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Peter E, Dumez P, Honnorat J, Desestret V. Mechanisms of immune tolerance breakdown in paraneoplastic neurological syndromes. Rev Neurol (Paris) 2024:S0035-3787(24)00582-4. [PMID: 39299842 DOI: 10.1016/j.neurol.2024.08.002] [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: 06/02/2024] [Revised: 08/01/2024] [Accepted: 08/28/2024] [Indexed: 09/22/2024]
Abstract
Paraneoplastic neurological syndromes (PNS) are rare autoimmune disorders triggered by the presence of a cancer. The autoimmunity is herein directed against proteins expressed both in the tumor and in the nervous system, namely the onconeural antigens, against which are directed specific autoantibodies, each of them characterizing a neurological syndrome. The mechanisms of the immune tolerance breakdown in PNS leading to the production of specific autoantibodies directed against the nervous system and leading to the immune attack begins to be explained. Each syndrome is associated with a specific histo-molecular subtype of tumor suggesting a link between the PNS genesis and oncogenesis. The expression of the onconeural antigen by these tumors is insufficient to explain the immune tolerance breakdown. In some PNS tumors, alterations of the antigen have been identified: mutations, gene copy number variation and overexpression of transcript and protein. But in others PNS, no such molecular alterations of the onconeural antigens have been demonstrated. In these cases, other mechanisms of neoantigen generation that may be involved remain to be deciphered. Cancer outcomes of PNS tumors are also characterized by the high frequency of lymph node metastasis at diagnosis. At the primary tumor site, the antitumor immune reaction seems to be particularly intense and characterized by a prominence of B-cell and Ig-secreting plasma cells that may generate the autoantibody secretion. The immune control mechanisms leading to such organization of the immune attack are not known to date. Renewed research efforts are thus needed to better understand the mechanism of immune tolerance breakdown in each PNS and determine potential targets to meet the therapeutic challenges posed by these rare disorders.
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Affiliation(s)
- E Peter
- Inserm U1314/UMR CNRS5284, SynatAc Team, MeLis Institute, Lyon, France; French Reference Center on Paraneoplastic Neurological Syndromes, Hospices Civils de Lyon, Lyon, France; University of Lyon, Université Claude-Bernard Lyon 1, Lyon, France
| | - P Dumez
- Inserm U1314/UMR CNRS5284, SynatAc Team, MeLis Institute, Lyon, France; French Reference Center on Paraneoplastic Neurological Syndromes, Hospices Civils de Lyon, Lyon, France; University of Lyon, Université Claude-Bernard Lyon 1, Lyon, France
| | - J Honnorat
- Inserm U1314/UMR CNRS5284, SynatAc Team, MeLis Institute, Lyon, France; French Reference Center on Paraneoplastic Neurological Syndromes, Hospices Civils de Lyon, Lyon, France; University of Lyon, Université Claude-Bernard Lyon 1, Lyon, France
| | - V Desestret
- Inserm U1314/UMR CNRS5284, SynatAc Team, MeLis Institute, Lyon, France; French Reference Center on Paraneoplastic Neurological Syndromes, Hospices Civils de Lyon, Lyon, France; University of Lyon, Université Claude-Bernard Lyon 1, Lyon, France.
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2
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Bartley CM, Ngo TT, Duy Do L, Zekeridou A, Dandekar R, Muñiz-Castrillo S, Alvarenga BD, Zorn KC, Tubati A, Pinto AL, Browne WD, Hullett PW, Terrelonge M, Schubert RD, Piquet AL, Yang B, Montalvo Perero MJ, Kung AF, Mann SA, Shah MP, Geschwind MD, Gelfand JM, DeRisi JL, Pittock SJ, Honnorat J, Pleasure SJ, Wilson MR. Detection of High-Risk Paraneoplastic Antibodies against TRIM9 and TRIM67 Proteins. Ann Neurol 2023; 94:1086-1101. [PMID: 37632288 PMCID: PMC10842626 DOI: 10.1002/ana.26776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 08/22/2023] [Accepted: 08/22/2023] [Indexed: 08/27/2023]
Abstract
OBJECTIVE Co-occurring anti-tripartite motif-containing protein 9 and 67 autoantibodies (TRIM9/67-IgG) have been reported in only a very few cases of paraneoplastic cerebellar syndrome. The value of these biomarkers and the most sensitive methods of TRIM9/67-IgG detection are not known. METHODS We performed a retrospective, multicenter study to evaluate the cerebrospinal fluid and serum of candidate TRIM9/67-IgG cases by tissue-based immunofluorescence, peptide phage display immunoprecipitation sequencing, overexpression cell-based assay (CBA), and immunoblot. Cases in which TRIM9/67-IgG was detected by at least 2 assays were considered TRIM9/67-IgG positive. RESULTS Among these cases (n = 13), CBA was the most sensitive (100%) and revealed that all cases had TRIM9 and TRIM67 autoantibodies. Of TRIM9/67-IgG cases with available clinical history, a subacute cerebellar syndrome was the most common presentation (n = 7/10), followed by encephalitis (n = 3/10). Of these 10 patients, 70% had comorbid cancer (7/10), 85% of whom (n = 6/7) had confirmed metastatic disease. All evaluable cancer biopsies expressed TRIM9 protein (n = 5/5), whose expression was elevated in the cancerous regions of the tissue in 4 of 5 cases. INTERPRETATION TRIM9/67-IgG is a rare but likely high-risk paraneoplastic biomarker for which CBA appears to be the most sensitive diagnostic assay. ANN NEUROL 2023;94:1086-1101.
