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Rothschild S, Sobottka-Brillout A, Tochtermann G, Trueb M, Nowak M, Alborelli I, Leonards K, Manzo M, Keller E, Herzig P, Schmid D, Hayoz S, Chiquet S, Schneider M, Pless M, Jermann P, Zippelius A, Prince SS, Koelzer V. 188P SAKK 16/14: Immune profiling of pre-operative biopsies correlates with survival and immune activation in stage IIIA (N2) NSCLC after neoadjuvant immunotherapy. J Thorac Oncol 2023. [DOI: 10.1016/s1556-0864(23)00441-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
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2
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Sobottka B, Tochtermann G, Trueb M, Nowack M, Alborelli I, Leonards K, Manzo M, Keller E, Herzig P, Schmid D, Eboulet E, Hayoz S, Godar G, Schneider M, Jermann P, Savic Prince S, König D, Pless M, Zippelius A, Rothschild S, Koelzer V. MA12.04 SAKK 16/14: CD8 T Cell Positioning Correlates with Survivalin Stage IIIA(N2) NSCLC After Neoadjuvant Immunotherapy. J Thorac Oncol 2022. [DOI: 10.1016/j.jtho.2022.07.144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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3
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Alborelli I, Leonards K, Manzo M, Keller E, Herzig P, Trüb M, Schmid D, Eboulet E, Godar G, Pless M, Zippelius A, Jermann P, Prince SS, Rothschild S. MA09.02 SAKK 16/14 - T-Cell Receptor Repertoire Metrics Predict Response to Neoadjuvant Durvalumab in Patients With Stage IIIA(N2) NSCLC. J Thorac Oncol 2021. [DOI: 10.1016/j.jtho.2021.08.153] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Fenizia F, Alborelli I, Costa JL, Vollbrecht C, Bellosillo B, Dinjens W, Endris V, Heydt C, Leonards K, Merkelback-Bruse S, Pfarr N, van Marion R, Allen C, Chaudhary R, Gottimukkala R, Hyland F, Wong-Ho E, Jermann P, Machado JC, Hummel M, Stenzinger A, Normanno N. Validation of a Targeted Next-Generation Sequencing Panel for Tumor Mutation Burden Analysis: Results from the Onconetwork Immuno-Oncology Consortium. J Mol Diagn 2021; 23:882-893. [PMID: 33964449 DOI: 10.1016/j.jmoldx.2021.04.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 03/26/2021] [Accepted: 04/12/2021] [Indexed: 12/22/2022] Open
Abstract
Tumor mutation burden (TMB) is evaluated as a biomarker of response to immunotherapy. We present the efforts of the Onconetwork Immuno-Oncology Consortium to validate a commercial targeted sequencing test for TMB calculation. A three-phase study was designed to validate the Oncomine Tumor Mutational Load (OTML) assay at nine European laboratories. Phase 1 evaluated reproducibility and accuracy on seven control samples. In phase 2, six formalin-fixed, paraffin-embedded samples tested with FoundationOne were reanalyzed with the OTML panel to evaluate concordance and reproducibility. Phase 3 involved analysis of 90 colorectal cancer samples with known microsatellite instability (MSI) status to evaluate TMB and MSI association. High reproducibility of TMB was demonstrated among the sites in the first and second phases. Strong correlation was also detected between mean and expected TMB in phase 1 (r2 = 0.998) and phase 2 (r2 = 0.96). Detection of actionable mutations was also confirmed. In colorectal cancer samples, the expected pattern of MSI-high/high-TMB and microsatellite stability/low-TMB was present, and gene signatures produced by the panel suggested the presence of a POLE mutation in two samples. The OTML panel demonstrated robustness and reproducibility for TMB evaluation. Results also suggest the possibility of using the panel for mutational signatures and variant detection. Collaborative efforts between academia and companies are crucial to accelerate the translation of new biomarkers into clinical research.
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Affiliation(s)
- Francesca Fenizia
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, Naples, Italy
| | - Ilaria Alborelli
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Jose Luis Costa
- Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
| | - Claudia Vollbrecht
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Pathology, Berlin, Germany
| | | | - Winand Dinjens
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, the Netherlands
| | - Volker Endris
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Carina Heydt
- Institute of Pathology, University Hospital Cologne, Cologne, France
| | - Katharina Leonards
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | | | - Nicole Pfarr
- Institute of Pathology, Technical University Munich, Munich, Germany
| | - Ronald van Marion
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, the Netherlands
| | - Christopher Allen
- Clinical Next-Generation Sequencing Division, Thermo Fisher Scientific, Waltham, Massachusetts
| | - Ruchi Chaudhary
- Clinical Next-Generation Sequencing Division, Thermo Fisher Scientific, Waltham, Massachusetts
| | - Rajesh Gottimukkala
- Clinical Next-Generation Sequencing Division, Thermo Fisher Scientific, Waltham, Massachusetts
| | - Fiona Hyland
- Clinical Next-Generation Sequencing Division, Thermo Fisher Scientific, Waltham, Massachusetts
| | - Elaine Wong-Ho
- Clinical Next-Generation Sequencing Division, Thermo Fisher Scientific, Waltham, Massachusetts
| | - Philip Jermann
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Jose Carlos Machado
- Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
| | - Michael Hummel
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Pathology, Berlin, Germany
| | | | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, Naples, Italy.
