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Marrer-Berger E, Nicastri A, Augustin A, Kramar V, Liao H, Hanisch LJ, Carpy A, Weinzierl T, Durr E, Schaub N, Nudischer R, Ortiz-Franyuti D, Breous-Nystrom E, Stucki J, Hobi N, Raggi G, Cabon L, Lezan E, Umaña P, Woodhouse I, Bujotzek A, Klein C, Ternette N. The physiological interactome of TCR-like antibody therapeutics in human tissues. Nat Commun 2024; 15:3271. [PMID: 38627373 PMCID: PMC11021511 DOI: 10.1038/s41467-024-47062-5] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 03/19/2024] [Indexed: 04/19/2024] Open
Abstract
Selective binding of TCR-like antibodies that target a single tumour-specific peptide antigen presented by human leukocyte antigens (HLA) is the absolute prerequisite for their therapeutic suitability and patient safety. To date, selectivity assessment has been limited to peptide library screening and predictive modeling. We developed an experimental platform to de novo identify interactomes of TCR-like antibodies directly in human tissues using mass spectrometry. As proof of concept, we confirm the target epitope of a MAGE-A4-specific TCR-like antibody. We further determine cross-reactive peptide sequences for ESK1, a TCR-like antibody with known off-target activity, in human liver tissue. We confirm off-target-induced T cell activation and ESK1-mediated liver spheroid killing. Off-target sequences feature an amino acid motif that allows a structural groove-coordination mimicking that of the target peptide, therefore allowing the interaction with the engager molecule. We conclude that our strategy offers an accurate, scalable route for evaluating the non-clinical safety profile of TCR-like antibody therapeutics prior to first-in-human clinical application.
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Affiliation(s)
- Estelle Marrer-Berger
- Roche Pharma Research & Early Development, Roche Innovation Center Basel, 4070, Basel, Switzerland
| | - Annalisa Nicastri
- The Jenner Institute, Old Road Campus Research Building, Oxford, OX37DQ, UK
- Centre for Immuno-Oncology, Old Road Campus Research Building, Oxford, OX37DQ, UK
| | - Angelique Augustin
- Roche Pharma Research & Early Development, Roche Innovation Center Basel, 4070, Basel, Switzerland
| | - Vesna Kramar
- Roche Innovation Center Zürich, 8952, Schlieren, Switzerland
| | - Hanqing Liao
- The Jenner Institute, Old Road Campus Research Building, Oxford, OX37DQ, UK
- Centre for Immuno-Oncology, Old Road Campus Research Building, Oxford, OX37DQ, UK
| | | | - Alejandro Carpy
- Roche Pharma Research & Early Development, Roche Innovation Center Munich, 82377, Penzberg, Germany
| | - Tina Weinzierl
- Roche Innovation Center Zürich, 8952, Schlieren, Switzerland
| | - Evelyne Durr
- Roche Pharma Research & Early Development, Roche Innovation Center Basel, 4070, Basel, Switzerland
| | - Nathalie Schaub
- Roche Pharma Research & Early Development, Roche Innovation Center Basel, 4070, Basel, Switzerland
| | - Ramona Nudischer
- Roche Pharma Research & Early Development, Roche Innovation Center Basel, 4070, Basel, Switzerland
| | - Daniela Ortiz-Franyuti
- Roche Pharma Research & Early Development, Roche Innovation Center Basel, 4070, Basel, Switzerland
| | - Ekaterina Breous-Nystrom
- Roche Pharma Research & Early Development, Roche Innovation Center Basel, 4070, Basel, Switzerland
| | - Janick Stucki
- Alveolix AG, Swiss Organs-on-Chip Innovation, 3010, Bern, Switzerland
| | - Nina Hobi
- Alveolix AG, Swiss Organs-on-Chip Innovation, 3010, Bern, Switzerland
| | - Giulia Raggi
- Alveolix AG, Swiss Organs-on-Chip Innovation, 3010, Bern, Switzerland
| | - Lauriane Cabon
- Roche Pharma Research & Early Development, Roche Innovation Center Basel, 4070, Basel, Switzerland
| | - Emmanuelle Lezan
- Roche Pharma Research & Early Development, Roche Innovation Center Basel, 4070, Basel, Switzerland
| | - Pablo Umaña
- Roche Innovation Center Zürich, 8952, Schlieren, Switzerland
| | - Isaac Woodhouse
- The Jenner Institute, Old Road Campus Research Building, Oxford, OX37DQ, UK
- Centre for Immuno-Oncology, Old Road Campus Research Building, Oxford, OX37DQ, UK
| | - Alexander Bujotzek
- Roche Pharma Research & Early Development, Roche Innovation Center Munich, 82377, Penzberg, Germany
| | - Christian Klein
- Roche Innovation Center Zürich, 8952, Schlieren, Switzerland.
| | - Nicola Ternette
- The Jenner Institute, Old Road Campus Research Building, Oxford, OX37DQ, UK.
- Centre for Immuno-Oncology, Old Road Campus Research Building, Oxford, OX37DQ, UK.
- Department of Pharmaceutical Sciences, University of Utrecht, 3584, CH, Utrecht, The Netherlands.
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2
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Hogan MJ, Maheshwari N, Begg BE, Nicastri A, Hedgepeth EJ, Muramatsu H, Pardi N, Miller MA, Reilly SP, Brossay L, Lynch KW, Ternette N, Eisenlohr LC. Cryptic MHC-E epitope from influenza elicits a potent cytolytic T cell response. Nat Immunol 2023; 24:1933-1946. [PMID: 37828378 DOI: 10.1038/s41590-023-01644-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 09/08/2023] [Indexed: 10/14/2023]
Abstract
The extent to which unconventional forms of antigen presentation drive T cell immunity is unknown. By convention, CD8 T cells recognize viral peptides, or epitopes, in association with classical major histocompatibility complex (MHC) class I, or MHC-Ia, but immune surveillance can, in some cases, be directed against peptides presented by nonclassical MHC-Ib, in particular the MHC-E proteins (Qa-1 in mice and HLA-E in humans); however, the overall importance of nonclassical responses in antiviral immunity remains unclear. Similarly uncertain is the importance of 'cryptic' viral epitopes, defined as those undetectable by conventional mapping techniques. Here we used an immunopeptidomic approach to search for unconventional epitopes that drive T cell responses in mice infected with influenza virus A/Puerto Rico/8/1934. We identified a nine amino acid epitope, termed M-SL9, that drives a co-immunodominant, cytolytic CD8 T cell response that is unconventional in two major ways: first, it is presented by Qa-1, and second, it has a cryptic origin, mapping to an unannotated alternative reading frame product of the influenza matrix gene segment. Presentation and immunogenicity of M-SL9 are dependent on the second AUG codon of the positive sense matrix RNA segment, suggesting translation initiation by leaky ribosomal scanning. During influenza virus A/Puerto Rico/8/1934 infection, M-SL9-specific T cells exhibit a low level of egress from the lungs and strong differentiation into tissue-resident memory cells. Importantly, we show that M-SL9/Qa-1-specific T cells can be strongly induced by messenger RNA vaccination and that they can mediate antigen-specific cytolysis in vivo. Our results demonstrate that noncanonical translation products can account for an important fraction of the T cell repertoire and add to a growing body of evidence that MHC-E-restricted T cells could have substantial therapeutic value.
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Affiliation(s)
- Michael J Hogan
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
| | - Nikita Maheshwari
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pathology, University of Chicago, Chicago, IL, USA
| | - Bridget E Begg
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Annalisa Nicastri
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Emma J Hedgepeth
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Hiromi Muramatsu
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Norbert Pardi
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael A Miller
- Department of Microbiology and Immunology, Thomas Jefferson University, Philadelphia, PA, USA
- Century Therapeutics, Philadelphia, PA, USA
| | - Shanelle P Reilly
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, USA
| | - Laurent Brossay
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, USA
| | - Kristen W Lynch
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Nicola Ternette
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Laurence C Eisenlohr
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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3
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Carré A, Zhou Z, Perez-Hernandez J, Samassa F, Lekka C, Manganaro A, Oshima M, Liao H, Parker R, Nicastri A, Brandao B, Colli ML, Eizirik DL, Göransson M, Morales OB, Anderson A, Landry L, Kobaisi F, Scharfmann R, Marselli L, Marchetti P, You S, Nakayama M, Hadrup SR, Kent SC, Richardson SJ, Ternette N, Mallone R. Interferon-α promotes neo-antigen formation and preferential HLA-B-restricted antigen presentation in pancreatic β-cells. bioRxiv 2023:2023.09.15.557918. [PMID: 37745505 PMCID: PMC10516036 DOI: 10.1101/2023.09.15.557918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Interferon (IFN)-α is the earliest cytokine signature observed in individuals at risk for type 1 diabetes (T1D), but its effect on the repertoire of HLA Class I (HLA-I)-bound peptides presented by pancreatic β-cells is unknown. Using immunopeptidomics, we characterized the peptide/HLA-I presentation in in-vitro resting and IFN-α-exposed β-cells. IFN-α increased HLA-I expression and peptide presentation, including neo-sequences derived from alternative mRNA splicing, post-translational modifications - notably glutathionylation - and protein cis-splicing. This antigenic landscape relied on processing by both the constitutive and immune proteasome. The resting β-cell immunopeptidome was dominated by HLA-A-restricted ligands. However, IFN-α only marginally upregulated HLA-A and largely favored HLA-B, translating into a major increase in HLA-B-restricted peptides and into an increased activation of HLA-B-restricted vs. HLA-A-restricted CD8+ T-cells. A preferential HLA-B hyper-expression was also observed in the islets of T1D vs. non-diabetic donors, and we identified islet-infiltrating CD8+ T-cells from T1D donors reactive to HLA-B-restricted granule peptides. Thus, the inflammatory milieu of insulitis may skew the autoimmune response toward epitopes presented by HLA-B, hence recruiting a distinct T-cell repertoire that may be relevant to T1D pathogenesis.
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Affiliation(s)
- Alexia Carré
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France
| | - Zhicheng Zhou
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France
| | - Javier Perez-Hernandez
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France
- Department of Nutrition and Health, Valencian International University (VIU), Valencia, Spain
| | | | - Christiana Lekka
- Islet Biology Group, Exeter Centre of Excellence in Diabetes Research, University of Exeter Medical School, Exeter, UK
| | - Anthony Manganaro
- Diabetes Center of Excellence, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Masaya Oshima
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France
| | - Hanqing Liao
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, UK
| | - Robert Parker
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, UK
| | - Annalisa Nicastri
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, UK
| | - Barbara Brandao
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France
| | - Maikel L. Colli
- ULB Center for Diabetes Research, Université Libre de Bruxelles, Brussels, Belgium
| | - Decio L. Eizirik
- ULB Center for Diabetes Research, Université Libre de Bruxelles, Brussels, Belgium
| | - Marcus Göransson
- Department of Health Technology, Technical University of Denmark, Copenhagen, Denmark
| | | | - Amanda Anderson
- Barbara Davis Center for Diabetes, University of Colorado School of Medicine, Aurora, CO, USA
| | - Laurie Landry
- Barbara Davis Center for Diabetes, University of Colorado School of Medicine, Aurora, CO, USA
| | - Farah Kobaisi
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France
| | | | - Lorella Marselli
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Piero Marchetti
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Sylvaine You
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France
- Indiana Biosciences Research Institute, Indianapolis, IN, USA
| | - Maki Nakayama
- Barbara Davis Center for Diabetes, University of Colorado School of Medicine, Aurora, CO, USA
| | - Sine R. Hadrup
- Department of Health Technology, Technical University of Denmark, Copenhagen, Denmark
| | - Sally C. Kent
- Diabetes Center of Excellence, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Sarah J. Richardson
- Islet Biology Group, Exeter Centre of Excellence in Diabetes Research, University of Exeter Medical School, Exeter, UK
| | - Nicola Ternette
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, UK
| | - Roberto Mallone
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France
- Indiana Biosciences Research Institute, Indianapolis, IN, USA
- Assistance Publique Hôpitaux de Paris, Service de Diabétologie et Immunologie Clinique, Cochin Hospital, Paris, France
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4
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Peng X, Woodhouse I, Hancock G, Parker R, Marx K, Müller J, Salatino S, Partridge T, Nicastri A, Liao H, Kruppa G, Hellner K, Dorrell L, Ternette N. Novel canonical and non-canonical viral antigens extend current targets for immunotherapy of HPV-driven cervical cancer. iScience 2023; 26:106101. [PMID: 36876126 PMCID: PMC9978627 DOI: 10.1016/j.isci.2023.106101] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 08/30/2022] [Accepted: 01/26/2023] [Indexed: 02/05/2023] Open
Abstract
Current immunotherapeutic approaches for human papillomavirus (HPV)-driven cervical cancer target the viral oncogenes E6 and E7. We report viral canonical and alternative reading frame (ARF)-derived sequences presented on cervical tumor cells, including antigens encoded by the conserved viral gene E1. We confirm immunogenicity of the identified viral peptides in HPV-positive women, and women with cervical intraepithelial neoplasia. We observe consistent transcription of the E1, E6, and E7 genes in 10 primary cervical tumor resections from the four most common high-risk HPV subtypes (HPV16, 18, 31, and 45), suggesting the suitability of E1 as therapeutic target. We finally confirm HLA presentation of canonical peptides derived from E6 and E7, and ARF-derived viral peptides from a reverse-strand transcript spanning the HPV E1 and E2 genes in primary human cervical tumor tissue. Our results extend currently known viral immunotherapeutic targets in cervical cancer and highlight E1 as an important cervical cancer antigen.