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Affiliation(s)
- Christopher M. Bartley
- Weill Institute for Neurosciences, University of California, San Francisco, California
- Department of Psychiatry and Behavioral Sciences, University of California San Francisco, California
| | - Thomas T. Ngo
- Weill Institute for Neurosciences, University of California, San Francisco, California
- Department of Psychiatry and Behavioral Sciences, University of California San Francisco, California
- Department of Neurology, University of California, San Francisco, California
| | - Le Duy Do
- French Reference Center on Paraneoplastic Neurological Syndromes and Autoimmune Encephalitis, Hospices Civils de Lyon and SynatAc Team, Institut MELiS, INSERM U1314/CNRS UMR 5284, Universités de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Anastasia Zekeridou
- Department of Neurology, Center MS and Autoimmune Neurology, Mayo Clinic
- Department of Laboratory Medicine and Pathology, Mayo Clinic
| | - Ravi Dandekar
- Weill Institute for Neurosciences, University of California, San Francisco, California
- Department of Neurology, University of California, San Francisco, California
| | - Sergio Muñiz-Castrillo
- French Reference Center on Paraneoplastic Neurological Syndromes and Autoimmune Encephalitis, Hospices Civils de Lyon and SynatAc Team, Institut MELiS, INSERM U1314/CNRS UMR 5284, Universités de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Bonny D. Alvarenga
- Weill Institute for Neurosciences, University of California, San Francisco, California
- Department of Neurology, University of California, San Francisco, California
| | - Kelsey C. Zorn
- Department of Biochemistry and Biophysics, University of California, San Francisco, California
| | - Asritha Tubati
- Weill Institute for Neurosciences, University of California, San Francisco, California
- Department of Neurology, University of California, San Francisco, California
| | - Anne-Laurie Pinto
- French Reference Center on Paraneoplastic Neurological Syndromes and Autoimmune Encephalitis, Hospices Civils de Lyon and SynatAc Team, Institut MELiS, INSERM U1314/CNRS UMR 5284, Universités de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Weston D. Browne
- Weill Institute for Neurosciences, University of California, San Francisco, California
- Department of Neurology, University of California, San Francisco, California
| | - Patrick W. Hullett
- Weill Institute for Neurosciences, University of California, San Francisco, California
- Department of Neurology, University of California, San Francisco, California
| | - Mark Terrelonge
- Weill Institute for Neurosciences, University of California, San Francisco, California
- Department of Neurology, University of California, San Francisco, California
| | - Ryan D. Schubert
- Weill Institute for Neurosciences, University of California, San Francisco, California
- Department of Neurology, University of California, San Francisco, California
| | - Amanda L. Piquet
- Department of Neurology, University of Colorado Anschutz Medical Campus, School of Medicine, Aurora, Colorado
| | - Binxia Yang
- Department of Laboratory Medicine and Pathology, Mayo Clinic
| | | | - Andrew F. Kung
- University of California San Francisco, School of Medicine, San Francisco, California
| | - Sabrina A. Mann
- Chan Zuckerberg Biohub, San Francisco, California
- Department of Biochemistry and Biophysics, University of California, San Francisco, California
| | - Maulik P. Shah
- Weill Institute for Neurosciences, University of California, San Francisco, California
- Department of Neurology, University of California, San Francisco, California
| | - Michael D. Geschwind
- Weill Institute for Neurosciences, University of California, San Francisco, California
- Department of Neurology, University of California, San Francisco, California
| | - Jeffrey M. Gelfand
- Weill Institute for Neurosciences, University of California, San Francisco, California
- Department of Neurology, University of California, San Francisco, California
| | - Joseph L. DeRisi
- Chan Zuckerberg Biohub, San Francisco, California
- Department of Biochemistry and Biophysics, University of California, San Francisco, California
| | - Sean J. Pittock
- Department of Neurology, Center MS and Autoimmune Neurology, Mayo Clinic
- Department of Laboratory Medicine and Pathology, Mayo Clinic
| | - Jérôme Honnorat
- French Reference Center on Paraneoplastic Neurological Syndromes and Autoimmune Encephalitis, Hospices Civils de Lyon and SynatAc Team, Institut MELiS, INSERM U1314/CNRS UMR 5284, Universités de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Samuel J. Pleasure
- Weill Institute for Neurosciences, University of California, San Francisco, California
- Department of Neurology, University of California, San Francisco, California
| | - Michael R. Wilson
- Weill Institute for Neurosciences, University of California, San Francisco, California
- Department of Neurology, University of California, San Francisco, California
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Song Y, Hu Q, Zhang Q. Anti-Kelch-like protein 11 antibody encephalitis: a case report and literature review. Front Neurol 2023; 14:1273051. [PMID: 37954647 PMCID: PMC10637383 DOI: 10.3389/fneur.2023.1273051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 10/02/2023] [Indexed: 11/14/2023] Open
Abstract
Anti-Kelch-like protein 11 (KLHL11) antibody encephalitis is a rare clinical condition characterized by autoimmune-mediated encephalomyelitis associated with the presence of KLHL11 antibodies. Diagnosis requires the detection of serum and cerebrospinal fluid anti-KLHL11 antibodies, while immunotherapy serves as the principal treatment approach. This paper presents a case report highlighting the emergence of anti-KLHL11 antibody encephalitis. A 66-year-old male patient presented with seizures, impaired cognitive function, disturbance of consciousness, apathy, hypologia, dysphoria, and ataxia. Serum and cerebrospinal fluid (CSF) were identified as positive for anti-KLHL11 antibodies, leading to a diagnosis of autoimmune encephalitis associated with KLHL11 antibodies. After treatment with glucocorticoid, the patient did not experience further convulsions and recovered consciousness, with improved cognitive function. Tumor screening suggested the presence of an underlying malignancy. The clinical manifestations of anti-KLHL11 antibody encephalitis vary widely, and timely identification and treatment can improve prognosis.