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5
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Alborelli I, Bratic Hench I, Chijioke O, Prince SS, Bubendorf L, Leuenberger LP, Tolnay M, Leonards K, Quagliata L, Jermann P, Matter MS. Robust assessment of tumor mutational burden in cytological specimens from lung cancer patients. Lung Cancer 2020; 149:84-89. [PMID: 32980613 DOI: 10.1016/j.lungcan.2020.08.019] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 08/23/2020] [Accepted: 08/31/2020] [Indexed: 12/28/2022]
Abstract
OBJECTIVES Tumor mutational burden (TMB) has emerged as a promising predictive biomarker for immune checkpoint inhibitor therapy. While the feasibility of TMB analysis on formalin-fixed paraffin-embedded (FFPE) samples has been thoroughly evaluated, only limited analyses have been performed on cytological samples, and no dedicated study has investigated concordance of TMB between different sample types. Here, we assessed TMB on matched histological and cytological samples from lung cancer patients and evaluated the accuracy of TMB estimation in these sample types. MATERIALS AND METHODS We analyzed mutations and resulting TMB in FFPE samples and matched ethanol-fixed cytological smears (n = 12 matched pairs) by using a targeted next-generation sequencing assay (Oncomine™ Tumor Mutational Load). Two different variant allele frequency (VAF) thresholds were used to estimate TMB (VAF = 5% or 10%). RESULTS At 5% VAF threshold, 73% (107/147) of mutations were concordantly detected in matched histological and cytological samples. Discordant variants were mainly unique to FFPE samples (34/40 discordant variants) and mostly C:G > T:A transitions with low allelic frequency, likely indicating formalin fixation artifacts. Increasing the VAF threshold to 10% clearly increased the number of concordantly detected mutations in matched histological and cytological samples to 96% (100/106 mutations), and drastically reduced the number of FFPE-only mutations (from 34 to 4 mutations). In contrast, cytological samples showed consistent mutation count and TMB values at both VAF thresholds. Using FFPE samples, 2 out of 12 patients were classified as TMB-high at VAF cutoff of 5% but TMB-low at 10%, whereas cytological specimens allowed consistent patient classification independently from VAF cutoff. CONCLUSION Our results show that cytological smears provide more consistent TMB values due to high DNA quality and lack of formalin-fixation induced artifacts. Therefore, cytological samples should be the preferred sample type for robust TMB estimation.
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Affiliation(s)
- Ilaria Alborelli
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Switzerland.
| | - Ivana Bratic Hench
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Switzerland
| | - Obinna Chijioke
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Switzerland
| | - Spasenija Savic Prince
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Switzerland
| | - Lukas Bubendorf
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Switzerland
| | - Laura P Leuenberger
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Switzerland
| | - Markus Tolnay
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Switzerland
| | - Katharina Leonards
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Switzerland
| | | | - Philip Jermann
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Switzerland
| | - Matthias S Matter
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Switzerland
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6
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Leonards K, Almosailleakh M, Tauchmann S, Bagger FO, Thirant C, Juge S, Bock T, Méreau H, Bezerra MF, Tzankov A, Ivanek R, Losson R, Peters AHFM, Mercher T, Schwaller J. Nuclear interacting SET domain protein 1 inactivation impairs GATA1-regulated erythroid differentiation and causes erythroleukemia. Nat Commun 2020; 11:2807. [PMID: 32533074 PMCID: PMC7293310 DOI: 10.1038/s41467-020-16179-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 04/17/2020] [Indexed: 12/20/2022] Open
Abstract
The nuclear receptor binding SET domain protein 1 (NSD1) is recurrently mutated in human cancers including acute leukemia. We show that NSD1 knockdown alters erythroid clonogenic growth of human CD34+ hematopoietic cells. Ablation of Nsd1 in the hematopoietic system of mice induces a transplantable erythroleukemia. In vitro differentiation of Nsd1−/− erythroblasts is majorly impaired despite abundant expression of GATA1, the transcriptional master regulator of erythropoiesis, and associated with an impaired activation of GATA1-induced targets. Retroviral expression of wildtype NSD1, but not a catalytically-inactive NSD1N1918Q SET-domain mutant induces terminal maturation of Nsd1−/− erythroblasts. Despite similar GATA1 protein levels, exogenous NSD1 but not NSDN1918Q significantly increases the occupancy of GATA1 at target genes and their expression. Notably, exogenous NSD1 reduces the association of GATA1 with the co-repressor SKI, and knockdown of SKI induces differentiation of Nsd1−/− erythroblasts. Collectively, we identify the NSD1 methyltransferase as a regulator of GATA1-controlled erythroid differentiation and leukemogenesis. Loss of function mutations of NSD1 occur in blood cancers. Here, the authors report that NSD1 loss blocks erythroid differentiation which leads to an erythroleukemia-like disease in mice by impairing GATA1-induced target gene activation.