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Affiliation(s)
- Xu Peng
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, OX3 7DQ Oxford, UK
| | - Isaac Woodhouse
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, OX3 7DQ Oxford, UK
| | - Gemma Hancock
- Nuffield Department of Medicine, University of Oxford, OX3 7FZ Oxford, UK
| | - Robert Parker
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, OX3 7DQ Oxford, UK
- The Jenner Institute, University of Oxford, OX3 7DQ Oxford, UK
| | - Kristina Marx
- Bruker Daltonics, Fahrenheitstraße 4, 28359 Bremen, Germany
| | - Julius Müller
- The Jenner Institute, University of Oxford, OX3 7DQ Oxford, UK
| | - Silvia Salatino
- Wellcome Centre Human Genetics, University of Oxford, OX3 7BN Oxford, UK
| | - Thomas Partridge
- Nuffield Department of Medicine, University of Oxford, OX3 7FZ Oxford, UK
| | - Annalisa Nicastri
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, OX3 7DQ Oxford, UK
- The Jenner Institute, University of Oxford, OX3 7DQ Oxford, UK
| | - Hanqing Liao
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, OX3 7DQ Oxford, UK
- The Jenner Institute, University of Oxford, OX3 7DQ Oxford, UK
| | - Gary Kruppa
- Bruker Daltonics, Fahrenheitstraße 4, 28359 Bremen, Germany
| | - Karin Hellner
- Nuffield Department of Women’s and Reproductive Health, University of Oxford, John Radcliffe Hospital, OX3 9DU Oxford, UK
| | - Lucy Dorrell
- Nuffield Department of Medicine, University of Oxford, OX3 7FZ Oxford, UK
- The Jenner Institute, University of Oxford, OX3 7DQ Oxford, UK
- Immunocore Ltd., OX14 4RY Abingdon, UK
| | - Nicola Ternette
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, OX3 7DQ Oxford, UK
- The Jenner Institute, University of Oxford, OX3 7DQ Oxford, UK
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5
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Karnaukhov V, Paes W, Woodhouse IB, Partridge T, Nicastri A, Brackenridge S, Shcherbinin D, Chudakov DM, Zvyagin IV, Ternette N, Koohy H, Borrow P, Shugay M. HLA variants have different preferences to present proteins with specific molecular functions which are complemented in frequent haplotypes. Front Immunol 2022; 13:1067463. [PMID: 36605212 PMCID: PMC9808399 DOI: 10.3389/fimmu.2022.1067463] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/21/2022] [Indexed: 12/24/2022] Open
Abstract
Human leukocyte antigen (HLA) genes are the most polymorphic loci in the human genome and code for proteins that play a key role in guiding adaptive immune responses by presenting foreign and self peptides (ligands) to T cells. Each person carries up to 6 HLA class I variants (maternal and paternal copies of HLA-A, HLA-B and HLA-C genes) and also multiple HLA class II variants, which cumulatively define the landscape of peptides presented to T cells. Each HLA variant has its own repertoire of presented peptides with a certain sequence motif which is mainly defined by peptide anchor residues (typically the second and the last positions for HLA class I ligands) forming key interactions with the peptide-binding groove of HLA. In this study, we aimed to characterize HLA binding preferences in terms of molecular functions of presented proteins. To focus on the ligand presentation bias introduced specifically by HLA-peptide interaction we performed large-scale in silico predictions of binding of all peptides from human proteome for a wide range of HLA variants and established which functions are characteristic for proteins that are more or less preferentially presented by different HLA variants using statistical calculations and gene ontology (GO) analysis. We demonstrated marked distinctions between HLA variants in molecular functions of preferentially presented proteins (e.g. some HLA variants preferentially present membrane and receptor proteins, while others - ribosomal and DNA-binding proteins) and reduced presentation of extracellular matrix and collagen proteins by the majority of HLA variants. To explain these observations we demonstrated that HLA preferentially presents proteins enriched in amino acids which are required as anchor residues for the particular HLA variant. Our observations can be extrapolated to explain the protective effect of certain HLA alleles in infectious diseases, and we hypothesize that they can also explain susceptibility to certain autoimmune diseases and cancers. We demonstrate that these differences lead to differential presentation of HIV, influenza virus, SARS-CoV-1 and SARS-CoV-2 proteins by various HLA alleles. Taking into consideration that HLA alleles are inherited in haplotypes, we hypothesized that haplotypes composed of a combination of HLA variants with different presentation preferences should be more advantageous as they allow presenting a larger repertoire of peptides and avoiding holes in immunopeptidome. Indeed, we demonstrated that HLA-A/HLA-B and HLA-A/HLA-C haplotypes which have a high frequency in the human population are comprised of HLA variants that are more distinct in terms of functions of preferentially presented proteins than the control pairs.
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Affiliation(s)
- Vadim Karnaukhov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia
| | - Wayne Paes
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Isaac B. Woodhouse
- Medical Research Council (MRC) Human Immunology Unit, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom,Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM) Centre for Computational Biology, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), University of Oxford, Oxford, United Kingdom
| | - Thomas Partridge
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Annalisa Nicastri
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Simon Brackenridge
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Dmitrii Shcherbinin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Dmitry M. Chudakov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Ivan V. Zvyagin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Nicola Ternette
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Hashem Koohy
- Medical Research Council (MRC) Human Immunology Unit, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom,Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM) Centre for Computational Biology, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), University of Oxford, Oxford, United Kingdom
| | - Persephone Borrow
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Mikhail Shugay
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia,*Correspondence: Mikhail Shugay,
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6
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Connelley T, Nicastri A, Sheldrake T, Vrettou C, Fisch A, Reynisson B, Buus S, Hill A, Morrison I, Nielsen M, Ternette N. Immunopeptidomic Analysis of BoLA-I and BoLA-DR Presented Peptides from Theileria parva Infected Cells. Vaccines (Basel) 2022; 10:vaccines10111907. [PMID: 36423003 PMCID: PMC9699068 DOI: 10.3390/vaccines10111907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 11/03/2022] [Accepted: 11/04/2022] [Indexed: 11/16/2022] Open
Abstract
The apicomplexan parasite Theileria parva is the causative agent of East Coast fever, usually a fatal disease for cattle, which is prevalent in large areas of eastern, central, and southern Africa. Protective immunity against T. parva is mediated by CD8+ T cells, with CD4+ T-cells thought to be important in facilitating the full maturation and development of the CD8+ T-cell response. T. parva has a large proteome, with >4000 protein-coding genes, making T-cell antigen identification using conventional screening approaches laborious and expensive. To date, only a limited number of T-cell antigens have been described. Novel approaches for identifying candidate antigens for T. parva are required to replace and/or complement those currently employed. In this study, we report on the use of immunopeptidomics to study the repertoire of T. parva peptides presented by both BoLA-I and BoLA-DR molecules on infected cells. The study reports on peptides identified from the analysis of 13 BoLA-I and 6 BoLA-DR datasets covering a range of different BoLA genotypes. This represents the most comprehensive immunopeptidomic dataset available for any eukaryotic pathogen to date. Examination of the immunopeptidome data suggested the presence of a large number of coprecipitated and non-MHC-binding peptides. As part of the work, a pipeline to curate the datasets to remove these peptides was developed and used to generate a final list of 74 BoLA-I and 15 BoLA-DR-presented peptides. Together, the data demonstrated the utility of immunopeptidomics as a method to identify novel T-cell antigens for T. parva and the importance of careful curation and the application of high-quality immunoinformatics to parse the data generated.
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Affiliation(s)
- Timothy Connelley
- The Roslin Institute, The Royal (Dick) School of Veterinary Science, The University of Edinburgh, Edinburgh EH25 9RG, UK
- Correspondence:
| | - Annalisa Nicastri
- The Jenner Institute, Nuffield Department of Medicine, The University of Oxford, Oxford OX3 7BN, UK
| | - Tara Sheldrake
- The Roslin Institute, The Royal (Dick) School of Veterinary Science, The University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Christina Vrettou
- The Roslin Institute, The Royal (Dick) School of Veterinary Science, The University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Andressa Fisch
- Ribeirão Preto College of Nursing, University of São Paulo, Av Bandeirantes, Ribeirão Preto 3900, Brazil
| | - Birkir Reynisson
- Department of Health Technology, Technical University of Denmark, DK-2800 Copenhagen, Denmark
| | - Soren Buus
- Laboratory of Experimental Immunology, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Adrian Hill
- The Jenner Institute, Nuffield Department of Medicine, The University of Oxford, Oxford OX3 7BN, UK
| | - Ivan Morrison
- The Roslin Institute, The Royal (Dick) School of Veterinary Science, The University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Morten Nielsen
- Department of Health Technology, Technical University of Denmark, DK-2800 Copenhagen, Denmark
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, San Martín CP1650, Argentina
| | - Nicola Ternette
- The Jenner Institute, Nuffield Department of Medicine, The University of Oxford, Oxford OX3 7BN, UK
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7
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Tailor A, Estephan H, Parker R, Woodhouse I, Abdulghani M, Nicastri A, Jones K, Salatino S, Muschel R, Humphrey T, Giaccia A, Ternette N. Ionizing Radiation Drives Key Regulators of Antigen Presentation and a Global Expansion of the Immunopeptidome. Mol Cell Proteomics 2022; 21:100410. [PMID: 36089194 PMCID: PMC9579046 DOI: 10.1016/j.mcpro.2022.100410] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 08/04/2022] [Accepted: 08/06/2022] [Indexed: 01/18/2023] Open
Abstract
Little is known about the pathways regulating MHC antigen presentation and the identity of treatment-specific T cell antigens induced by ionizing radiation. For this reason, we investigated the radiation-specific changes in the colorectal tumor cell proteome. We found an increase in DDX58 and ZBP1 protein expression, two nucleic acid sensing molecules likely involved in induction of the dominant interferon response signature observed after genotoxic insult. We further observed treatment-induced changes in key regulators and effector proteins of the antigen processing and presentation machinery. Differential regulation of MHC allele expression was further driving the presentation of a significantly broader MHC-associated peptidome postirradiation, defining a radiation-specific peptide repertoire. Interestingly, treatment-induced peptides originated predominantly from proteins involved in catecholamine synthesis and metabolic pathways. A nuanced relationship between protein expression and antigen presentation was observed where radiation-induced changes in proteins do not correlate with increased presentation of associated peptides. Finally, we detected an increase in the presentation of a tumor-specific neoantigen derived from Mtch1. This study provides new insights into how radiation enhances antigen processing and presentation that could be suitable for the development of combinatorial therapies. Data are available via ProteomeXchange with identifier PXD032003.
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Affiliation(s)
- Arun Tailor
- Oxford Cancer Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom; The Jenner Institute, University of Oxford, Oxford, United Kingdom.
| | - Hala Estephan
- Oxford Institute of Radiation Oncology, Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Robert Parker
- Oxford Cancer Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom; The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Isaac Woodhouse
- Oxford Cancer Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Majd Abdulghani
- Oxford Institute of Radiation Oncology, Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Annalisa Nicastri
- Oxford Cancer Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom; The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Keaton Jones
- Nuffield Department of Surgical Sciences, John Radcliffe Hospital, Oxford, United Kingdom
| | - Silvia Salatino
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics, Oxford, Unitied Kingdom
| | - Ruth Muschel
- Oxford Institute of Radiation Oncology, Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Timothy Humphrey
- Oxford Institute of Radiation Oncology, Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Amato Giaccia
- Oxford Institute of Radiation Oncology, Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Nicola Ternette
- Oxford Cancer Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom; The Jenner Institute, University of Oxford, Oxford, United Kingdom.