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Affiliation(s)
- Yanling Song
- School of Clinical Medicine, Ningxia Medical University, Yinchuan, Ningxia, China
| | - Quanzhong Hu
- Department of Neurology, Qinghai Provincial People’s Hospital, Xining, Qinghai, China
| | - Qing Zhang
- Department of Neurology, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, China
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Yu H, Mao G, Pei Z, Cen J, Meng W, Wang Y, Zhang S, Li S, Xu Q, Sun M, Xiao K. In Vitro Affinity Maturation of Nanobodies against Mpox Virus A29 Protein Based on Computer-Aided Design. Molecules 2023; 28:6838. [PMID: 37836685 PMCID: PMC10574621 DOI: 10.3390/molecules28196838] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/20/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
Mpox virus (MPXV), the most pathogenic zoonotic orthopoxvirus, caused worldwide concern during the SARS-CoV-2 epidemic. Growing evidence suggests that the MPXV surface protein A29 could be a specific diagnostic marker for immunological detection. In this study, a fully synthetic phage display library was screened, revealing two nanobodies (A1 and H8) that specifically recognize A29. Subsequently, an in vitro affinity maturation strategy based on computer-aided design was proposed by building and docking the A29 and A1 three-dimensional structures. Ligand-receptor binding and molecular dynamics simulations were performed to predict binding modes and key residues. Three mutant antibodies were predicted using the platform, increasing the affinity by approximately 10-fold compared with the parental form. These results will facilitate the application of computers in antibody optimization and reduce the cost of antibody development; moreover, the predicted antibodies provide a reference for establishing an immunological response against MPXV.
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Affiliation(s)
- Haiyang Yu
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China;
- Lab of Toxicology and Pharmacology, Faculty of Naval Medicine, Naval Medical University, Shanghai 200433, China; (G.M.); (Z.P.); (J.C.); (W.M.); (Y.W.); (S.Z.); (S.L.)
| | - Guanchao Mao
- Lab of Toxicology and Pharmacology, Faculty of Naval Medicine, Naval Medical University, Shanghai 200433, China; (G.M.); (Z.P.); (J.C.); (W.M.); (Y.W.); (S.Z.); (S.L.)
| | - Zhipeng Pei
- Lab of Toxicology and Pharmacology, Faculty of Naval Medicine, Naval Medical University, Shanghai 200433, China; (G.M.); (Z.P.); (J.C.); (W.M.); (Y.W.); (S.Z.); (S.L.)
| | - Jinfeng Cen
- Lab of Toxicology and Pharmacology, Faculty of Naval Medicine, Naval Medical University, Shanghai 200433, China; (G.M.); (Z.P.); (J.C.); (W.M.); (Y.W.); (S.Z.); (S.L.)
| | - Wenqi Meng
- Lab of Toxicology and Pharmacology, Faculty of Naval Medicine, Naval Medical University, Shanghai 200433, China; (G.M.); (Z.P.); (J.C.); (W.M.); (Y.W.); (S.Z.); (S.L.)
| | - Yunqin Wang
- Lab of Toxicology and Pharmacology, Faculty of Naval Medicine, Naval Medical University, Shanghai 200433, China; (G.M.); (Z.P.); (J.C.); (W.M.); (Y.W.); (S.Z.); (S.L.)
| | - Shanshan Zhang
- Lab of Toxicology and Pharmacology, Faculty of Naval Medicine, Naval Medical University, Shanghai 200433, China; (G.M.); (Z.P.); (J.C.); (W.M.); (Y.W.); (S.Z.); (S.L.)