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Affiliation(s)
- Katharina Leonards
- University Children's Hospital Basel, Basel, Switzerland.,Department of Biomedicine, University of Basel, 4031, Basel, Switzerland
| | - Marwa Almosailleakh
- University Children's Hospital Basel, Basel, Switzerland.,Department of Biomedicine, University of Basel, 4031, Basel, Switzerland
| | - Samantha Tauchmann
- University Children's Hospital Basel, Basel, Switzerland.,Department of Biomedicine, University of Basel, 4031, Basel, Switzerland
| | - Frederik Otzen Bagger
- University Children's Hospital Basel, Basel, Switzerland.,Department of Biomedicine, University of Basel, 4031, Basel, Switzerland.,Swiss Institute of Bioinfomatics, 4031, Basel, Switzerland.,Genomic Medicine, Righospitalet, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Cécile Thirant
- INSERM U1170, Equipe Labellisée Ligue Contre le Cancer, Gustave Roussy Institute, Université Paris Diderot, Université Paris-Sud, Villejuif, 94800, France
| | - Sabine Juge
- University Children's Hospital Basel, Basel, Switzerland.,Department of Biomedicine, University of Basel, 4031, Basel, Switzerland
| | - Thomas Bock
- Proteomics Core Facility, Biozentrum University of Basel, Basel, Switzerland
| | - Hélène Méreau
- Department of Biomedicine, University of Basel, 4031, Basel, Switzerland
| | - Matheus F Bezerra
- University Children's Hospital Basel, Basel, Switzerland.,Department of Biomedicine, University of Basel, 4031, Basel, Switzerland.,Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife, Brazil
| | - Alexandar Tzankov
- Institute for Pathology, University Hospital Basel, 4031, Basel, Switzerland
| | - Robert Ivanek
- Department of Biomedicine, University of Basel, 4031, Basel, Switzerland.,Swiss Institute of Bioinfomatics, 4031, Basel, Switzerland
| | - Régine Losson
- Institute de Génétique et de Biologie Moléculaire et Cellulaire (I.G.B.M.C.), CNRS/INSERM Université de Strasbourg, BP10142, 67404, Illkirch Cedex, France
| | - Antoine H F M Peters
- Friedrich Miescher Institute for Biomedical Research, 4058, Basel, Switzerland.,Faculty of Sciences, University of Basel, 4056, Basel, Switzerland
| | - Thomas Mercher
- INSERM U1170, Equipe Labellisée Ligue Contre le Cancer, Gustave Roussy Institute, Université Paris Diderot, Université Paris-Sud, Villejuif, 94800, France
| | - Juerg Schwaller
- University Children's Hospital Basel, Basel, Switzerland. .,Department of Biomedicine, University of Basel, 4031, Basel, Switzerland.
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7
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Alborelli I, Leonards K, Rothschild SI, Leuenberger LP, Savic Prince S, Mertz KD, Poechtrager S, Buess M, Zippelius A, Läubli H, Haegele J, Tolnay M, Bubendorf L, Quagliata L, Jermann P. Tumor mutational burden assessed by targeted NGS predicts clinical benefit from immune checkpoint inhibitors in non-small cell lung cancer. J Pathol 2019; 250:19-29. [PMID: 31471895 PMCID: PMC6972587 DOI: 10.1002/path.5344] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [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: 03/14/2019] [Revised: 07/22/2019] [Accepted: 08/22/2019] [Indexed: 02/06/2023]
Abstract
In non‐small cell lung cancer (NSCLC), immune checkpoint inhibitors (ICIs) significantly improve overall survival (OS). Tumor mutational burden (TMB) has emerged as a predictive biomarker for patients treated with ICIs. Here, we evaluated the predictive power of TMB measured by the Oncomine™ Tumor Mutational Load targeted sequencing assay in 76 NSCLC patients treated with ICIs. TMB was assessed retrospectively in 76 NSCLC patients receiving ICI therapy. Clinical data (RECIST 1.1) were collected and patients were classified as having either durable clinical benefit (DCB) or no durable benefit (NDB). Additionally, genetic alterations and PD‐L1 expression were assessed and compared with TMB and response rate. TMB was significantly higher in patients with DCB than in patients with NDB (median TMB = 8.5 versus 6.0 mutations/Mb, Mann–Whitney p = 0.0244). 64% of patients with high TMB (cut‐off = third tertile, TMB ≥ 9) were responders (DCB) compared to 33% and 29% of patients with intermediate and low TMB, respectively (cut‐off = second and first tertile, TMB = 5–9 and TMB ≤ 4, respectively). TMB‐high patients showed significantly longer progression‐free survival (PFS) and OS (log‐rank test p = 0.0014 for PFS and 0.0197 for OS). While identifying different subgroups of patients, combining PD‐L1 expression and TMB increased the predictive power (from AUC 0.63 to AUC 0.65). Our results show that the TML panel is an effective tool to stratify patients for ICI treatment. A combination of biomarkers might maximize the predictive precision for patient stratification. Our study supports TMB evaluation through targeted NGS in NSCLC patient samples as a tool to predict response to ICI therapy. We offer recommendations for a reliable and cost‐effective assessment of TMB in a routine diagnostic setting. © 2019 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Ilaria Alborelli