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Paes W, Leishman A, Anderton K, Liao H, Woodhouse I, Parker R, Nicastri A, Joyce P, Ternette N. Abstract 4153: First-in-class inhibitors of ERAP1 alter the HLA-I-restricted cancer immunopeptidome leading to the generation of novel peptides presented for immune recognition. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-4153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The antigen processing machinery of a cell shapes the repertoire of peptides presented for immune recognition on the cell surface. Human leukocyte antigen class I (HLA-I) molecules present peptides that are recognised by both CD8+ T cells and NK cells, and these complexes play a vital role in the recognition and eradication of malignant cells. During direct presentation, the endoplasmic reticulum aminopeptidase 1 (ERAP1) enzyme processes a subset of HLA-I ligand precursors which are translocated into the endoplasmic reticulum (ER) following intracellular proteasomal degradation. Here, we show that inhibition of ERAP1 with highly potent and selective small molecule inhibitors drives significant qualitative and quantitative changes in the HLA-I-restricted immunopeptidome, resulting in the generation of altered and novel peptides from tumour-associated antigens that are then presented on HLA-I molecules. A major consequence of inhibiting the processing of precursor ligands by ERAP1 within the ER of cancer cells was not only the generation of unique peptides which were not detectable under baseline conditions, but a shift in the peptide length distribution towards longer HLA-I-restricted peptides. Importantly, we demonstrate that the degree of bias towards longer HLA-I-bound ligands uniquely presented following ERAP1 inhibition was governed by both ERAP1 and HLA-I haplotypes. Such dramatic changes in the peptide repertoire presented for immune recognition have the potential to enhance anti-tumoural immunogenicity through T cell recognition of a novel cancer immunopeptidome, and, in addition to global shifts in the peptide length distributions, unique peptides presented for immune recognition during ERAP1 inhibition may be used as biomarkers for monitoring activity of this novel therapeutic approach in the clinic.
Citation Format: Wayne Paes, Andrew Leishman, Kate Anderton, Hanqing Liao, Isaac Woodhouse, Robert Parker, Annalisa Nicastri, Peter Joyce, Nicola Ternette. First-in-class inhibitors of ERAP1 alter the HLA-I-restricted cancer immunopeptidome leading to the generation of novel peptides presented for immune recognition [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 4153.
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Affiliation(s)
- Wayne Paes
- 1University of Oxford, Oxford, United Kingdom
| | | | | | | | | | | | | | - Peter Joyce
- 2Grey Wolf Therapeutics, Oxford, United Kingdom
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9
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Paes W, Leonov G, Partridge T, Nicastri A, Ternette N, Borrow P. Corrigendum: Elucidation of the Signatures of Proteasome-Catalysed Peptide Splicing. Front Immunol 2021; 12:755002. [PMID: 34630434 PMCID: PMC8496456 DOI: 10.3389/fimmu.2021.755002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 08/25/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Wayne Paes
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - German Leonov
- York Cross-Disciplinary Centre for Systems Analysis, University of York, York, United Kingdom
| | - Thomas Partridge
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Annalisa Nicastri
- Nuffield Department of Clinical Medicine, The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Nicola Ternette
- Nuffield Department of Clinical Medicine, The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Persephone Borrow
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
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10
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Parker R, Tailor A, Peng X, Nicastri A, Zerweck J, Reimer U, Wenschuh H, Schnatbaum K, Ternette N. The Choice of Search Engine Affects Sequencing Depth and HLA Class I Allele-Specific Peptide Repertoires. Mol Cell Proteomics 2021; 20:100124. [PMID: 34303857 PMCID: PMC8724928 DOI: 10.1016/j.mcpro.2021.100124] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 07/09/2021] [Accepted: 07/12/2021] [Indexed: 12/26/2022] Open
Abstract
Standardization of immunopeptidomics experiments across laboratories is a pressing issue within the field, and currently a variety of different methods for sample preparation and data analysis tools are applied. Here, we compared different software packages to interrogate immunopeptidomics datasets and found that Peaks reproducibly reports substantially more peptide sequences (~30-70%) compared with Maxquant, Comet, and MS-GF+ at a global false discovery rate (FDR) of <1%. We noted that these differences are driven by search space and spectral ranking. Furthermore, we observed differences in the proportion of peptides binding the human leukocyte antigen (HLA) alleles present in the samples, indicating that sequence-related differences affected the performance of each tested engine. Utilizing data from single HLA allele expressing cell lines, we observed significant differences in amino acid frequency among the peptides reported, with a broadly higher representation of hydrophobic amino acids L, I, P, and V reported by Peaks. We validated these results using data generated with a synthetic library of 2000 HLA-associated peptides from four common HLA alleles with distinct anchor residues. Our investigation highlights that search engines create a bias in peptide sequence depth and peptide amino acid composition, and resulting data should be interpreted with caution.
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Affiliation(s)
- Robert Parker
- Nuffield Department of Medicine, Centre for Cellar and Medical Physiology, University of Oxford, Oxford, UK.
| | - Arun Tailor
- Nuffield Department of Medicine, Centre for Cellar and Medical Physiology, University of Oxford, Oxford, UK
| | - Xu Peng
- Nuffield Department of Medicine, Centre for Cellar and Medical Physiology, University of Oxford, Oxford, UK
| | - Annalisa Nicastri
- Nuffield Department of Medicine, Centre for Cellar and Medical Physiology, University of Oxford, Oxford, UK
| | | | - Ulf Reimer
- JPT Peptide Technologies GmbH, Berlin, Germany
| | | | | | - Nicola Ternette
- Nuffield Department of Medicine, Centre for Cellar and Medical Physiology, University of Oxford, Oxford, UK.
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11
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Hogan MJ, Maheshwari N, Nicastri A, Ternette N, Eisenlohr LC. Immunodominant, Qa-1-restricted CD8 T cell response elicited against a non-canonical translation product in influenza A virus. The Journal of Immunology 2021. [DOI: 10.4049/jimmunol.206.supp.103.05] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Abstract
The extent to which non-canonical translation products drive antiviral T cell responses is incompletely understood. We explored this question using an immunopeptidomic approach in an influenza virus model. C57Bl/6 mouse-derived cells were infected with influenza virus A/Puerto Rico/8/1934 (PR8), and MHC-bound peptides were eluted and analyzed by tandem mass spectrometry. Mass spectra were searched against a database of all viral gene segments translated in all possible reading frames, irrespective of the presence of start codons. We identified a 9-mer peptide, here termed M-SL9, that maps to an alternative reading frame of the sequence encoding matrix protein 1 (M1). To validate M-SL9 as a T cell epitope, we infected C57Bl/6 mice with PR8, collected tissues, and measured T cell reactivation by synthetic M-SL9 peptide. Remarkably, 10% of all CD8 T cells in the lung were specifically reactivated by M-SL9 peptide, and the vast majority of these were polyfunctional, producing two or more Th1 cytokines. An analysis of M-SL9 processing and presentation revealed that M-SL9 is restricted to the non-classical MHC class Ib molecule, Qa-1, and that presentation is dependent on the second 5′-proximal AUG codon within the M1-coding sequence, suggesting that its translation results from leaky ribosomal scanning. These data contribute to a growing body of work showing the importance of non-canonical MHC presentation in protective immune responses.
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Fisch A, Reynisson B, Benedictus L, Nicastri A, Vasoya D, Morrison I, Buus S, Ferreira BR, Kinney Ferreira de Miranda Santos I, Ternette N, Connelley T, Nielsen M. Integral Use of Immunopeptidomics and Immunoinformatics for the Characterization of Antigen Presentation and Rational Identification of BoLA-DR-Presented Peptides and Epitopes. J Immunol 2021; 206:2489-2497. [PMID: 33789985 DOI: 10.4049/jimmunol.2001409] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 03/01/2021] [Indexed: 02/04/2023]
Abstract
MHC peptide binding and presentation is the most selective event defining the landscape of T cell epitopes. Consequently, understanding the diversity of MHC alleles in a given population and the parameters that define the set of ligands that can be bound and presented by each of these alleles (the immunopeptidome) has an enormous impact on our capacity to predict and manipulate the potential of protein Ags to elicit functional T cell responses. Liquid chromatography-mass spectrometry analysis of MHC-eluted ligand data has proven to be a powerful technique for identifying such peptidomes, and methods integrating such data for prediction of Ag presentation have reached a high level of accuracy for both MHC class I and class II. In this study, we demonstrate how these techniques and prediction methods can be readily extended to the bovine leukocyte Ag class II DR locus (BoLA-DR). BoLA-DR binding motifs were characterized by eluted ligand data derived from bovine cell lines expressing a range of DRB3 alleles prevalent in Holstein-Friesian populations. The model generated (NetBoLAIIpan, available as a Web server at www.cbs.dtu.dk/services/NetBoLAIIpan) was shown to have unprecedented predictive power to identify known BoLA-DR-restricted CD4 epitopes. In summary, the results demonstrate the power of an integrated approach combining advanced mass spectrometry peptidomics with immunoinformatics for characterization of the BoLA-DR Ag presentation system and provide a prediction tool that can be used to assist in rational evaluation and selection of bovine CD4 T cell epitopes.
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Affiliation(s)
- Andressa Fisch
- Ribeirão Preto College of Nursing, University of São Paulo, Av Bandeirantes, Ribeirão Preto, Brazil
| | - Birkir Reynisson
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | | | - Annalisa Nicastri
- The Jenner Institute, Nuffield Department of Medicine, Oxford, United Kingdom
| | - Deepali Vasoya
- The Roslin Institute, Edinburgh, Midlothian, United Kingdom
| | - Ivan Morrison
- The Roslin Institute, Edinburgh, Midlothian, United Kingdom
| | - Søren Buus
- Laboratory of Experimental Immunology, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Nicola Ternette
- The Jenner Institute, Nuffield Department of Medicine, Oxford, United Kingdom
| | - Tim Connelley
- The Roslin Institute, Edinburgh, Midlothian, United Kingdom
| | - Morten Nielsen
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark .,Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, San Martín, Argentina
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Karnaukhov V, Paes W, Woodhouse IB, Partridge T, Nicastri A, Brackenridge S, Scherbinin D, Chudakov DM, Zvyagin IV, Ternette N, Koohy H, Borrow P, Shugay M. HLA binding of self-peptides is biased towards proteins with specific molecular functions. bioRxiv 2021:2021.02.16.431395. [PMID: 33619495 PMCID: PMC7899460 DOI: 10.1101/2021.02.16.431395] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Human leukocyte antigen (HLA) is highly polymorphic and plays a key role in guiding adaptive immune responses by presenting foreign and self peptides to T cells. Each HLA variant selects a minor fraction of peptides that match a certain motif required for optimal interaction with the peptide-binding groove. These restriction rules define the landscape of peptides presented to T cells. Given these limitations, one might suggest that the choice of peptides presented by HLA is non-random and there is preferential presentation of an array of peptides that is optimal for distinguishing self and foreign proteins. In this study we explore these preferences with a comparative analysis of self peptides enriched and depleted in HLA ligands. We show that HLAs exhibit preferences towards presenting peptides from certain proteins while disfavoring others with specific functions, and highlight differences between various HLA genes and alleles in those preferences. We link those differences to HLA anchor residue propensities and amino acid composition of preferentially presented proteins. The set of proteins that peptides presented by a given HLA are most likely to be derived from can be used to distinguish between class I and class II HLAs and HLA alleles. Our observations can be extrapolated to explain the protective effect of certain HLA alleles in infectious diseases, and we hypothesize that they can also explain susceptibility to certain autoimmune diseases and cancers. We demonstrate that these differences lead to differential presentation of HIV, influenza virus, SARS-CoV-1 and SARS-CoV-2 proteins by various HLA alleles. Finally, we show that the reported self peptidome preferences of distinct HLA variants can be compensated by combinations of HLA-A/HLA-B and HLA-A/HLA-C alleles in frequent haplotypes.