| | - Songling Li
- Lab of Toxicology and Pharmacology, Faculty of Naval Medicine, Naval Medical University, Shanghai 200433, China; (G.M.); (Z.P.); (J.C.); (W.M.); (Y.W.); (S.Z.); (S.L.)
| | - Qingqiang Xu
- Lab of Toxicology and Pharmacology, Faculty of Naval Medicine, Naval Medical University, Shanghai 200433, China; (G.M.); (Z.P.); (J.C.); (W.M.); (Y.W.); (S.Z.); (S.L.)
| | - Mingxue Sun
- Lab of Toxicology and Pharmacology, Faculty of Naval Medicine, Naval Medical University, Shanghai 200433, China; (G.M.); (Z.P.); (J.C.); (W.M.); (Y.W.); (S.Z.); (S.L.)
| | - Kai Xiao
- Lab of Toxicology and Pharmacology, Faculty of Naval Medicine, Naval Medical University, Shanghai 200433, China; (G.M.); (Z.P.); (J.C.); (W.M.); (Y.W.); (S.Z.); (S.L.)
- Marine Biomedical Science and Technology Innovation Platform of Lingang Special Area, Shanghai 201306, China
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5
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Li Y, Yang KD, Duan HY, Du YN, Ye JF. Phage-based peptides for pancreatic cancer diagnosis and treatment: alternative approach. Front Microbiol 2023; 14:1231503. [PMID: 37601380 PMCID: PMC10433397 DOI: 10.3389/fmicb.2023.1231503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 07/06/2023] [Indexed: 08/22/2023] Open
Abstract
Pancreatic cancer is a devastating disease with a high mortality rate and a lack of effective therapies. The challenges associated with early detection and the highly aggressive nature of pancreatic cancer have limited treatment options, underscoring the urgent need for better disease-modifying therapies. Peptide-based biotherapeutics have become an attractive area of research due to their favorable properties such as high selectivity and affinity, chemical modifiability, good tissue permeability, and easy metabolism and excretion. Phage display, a powerful technique for identifying peptides with high affinity and specificity for their target molecules, has emerged as a key tool in the discovery of peptide-based drugs. Phage display technology involves the use of bacteriophages to express peptide libraries, which are then screened against a target of interest to identify peptides with desired properties. This approach has shown great promise in cancer diagnosis and treatment, with potential applications in targeting cancer cells and developing new therapies. In this comprehensive review, we provide an overview of the basic biology of phage vectors, the principles of phage library construction, and various methods for binding affinity assessment. We then describe the applications of phage display in pancreatic cancer therapy, targeted drug delivery, and early detection. Despite its promising potential, there are still challenges to be addressed, such as optimizing the selection process and improving the pharmacokinetic properties of phage-based drugs. Nevertheless, phage display represents a promising approach for the development of novel targeted therapies in pancreatic cancer and other tumors.
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Affiliation(s)
- Yang Li
- General Surgery Center, First Hospital of Jilin University, Changchun, China
- School of Nursing, Jilin University, Changchun, China
| | - Kai-di Yang
- General Surgery Center, First Hospital of Jilin University, Changchun, China
- School of Nursing, Jilin University, Changchun, China
| | - Hao-yu Duan
- General Surgery Center, First Hospital of Jilin University, Changchun, China
- School of Nursing, Jilin University, Changchun, China
| | - Ya-nan Du
- General Surgery Center, First Hospital of Jilin University, Changchun, China
- School of Nursing, Jilin University, Changchun, China
| | - Jun-feng Ye
- General Surgery Center, First Hospital of Jilin University, Changchun, China
- School of Nursing, Jilin University, Changchun, China
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Mandel-Brehm C, Vazquez SE, Liverman C, Cheng M, Quandt Z, Kung AF, Parent A, Miao B, Disse E, Cugnet-Anceau C, Dalle S, Orlova E, Frolova E, Alba D, Michels A, Oftedal BE, Lionakis MS, Husebye ES, Agarwal AK, Li X, Zhu C, Li Q, Oral E, Brown R, Anderson MS, Garg A, DeRisi JL. Autoantibodies to Perilipin-1 Define a Subset of Acquired Generalized Lipodystrophy. Diabetes 2023; 72:59-70. [PMID: 35709010 PMCID: PMC9797316 DOI: 10.2337/db21-1172] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 06/06/2022] [Indexed: 02/04/2023]
Abstract
Acquired lipodystrophy is often characterized as an idiopathic subtype of lipodystrophy. Despite suspicion of an immune-mediated pathology, biomarkers such as autoantibodies are generally lacking. Here, we used an unbiased proteome-wide screening approach to identify autoantibodies to the adipocyte-specific lipid droplet protein perilipin 1 (PLIN1) in a murine model of autoimmune polyendocrine syndrome type 1 (APS1). We then tested for PLIN1 autoantibodies in human subjects with acquired lipodystrophy with two independent severe breaks in immune tolerance (including APS1) along with control subjects using a specific radioligand binding assay and indirect immunofluorescence on fat tissue. We identified autoantibodies to PLIN1 in these two cases, including the first reported case of APS1 with acquired lipodystrophy and a second patient who acquired lipodystrophy as an immune-related adverse event following cancer immunotherapy. Lastly, we also found PLIN1 autoantibodies to be specifically enriched in a subset of patients with acquired generalized lipodystrophy (17 of 46 [37%]), particularly those with panniculitis and other features of autoimmunity. These data lend additional support to new literature that suggests that PLIN1 autoantibodies represent a marker of acquired autoimmune lipodystrophies and further link them to a break in immune tolerance.