- Department of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Katharina Leonards
- Department of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Sacha I Rothschild
- Laboratory of Cancer Immunology, Department of Biomedicine, University Hospital Basel, Basel, Switzerland.,Department of Medical Oncology, Department of Internal Medicine, University Hospital Basel, Basel, Switzerland
| | - Laura P Leuenberger
- Department of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Spasenija Savic Prince
- Department of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Kirsten D Mertz
- Department of Pathology, Cantonal Hospital Baselland, Liestal, Switzerland
| | | | - Martin Buess
- Department of Medical Oncology, St. Claraspital, Basel, Switzerland
| | - Alfred Zippelius
- Laboratory of Cancer Immunology, Department of Biomedicine, University Hospital Basel, Basel, Switzerland.,Department of Medical Oncology, Department of Internal Medicine, University Hospital Basel, Basel, Switzerland
| | - Heinz Läubli
- Laboratory of Cancer Immunology, Department of Biomedicine, University Hospital Basel, Basel, Switzerland.,Department of Medical Oncology, Department of Internal Medicine, University Hospital Basel, Basel, Switzerland
| | - Jasmin Haegele
- Department of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Markus Tolnay
- Department of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Lukas Bubendorf
- Department of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Luca Quagliata
- Department of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Philip Jermann
- Department of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
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8
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Jermann P, Leonards K, Looney T, Alborelli I, Rothschild S, Savic Prince S, Mertz K, Zippelius A, Bubendorf L. TCR-beta repertoire convergence and evenness are associated with response to immune checkpoint inhibitors. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz394.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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9
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Rothschild S, Alborelli I, Leonards K, Leuenberger LP, Savic Prince S, Mertz KD, Poechtrager S, Zippelius A, Laubli HP, Haegele J, Tolnay M, Bubendorf L, Quagliata L, Jermann P. Tumor mutational burden assessed by a targeted NGS assay to predict clinical benefit from immune checkpoint inhibitors in non-small cell lung cancer. J Clin Oncol 2019. [DOI: 10.1200/jco.2019.37.15_suppl.e14266] [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
e14266 Background: In non-small cell lung cancer (NSCLC) immune checkpoint inhibitors (ICIs) significantly improve overall survival (OS). Tumor mutational burden (TMB) has emerged as a predictive biomarker for patients treated with ICIs. Here we evaluated the predictive power of TMB measured through / by the Oncomine Tumor Mutational Load (TML - Thermo Fisher Scientific) targeted sequencing assay in 71 NSCLC patients treated with ICIs. Methods: TMB was assessed retrospectively in 71 metastatic NSCLC patients receiving ICI therapy. Clinical data (RECIST 1.1) were collected and patients were characterized as either having durable clinical benefit (DCB) or no durable benefit (NDB). Additionally, genetic alterations and PD-L1 expression were assessed and compared with TMB and response rate. Results: TMB was significantly higher in patients with DCB compared to patients with NDB (median TMB = 9.2 versus 5.3 mutations/Mb, Mann-Whitney p = 0.014). 70% of patients with high TMB (cutoff = 3rd tertile, TMB ≥ 9.2) were responders (DCB) compared to 29% of patients with low TMB (cutoff = 1st tertile, TMB ≤ 4.5). TMB-high patients showed significantly longer progression-free survival (PFS) and OS (log rank test, p = .0030 for PFS and 0 .0375 for OS, respectively). Combining PD-L1 expression and TMB value increased the predictive power of TMB. Conclusions: Our results show that the TML panel is an effective tool to stratify patients for ICI treatment. We believe that a combination of biomarkers will maximize the precision of patient selection.