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Affiliation(s)
- Vadim Karnaukhov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Wayne Paes
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Isaac B. Woodhouse
- Medical Research Council (MRC) Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, UK
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, UK
| | - Thomas Partridge
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Annalisa Nicastri
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Simon Brackenridge
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Dmitrii Scherbinin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Dmitry M. Chudakov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Ivan V. Zvyagin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Nicola Ternette
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Hashem Koohy
- Medical Research Council (MRC) Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, UK
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, UK
| | - Persephone Borrow
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Mikhail Shugay
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
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Nicastri A, Liao H, Muller J, Purcell AW, Ternette N. The Choice of HLA‐Associated Peptide Enrichment and Purification Strategy Affects Peptide Yields and Creates a Bias in Detected Sequence Repertoire. Proteomics 2020; 20:e2070175. [DOI: 10.1002/pmic.202070175] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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15
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Paes W, Leonov G, Partridge T, Nicastri A, Ternette N, Borrow P. Elucidation of the Signatures of Proteasome-Catalyzed Peptide Splicing. Front Immunol 2020; 11:563800. [PMID: 33072102 PMCID: PMC7541919 DOI: 10.3389/fimmu.2020.563800] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 08/26/2020] [Indexed: 01/10/2023] Open
Abstract
Proteasomes catalyze the degradation of endogenous proteins into oligopeptides, but can concurrently create spliced oligopeptides through ligation of previously non-contiguous peptide fragments. Recent studies have uncovered a formerly unappreciated role for proteasome-catalyzed peptide splicing (PCPS) in the generation of non-genomically templated human leukocyte antigen class I (HLA-I)-bound cis-spliced peptides that can be targeted by CD8+ T cells in cancer and infection. However, the mechanisms defining PCPS reactions are poorly understood. Here, we experimentally define the biochemical constraints of proteasome-catalyzed cis-splicing reactions by examination of in vitro proteasomal digests of a panel of viral- and self-derived polypeptide substrates using a tailored mass-spectrometry-based de novo sequencing workflow. We show that forward and reverse PCPS reactions display unique splicing signatures, defined by preferential fusion of distinct amino acid residues with stringent peptide length distributions, suggesting sequence- and size-dependent accessibility of splice reactants for proteasomal substrate binding pockets. Our data provide the basis for a more informed mechanistic understanding of PCPS that will facilitate future prediction of spliced peptides from protein sequences.
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Affiliation(s)
- Wayne Paes
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - German Leonov
- York Cross-Disciplinary Center for Systems Analysis, University of York, York, United Kingdom
| | - Thomas Partridge
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Annalisa Nicastri
- Nuffield Department of Clinical Medicine, The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Nicola Ternette
- Nuffield Department of Clinical Medicine, The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Persephone Borrow
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
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16
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Nicastri A, Liao H, Muller J, Purcell AW, Ternette N. The Choice of HLA-Associated Peptide Enrichment and Purification Strategy Affects Peptide Yields and Creates a Bias in Detected Sequence Repertoire. Proteomics 2020; 20:e1900401. [PMID: 32359108 DOI: 10.1002/pmic.201900401] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 04/14/2020] [Indexed: 11/06/2022]
Abstract
Understanding the most appropriate workflow for biochemical human leukocyte antigen (HLA)-associated peptide enrichment prior to ligand sequencing is essential to achieve optimal sensitivity in immunopeptidomics experiments. The use of different detergents for HLA solubilization as well as complementary workflows to separate HLA-bound peptides from HLA protein complex components after their immunoprecipitation including HPLC, C18 cartridge, and 5 kDa filter are described. It is observed that all solubilization approaches tested led to similar peptide ligand identification rates; however, a higher number of peptides are identified in samples lysed with CHAPS compared with other methods. The HPLC method is superior in terms of HLA-I peptide recovery compared with 5 kDa filter and C18 cartridge peptide purification methods. Most importantly, it is observed that both the choice of detergent and peptide purification strategy creates a significant bias for the identified peptide sequences, and that allele-specific peptide repertoires are affected depending on the workflow of choice. The results highlight the importance of employing a suitable strategy for HLA peptide enrichment and that the obtained peptide repertoires do not necessarily reflect the true distributions of peptide sequences in the sample.
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Affiliation(s)
- Annalisa Nicastri
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
| | - Hanqing Liao
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
| | | | - Anthony W Purcell
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia
| | - Nicola Ternette
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
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17
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Chen L, Shi H, Koftori D, Sekine T, Nicastri A, Ternette N, Bowness P. Identification of an Unconventional Subpeptidome Bound to the Behçet's Disease-associated HLA-B*51:01 that is Regulated by Endoplasmic Reticulum Aminopeptidase 1 (ERAP1). Mol Cell Proteomics 2020; 19:871-883. [PMID: 32161166 PMCID: PMC7196583 DOI: 10.1074/mcp.ra119.001617] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 03/10/2020] [Indexed: 01/31/2023] Open
Abstract
Human leukocyte antigen (HLA) B*51:01 and endoplasmic reticulum aminopeptidase 1 (ERAP1) are strongly genetically associated with Behçet's disease (BD). Previous studies have defined two subgroups of HLA-B*51 peptidome containing proline (Pro) or alanine (Ala) at position 2 (P2). Little is known about the unconventional non-Pro/Ala2 HLA-B*51-bound peptides. We aimed to study the features of this novel subpeptidome, and investigate its regulation by ERAP1. CRISPR-Cas9 was used to generate an HLA-ABC-triple knockout HeLa cell line (HeLa.ABC-KO), which was subsequently transduced to express HLA-B*51:01 (HeLa.ABC-KO.B51). ERAP1 was silenced using lentiviral shRNA. Peptides bound to HLA-B*51:01 were eluted and analyzed by mass spectrometry. The characteristics of non-Pro/Ala2, Pro2, and Ala2 peptides and their alteration by ERAP1 silencing were investigated. Effects of ERAP1 silencing on cell surface expression of HLA-B*51:01 were studied using flow cytometry. More than 20% of peptides eluted from HLA-B*51:01 lacked Pro or Ala at P2. This unconventional group of HLA-B*51:01-bound peptides was relatively enriched for 8-mers (with relatively fewer 9-mers) compared with the Pro2 and Ala2 subpeptidomes and had similar N-terminal and C-terminal residue usages to Ala2 peptides (with the exception of the less abundant leucine at position Ω). Knockdown of ERAP1 increased the percentage of non-Pro/Ala2 from 20% to ∼40%, increased the percentage of longer (10-mer and 11-mer) peptides eluted from HLA-B*51:01 complexes, and abrogated the predominance of leucine at P1. Interestingly knockdown of ERAP1 altered the length and N-terminal residue usage of non-Ala2&Pro2 and Ala2 but not the Pro2 peptides. Finally, ERAP1 silencing regulated the expression levels of cell surface HLA-B*51 in a cell-type-dependent manner. In conclusion, we have used a novel methodology to identify an unconventional but surprisingly abundant non-Pro/Ala2 HLA-B*51:01 subpeptidome. It is increased by knockdown of ERAP1, a gene affecting the risk of developing BD. This has implications for theories of disease pathogenesis.
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Affiliation(s)
- Liye Chen
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK.
| | - Hui Shi
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Danai Koftori
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Takuya Sekine
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | | | - Nicola Ternette
- Target Discovery Institute, University of Oxford, Oxford, UK
| | - Paul Bowness
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
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Bettencourt P, Müller J, Nicastri A, Cantillon D, Madhavan M, Charles PD, Fotso CB, Wittenberg R, Bull N, Pinpathomrat N, Waddell SJ, Stylianou E, Hill AVS, Ternette N, McShane H. Identification of antigens presented by MHC for vaccines against tuberculosis. NPJ Vaccines 2020; 5:2. [PMID: 31908851 PMCID: PMC6941960 DOI: 10.1038/s41541-019-0148-y] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 11/25/2019] [Indexed: 11/09/2022] Open
Abstract
Mycobacterium tuberculosis (M.tb) is responsible for more deaths globally than any other pathogen. The only available vaccine, bacillus Calmette-Guérin (BCG), has variable efficacy throughout the world. A more effective vaccine is urgently needed. The immune response against tuberculosis relies, at least in part, on CD4+ T cells. Protective vaccines require the induction of antigen-specific CD4+ T cells via mycobacterial peptides presented by MHC class-II in infected macrophages. In order to identify mycobacterial antigens bound to MHC, we have immunoprecipitated MHC class-I and class-II complexes from THP-1 macrophages infected with BCG, purified MHC class-I and MHC class-II peptides and analysed them by liquid chromatography tandem mass spectrometry. We have successfully identified 94 mycobacterial peptides presented by MHC-II and 43 presented by MHC-I, from 76 and 41 antigens, respectively. These antigens were found to be highly expressed in infected macrophages. Gene ontology analysis suggests most of these antigens are associated with membranes and involved in lipid biosynthesis and transport. The sequences of selected peptides were confirmed by spectral match validation and immunogenicity evaluated by IFN-gamma ELISpot against peripheral blood mononuclear cell from volunteers vaccinated with BCG, M.tb latently infected subjects or patients with tuberculosis disease. Three antigens were expressed in viral vectors, and evaluated as vaccine candidates alone or in combination in a murine aerosol M.tb challenge model. When delivered in combination, the three candidate vaccines conferred significant protection in the lungs and spleen compared with BCG alone, demonstrating proof-of-concept for this unbiased approach to identifying new candidate antigens. Protective vaccines against Mycobacterium tuberculosis (M.tb), such as bacillus Calmette-Guérin (BCG), trigger strong CD4 T-cell responses specific to mycobacterium peptides, but their efficacy is variable. Paulo Bettencourt and colleagues now identify a set of mycobacterium peptides presented by BCG-infected macrophages via major compatibility complexes (MHC), and show that three of these antigens can be combined to formulate a vaccine that confers improved protection to Mtb infection in mice. After identifying 94 MHC-II-associated and 43 MHC-I-associated mycobacterium peptides, the researchers performed immunogenicity assays with peripheral blood mononuclear cells from BCG-vaccinated donors, latent Mtb-infected patients and patients with tuberculosis, and show that a set of these peptides was recognised by the immune cells, validating their potential as possible components for new Mtb vaccine formulations. These findings further support the value of immunopeptidomics for the identification of new antigens for effective vaccine alternatives.
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Affiliation(s)
| | - Julius Müller
- 1Jenner Institute, University of Oxford, Oxford, OX3 7DQ UK
| | - Annalisa Nicastri
- 2Target Discovery Institute, University of Oxford, Oxford, OX3 7FZ UK
| | - Daire Cantillon
- 3Department of Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Brighton, BN1 9PX UK
| | - Meera Madhavan
- 1Jenner Institute, University of Oxford, Oxford, OX3 7DQ UK
| | - Philip D Charles
- 2Target Discovery Institute, University of Oxford, Oxford, OX3 7FZ UK
| | - Carine B Fotso
- 1Jenner Institute, University of Oxford, Oxford, OX3 7DQ UK
| | | | - Naomi Bull
- 1Jenner Institute, University of Oxford, Oxford, OX3 7DQ UK
| | | | - Simon J Waddell
- 3Department of Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Brighton, BN1 9PX UK
| | | | | | - Nicola Ternette
- 1Jenner Institute, University of Oxford, Oxford, OX3 7DQ UK.,2Target Discovery Institute, University of Oxford, Oxford, OX3 7FZ UK
| | - Helen McShane
- 1Jenner Institute, University of Oxford, Oxford, OX3 7DQ UK
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19
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Paes W, Leonov G, Partridge T, Chikata T, Murakoshi H, Frangou A, Brackenridge S, Nicastri A, Smith AG, Learn GH, Li Y, Parker R, Oka S, Pellegrino P, Williams I, Haynes BF, McMichael AJ, Shaw GM, Hahn BH, Takiguchi M, Ternette N, Borrow P. Contribution of proteasome-catalyzed peptide cis-splicing to viral targeting by CD8 + T cells in HIV-1 infection. Proc Natl Acad Sci U S A 2019; 116:24748-24759. [PMID: 31748275 PMCID: PMC6900506 DOI: 10.1073/pnas.1911622116] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Peptides generated by proteasome-catalyzed splicing of noncontiguous amino acid sequences have been shown to constitute a source of nontemplated human leukocyte antigen class I (HLA-I) epitopes, but their role in pathogen-specific immunity remains unknown. CD8+ T cells are key mediators of HIV type 1 (HIV-1) control, and identification of novel epitopes to enhance targeting of infected cells is a priority for prophylactic and therapeutic strategies. To explore the contribution of proteasome-catalyzed peptide splicing (PCPS) to HIV-1 epitope generation, we developed a broadly applicable mass spectrometry-based discovery workflow that we employed to identify spliced HLA-I-bound peptides on HIV-infected cells. We demonstrate that HIV-1-derived spliced peptides comprise a relatively minor component of the HLA-I-bound viral immunopeptidome. Although spliced HIV-1 peptides may elicit CD8+ T cell responses relatively infrequently during infection, CD8+ T cells primed by partially overlapping contiguous epitopes in HIV-infected individuals were able to cross-recognize spliced viral peptides, suggesting a potential role for PCPS in restricting HIV-1 escape pathways. Vaccine-mediated priming of responses to spliced HIV-1 epitopes could thus provide a novel means of exploiting epitope targets typically underutilized during natural infection.