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Affiliation(s)
- Caleigh Mandel-Brehm
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA
| | - Sara E. Vazquez
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA
- Diabetes Center, University of California, San Francisco, San Francisco, CA
| | - Christopher Liverman
- Department of Pathology, University of California, San Francisco, San Francisco, CA
| | - Mickie Cheng
- Diabetes Center, University of California, San Francisco, San Francisco, CA
| | - Zoe Quandt
- Diabetes Center, University of California, San Francisco, San Francisco, CA
- Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Andrew F. Kung
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA
| | - Audrey Parent
- Diabetes Center, University of California, San Francisco, San Francisco, CA
| | - Brenda Miao
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA
- Diabetes Center, University of California, San Francisco, San Francisco, CA
| | - Emmanuel Disse
- Endocrinology Diabetology and Nutrition Department, Lyon Sud Hospital, Hospices Civils de Lyon, Pierre-Bénite, France
- ImmuCare, Cancer Institute of Hospices Civils de Lyon (IC-HCL), Lyon, France
| | - Christine Cugnet-Anceau
- Endocrinology Diabetology and Nutrition Department, Lyon Sud Hospital, Hospices Civils de Lyon, Pierre-Bénite, France
- ImmuCare, Cancer Institute of Hospices Civils de Lyon (IC-HCL), Lyon, France
| | - Stéphane Dalle
- ImmuCare, Cancer Institute of Hospices Civils de Lyon (IC-HCL), Lyon, France
- Dermatology Department, Lyon Sud Hospital, Hospices Civils de Lyon, Pierre-Bénite, France
| | - Elizaveta Orlova
- Endocrinology Research Centre, Institute of Paediatric Endocrinology, Moscow, Russia
| | - Elena Frolova
- National Medical Research Center of Children’s Health, Moscow, Russia
| | - Diana Alba
- Diabetes Center, University of California, San Francisco, San Francisco, CA
- Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Aaron Michels
- Barbara Davis Center for Childhood Diabetes, University of Colorado School of Medicine, Aurora, CO
| | - Bergithe E. Oftedal
- University of Bergen, Bergen, Norway
- Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Michail S. Lionakis
- Fungal Pathogenesis Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Eystein S. Husebye
- Department of Medicine, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Science and K.G. Jebsen Center for Autoimmune Disorders, University of Bergen, Bergen, Norway
| | - Anil K. Agarwal
- Division of Nutrition and Metabolic Diseases, Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX
| | - Xilong Li
- Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX
| | - Chengsong Zhu
- Department of Immunology, UT Southwestern Medical Center, Dallas, TX
| | - Quan Li
- Department of Immunology, UT Southwestern Medical Center, Dallas, TX
| | - Elif Oral
- Division of Metabolism, Endocrinology & Diabetes and Caswell Diabetes Institute, University of Michigan, Ann Arbor, MI
| | - Rebecca Brown
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Mark S. Anderson
- Diabetes Center, University of California, San Francisco, San Francisco, CA
- Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Abhimanyu Garg
- Division of Nutrition and Metabolic Diseases, Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX
| | - Joseph L. DeRisi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA
- Chan Zuckerberg Biohub, San Francisco, CA
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Zhang X, Li S, Luo H, He S, Yang H, Li L, Tian T, Han Q, Ye J, Huang C, Liu A, Jiang Y. Identification of heptapeptides targeting a lethal bacterial strain in septic mice through an integrative approach. Signal Transduct Target Ther 2022; 7:245. [PMID: 35871689 PMCID: PMC9309159 DOI: 10.1038/s41392-022-01035-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 04/06/2022] [Accepted: 05/18/2022] [Indexed: 11/11/2022] Open
Abstract
Effectively killing pathogenic bacteria is key for the treatment of sepsis. Although various anti-infective drugs have been used for the treatment of sepsis, the therapeutic effect is largely limited by the lack of a specific bacterium-targeting delivery system. This study aimed to develop antibacterial peptides that specifically target pathogenic bacteria for the treatment of sepsis. The lethal bacterial strain Escherichia coli MSI001 was isolated from mice of a cecal ligation and puncture (CLP) model and was used as a target to screen bacterial binding heptapeptides through an integrative bioinformatics approach based on phage display technology and high-throughput sequencing (HTS). Heptapeptides binding to E. coli MSI001 with high affinity were acquired after normalization by the heptapeptide frequency of the library. A representative heptapeptide VTKLGSL (VTK) was selected for fusion with the antibacterial peptide LL-37 to construct the specific-targeting antibacterial peptide VTK-LL37. We found that, in comparison with LL37, VTK-LL37 showed prominent bacteriostatic activity and an inhibitive effect on biofilm formation in vitro. In vivo experiments demonstrated that VTK-LL37 significantly inhibited bacterial growth, reduced HMGB1 expression, alleviated lesions of vital organs and improved the survival of mice subjected to CLP modeling. Furthermore, membrane DEGP and DEGQ were identified as VTK-binding proteins by proteomic methods. This study provides a novel strategy for targeted pathogen killing, which is helpful for the treatment of sepsis in the era of precise medicine.
