Biochemistry 2019; 58:2750-2759. [DOI: 10.1021/acs.biochem.9b00251] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Laila I. Sakhnini
- Global Research Technologies, Novo Nordisk A/S, 2760 Måløv, Denmark
- Department of Pure and Applied Biochemistry, Lund University, 223 62 Lund, Sweden
| | - Per J. Greisen
- Global Research Technologies, Novo Nordisk A/S, 2760 Måløv, Denmark
| | - Charlotte Wiberg
- Global Research Technologies, Novo Nordisk A/S, 2760 Måløv, Denmark
| | - Zoltan Bozoky
- Global Research Technologies, Novo Nordisk A/S, 2760 Måløv, Denmark
| | - Søren Lund
- Global Research Technologies, Novo Nordisk A/S, 2760 Måløv, Denmark
| | | | - Hanne S. Karkov
- Global Research Technologies, Novo Nordisk A/S, 2760 Måløv, Denmark
| | - Kasper Huus
- Global Research Technologies, Novo Nordisk A/S, 2760 Måløv, Denmark
| | | | - Leif Bülow
- Department of Pure and Applied Biochemistry, Lund University, 223 62 Lund, Sweden
| | - Nikolai Lorenzen
- Global Research Technologies, Novo Nordisk A/S, 2760 Måløv, Denmark
| | - Maria B. Dainiak
- Global Research Technologies, Novo Nordisk A/S, 2760 Måløv, Denmark
| | - Anja K. Pedersen
- Chemistry, Manufacturing and Control, Novo Nordisk A/S, 2820 Gentofte, Denmark
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7
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Sakhnini LI, Pedersen AK, León IR, Greisen PJ, Hansen JJ, Vester-Christensen MB, Bülow L, Dainiak MB. Optimizing selectivity of anion hydrophobic multimodal chromatography for purification of a single-chain variable fragment. Eng Life Sci 2019; 19:490-501. [PMID: 32625026 DOI: 10.1002/elsc.201800207] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 03/14/2019] [Accepted: 04/24/2019] [Indexed: 11/11/2022] Open
Abstract
Single-chain variable fragments (scFv) are widely used in several fields. However, they can be challenging to purify unless using expensive Protein L-based affinity adsorbents or affinity tags. In this work, a purification process for a scFv using mixed-mode (MM) chromatography was developed by design of experiments (DoE) and proteomics for host cell protein (HCP) quantification. Capture of scFv from human embryonic kidney 293 (HEK293) cell feedstocks was performed by hydrophobic charge induction chromatography (MEP HyperCel™), whereafter polishing was performed by anion hydrophobic MM chromatography (Capto Adhere™). The DoE designs of the polishing step included both binding and flow-through modes, the latter being the standard mode for HCP removal. Chromatography with Capto Adhere™ in binding-mode with elution by linear salt gradient at pH 7.5 resulted in optimal yield, purity and HCP reduction factor of 98.9 > 98.5%, and 14, respectively. Totally, 258 different HCPs were removed, corresponding to 84% of identified HCPs. The optimized conditions enabled binding of the scFv to Capto Adhere™ below its theoretical pI, while the majority of HCPs were in the flow-through. Surface property maps indicated the presence of hydrophobic patches in close proximity to negatively charged patches that could potentially play a role in this unique selectivity.
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Affiliation(s)
- Laila I Sakhnini
- Department of Downstream Technologies Novo Nordisk A/S Måløv Denmark.,Department of Pure and Applied Biochemistry Lund University Lund Sweden
| | - Anja K Pedersen
- Department of Protein Purification Development Novo Nordisk A/S Gentofte Denmark
| | | | - Per J Greisen
- Department of Modelling & Predictive Technologies Novo Nordisk A/S Måløv Denmark
| | - Jens Jacob Hansen
- Department of Expression Technologies Novo Nordisk A/S Måløv Denmark
| | | | - Leif Bülow
- Department of Pure and Applied Biochemistry Lund University Lund Sweden
| | - Maria B Dainiak
- Department of Downstream Technologies Novo Nordisk A/S Måløv Denmark
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Wang N, Xu P, Wu C, Wu R, Shou D. Preparation of micro-cell membrane chromatographic columns with polyvinyl alcohol-modified polyether ether ketone tube as cellular membrane carrier. J Chromatogr B Analyt Technol Biomed Life Sci 2019; 1104:102-108. [PMID: 30448628 DOI: 10.1016/j.jchromb.2018.11.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 11/06/2018] [Accepted: 11/08/2018] [Indexed: 12/31/2022]
Abstract
Cell membrane chromatography is a promising technique for screening active components from complex matrices. Unfortunately, the large consumption of cells and low resolutions of analytes limit the applications of this method. Herein, we report polyether ether ketone tube as a novel cellular membrane carrier for cell membrane chromatography. Its inner surface is firstly coated by polyvinyl alcohol and then cell membranes are physically adsorbed onto the polyvinyl alcohol layer. To verify this approach, osteoclast and osteoblast micro-column were prepared and characterized by calcitonin and verapamil, respectively. Comparing with common cell membrane chromatographic column, the micro-cell membrane chromatographic columns showed about 1000-fold decrease of cell consumption and satisfactory retention behavior. The developed column was applied to screen potential active components from Cortex Phellodendri Chinensis. A total of 18 components in Cortex Phellodendri Chinensis extract were observed as having retention property of osteoclast micro-cell membrane chromatographic column, while 10 components retained on osteoblast micro-cell membrane chromatographic column. The results of in vitro assay showed that berberine, obacunoic acid and phellodendrine had an obvious inhibitory effect on osteoclast differentiation and function. Berberine and tetrahydropalmatine increased the osteoblast proliferations and mineralized nodules density. This cell membrane/polyvinyl alcohol column can be applied to various biological chromatography models.