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Affiliation(s)
- Sacha Rothschild
- Medical Oncology, Department of Internal Medicine, University Hospital Basel, Basel, Switzerland
| | - Ilaria Alborelli
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Katharina Leonards
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Laura P Leuenberger
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Spasenija Savic Prince
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Kirsten D Mertz
- Institute of Pathology, Cantonal Hospital Baselland, Liestal, Liestal, Switzerland
| | - Severin Poechtrager
- Department Oncology, Hematology and Immunotherapy, Cantonal Hospital Baselland, Liestal, Liestal, Switzerland
| | - Alfred Zippelius
- Medical Oncology, Department of Internal Medicine, University Hospital Basel, Basel, Switzerland
| | - Heinz Philipp Laubli
- Medical Oncology, Department of Internal Medicine, University Hospital Basel, Basel, Switzerland
| | - Jasmin Haegele
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Markus Tolnay
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Lukas Bubendorf
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | | | - Philip Jermann
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
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10
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Jermann P, Alborelli I, Leonards K, Rothschild S, Leuenberger L, Savic Prince S, Mertz K, Poechtrager S, Zippelius A, Quagliata L, Bubendorf L. Tumor mutational burden assessed by a targeted NGS assay predicts clinical benefit from immune checkpoint inhibitors in non-small cell lung cancer. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz063.059] [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: 11/13/2022] Open
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11
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Picaud S, Leonards K, Lambert JP, Dovey O, Wells C, Fedorov O, Monteiro O, Fujisawa T, Wang CY, Lingard H, Tallant C, Nikbin N, Guetzoyan L, Ingham R, Ley SV, Brennan P, Muller S, Samsonova A, Gingras AC, Schwaller J, Vassiliou G, Knapp S, Filippakopoulos P. Promiscuous targeting of bromodomains by bromosporine identifies BET proteins as master regulators of primary transcription response in leukemia. Sci Adv 2016; 2:e1600760. [PMID: 27757418 PMCID: PMC5061470 DOI: 10.1126/sciadv.1600760] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Accepted: 08/22/2016] [Indexed: 06/06/2023]
Abstract
Bromodomains (BRDs) have emerged as compelling targets for cancer therapy. The development of selective and potent BET (bromo and extra-terminal) inhibitors and their significant activity in diverse tumor models have rapidly translated into clinical studies and have motivated drug development efforts targeting non-BET BRDs. However, the complex multidomain/subunit architecture of BRD protein complexes complicates predictions of the consequences of their pharmacological targeting. To address this issue, we developed a promiscuous BRD inhibitor [bromosporine (BSP)] that broadly targets BRDs (including BETs) with nanomolar affinity, creating a tool for the identification of cellular processes and diseases where BRDs have a regulatory function. As a proof of principle, we studied the effects of BSP on leukemic cell lines known to be sensitive to BET inhibition and found, as expected, strong antiproliferative activity. Comparison of the modulation of transcriptional profiles by BSP after a short exposure to the inhibitor resulted in a BET inhibitor signature but no significant additional changes in transcription that could account for inhibition of other BRDs. Thus, nonselective targeting of BRDs identified BETs, but not other BRDs, as master regulators of context-dependent primary transcription response.
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Affiliation(s)
- Sarah Picaud
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K
| | - Katharina Leonards
- Laboratory of Childhood Leukemia, Department of Biomedicine, University of Basel and Basel University Children’s Hospital, Hebelstrasse 20, CH-4031 Basel, Switzerland
| | - Jean-Philippe Lambert
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Oliver Dovey
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, U.K
| | - Christopher Wells
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K
| | - Oleg Fedorov
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K
- Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, U.K
| | - Octovia Monteiro
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K
- Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, U.K
| | - Takao Fujisawa
- Ludwig Institute for Cancer Research, University of Oxford, Oxford OX3 7DQ, U.K
| | - Chen-Yi Wang
- Ludwig Institute for Cancer Research, University of Oxford, Oxford OX3 7DQ, U.K
| | - Hannah Lingard
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K
| | - Cynthia Tallant
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K
- Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, U.K
| | - Nikzad Nikbin
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Lucie Guetzoyan
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Richard Ingham
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Steven V. Ley
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Paul Brennan