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Rasquinha MT, Lasrado N, Petro-Turnquist E, Weaver E, Venkataraman T, Anderson D, Laserson U, Larman HB, Reddy J. PhIP-Seq Reveals Autoantibodies for Ubiquitously Expressed Antigens in Viral Myocarditis. BIOLOGY 2022; 11:biology11071055. [PMID: 36101433 PMCID: PMC9312229 DOI: 10.3390/biology11071055] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/09/2022] [Accepted: 07/11/2022] [Indexed: 12/01/2022]
Abstract
Simple Summary Myocarditis is the inflammation of the heart muscle, and viral infections are a common cause of this disease. Myocarditis in some patients can progress to dilated cardiomyopathy (DCM). The mouse model of coxsackievirus B3 (CVB3) is commonly used to understand this disease progression in DCM patients. In this paper, we have attempted to analyze antibodies for heart antigens that could be produced as a result of heart damage in animals infected with CVB3 using a technique called Phage ImmunoPrecipitation Sequencing (PhIP-Seq). The analyses led us to identify antibodies for several proteins that were not previously reported that may have relevance to human disease. Abstract Enteroviruses such as group B coxsackieviruses (CVB) are commonly suspected as causes of myocarditis that can lead to dilated cardiomyopathy (DCM), and the mouse model of CVB3 myocarditis is routinely used to understand DCM pathogenesis. Mechanistically, autoimmunity is suspected due to the presence of autoantibodies for select antigens. However, their role continues to be enigmatic, which also raises the question of whether the breadth of autoantibodies is sufficiently characterized. Here, we attempted to comprehensively analyze the autoantibody repertoire using Phage ImmunoPrecipitation Sequencing (PhIP-Seq), a versatile and high-throughput platform, in the mouse model of CVB3 myocarditis. First, PhIP-Seq analysis using the VirScan library revealed antibody reactivity only to CVB3 in the infected group but not in controls, thus validating the technique in this model. Second, using the mouse peptide library, we detected autoantibodies to 32 peptides from 25 proteins in infected animals that are ubiquitously expressed and have not been previously reported. Third, by using ELISA as a secondary assay, we confirmed antibody reactivity in sera from CVB3-infected animals to cytochrome c oxidase assembly factor 4 homolog (COA4) and phosphoinositide-3-kinase adaptor protein 1 (PIK3AP1), indicating the specificity of antibody detection by PhIP-Seq technology. Fourth, we noted similar antibody reactivity patterns in CVB3 and CVB4 infections, suggesting that the COA4- and PIK3AP1-reactive antibodies could be common to multiple CVB infections. The specificity of the autoantibodies was affirmed with influenza-infected animals that showed no reactivity to any of the antigens tested. Taken together, our data suggest that the autoantibodies identified by PhIP-Seq may have relevance to CVB pathogenesis, with a possibility that similar reactivity could be expected in human DCM patients.
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Affiliation(s)
- Mahima T. Rasquinha
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, USA; (M.T.R.); (N.L.)
| | - Ninaad Lasrado
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, USA; (M.T.R.); (N.L.)
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Erika Petro-Turnquist
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA; (E.P.-T.); (E.W.)
| | - Eric Weaver
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA; (E.P.-T.); (E.W.)
| | - Thiagarajan Venkataraman
- Division of Immunology, Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA;
| | - Daniel Anderson
- Department of Internal Medicine, Division of Cardiovascular Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA;
| | - Uri Laserson
- Department of Genetics and Genomic Sciences and Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
| | - H. Benjamin Larman
- Division of Immunology, Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA;
- Correspondence: (H.B.L.); (J.R.); Tel.: +1-(410)-614-6525 (H.B.L); +1-(402)-472-8541 (J.R.)
| | - Jay Reddy
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, USA; (M.T.R.); (N.L.)
- Correspondence: (H.B.L.); (J.R.); Tel.: +1-(410)-614-6525 (H.B.L); +1-(402)-472-8541 (J.R.)
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9
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Ochoa R, Soler MA, Gladich I, Battisti A, Minovski N, Rodriguez A, Fortuna S, Cossio P, Laio A. Computational Evolution Protocol for Peptide Design. Methods Mol Biol 2022; 2405:335-359. [PMID: 35298821 DOI: 10.1007/978-1-0716-1855-4_16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Computational peptide design is useful for therapeutics, diagnostics, and vaccine development. To select the most promising peptide candidates, the key is describing accurately the peptide-target interactions at the molecular level. We here review a computational peptide design protocol whose key feature is the use of all-atom explicit solvent molecular dynamics for describing the different peptide-target complexes explored during the optimization. We describe the milestones behind the development of this protocol, which is now implemented in an open-source code called PARCE. We provide a basic tutorial to run the code for an antibody fragment design example. Finally, we describe three additional applications of the method to design peptides for different targets, illustrating the broad scope of the proposed approach.