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Affiliation(s)
- Wayne Paes
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7FZ, United Kingdom;
| | - German Leonov
- York Cross-Disciplinary Centre for Systems Analysis, University of York, York YO10 5DD, United Kingdom
| | - Thomas Partridge
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7FZ, United Kingdom
| | - Takayuki Chikata
- Centre for AIDS Research, Kumamoto University, Kumamoto 860-0811, Japan
| | - Hayato Murakoshi
- Centre for AIDS Research, Kumamoto University, Kumamoto 860-0811, Japan
| | - Anna Frangou
- Big Data Institute, University of Oxford, Oxford OX3 7LF, United Kingdom
| | - Simon Brackenridge
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7FZ, United Kingdom
| | - Annalisa Nicastri
- Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Andrew G Smith
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Gerald H Learn
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Yingying Li
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Robert Parker
- Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Shinichi Oka
- Centre for AIDS Research, Kumamoto University, Kumamoto 860-0811, Japan
- AIDS Clinical Centre, National Centre for Global Health and Medicine, Tokyo 162-8655, Japan
| | - Pierre Pellegrino
- Centre for Sexual Health and HIV Research, University College London, London WC1E 6JB, United Kingdom
| | - Ian Williams
- Centre for Sexual Health and HIV Research, University College London, London WC1E 6JB, United Kingdom
| | - Barton F Haynes
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710
| | - Andrew J McMichael
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7FZ, United Kingdom
| | - George M Shaw
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Beatrice H Hahn
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | | | - Nicola Ternette
- Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, United Kingdom;
| | - Persephone Borrow
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7FZ, United Kingdom;
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20
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Andreatta M, Nicastri A, Peng X, Hancock G, Dorrell L, Ternette N, Nielsen M. MS-Rescue: A Computational Pipeline to Increase the Quality and Yield of Immunopeptidomics Experiments. Proteomics 2019; 19:e1800357. [DOI: 10.1002/pmic.201800357] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 12/12/2018] [Indexed: 01/01/2023]
Affiliation(s)
- Massimo Andreatta
- Instituto de Investigaciones Biotecnológicas; Universidad Nacional de San Martín; Av. 25 de Mayo y Francia CP(1650) San Martín Argentina
| | - Annalisa Nicastri
- Nuffield Department of Medicine; University of Oxford; Oxford OX3 7BN UK
| | - Xu Peng
- Nuffield Department of Medicine; University of Oxford; Oxford OX3 7BN UK
| | - Gemma Hancock
- Nuffield Department of Medicine; University of Oxford; Oxford OX3 7BN UK
| | - Lucy Dorrell
- Nuffield Department of Medicine; University of Oxford; Oxford OX3 7BN UK
- Oxford NIHR Biomedical Research Centre; Oxford OX4 2PG UK
| | - Nicola Ternette
- The Jenner Institute; University of Oxford; Oxford OX3 7DQ UK
| | - Morten Nielsen
- Instituto de Investigaciones Biotecnológicas; Universidad Nacional de San Martín; Av. 25 de Mayo y Francia CP(1650) San Martín Argentina
- Department of Bio and Health Informatics; Technical University of Denmark; 2800Kgs. Lyngby Denmark
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21
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Gabriele C, Cantiello F, Nicastri A, Crocerossa F, Russo GI, Cicione A, Vartolomei MD, Ferro M, Morgia G, Lucarelli G, Cuda G, Damiano R, Gaspari M. High-throughput detection of low abundance sialylated glycoproteins in human serum by TiO 2 enrichment and targeted LC-MS/MS analysis: application to a prostate cancer sample set. Anal Bioanal Chem 2018; 411:755-763. [PMID: 30483857 DOI: 10.1007/s00216-018-1497-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 11/03/2018] [Accepted: 11/13/2018] [Indexed: 12/22/2022]
Abstract
Glycopeptide enrichment can be a strategy to allow the detection of peptides belonging to low abundance proteins in complex matrixes such as blood serum or plasma. Though several glycopeptide enrichment protocols have shown excellent sensitivities in this respect, few reports have demonstrated the applicability of these methods to relatively large sample cohorts. In this work, a fast protocol based on TiO2 enrichment and highly sensitive mass spectrometric analysis by Selected Reaction Monitoring (SRM) has been applied to a cohort of serum samples from prostate cancer and benign prostatic hyperplasia patients in order to detect low abundance proteins in a single LC-MS/MS analysis in nanoscale format, without immunodepletion or peptide fractionation. A peptide library of over 700 formerly N-glycosylated peptides was created by data dependent analysis. Then, 16 medium to low abundance proteins were selected for detection by single injection LC-MS/MS based on selected-reaction monitoring. Results demonstrated the consistent detection of the low-level proteins under investigation. Following label-free quantification, four proteins (Adipocyte plasma membrane-associated protein, Periostin, Cathepsin D and Lysosome-associated membrane glycoprotein 2) were found significantly increased in prostate cancer sera compared to the control group. Graphical abstract ᅟ.
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Affiliation(s)
- Caterina Gabriele
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, Campus "S. Venuta", Viale Europa, Loc. Germaneto, 88100, Catanzaro, Italy
| | - Francesco Cantiello
- Urology Unit, Magna Graecia University of Catanzaro, Campus "S. Venuta", Viale Europa, Loc. Germaneto, 88100, Catanzaro, Italy.
| | - Annalisa Nicastri
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, Campus "S. Venuta", Viale Europa, Loc. Germaneto, 88100, Catanzaro, Italy
| | - Fabio Crocerossa
- Urology Unit, Magna Graecia University of Catanzaro, Campus "S. Venuta", Viale Europa, Loc. Germaneto, 88100, Catanzaro, Italy
| | - Giorgio Ivan Russo
- Urology Section, Department of Surgery, University of Catania, 95131, Catania, Italy
| | - Antonio Cicione
- Urology Unit, Magna Graecia University of Catanzaro, Campus "S. Venuta", Viale Europa, Loc. Germaneto, 88100, Catanzaro, Italy
| | - Mihai D Vartolomei
- Department of Urology, European Institute of Oncology, 20141, Milan, Italy.,Department of Cell and Molecular Biology, University of Medicine, Pharmacy, Sciences and Technology, 540139, Targu Mures, Romania
| | - Matteo Ferro
- Department of Urology, European Institute of Oncology, 20141, Milan, Italy
| | - Giuseppe Morgia
- Urology Section, Department of Surgery, University of Catania, 95131, Catania, Italy
| | - Giuseppe Lucarelli
- Urology, Andrology & Kidney Transplantation Unit, Department of Emergency & Organ Transplantation, University of Bari, 70121, Bari, Italy
| | - Giovanni Cuda
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, Campus "S. Venuta", Viale Europa, Loc. Germaneto, 88100, Catanzaro, Italy
| | - Rocco Damiano
- Urology Unit, Magna Graecia University of Catanzaro, Campus "S. Venuta", Viale Europa, Loc. Germaneto, 88100, Catanzaro, Italy
| | - Marco Gaspari
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, Campus "S. Venuta", Viale Europa, Loc. Germaneto, 88100, Catanzaro, Italy.
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22
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Ternette N, Olde Nordkamp MJM, Müller J, Anderson AP, Nicastri A, Hill AVS, Kessler BM, Li D. Immunopeptidomic Profiling of HLA-A2-Positive Triple Negative Breast Cancer Identifies Potential Immunotherapy Target Antigens. Proteomics 2018; 18:e1700465. [PMID: 29786170 PMCID: PMC6032843 DOI: 10.1002/pmic.201700465] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 04/26/2018] [Indexed: 11/06/2022]
Abstract
The recent development in immune checkpoint inhibitors and chimeric antigen receptor (CAR) T-cells in the treatment of cancer has not only demonstrated the potency of utilizing T-cell reactivity for cancer therapy, but has also highlighted the need for developing new approaches to discover targets suitable for such novel therapeutics. Here we analyzed the immunopeptidomes of six HLA-A2-positive triple negative breast cancer (TNBC) samples by nano-ultra performance liquid chromatography tandem mass spectrometry (nUPLC-MS2 ). Immunopeptidomic profiling identified a total of 19 675 peptides from tumor and adjacent normal tissue and 130 of the peptides were found to have higher abundance in tumor than in normal tissues. To determine potential therapeutic target proteins, we calculated the average tumor-associated cohort coverage (aTaCC) that represents the percentage coverage of each protein in this cohort by peptides that had higher tumoral abundance. Cofilin-1 (CFL-1), interleukin-32 (IL-32), proliferating cell nuclear antigen (PCNA), syntenin-1 (SDCBP), and ribophorin-2 (RPN-2) were found to have the highest aTaCC scores. We propose that these antigens could be evaluated further for their potential as targets in breast cancer immunotherapy and the small cohort immunopeptidomics analysis technique could be used in a wide spectrum of target discovery. Data are available via ProteomeXchange with identifier PXD009738.
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Affiliation(s)
- Nicola Ternette
- The Jenner InstituteUniversity of OxfordOxfordOX3 7FZUK
- Target Discovery InstituteNuffield Department of MedicineOxfordOX3 7FZUK
| | - Marloes J. M. Olde Nordkamp
- Nuffield Division of Clinical Laboratory SciencesRadcliffe Department of MedicineUniversity of OxfordOxfordOX3 9DUUK
| | - Julius Müller
- The Jenner InstituteUniversity of OxfordOxfordOX3 7FZUK
| | - Amanda P. Anderson
- Nuffield Division of Clinical Laboratory SciencesRadcliffe Department of MedicineUniversity of OxfordOxfordOX3 9DUUK
| | - Annalisa Nicastri
- Target Discovery InstituteNuffield Department of MedicineOxfordOX3 7FZUK
| | | | | | - Demin Li
- Nuffield Division of Clinical Laboratory SciencesRadcliffe Department of MedicineUniversity of OxfordOxfordOX3 9DUUK
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23
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Ternette N, Olde Nordkamp MJM, Müller J, Anderson AP, Nicastri A, Hill AVS, Kessler BM, Li D. Back Cover: Immunopeptidomic Profiling of HLA-A2-Positive Triple Negative Breast Cancer Identifies Potential Immunotherapy Target Antigens. Proteomics 2018. [DOI: 10.1002/pmic.201870106] [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: 11/06/2022]
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24
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Partridge T, Nicastri A, Kliszczak AE, Yindom LM, Kessler BM, Ternette N, Borrow P. Discrimination Between Human Leukocyte Antigen Class I-Bound and Co-Purified HIV-Derived Peptides in Immunopeptidomics Workflows. Front Immunol 2018; 9:912. [PMID: 29780384 PMCID: PMC5946011 DOI: 10.3389/fimmu.2018.00912] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 04/12/2018] [Indexed: 12/24/2022] Open
Abstract
Elucidation of novel peptides presented by human leukocyte antigen (HLA) class I alleles by immunopeptidomics constitutes a powerful approach that can inform the rational design of CD8+ T cell inducing vaccines to control infection with pathogens such as human immunodeficiency virus type 1 (HIV-1) or to combat tumors. Recent advances in the sensitivity of liquid chromatography tandem mass spectrometry instrumentation have facilitated the discovery of thousands of natural HLA-restricted peptides in a single measurement. However, the extent of contamination of class I-bound peptides identified using HLA immunoprecipitation (IP)-based immunopeptidomics approaches with peptides from other sources has not previously been evaluated in depth. Here, we investigated the specificity of the IP-based immunopeptidomics methodology using HLA class I- or II-deficient cell lines and membrane protein-specific antibody IPs. We demonstrate that the 721.221 B lymphoblastoid cell line, widely regarded to be HLA class Ia-deficient, actually expresses and presents peptides on HLA-C*01:02. Using this cell line and the C8166 (HLA class I- and II-expressing) cell line, we show that some HLA class II-bound peptides were co-purified non-specifically during HLA class I and membrane protein IPs. Furthermore, IPs of "irrelevant" membrane proteins from HIV-1-infected HLA class I- and/or II-expressing cells revealed that unusually long HIV-1-derived peptides previously reported by us and other immunopeptidomics studies as potentially novel CD8+ T cell epitopes were non-specifically co-isolated, and so constitute a source of contamination in HLA class I IPs. For example, a 16-mer (FLGKIWPSYKGRPGNF), which was detected in all samples studied represents the full p1 segment of the abundant intracellular or virion-associated proteolytically-processed HIV-1 Gag protein. This result is of importance, as these long co-purified HIV-1 Gag peptides may not elicit CD8+ T cell responses when incorporated into candidate vaccines. These results have wider implications for HLA epitope discovery from abundant or membrane-associated antigens by immunopeptidomics in the context of infectious diseases, cancer, and autoimmunity.