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Affiliation(s)
- Nani Wang
- Department of Medicine, Zhejiang Academy of Traditional Chinese Medicine, Hangzhou, Zhejiang 310007, China; School of Pharmacy, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Pingcui Xu
- School of Pharmacy, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Can Wu
- Department of Chemsitry, Zhejiang University, Hangzhou 310007, China
| | - Renjie Wu
- Department of Medicine, Zhejiang Academy of Traditional Chinese Medicine, Hangzhou, Zhejiang 310007, China
| | - Dan Shou
- Department of Medicine, Zhejiang Academy of Traditional Chinese Medicine, Hangzhou, Zhejiang 310007, China.
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9
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Lin WW, Cheng YA, Kao CH, Roffler SR, Lee YC, Chen BM, Hsieh YC, Chen IJ, Huang BC, Wang YT, Tung YC, Huang MY, Chen FM, Cheng TL. Enhancement Effect of a Variable Topology of a Membrane-Tethered Anti-Poly(ethylene glycol) Antibody on the Sensitivity for Quantifying PEG and PEGylated Molecules. Anal Chem 2017; 89:6082-6090. [DOI: 10.1021/acs.analchem.7b00730] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Wen-Wei Lin
- Institute
of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung, Taiwan
| | | | | | - Steve R. Roffler
- Institute
of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | | | - Bing-Mae Chen
- Institute
of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | | | | | - Bo-Cheng Huang
- Institute
of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung, Taiwan
| | | | | | | | | | - Tian-Lu Cheng
- Institute
of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung, Taiwan
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10
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Eliaz I, Patil A, Navarro-Alvarez N, Wang Z, Eliaz A, Weil E, Wilk B, Sachs DH, Huang CA. Methods for the detection and serum depletion of porcine galectin-3. J Clin Apher 2017; 32:335-341. [PMID: 28083958 DOI: 10.1002/jca.21521] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 10/26/2016] [Accepted: 12/01/2016] [Indexed: 12/31/2022]
Abstract
BACKGROUND Circulating galectin-3 (Gal-3) is elevated in systemic inflammatory disorders, fibrotic diseases, and in cancers. Gal-3 is a promising cancer target where it promotes tumorigenesis and metastasis, as well as in renal, pulmonary, hepatic, and cardiovascular diseases, because of its role as a driver of fibrotic remodeling. This reports goal was to establish methods for the detection and removal of porcine Gal-3 that will enable further studies of the therapeutic potential of Gal-3 depletion by apheresis in porcine disease models. The long-term aim is to develop a safe, effective method of removing Gal-3 via apheresis as a standalone therapeutic tool and as an adjuvant to other therapies. METHODS Purified recombinant porcine Gal-3 was prepared and used as the standard for development of a porcine Gal-3 enzyme-linked immunosorbent assay (ELISA). Different affinity column matrices that incorporated either a rat IgG2a anti-Gal-3 monoclonal antibody or carbohydrate ligand were assessed for depletion of Gal-3 from porcine serum. RESULTS A porcine Gal-3 ELISA with a linear range from 0.3 to 20 ng/mL was able to detect native porcine Gal-3 in both fetal (∼150-200 ng/mL) and juvenile (∼5-15 ng/mL) porcine serum samples. Use of an anti-Gal-3 monoclonal antibody affinity column depleted Gal-3 from porcine serum to at least 313 pg/mL, the limit of ELISA detection. CONCLUSIONS Methods have been developed for the detection and depletion of porcine Gal-3. These methods will be used to study the specific effects of Gal-3 depletion via apheresis in porcine models of disease.
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Affiliation(s)
- Isaac Eliaz
- Eliaz Therapeutics Inc, Santa Rosa, California
| | - Aarti Patil
- Center for Transplantation Sciences, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Nalu Navarro-Alvarez
- Center for Transplantation Sciences, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Zhirui Wang
- Center for Transplantation Sciences, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Amity Eliaz
- University of California, Los Angeles, California
| | - Elaine Weil
- Eliaz Therapeutics Inc, Santa Rosa, California
| | - Barry Wilk
- Eliaz Therapeutics Inc, Santa Rosa, California
| | - David H Sachs
- Center for Transplantation Sciences, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Christene A Huang
- Center for Transplantation Sciences, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
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