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Affiliation(s)
- Rodrigo Ochoa
- Biophysics of Tropical Diseases, Max Planck Tandem Group, University of Antioquia, Medellin, Colombia
| | | | - Ivan Gladich
- Qatar Environment and Energy Research Institute, Hamad Bin Khalifa University, Doha, Qatar
- SISSA, Trieste, Italy
| | | | - Nikola Minovski
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
- Theory Department, Laboratory for Cheminformatics, National Institute of Chemistry, Ljubljana, Slovenia
| | - Alex Rodriguez
- The Abdus Salam International Centre for Theoretical Physics, Trieste, Italy
| | - Sara Fortuna
- Italian Institute of Technology (IIT), Genova, Italy
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Pilar Cossio
- Biophysics of Tropical Diseases, Max Planck Tandem Group, University of Antioquia, Medellin, Colombia
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Alessandro Laio
- The Abdus Salam International Centre for Theoretical Physics, Trieste, Italy
- SISSA, Trieste, Italy
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10
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Jaroszewicz W, Morcinek-Orłowska J, Pierzynowska K, Gaffke L, Węgrzyn G. Phage display and other peptide display technologies. FEMS Microbiol Rev 2021; 46:6407522. [PMID: 34673942 DOI: 10.1093/femsre/fuab052] [Citation(s) in RCA: 97] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 10/19/2021] [Indexed: 12/13/2022] Open
Abstract
Phage display technology, which is based on the presentation of peptide sequences on the surface of bacteriophage virions, was developed over 30 years ago. Improvements in phage display systems have allowed us to employ this method in numerous fields of biotechnology, as diverse as immunological and biomedical applications, the formation of novel materials and many others. The importance of phage display platforms was recognized by awarding the Nobel Prize in 2018 "for the phage display of peptides and antibodies". In contrast to many review articles concerning specific applications of phage display systems published in recent years, we present an overview of this technology, including a comparison of various display systems, their advantages and disadvantages, and examples of applications in various fields of science, medicine, and the broad sense of biotechnology. Other peptide display technologies, which employ bacterial, yeast and mammalian cells, as well as eukaryotic viruses and cell-free systems, are also discussed. These powerful methods are still being developed and improved; thus, novel sophisticated tools based on phage display and other peptide display systems are constantly emerging, and new opportunities to solve various scientific, medical and technological problems can be expected to become available in the near future.
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Affiliation(s)
- Weronika Jaroszewicz
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | | | - Karolina Pierzynowska
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Lidia Gaffke
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
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11
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Salinas VH, Stüve O. Systems Approaches to Unravel T Cell Function and Therapeutic Potential in Autoimmune Disease. THE JOURNAL OF IMMUNOLOGY 2021; 206:669-675. [PMID: 33526601 DOI: 10.4049/jimmunol.2000954] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 11/02/2020] [Indexed: 12/22/2022]
Abstract
Producing Ag-specific immune responses constrained to target tissues or cells that can be engaged or disengaged at will is predicated on understanding the network of genes governing immune cell function, defining the rules underlying Ag specificity, and synthesizing the tools to engineer them. The successes and limitations of chimeric Ag receptor (CAR) T cells emphasize this goal, and advances in high-throughput sequencing, large-scale genomic screens, single-cell profiling, and genetic modification are providing the necessary data to bring it to fruition-including a broader application into the treatment of autoimmune diseases. In this review, we delve into the implementation of these developments, survey the relevant works, and propose a framework for generating the next generation of synthetic T cells informed by the principles learned from these systems approaches.
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Affiliation(s)
- Victor H Salinas
- Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, TX 75390; and
| | - Olaf Stüve
- Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, TX 75390; and .,Neurology Section, Medical Service, U.S. Department of Veterans Affairs, North Texas Health Care System, Dallas, TX 75216
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12
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Gelbard A, Wanjalla C, Wootten CT, Drake WP, Lowery AS, Wheeler DA, Cardenas MF, Sikora AG, Pathak RR, McDonnell W, Mallal S, Pilkinton M. The Proximal Airway Is a Reservoir for Adaptive Immunologic Memory in Idiopathic Subglottic Stenosis. Laryngoscope 2021; 131:610-617. [PMID: 32603507 PMCID: PMC7951501 DOI: 10.1002/lary.28840] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/18/2020] [Accepted: 05/21/2020] [Indexed: 01/20/2023]
Abstract
OBJECTIVES/HYPOTHESIS Characterization of the localized adaptive immune response in the airway scar of patients with idiopathic subglottic stenosis (iSGS). STUDY DESIGN Basic Science. METHODS Utilizing 36 patients with subglottic stenosis (25 idiopathic subglottic stenosis [iSGS], 10 iatrogenic post-intubation stenosis [iLTS], and one granulomatosis with polyangiitis [GPA]) we applied immunohistochemical and immunologic techniques coupled with RNA sequencing. RESULTS iSGS, iLTS, and GPA demonstrate a significant immune infiltrate in the subglottic scar consisting of adaptive cell subsets (T cells along with dendritic cells). Interrogation of T cell subtypes showed significantly more CD69+ CD103+ CD8+ tissue resident memory T cells (TRM ) in the iSGS airway scar than iLTS specimens (iSGS vs. iLTS; 50% vs. 28%, P = .0065). Additionally, subglottic CD8+ clones possessed T-cell receptor (TCR) sequences with known antigen specificity for viral and intracellular pathogens. CONCLUSIONS The human subglottis is significantly enriched for CD8+ tissue resident memory T cells in iSGS, which possess TCR sequences proven to recognize viral and intracellular pathogens. These results inform our understanding of iSGS, provide a direction for future discovery, and demonstrate immunologic function in the human proximal airway. Laryngoscope, 131:610-617, 2021.