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Affiliation(s)
- Thomas Partridge
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Annalisa Nicastri
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, United Kingdom
| | - Anna E Kliszczak
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Louis-Marie Yindom
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Benedikt M Kessler
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, United Kingdom
| | - Nicola Ternette
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, United Kingdom.,The Jenner Institute, Target Discovery Institute Mass Spectrometry Laboratory, University of Oxford, Oxford, United Kingdom
| | - Persephone Borrow
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
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25
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Gaspari M, Chiesa L, Nicastri A, Gabriele C, Harper V, Britti D, Cuda G, Procopio A. Proteome Speciation by Mass Spectrometry: Characterization of Composite Protein Mixtures in Milk Replacers. Anal Chem 2016; 88:11568-11574. [PMID: 27792874 DOI: 10.1021/acs.analchem.6b02848] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The ability of tandem mass spectrometry to determine the primary structure of proteolytic peptides can be exploited to trace back the organisms from which the corresponding proteins were extracted. This information can be important when food products, such as protein powders, can be supplemented with lower-quality starting materials. In order to dissect the origin of proteinaceous material composing a given unknown mixture, a two-step database search strategy for bottom-up nanoscale liquid chromatography-tandem mass spectrometry (nanoLC-MS/MS) data was implemented. A single nanoLC-MS/MS analysis was sufficient not only to determine the qualitative composition of the mixtures under examination, but also to assess the relative percent composition of the various proteomes, if dedicated calibration curves were previously generated. The approach of two-step database search for qualitative analysis and proteome total ion current (pTIC) calculation for quantitative analysis was applied to several binary and ternary mixtures which mimic the composition of milk replacers typically used in calf feeding.
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Affiliation(s)
- Marco Gaspari
- Research Center for Advanced Biochemistry and Molecular Biology, Department of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro , 88100 Catanzaro, Italy
| | - Luca Chiesa
- Department of Veterinary Sciences and Public Health, University of Milan , 20122 Milan, Italy
| | - Annalisa Nicastri
- Research Center for Advanced Biochemistry and Molecular Biology, Department of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro , 88100 Catanzaro, Italy
| | - Caterina Gabriele
- Research Center for Advanced Biochemistry and Molecular Biology, Department of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro , 88100 Catanzaro, Italy
| | | | - Domenico Britti
- Department of Health Sciences, Magna Græcia University of Catanzaro , 88100 Catanzaro, Italy
| | - Giovanni Cuda
- Research Center for Advanced Biochemistry and Molecular Biology, Department of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro , 88100 Catanzaro, Italy
| | - Antonio Procopio
- Department of Health Sciences, Magna Græcia University of Catanzaro , 88100 Catanzaro, Italy
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26
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Das G, Alrasheed S, Coluccio ML, Gentile F, Nicastri A, Candeloro P, Cuda G, Perozziello G, Di Fabrizio E. Few molecule SERS detection using nanolens based plasmonic nanostructure: application to point mutation detection. RSC Adv 2016. [DOI: 10.1039/c6ra23301e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Self-similar chain based nanolens plasmonic devices were fabricated for detecting single point mutations.
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Affiliation(s)
- Gobind Das
- Physical Sciences and Engineering (PSE)
- King Abdullah University of Science and Technology (KAUST)
- Thuwal 23955-6900
- Kingdom of Saudi Arabia
| | - Salma Alrasheed
- Physical Sciences and Engineering (PSE)
- King Abdullah University of Science and Technology (KAUST)
- Thuwal 23955-6900
- Kingdom of Saudi Arabia
| | - Maria Laura Coluccio
- Bio-Nanotechnology and Engineering for Medicine (BIONEM)
- Department of Experimental and Clinical Medicine
- University of Magna Graecia Viale Europa
- Catanzaro 88100
- Italy
| | - Francesco Gentile
- Bio-Nanotechnology and Engineering for Medicine (BIONEM)
- Department of Experimental and Clinical Medicine
- University of Magna Graecia Viale Europa
- Catanzaro 88100
- Italy
| | - Annalisa Nicastri
- Advanced Research Center on Biochemistry and Molecular Biology
- Department of Experimental and Clinical Medicine
- University of Magna Graecia Viale Europa
- Catanzaro 88100
- Italy
| | - Patrizio Candeloro
- Bio-Nanotechnology and Engineering for Medicine (BIONEM)
- Department of Experimental and Clinical Medicine
- University of Magna Graecia Viale Europa
- Catanzaro 88100
- Italy
| | - Giovanni Cuda
- Advanced Research Center on Biochemistry and Molecular Biology
- Department of Experimental and Clinical Medicine
- University of Magna Graecia Viale Europa
- Catanzaro 88100
- Italy
| | - Gerardo Perozziello
- Bio-Nanotechnology and Engineering for Medicine (BIONEM)
- Department of Experimental and Clinical Medicine
- University of Magna Graecia Viale Europa
- Catanzaro 88100
- Italy
| | - Enzo Di Fabrizio
- Physical Sciences and Engineering (PSE)
- King Abdullah University of Science and Technology (KAUST)
- Thuwal 23955-6900
- Kingdom of Saudi Arabia
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27
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Coluccio ML, Gentile F, Das G, Nicastri A, Perri AM, Candeloro P, Perozziello G, Proietti Zaccaria R, Gongora JST, Alrasheed S, Fratalocchi A, Limongi T, Cuda G, Di Fabrizio E. Detection of single amino acid mutation in human breast cancer by disordered plasmonic self-similar chain. Sci Adv 2015; 1:e1500487. [PMID: 26601267 PMCID: PMC4643778 DOI: 10.1126/sciadv.1500487] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 06/13/2015] [Indexed: 05/15/2023]
Abstract
Control of the architecture and electromagnetic behavior of nanostructures offers the possibility of designing and fabricating sensors that, owing to their intrinsic behavior, provide solutions to new problems in various fields. We show detection of peptides in multicomponent mixtures derived from human samples for early diagnosis of breast cancer. The architecture of sensors is based on a matrix array where pixels constitute a plasmonic device showing a strong electric field enhancement localized in an area of a few square nanometers. The method allows detection of single point mutations in peptides composing the BRCA1 protein. The sensitivity demonstrated falls in the picomolar (10(-12) M) range. The success of this approach is a result of accurate design and fabrication control. The residual roughness introduced by fabrication was taken into account in optical modeling and was a further contributing factor in plasmon localization, increasing the sensitivity and selectivity of the sensors. This methodology developed for breast cancer detection can be considered a general strategy that is applicable to various pathologies and other chemical analytical cases where complex mixtures have to be resolved in their constitutive components.
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Affiliation(s)
- Maria Laura Coluccio
- Bio-Nanotechnology and Engineering for Medicine (BIONEM), Department of Experimental and Clinical Medicine, University of Magna Graecia Viale Europa, Germaneto, Catanzaro 88100, Italy
| | - Francesco Gentile
- Bio-Nanotechnology and Engineering for Medicine (BIONEM), Department of Experimental and Clinical Medicine, University of Magna Graecia Viale Europa, Germaneto, Catanzaro 88100, Italy
- Department of Electrical Engineering and Information Technology, University of Naples, Naples 80125, Italy
| | - Gobind Das
- Physical Sciences and Engineering (PSE) and Biological and Environment Science and Engineering Divisions (BESE), King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Annalisa Nicastri
- Bio-Nanotechnology and Engineering for Medicine (BIONEM), Department of Experimental and Clinical Medicine, University of Magna Graecia Viale Europa, Germaneto, Catanzaro 88100, Italy
| | - Angela Mena Perri
- Bio-Nanotechnology and Engineering for Medicine (BIONEM), Department of Experimental and Clinical Medicine, University of Magna Graecia Viale Europa, Germaneto, Catanzaro 88100, Italy
| | - Patrizio Candeloro
- Bio-Nanotechnology and Engineering for Medicine (BIONEM), Department of Experimental and Clinical Medicine, University of Magna Graecia Viale Europa, Germaneto, Catanzaro 88100, Italy
| | - Gerardo Perozziello
- Bio-Nanotechnology and Engineering for Medicine (BIONEM), Department of Experimental and Clinical Medicine, University of Magna Graecia Viale Europa, Germaneto, Catanzaro 88100, Italy
| | | | - Juan Sebastian Totero Gongora
- PRIMALIGHT, Electrical Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Salma Alrasheed
- Physical Sciences and Engineering (PSE) and Biological and Environment Science and Engineering Divisions (BESE), King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Andrea Fratalocchi
- PRIMALIGHT, Electrical Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Tania Limongi
- Physical Sciences and Engineering (PSE) and Biological and Environment Science and Engineering Divisions (BESE), King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Giovanni Cuda
- Bio-Nanotechnology and Engineering for Medicine (BIONEM), Department of Experimental and Clinical Medicine, University of Magna Graecia Viale Europa, Germaneto, Catanzaro 88100, Italy
| | - Enzo Di Fabrizio
- Bio-Nanotechnology and Engineering for Medicine (BIONEM), Department of Experimental and Clinical Medicine, University of Magna Graecia Viale Europa, Germaneto, Catanzaro 88100, Italy
- Physical Sciences and Engineering (PSE) and Biological and Environment Science and Engineering Divisions (BESE), King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
- Corresponding author. E-mail:
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Nicastri A, Gaspari M, Sacco R, Elia L, Gabriele C, Romano R, Rizzuto A, Cuda G. N-glycoprotein analysis discovers new up-regulated glycoproteins in colorectal cancer tissue. J Proteome Res 2014; 13:4932-41. [PMID: 25247386 DOI: 10.1021/pr500647y] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Colorectal cancer is one of the leading causes of death due to cancer worldwide. Therefore, the identification of high-specificity and -sensitivity biomarkers for the early detection of colorectal cancer is urgently needed. Post-translational modifications, such as glycosylation, are known to play an important role in cancer progression. In the present work, we used a quantitative proteomic technique based on (18)O stable isotope labeling to identify differentially expressed N-linked glycoproteins in colorectal cancer tissue samples compared with healthy colorectal tissue from 19 patients undergoing colorectal cancer surgery. We identified 54 up-regulated glycoproteins in colorectal cancer samples, therefore potentially involved in the biological processes of tumorigenesis. In particular, nine of these (PLOD2, DPEP1, SE1L1, CD82, PAR1, PLOD3, S12A2, LAMP3, OLFM4) were found to be up-regulated in the great majority of the cohort, and, interestingly, the association with colorectal cancer of four (PLOD2, S12A2, PLOD3, CD82) has not been hitherto described.
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Affiliation(s)
- Annalisa Nicastri
- Proteomics@UMG, Department of Experimental and Clinical Medicine and ‡Surgery Unit, Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro , viale Europa, 88100 Catanzaro, Italy
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Perozziello G, Candeloro P, Gentile F, Nicastri A, Perri A, Coluccio ML, Adamo A, Pardeo F, Catalano R, Parrotta E, Espinosa HD, Cuda G, Di Fabrizio E. Microfluidics & nanotechnology: towards fully integrated analytical devices for the detection of cancer biomarkers. RSC Adv 2014. [DOI: 10.1039/c4ra10486b] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
In this paper, we describe an innovative modular microfluidic platform allowing filtering, concentration and analysis of peptides from a complex mixture.