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K
- Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, U.K
- Alzheimer’s Research UK Oxford, Nuffield Department of Medicine Research Building, University of Oxford, Oxford OX3 7FZ, U.K
| | - Susanne Muller
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K
- Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, U.K
| | - Anastasia Samsonova
- Department of Oncology, CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford, Oxford OX3 7DQ, U.K
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Juerg Schwaller
- Laboratory of Childhood Leukemia, Department of Biomedicine, University of Basel and Basel University Children’s Hospital, Hebelstrasse 20, CH-4031 Basel, Switzerland
| | - George Vassiliou
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, U.K
- Department of Haematology, Cambridge University Hospitals NHS Trust, Cambridge CB2 0QQ, U.K
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0XY, U.K
| | - Stefan Knapp
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K
- Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, U.K
- Institute for Pharmaceutical Chemistry and Buchmann Institute for Life Sciences, Goethe University, Max-von Laue Str. 9, 60438 Frankfurt am Main, Germany
| | - Panagis Filippakopoulos
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K
- Ludwig Institute for Cancer Research, University of Oxford, Oxford OX3 7DQ, U.K
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12
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Picaud S, Fedorov O, Thanasopoulou A, Leonards K, Jones K, Meier J, Olzscha H, Monteiro O, Martin S, Philpott M, Tumber A, Filippakopoulos P, Yapp C, Wells C, Che KH, Bannister A, Robson S, Kumar U, Parr N, Lee K, Lugo D, Jeffrey P, Taylor S, Vecellio ML, Bountra C, Brennan PE, O’Mahony A, Velichko S, Müller S, Hay D, Daniels DL, Urh M, La Thangue NB, Kouzarides T, Prinjha R, Schwaller J, Knapp S. Generation of a Selective Small Molecule Inhibitor of the CBP/p300 Bromodomain for Leukemia Therapy. Cancer Res 2015; 75:5106-5119. [PMID: 26552700 PMCID: PMC4948672 DOI: 10.1158/0008-5472.can-15-0236] [Citation(s) in RCA: 165] [Impact Index Per Article: 18.3] [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: 01/28/2015] [Accepted: 08/07/2015] [Indexed: 01/11/2023]
Abstract
The histone acetyltransferases CBP/p300 are involved in recurrent leukemia-associated chromosomal translocations and are key regulators of cell growth. Therefore, efforts to generate inhibitors of CBP/p300 are of clinical value. We developed a specific and potent acetyl-lysine competitive protein-protein interaction inhibitor, I-CBP112, that targets the CBP/p300 bromodomains. Exposure of human and mouse leukemic cell lines to I-CBP112 resulted in substantially impaired colony formation and induced cellular differentiation without significant cytotoxicity. I-CBP112 significantly reduced the leukemia-initiating potential of MLL-AF9(+) acute myeloid leukemia cells in a dose-dependent manner in vitro and in vivo. Interestingly, I-CBP112 increased the cytotoxic activity of BET bromodomain inhibitor JQ1 as well as doxorubicin. Collectively, we report the development and preclinical evaluation of a novel, potent inhibitor targeting CBP/p300 bromodomains that impairs aberrant self-renewal of leukemic cells. The synergistic effects of I-CBP112 and current standard therapy (doxorubicin) as well as emerging treatment strategies (BET inhibition) provide new opportunities for combinatorial treatment of leukemia and potentially other cancers.
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Affiliation(s)
- Sarah Picaud
- Nuffield Department of Clinical Medicine, University of Oxford,
Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive,
Oxford OX3 7DQ, UK
- Nuffield Department of Clinical Medicine, University of Oxford,
Ludwig Institute for Cancer Research (LICR), Roosevelt Drive, Oxford OX3 7DQ,
UK
| | - Oleg Fedorov
- Nuffield Department of Clinical Medicine, University of Oxford,
Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive,
Oxford OX3 7DQ, UK
- Nuffield Department of Clinical Medicine, University of Oxford,
Target Discovery Institute (TDI), Roosevelt Drive, Oxford OX3 7BN, UK
| | - Angeliki Thanasopoulou
- Laboratory of Childhood Leukemia, Department of Biomedicine,
University of Basel and Basel University Children’s Hospital, Hebelstrasse 20
CH - 4031 Basel, Switzerland
| | - Katharina Leonards
- Laboratory of Childhood Leukemia, Department of Biomedicine,
University of Basel and Basel University Children’s Hospital, Hebelstrasse 20
CH - 4031 Basel, Switzerland
| | - Katherine Jones
- Epinova DPU, Immuno-Inflammation Therapy Area Unit, GlaxoSmithKline,
Medicines Research Centre, Stevenage SG1 2NY, UK
| | - Julia Meier
- Nuffield Department of Clinical Medicine, University of Oxford,
Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive,
Oxford OX3 7DQ, UK
- Nuffield Department of Clinical Medicine, University of Oxford,
Target Discovery Institute (TDI), Roosevelt Drive, Oxford OX3 7BN, UK
| | - Heidi Olzscha
- Laboratory of Cancer Biology, Department of Oncology, Medical
Sciences Division, University of Oxford, Old Road Campus Research Building,
Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Octovia Monteiro
- Nuffield Department of Clinical Medicine, University of Oxford,
Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive,
Oxford OX3 7DQ, UK
- Nuffield Department of Clinical Medicine, University of Oxford,
Target Discovery Institute (TDI), Roosevelt Drive, Oxford OX3 7BN, UK
| | - Sarah Martin
- Nuffield Department of Clinical Medicine, University of Oxford,
Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive,
Oxford OX3 7DQ, UK
- Nuffield Department of Clinical Medicine, University of Oxford,
Target Discovery Institute (TDI), Roosevelt Drive, Oxford OX3 7BN, UK
| | - Martin Philpott
- Nuffield Department of Clinical Medicine, University of Oxford,
Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive,
Oxford OX3 7DQ, UK
- Nuffield Department of Clinical Medicine, University of Oxford,
Target Discovery Institute (TDI), Roosevelt Drive, Oxford OX3 7BN, UK
| | - Anthony Tumber
- Nuffield Department of Clinical Medicine, University of Oxford,
Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive,
Oxford OX3 7DQ, UK
- Nuffield Department of Clinical Medicine, University of Oxford,
Target Discovery Institute (TDI), Roosevelt Drive, Oxford OX3 7BN, UK
| | - Panagis Filippakopoulos
- Nuffield Department of Clinical Medicine, University of Oxford,
Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive,
Oxford OX3 7DQ, UK
- Nuffield Department of Clinical Medicine, University of Oxford,
Ludwig Institute for Cancer Research (LICR), Roosevelt Drive, Oxford OX3 7DQ,
UK
| | - Clarence Yapp
- Nuffield Department of Clinical Medicine, University of Oxford,
Target Discovery Institute (TDI), Roosevelt Drive, Oxford OX3 7BN, UK
| | - Christopher Wells
- Nuffield Department of Clinical Medicine, University of Oxford,
Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive,
Oxford OX3 7DQ, UK
- Nuffield Department of Clinical Medicine, University of Oxford,
Target Discovery Institute (TDI), Roosevelt Drive, Oxford OX3 7BN, UK
| | - Ka Hing Che
- Gurdon Institute and Department of Pathology, University of
Cambridge, Cambridge CB2 1QN, UK
| | - Andrew Bannister
- Gurdon Institute and Department of Pathology, University of
Cambridge, Cambridge CB2 1QN, UK
| | - Samuel Robson
- Gurdon Institute and Department of Pathology, University of
Cambridge, Cambridge CB2 1QN, UK
| | - Umesh Kumar
- Epinova DPU, Immuno-Inflammation Therapy Area Unit, GlaxoSmithKline,
Medicines Research Centre, Stevenage SG1 2NY, UK
| | - Nigel Parr
- Epinova DPU, Immuno-Inflammation Therapy Area Unit, GlaxoSmithKline,
Medicines Research Centre, Stevenage SG1 2NY, UK
| | - Kevin Lee
- Epinova DPU, Immuno-Inflammation Therapy Area Unit, GlaxoSmithKline,
Medicines Research Centre, Stevenage SG1 2NY, UK
| | - Dave Lugo
- Experimental Medicines Unit, GlaxoSmithKline, Medicines Research
Centre, Stevenage, UK
| | - Philip Jeffrey
- Experimental Medicines Unit, GlaxoSmithKline, Medicines Research
Centre, Stevenage, UK
| | - Simon Taylor
- Experimental Medicines Unit, GlaxoSmithKline, Medicines Research
Centre, Stevenage, UK
| | - Matteo L. Vecellio
- Nuffield Department of Clinical Medicine, University of Oxford,
Target Discovery Institute (TDI), Roosevelt Drive, Oxford OX3 7BN, UK
| | - Chas Bountra
- Nuffield Department of Clinical Medicine, University of Oxford,
Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive,
Oxford OX3 7DQ, UK
| | - Paul E. Brennan
- Nuffield Department of Clinical Medicine, University of Oxford,
Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive,
Oxford OX3 7DQ, UK
- Nuffield Department of Clinical Medicine, University of Oxford,
Target Discovery Institute (TDI), Roosevelt Drive, Oxford OX3 7BN, UK
| | - Alison O’Mahony
- BioSeek Division of DiscoveRx Corporation, 310 Utah Street, Suite
100, South San Francisco, CA, 94080, USA
| | - Sharlene Velichko
- BioSeek Division of DiscoveRx Corporation, 310 Utah Street, Suite
100, South San Francisco, CA, 94080, USA
| | - Susanne Müller
- Nuffield Department of Clinical Medicine, University of Oxford,
Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive,
Oxford OX3 7DQ, UK
- Nuffield Department of Clinical Medicine, University of Oxford,
Target Discovery Institute (TDI), Roosevelt Drive, Oxford OX3 7BN, UK
| | - Duncan Hay
- Nuffield Department of Clinical Medicine, University of Oxford,
Target Discovery Institute (TDI), Roosevelt Drive, Oxford OX3 7BN, UK
| | - Danette L. Daniels
- Promega Corporation, 2800 Woods Hollow Road, Madison, Wisconsin,
U.S.A 53711
| | - Marjeta Urh
- Promega Corporation, 2800 Woods Hollow Road, Madison, Wisconsin,
U.S.A 53711
| | - Nicholas B. La Thangue
- Laboratory of Cancer Biology, Department of Oncology, Medical
Sciences Division, University of Oxford, Old Road Campus Research Building,
Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Tony Kouzarides
- Gurdon Institute and Department of Pathology, University of
Cambridge, Cambridge CB2 1QN, UK
| | - Rab Prinjha
- Epinova DPU, Immuno-Inflammation Therapy Area Unit, GlaxoSmithKline,
Medicines Research Centre, Stevenage SG1 2NY, UK
| | - Jürg Schwaller
- Laboratory of Childhood Leukemia, Department of Biomedicine,
University of Basel and Basel University Children’s Hospital, Hebelstrasse 20
CH - 4031 Basel, Switzerland
| | - Stefan Knapp
- Nuffield Department of Clinical Medicine, University of Oxford,
Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive,
Oxford OX3 7DQ, UK