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Affiliation(s)
- Alexander Gelbard
- Dept. of Otolaryngology-Head & Neck Surgery, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Celestine Wanjalla
- Dept. of Medicine, Division of Infectious Disease, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Christopher T. Wootten
- Dept. of Otolaryngology-Head & Neck Surgery, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Wonder P. Drake
- Dept. of Molecular and Human Genetics, Baylor College of Medicine, Houston Texas
| | - Anne S Lowery
- Dept. of Otolaryngology-Head & Neck Surgery, Vanderbilt University Medical Center, Nashville, Tennessee
| | - David A. Wheeler
- Dept. of Molecular and Human Genetics, Baylor College of Medicine, Houston Texas
| | - Maria F. Cardenas
- Dept. of Molecular and Human Genetics, Baylor College of Medicine, Houston Texas
| | - Andrew G. Sikora
- Bobby R. Alford Dept. of Otolaryngology-Head & Neck Surgery, Baylor College of Medicine, Houston Texas
| | - Ravi R. Pathak
- Bobby R. Alford Dept. of Otolaryngology-Head & Neck Surgery, Baylor College of Medicine, Houston Texas
| | | | - Simon Mallal
- Dept. of Molecular and Human Genetics, Baylor College of Medicine, Houston Texas
| | - Mark Pilkinton
- Dept. of Medicine, Division of Infectious Disease, Vanderbilt University Medical Center, Nashville, Tennessee
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13
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Delgado-García G, Balint B. New Technique, New Antibody: Phage Display Identifies Kelch-Like Protein-11 Antibodies. Mov Disord Clin Pract 2021; 8:215-216. [PMID: 33553490 PMCID: PMC7853185 DOI: 10.1002/mdc3.13136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 12/03/2020] [Accepted: 12/06/2020] [Indexed: 12/01/2022] Open
Affiliation(s)
- Guillermo Delgado-García
- Department of Clinical Neurosciences, Cumming School of Medicine University of Calgary Calgary Alberta Canada
| | - Bettina Balint
- Department of Clinical and Movement Neurosciences UCL Queen Square Institute of Neurology London UK.,Department of Neurology University Hospital Heidelberg Heidelberg Germany
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14
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Computational Evolution of Beta-2-Microglobulin Binding Peptides for Nanopatterned Surface Sensors. Int J Mol Sci 2021; 22:ijms22020812. [PMID: 33467468 PMCID: PMC7831021 DOI: 10.3390/ijms22020812] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 12/24/2020] [Accepted: 01/04/2021] [Indexed: 11/17/2022] Open
Abstract
The bottom-up design of smart nanodevices largely depends on the accuracy by which each of the inherent nanometric components can be functionally designed with predictive methods. Here, we present a rationally designed, self-assembled nanochip capable of capturing a target protein by means of pre-selected binding sites. The sensing elements comprise computationally evolved peptides, designed to target an arbitrarily selected binding site on the surface of beta-2-Microglobulin (β2m), a globular protein that lacks well-defined pockets. The nanopatterned surface was generated by an atomic force microscopy (AFM)-based, tip force-driven nanolithography technique termed nanografting to construct laterally confined self-assembled nanopatches of single stranded (ss)DNA. These were subsequently associated with an ssDNA-peptide conjugate by means of DNA-directed immobilization, therefore allowing control of the peptide's spatial orientation. We characterized the sensitivity of such peptide-containing systems against β2m in solution by means of AFM-based differential topographic imaging and surface plasmon resonance (SPR) spectroscopy. Our results show that the confined peptides are capable of specifically capturing β2m from the surface-liquid interface with micromolar affinity, hence providing a viable proof-of-concept for our approach to peptide design.
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15
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Moritz CP, Paul S, Stoevesandt O, Tholance Y, Camdessanché JP, Antoine JC. Autoantigenomics: Holistic characterization of autoantigen repertoires for a better understanding of autoimmune diseases. Autoimmun Rev 2020; 19:102450. [DOI: 10.1016/j.autrev.2019.102450] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 10/16/2019] [Indexed: 12/13/2022]
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