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Affiliation(s)
- G. Perozziello
- BioNEM lab
- Department of Experimental and Clinical Medicine, University “Magna Graecia” of Catanzaro
- Catanzaro, Italy
- Department of Mechanical Engineering
- NorthWestern University
| | - P. Candeloro
- BioNEM lab
- Department of Experimental and Clinical Medicine, University “Magna Graecia” of Catanzaro
- Catanzaro, Italy
| | - F. Gentile
- BioNEM lab
- Department of Experimental and Clinical Medicine, University “Magna Graecia” of Catanzaro
- Catanzaro, Italy
| | - A. Nicastri
- Proteomics lab
- Department of Experimental and Clinical Medicine, University “Magna Graecia” of Catanzaro
- Catanzaro, Italy
| | - A. Perri
- Proteomics lab
- Department of Experimental and Clinical Medicine, University “Magna Graecia” of Catanzaro
- Catanzaro, Italy
| | - M. L. Coluccio
- BioNEM lab
- Department of Experimental and Clinical Medicine, University “Magna Graecia” of Catanzaro
- Catanzaro, Italy
| | - A. Adamo
- Department of Chemical Engineering
- Massachusetts Institute of Technology (MIT)
- Cambridge, USA
| | - F. Pardeo
- BioNEM lab
- Department of Experimental and Clinical Medicine, University “Magna Graecia” of Catanzaro
- Catanzaro, Italy
| | - R. Catalano
- BioNEM lab
- Department of Experimental and Clinical Medicine, University “Magna Graecia” of Catanzaro
- Catanzaro, Italy
| | - E. Parrotta
- Proteomics lab
- Department of Experimental and Clinical Medicine, University “Magna Graecia” of Catanzaro
- Catanzaro, Italy
| | - H. D. Espinosa
- Department of Mechanical Engineering
- NorthWestern University
- Evanston, USA
| | - G. Cuda
- Proteomics lab
- Department of Experimental and Clinical Medicine, University “Magna Graecia” of Catanzaro
- Catanzaro, Italy
| | - E. Di Fabrizio
- BioNEM lab
- Department of Experimental and Clinical Medicine, University “Magna Graecia” of Catanzaro
- Catanzaro, Italy
- King Abdullah University of Science and Technology (KAUST)
- Thuwal, Kingdom of Saudi Arabia
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Gentile F, La Rocca R, Marinaro G, Nicastri A, Toma A, Paonessa F, Cojoc G, Liberale C, Benfenati F, di Fabrizio E, Decuzzi P. Differential cell adhesion on mesoporous silicon substrates. ACS Appl Mater Interfaces 2012; 4:2903-11. [PMID: 22583790 DOI: 10.1021/am300519a] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Porous silicon (PSi) is a promising material in several biomedical applications because of its biocompatibility and biodegradability. Despite the plethora of studies focusing on the interaction of cells with micrometer and submicro geometrical features, limited information is available on the response of cells to substrates with a quasi-regular distribution of nanoscopic pores. Here, the behavior of four different cell types is analyzed on two mesoporous (MeP) silicon substrates, with an average pore size of ∼5 (MeP1) and ∼20 nm (MeP2), respectively. On both MeP substrates, cells are observed to spread and adhere in a larger number as compared to flat silicon wafers. At all considered time points, the surface density of the adhering cells nd is larger on the PSi substrate with the smaller average pore size (MeP1). At 60 h, nd is from ∼1.5 to 5 times larger on MeP1 than on MeP2 substrates, depending on the cell type. The higher rates of proliferation are observed for the two neuronal cell types, the mouse neuroblastoma cells (N2A) and the immortalized human cortical neuronal cells (HCN1A). It is speculated that the higher adhesion on MeP1 could be attributed to a preferential matching of the substrate topography with the recently observed multiscale molecular architecture of focal adhesions. These results have implications in the rational development of PSi substrates for supporting cell adhesion and controlling drug release in implants and scaffolds for tissue engineering applications.
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Affiliation(s)
- Francesco Gentile
- Laboratory of Proteomics and Mass Spectrometry, Department of Experimental and Clinical Medicine, University of Magna Graecia , Catanzaro 88100, Italy
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Das G, Nicastri A, Coluccio ML, Gentile F, Candeloro P, Cojoc G, Liberale C, De Angelis F, Di Fabrizio E. FT-IR, Raman, RRS measurements and DFT calculation for doxorubicin. Microsc Res Tech 2010; 73:991-5. [DOI: 10.1002/jemt.20849] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Reinersman M, Riely GJ, Nicastri A, Soff GA, Getinet A, Schwartz AG, Zakowski MF, Rusch VW, Kris MG, Ladanyi M. EGFR and KRAS mutation status of lung adenocarcinomas in African Americans. J Clin Oncol 2009. [DOI: 10.1200/jco.2009.27.15_suppl.11065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
11065 Background: The 2004 discovery of the tyrosine kinase inhibitor-sensitizing mutations in the epidermal growth factor receptor (EGFR) represents a major advance in the study and management of non-small cell lung cancer. Conversely, KRAS mutations in these cancers confer resistance to the EGFR tyrosine kinase inhibitors gefitinib and erlotinib. EGFR mutations occur almost exclusively in adenocarcinoma, and are more common in never smokers, women, and people born in East Asian (compared to Whites). No comprehensive studies exist of EGFR and KRAS mutations in lung cancers from African-American patients. Methods: We collected formalin-fixed paraffin-embedded material from 121 resected lung adenocarcinomas from African-American patients for DNA extraction. EGFR exon 19 deletions and exon 21 L858R point mutations were detected by sensitive mutation-specific PCR-based methods. KRAS codon 12 and 13 mutation testing was performed by mass-spectrometry (Sequenom)-based genotyping and direct sequencing. These data were compared to Memorial Sloan-Kettering data for EGFR and KRAS mutations in all resected adenocarcinomas in white patients. Results: EGFR mutations were detected in 23 of 121 cases (19%), while KRAS mutations were found in 21 (17%). Exon 19 deletions accounted for 18 of 23 of the EGFR mutations compared to 5 EGFR L858R mutations. KRAS mutations were primarily the transversion type mutations (17 of 21). When compared to data from Memorial Sloan-Kettering for White patients (81/273, 30%), the 17% rate of KRAS mutations in lung adenocarcinomas from African-Americans was significantly lower (p=0.01). EGFR mutation status was similar between African-Americans and Whites (19% vs 18%, p=0.9) and the proportion of exon 19 deletions and L858R mutations was comparable as well. Conclusions: This is the first large series reporting results of mutation testing in lung adenocarcinoma specimens from African-Americans. African-American patients are less likely than Whites to harbor KRAS mutations in their lung adenocarcinomas. There was no significant difference in the prevalence of EGFR mutations. Since biological characteristics underlie clinical factors, these differences may help explain differences in outcomes comparing African-Americans to other groups. No significant financial relationships to disclose.
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Affiliation(s)
- M. Reinersman
- Memorial Sloan-Kettering Cancer Center, New York, NY; SUNY Downstate Medical Center, Brooklyn, NY; Karmanos Cancer Institute, Wayne State University, Detroit, MI
| | - G. J. Riely
- Memorial Sloan-Kettering Cancer Center, New York, NY; SUNY Downstate Medical Center, Brooklyn, NY; Karmanos Cancer Institute, Wayne State University, Detroit, MI
| | - A. Nicastri
- Memorial Sloan-Kettering Cancer Center, New York, NY; SUNY Downstate Medical Center, Brooklyn, NY; Karmanos Cancer Institute, Wayne State University, Detroit, MI
| | - G. A. Soff
- Memorial Sloan-Kettering Cancer Center, New York, NY; SUNY Downstate Medical Center, Brooklyn, NY; Karmanos Cancer Institute, Wayne State University, Detroit, MI
| | - A. Getinet
- Memorial Sloan-Kettering Cancer Center, New York, NY; SUNY Downstate Medical Center, Brooklyn, NY; Karmanos Cancer Institute, Wayne State University, Detroit, MI
| | - A. G. Schwartz
- Memorial Sloan-Kettering Cancer Center, New York, NY; SUNY Downstate Medical Center, Brooklyn, NY; Karmanos Cancer Institute, Wayne State University, Detroit, MI
| | - M. F. Zakowski
- Memorial Sloan-Kettering Cancer Center, New York, NY; SUNY Downstate Medical Center, Brooklyn, NY; Karmanos Cancer Institute, Wayne State University, Detroit, MI
| | - V. W. Rusch
- Memorial Sloan-Kettering Cancer Center, New York, NY; SUNY Downstate Medical Center, Brooklyn, NY; Karmanos Cancer Institute, Wayne State University, Detroit, MI
| | - M. G. Kris
- Memorial Sloan-Kettering Cancer Center, New York, NY; SUNY Downstate Medical Center, Brooklyn, NY; Karmanos Cancer Institute, Wayne State University, Detroit, MI
| | - M. Ladanyi
- Memorial Sloan-Kettering Cancer Center, New York, NY; SUNY Downstate Medical Center, Brooklyn, NY; Karmanos Cancer Institute, Wayne State University, Detroit, MI
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Baldelli S, Merlini S, Perico N, Nicastri A, Cortinovis M, Gotti E, Remuzzi G, Cattaneo D. C-440T/T-331C polymorphisms in the UGT1A9 gene affect the pharmacokinetics of mycophenolic acid in kidney transplantation. Pharmacogenomics 2008; 8:1127-41. [PMID: 17924828 DOI: 10.2217/14622416.8.9.1127] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
INTRODUCTION The immunosuppressive agent mycophenolic acid (MPA) is metabolized by uridine diphosphate glucuronosyltransferase 1A9 (UGT1A9) to 7-O-glucuronide (MPAG) and excreted by multidrug resistance-associated protein 2 in the bile. By contrast, the production of the acyl MPAG, a minor MPA metabolite, was ascribed to UGT2B7 and UGT1A8. Several polymorphisms in the genes encoding for UGT1A9, UGT2B7 and MRP2 proteins have been described. However, their functional role in vivo on MPA metabolism remains poorly defined. METHODS A total of 40 Caucasian kidney transplant patients, given induction therapies (with Campath-(1)H or the combination basiliximab/rabbit antithymocyte globulin) and on maintenance immunosuppression with cyclosporine in combination with mycophenolate mofetil (MMF) in a steroid-free regimen, were enrolled in the pharmacogenetic study. Patients had clinical and hematochemical evaluations at month 6 after transplantation, as well as complete MPA pharmacokinetic assessment. They were genotyped for SNPs in UGT1A9 C-2152T, T-1887G, C-665T, C-440T, T-331C, T-275A, T98C, for the nonsynonymous C802T SNP in UGT2B7, and for ABCC2 SNPs C-24T and G1249A. The association of these polymorphisms with MPA pharmacokinetic parameters was investigated. RESULTS Differences in the MPA pharmacokinetic profiles confirmed large interpatient variability of MPA exposure, with AUC(0-12) values ranging from 7.9 to 50.1 mg*h/ml. MPA AUC(0-12) was significantly associated with the presence of UGT1A9 -440/-331 genotypes (TT/CC: 61.5 +/- 2.7 mg*h/ml/g MMF; TC/CT: 45.4 +/- 14.0 mg*h/ml/g MMF; CC/TT: 40.8 +/- 10.8 mg*h/ml/g MMF; p = 0.005), whereas MPAG exposure was mainly influenced by renal function. The positive association between MPA AUC and SNPs in position -440/-331 found in kidney transplant patients confirmed previous in vitro findings showing that the abovementioned SNPs had a significant impact on UGT1A9 protein content in the liver. The presence of ABCC2 promoter C-24T and exon 10 G1249A SNPs did not cause any significant variation in MPA and MPAG pharmacokinetic parameters. CONCLUSION The study demonstrated a significant impact of C-440T/T-331C SNPs in the promoter region of the UGT1A9 gene on MPA pharmacokinetics in renal allograft recipients.
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Affiliation(s)
- Sara Baldelli
- Mario Negri Institute for Pharmacological Research, Department of Medicine and Transplantation, Via Gavazzeni, 11-24125 Bergamo, Italy
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Cattaneo D, Merlini S, Baldelli S, Bartolini B, Nicastri A, Gotti E, Remuzzi G, Perico N. Mycophenolic Acid Formulation Affects Cyclosporine Pharmacokinetics in Stable Kidney Transplant Recipients. Ther Drug Monit 2006; 28:643-9. [PMID: 17038879 DOI: 10.1097/01.ftd.0000245379.87563.3b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
A novel monitoring strategy based on the blood concentration at two hours post-dose (C2) has been recently proposed for the assessment of cyclosporine (CsA) absorption and daily exposure, and therapeutic windows for C2 levels have been identified. These guidelines have been derived from patients given mycophenolate mofetil (MMF) or azathioprine, and never tested in those treated with the enteric-coated formulation of mycophenolic acid (EC-MPS). The authors have compared full CsA pharmacokinetic evaluations in 12 kidney transplant recipients given EC-MPS with those from 20 patients on MMF at months 6, 12, 18 and 24 postsurgery. At month 6 postsurgery, patients on EC-MPS had a shift to the right in the CsA peak concentration as compared to that in patients given MMF, an effect associated with significant differences in CsA Tmax (1.9 +/- 0.3 h vs. 1.5 +/- 0.6 h, P < 0.05), C2 (988 +/- 259 vs. 720 +/- 214 ng/mL, P < 0.01), and C3 levels (539 +/- 119 vs. 435 +/- 119 ng/mL, P < 0.05). Interestingly, the authors found that the majority of patients on EC-MPS had CsA peaking at 2-h postdosing, whereas most of patients on MMF had CsA Cmax at 1 h. Similar results were observed also at months 12, 18, and 24 postsurgery. These findings indicate that the pharmacokinetics of CsA is significantly affected by the concomitant administration of different MPA formulations. This would imply the need of specific algorithms to adequately estimate CsA dose adjustment in patients given, in addition to CsA, EC-MPS or MMF.
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Affiliation(s)
- Dario Cattaneo
- Department of Medicine and Transplantation, Ospedali Riuniti di Bergamo, Mario Negri Institute for Pharmacological Research, Bergamo, Italy.
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Abstract
Renal amyloidosis can occur as a primary or secondary, systemic or localized disorder. It is defined as a chronic infiltrative disorder characterized by impaired organ function caused by extracellular insoluble protein fibrils. Although colonic tuberculosis is not uncommon, the occurrence of reactive renal amyloidosis in such patients is not as prevalent. We report a single case of renal amyloidosis in a patient with tuberculosis of the cecum who presented with nephrotic syndrome.