- Nuffield Department of Clinical Medicine, University of Oxford,
Target Discovery Institute (TDI), Roosevelt Drive, Oxford OX3 7BN, UK
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13
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Fassel TA, Hui SW, Leonards K, Ohki S. Electron microscopic study of the calcium phosphate-induced aggregation and membrane destabilization of cytoskeleton-free erythrocyte vesicles. Biochim Biophys Acta 1988; 943:267-76. [PMID: 3401481 DOI: 10.1016/0005-2736(88)90558-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Cytoskeleton-free vesicles derived from human erythrocytes were treated with trypsin, chymotrypsin, or neuraminidase followed by calcium, phosphate, or combined calcium/phosphate treatments in order to study the roles of cell surface proteins and glycoproteins in calcium/phosphate-induced cell aggregation and fusion. Vesicle aggregation (a necessary pre-cursor to membrane fusion) and subsequent membrane destabilization (an essential component of fusion) were examined by freeze-fracture electron microscopy. Enzymatic treatment alone had no effect on the morphology of the cytoskeleton-free vesicles. Neither did separate calcium nor phosphate treatments, although the treatment of the cytoskeleton-free vesicles with calcium did reduce their size slightly. Enzymatic pretreatment had no effect on the calcium-induced size changes. In contrast, the combination of calcium and phosphate drastically disrupted the membrane integrity of aggregated cytoskeleton-free vesicles at pH 7.8, although the effect was reduced at lower pH values. The extent of this membrane destabilization was independent of enzyme treatment. Our results indicate: (1) that the cell surface proteins and glycoproteins have only secondary effects on calcium/phosphate-induced cell aggregation and membrane destabilization, (2) that these processes primarily depend on the reaction between calcium and phosphate ions at the membrane surface, and (3) that cytoskeletal elements probably play no active (positive) role in the Ca2+/PO4(3-) induced erythrocyte membrane fusion process, apart from maintaining cell shape.
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Affiliation(s)
- T A Fassel
- Biophysics Department, Roswell Park Memorial Institute, Buffalo, NY
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Abstract
Aggregation of acidic phospholipid vesicles induced by monovalent cations was studied for vesicles of small and large sizes. It was found that there were two phases in the aggregation of large acidic phospholipid vesicles. In the initial phase, observed in the range of 0.1-0.4 M monovalent salts, aggregation took place spontaneously after a change in salt concentration; in the second phase (greater than 0.4 M salt), aggregation progressed gradually with time. The order of capability for monovalent cations to induce the initial phase of aggregation of large phosphatidylserine vesicles (more than 1000 A in diameter) was Li+ greater than Na+ greater than K+ greater than TEA+. However, for the second phase of aggregation, the order was Na+ greater than Li+ greater than K+ greater than TEA+, which was the same as that to induce massive aggregation of small phosphatidylserine vesicles (250 A in diameter). A similar reversal in the order was observed in studies of the surface potential of the phosphatidylserine monolayer. In these studies, the order of the binding strength of monovalent cations was deduced from the change in surface potential produced by successive additions of MgCl2 to the subphase solution, which contained a certain level of monovalent salt initially. These measurements were carried out with monolayers that had a range of areas per molecule. The order was Na+ greater than Li+ greater than K+ for monolayers of large area (greater than 80 A2) per molecule and was Li+ greater than Na+ greater than K+ for those of small area (less than 80 A2) per molecule.(ABSTRACT TRUNCATED AT 250 WORDS)
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Abstract
The effects of proteins on divalent cation-induced phospholipid vesicle aggregation and phospholipid vesicle-monolayer membrane interactions (fusion) were examined. Glycophorin (from human erythrocytes) suppressed the membrane interactions more than N-2 protein (from human brain myelin) when these proteins were incorporated into acidic phospholipid vesicle membranes. The threshold concentrations of divalent cations which induced vesicle aggregation were increased by protein incorporation, and the rate of vesicle aggregation was reduced. A similar inhibitory effect by the proteins, incorporated into lipid vesicle membranes, was observed for Ca2+-induced lipid vesicle-monolayer interactions. However, when these proteins were incorporated only in the acidic phospholipid monolayers, the interaction (fusion) of the lipid vesicle-monolayer membranes, induced by divalent cations, was not appreciably altered by the presence of the proteins. In contrast to these two proteins, the presence of synexin in the solution did enhance the Ca2+-induced aggregation of phosphatidylserine vesicles, but did not seem to affect the degree of Ca2+-induced fusion between phosphatidylserine/phosphatidylcholine (1:1) and phosphatidylserine vesicles and monolayer membranes.
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