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Affiliation(s)
- A S El-Hennawy
- Department of Medicine, Renal Division, Coney Island Hospital, Brooklyn, N.Y. 11235, USA.
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Baqi N, Singh A, Balachandra S, Ahmad H, Nicastri A, Kytinski S, Homel P, Tejani A. The paucity of minimal change disease in adolescents with primary nephrotic syndrome. Pediatr Nephrol 1998; 12:105-7. [PMID: 9543365 DOI: 10.1007/s004670050414] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Data are sparse regarding the histological lesions associated with the primary nephrotic syndrome in adolescents. To our knowledge there are only two published articles that have specifically addressed the histopathological lesions that typify idiopathic nephrotic syndrome in the adolescent population. We reviewed our experience from the last 14 years of children between the ages of 12 and 18 years who were referred to our center for the evaluation of the nephrotic syndrome. A total of 29 adolescents met the inclusion criteria for this review. All patients were biopsied prior to the initiation of treatment. The sex ratio consisted of 52% males and 48% females and the racial breakdown was largely African-American, with 83% black adolescents, 7% Hispanic, and 10% Caucasian patients. Minimal change nephrotic syndrome (MCNS), the predominant lesion of children at an early age, was noted in only 20% of patients. The majority of patients (55.2%) had focal segmental glomerulosclerosis (FSGS); 7% had IgM nephropathy and 3.5% had diffuse mesangial hypercellularity. Only 7% of biopsied adolescents had membranoproliferative glomerulonephritis. Our results indicate that the most common lesion in this predominantly African-American patient population is FSGS, with only a small number showing MCNS. Thus, in our experience derived from a racially mixed population, adolescents with the nephrotic syndrome are less likely to have MCNS than younger children.
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Affiliation(s)
- N Baqi
- Division of Pediatric Nephrology, State University of New York HSC at Brooklyn, 11203, USA
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Baqi N, Singh A, Moazani S, Ahmad H, Nicastri A, Tejani A. Clinical quiz. Quiescent lupus nephritis with superimposed HUS. Pediatr Nephrol 1995; 9:669-70. [PMID: 8580036 DOI: 10.1007/bf00860969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- N Baqi
- Children's Medical Center of Brooklyn, Kings County Hospital Center, University Hospital of Brooklyn, New York, USA
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Abstract
We report here the cases of 15 children in whom nephrotic syndrome developed, from among 164 children (55% male, 90% black) followed in our acquired immunodeficiency syndrome clinic from 1984 through 1990. Mean age at onset of nephrotic syndrome was 4.9 +/- 2.6 years. Fourteen patients were black and one was Hispanic. Seventy-three percent of our patients with nephrotic syndrome were girls. The mean duration of clinical acquired immunodeficiency syndrome before development of nephrotic syndrome was 1.7 +/- 1.1 years. In eight patients, nephrotic syndrome appeared between 3 and 11 months after intravenous infusions of immune globulin or albumin were administered as part of a research protocol; this incidence (8/47) was higher than the incidence of nephrotic syndrome among those who did not receive intravenous infusions (7/117, p less than 0.05). Tissue for histologic examination was available for 80% of the patients, and histologic examination demonstrated mesangial hypercellularity (5 patients), focal segmental glomerulosclerosis (4 patients), minimal change disease (2 patients), and IgM nephropathy (1 patient). Deposition of one or more immunoglobulins was noted in all but one patient studied with immunofluorescence. Corresponding electron-dense deposits were seen by electron microscopy in 78% of specimens. Prednisone did not induce a remission of nephrotic syndrome in the 13 patients treated, whereas cyclosporine did so in the 3 patients to whom it was administered. Five patients were in the end stage of renal disease within 8 months. Successful maintenance peritoneal dialysis was performed in three patients, but 80% of patients have died of human immunodeficiency virus-related complications; one patient was lost to follow-up. We conclude that immune-complex deposition is consistently seen in children with human immunodeficiency virus-associated nephrotic syndrome. This nephrotic syndrome is resistant to steroid therapy, but we observed a remission of the proteinuria with cyclosporine therapy in three patients. For patients with end-stage renal disease, maintenance peritoneal dialysis may improve the quality of life.
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Affiliation(s)
- E Ingulli
- Renal Division, Children's Medical Center of Brooklyn, NY
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Abstract
Three cases are presented in which biopsy-proven diabetic nephropathy was found in nephrotic patients with no prior history of diabetes. One patient presented with advanced retinopathy and end-stage renal disease (ESRD), another with retinopathy and mild renal insufficiency, and a third with mild renal insufficiency alone. In each case, biopsy showed diffuse and nodular glomerulosclerosis with no evidence of kappa or lambda light chains. The patients had normal fasting serum glucose values, and two had normal oral glucose tolerance tests. Twenty-three similar cases in the literature were reviewed, and in most, some evidence of diabetes or hyperglycemia was found; five cases remained in which there was no evidence of hyperglycemia at any time. The cases reviewed included a disproportionate number of men (65%) and blacks (42%). It is concluded that diabetic nephropathy may exist in the absence of detectable hyperglycemia in a small number of extraordinarily susceptible individuals. Men and blacks appear to be at increased risk.
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Affiliation(s)
- J Macrae
- Department of Medicine, SUNY Health Science Center, Brooklyn 11203
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Trachtman H, Carroll F, Phadke K, Khawar M, Nicastri A, Chen CK, Tejani A. Paucity of minimal-change lesion in children with early frequently relapsing steroid-responsive nephrotic syndrome. Am J Nephrol 1987; 7:13-7. [PMID: 3578368 DOI: 10.1159/000167422] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
It is widely believed that the most common morphological lesion in children with the idiopathic nephrotic syndrome who manifest a frequently relapsing steroid-responsive course is the minimal-change lesion. However, there are no prospective renal biopsy studies in such patients to substantiate this assertion. We performed a renal biopsy in all children with early frequently relapsing steroid-responsive nephrotic syndrome during the years 1980-1984. In 16 affected children, only 4 (25%) had minimal-change lesion, 7 had IgM nephropathy, 3 had diffuse mesangial hypercellularity, and 2 had focal segmental glomerulosclerosis. Fourteen of these patients have required immunosuppressive therapy with cyclophosphamide. Long-term follow-up revealed that 10 patients have remained protein free, 4 have persistent proteinuria despite cyclophosphamide therapy, 1 had progressed to end-stage renal disease, and 1 is lost to follow-up. On the basis of these findings, we recommend that all children with nephrotic syndrome and an early frequently relapsing steroid-responsive course undergo a prompt renal biopsy. Such patients constitute a high-risk group with a spectrum of renal histopathological lesions characterized by an unpredictable response to therapy and an unfavorable prognosis.
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Abstract
Sickle cell nephropathy characterized by proteinuria and predominantly glomerular lesions has not been studied as extensively as renal tubular alterations in sickle cell disease. We reviewed our experience with this entity over a 14-year period. Of 13 children with either proteinuria or the nephrotic syndrome, 8 showed focal and segmental glomerulosclerosis, and 5 had mesangial proliferation. Children with focal and segmental glomerulosclerosis were older at onset of nephropathy and presented with the nephrotic syndrome more frequently than those with mesangial proliferation (p less than 0.05). All patients with mesangial proliferation and half of the focal and segmental glomerulosclerosis patients had supranormal renal clearances at onset of nephropathy suggesting hyperfiltration. Hyperfiltration seen in animals with reduced renal mass, and in human diabetic nephropathy before reduction in nephron units leads to mesangial proliferation and sclerosis. Our study suggests that sickle cell disease produces similar lesions in patients with sickle cell nephropathy.
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Tejani A, Phadke K, Nicastri A, Adamson O, Chen CK, Trachtman H, Tejani C. Efficacy of cyclophosphamide in steroid-sensitive childhood nephrotic syndrome with different morphological lesions. Nephron Clin Pract 1985; 41:170-3. [PMID: 4047274 DOI: 10.1159/000183575] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
We have reviewed the efficacy of cyclophosphamide in 39 steroid-sensitive frequently relapsing nephrotic children. Cyclophosphamide was used because of heavy steroid dependence and steroid toxicity. A percutaneous renal biopsy done prior to administration of cyclophosphamide showed the lesion to be minimal change in 7 children, IgM nephropathy in 17 children, and evolving from minimal change nephrotic syndrome to focal segmental sclerosis (FSGS) in 15 children. 100% of patients with minimal change nephrotic syndrome responded to cyclophosphamide, but only 58% of IgM patients responded (p less than 0.05). Only 1 of 15 FSGS patients responded (p less than 0.001 vs. minimal change nephrotic syndrome and p less than 0.01 vs. IgM). In view of the failure of cyclophosphamide to produce a remission in FSGS and its potential for long-term impairment of suppressor T cell function, we suggest that it should not be used in patients whose disease has evolved from minimal change to FSGS.
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Sillman F, Stanek A, Sedlis A, Rosenthal J, Lanks KW, Buchhagen D, Nicastri A, Boyce J. The relationship between human papillomavirus and lower genital intraepithelial neoplasia in immunosuppressed women. Am J Obstet Gynecol 1984; 150:300-8. [PMID: 6091459 DOI: 10.1016/s0002-9378(84)90369-7] [Citation(s) in RCA: 100] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
In a group of 20 immunosuppressed women with lower genital neoplasia, evidence of associated human papillomaviral infection was found in all patients on the basis of the histologic identification of koilocytes in the upper strata of areas of mild or moderate dysplasia. Immunohistochemical study of similar areas disclosed human papilloma structural antigens in the lesions in 60%, while 50% had lesions in which human papilloma virions were detected by the electron microscope. An abnormal immunologic status, indicated by an altered T-helper/T-suppressor ratio, a deficient response to mitogenic stimulation, or both, was confirmed in 80% of the patients studied. Twelve of the 20 patients had unusually persistent and recurrent intraepithelial neoplasia, and in one the disorder progressed to invasive epidermoid carcinoma. The progressive behavior of human papillomavirus-associated neoplasia in these immunosuppressed patients might represent an accelerated version of the long-term course of such lesions in immunocompetent hosts.
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Abstract
In two patients with systemic lupus erythematosus, acute renal failure was the initial manifestation. The diagnosis was eventually established on the basis of serologic tests and characteristic renal histopathologic findings. We emphasize the need to consider systemic lupus erythematosus as a cause of acute renal failure of glomerular origin, because appropriate therapy may alter the outcome of the disease.
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Tejani A, Nicastri A, Phadke K, Sen D, Adamson O, Dunn I, Calderon P. Familial focal segmental glomerulosclerosis. Int J Pediatr Nephrol 1983; 4:231-4. [PMID: 6229501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
We have observed the nephrotic syndrome in more than one sibling in three unrelated hispanic families. The histological lesion in the involved children was either focal segmental glomerulosclerosis or IgM nephropathy evolving into focal sclerosis. Tissue typing revealed the presence of HLA DRw8 in six out of eight patients. The frequency of this antigen in our patients, when compared with its frequency in a group of unrelated normal hispanic children was highly significant (p less than 0.0001). Our study suggests that there may be a genetic predilection towards developing focal segmental glomerulosclerosis.
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Avramides A, Leonidas JR, Chen CK, Nicastri A. Coexistence of Paget's disease and hyperparathyroidism. N Y State J Med 1981; 81:1660-2. [PMID: 6945499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Macasaet M, Brigati D, Boyce J, Nicastri A, Waxman M, Nelson J, Fruchter R. The significance of residual disease after radiotherapy in endometrial carcinoma: clinicopathologic correlation. Am J Obstet Gynecol 1980; 138:557-63. [PMID: 7425019 DOI: 10.1016/0002-9378(80)90286-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The extent and location of residual disease after radiotherapy in 91 patients with early invasive endometrial carcinoma was related to tumor grade, clinical stage, and outcome. In 20% the grade (according to the International Federation of Gynecology and Obstetrics) differed in curettage and hysterectomy specimens. In at least 12% the clinical stage was unreliable. Death from endometrial carcinoma was significantly more frequent in patients with residual disease after radiotherapy than in those without residual disease. The poorest prognostic features were blood vesel invasion in the myometrium, irrespective of depth of invasion, and residual disease outside the uterus. Treatment of endometrial carcinoma should be based on accurate knowledge or prognostic features determined by initial surgery.
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Stillman RM, Alfonso A, Nicastri A, Gardner B. Atypical appendiceal carcinoid. N Y State J Med 1979; 79:98-100. [PMID: 282480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Ray M, Nicastri A, Freidman EA. Sequential rat-to-mouse skin xenografts. J Pathol 1973; 109:259-62. [PMID: 4578325 DOI: 10.1002/path.1711090312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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