Swarm Intelligence-Enhanced Detection of Non-Small-Cell Lung Cancer Using Tumor-Educated Platelets.

Journal: Cancer cell
Published Date: Aug 14, 2017

Abstract

Blood-based liquid biopsies, including tumor-educated blood platelets (TEPs), have emerged as promising biomarker sources for non-invasive detection of cancer. Here we demonstrate that particle-swarm optimization (PSO)-enhanced algorithms enable efficient selection of RNA biomarker panels from platelet RNA-sequencing libraries (n = 779). This resulted in accurate TEP-based detection of early- and late-stage non-small-cell lung cancer (n = 518 late-stage validation cohort, accuracy, 88%; AUC, 0.94; 95% CI, 0.92-0.96; p < 0.001; n = 106 early-stage validation cohort, accuracy, 81%; AUC, 0.89; 95% CI, 0.83-0.95; p < 0.001), independent of age of the individuals, smoking habits, whole-blood storage time, and various inflammatory conditions. PSO enabled selection of gene panels to diagnose cancer from TEPs, suggesting that swarm intelligence may also benefit the optimization of diagnostics readout of other liquid biopsy biosources.

Authors

  • Myron G Best
    Department of Neurosurgery, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands; Department of Pathology, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands; Brain Tumor Center Amsterdam, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands. Electronic address: m.best@vumc.nl.
  • Nik Sol
    Brain Tumor Center Amsterdam, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands; Department of Neurology, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands.
  • Sjors G J G In 't Veld
    Department of Neurosurgery, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands; Brain Tumor Center Amsterdam, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands.
  • Adrienne Vancura
    Department of Neurosurgery, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands; Brain Tumor Center Amsterdam, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands.
  • Mirte Muller
    Department of Thoracic Oncology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands.
  • Anna-Larissa N Niemeijer
    Department of Pulmonary Diseases, VU University Medical Center, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands.
  • Aniko V Fejes
    Department of Neurosurgery, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands; Brain Tumor Center Amsterdam, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands; Clinical Institute of Laboratory Medicine, Medical University of Vienna, Spitalgasse 23, 1090 Vienna, Austria.
  • Lee-Ann Tjon Kon Fat
    Department of Radiation Sciences, Oncology, Umeå University, 90185 Umeå, Sweden.
  • Anna E Huis In 't Veld
    Department of Pulmonary Diseases, VU University Medical Center, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands.
  • Cyra Leurs
    Department of Neurology, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands; MS Center Amsterdam, VU University Medical Center, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands.
  • Tessa Y Le Large
    Department of Surgery, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands.
  • Laura L Meijer
    Department of Surgery, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands.
  • Irsan E Kooi
    Department of Clinical Genetics, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands.
  • François Rustenburg
    Department of Neurosurgery, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands; Department of Pathology, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands; Brain Tumor Center Amsterdam, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands.
  • Pepijn Schellen
    Department of Neurosurgery, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands; Brain Tumor Center Amsterdam, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands.
  • Heleen Verschueren
    Department of Neurosurgery, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands; Brain Tumor Center Amsterdam, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands; thromboDx B.V., 1098 EA Amsterdam, the Netherlands.
  • Edward Post
    Department of Neurosurgery, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands; Brain Tumor Center Amsterdam, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands; thromboDx B.V., 1098 EA Amsterdam, the Netherlands.
  • Laurine E Wedekind
    Department of Neurosurgery, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands; Brain Tumor Center Amsterdam, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands.
  • Jillian Bracht
    Department of Neurosurgery, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands.
  • Michelle Esenkbrink
    Department of Neurosurgery, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands.
  • Leon Wils
    Department of Neurosurgery, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands.
  • Francesca Favaro
    Department of Neurosurgery, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands.
  • Jilian D Schoonhoven
    Department of Neurosurgery, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands.
  • Jihane Tannous
    Department of Neurology, Massachusetts General Hospital and Neuroscience Program, Harvard Medical School, 149 13(th) Street, Charlestown, MA 02129, USA.
  • Hanne Meijers-Heijboer
    Department of Clinical Genetics, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands.
  • Geert Kazemier
    Department of Surgery, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands.
  • Elisa Giovannetti
    Department of Medical Oncology, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands.
  • Jaap C Reijneveld
    Brain Tumor Center Amsterdam, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands; Department of Neurology, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands.
  • Sander Idema
    Department of Neurosurgery, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands.
  • Joep Killestein
    Department of Neurology, Neuroscience Campus Amsterdam, VUmc MS Center Amsterdam, VU University Medical Center Amsterdam, Amsterdam, The Netherlands.
  • Michal Heger
    Department of Surgery, Amsterdam Medical Center, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands.
  • Saskia C de Jager
    Department of Experimental Cardiology, Utrecht University Medical Center, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands.
  • Rolf T Urbanus
    Laboratory of Clinical Chemistry and Hematology, Utrecht University Medical Center, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands.
  • Imo E Hoefer
    Central Diagnostic Laboratory, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands.
  • Gerard Pasterkamp
    Department of Experimental Cardiology, Utrecht University Medical Center, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands.
  • Christine Mannhalter
    Clinical Institute of Laboratory Medicine, Medical University of Vienna, Spitalgasse 23, 1090 Vienna, Austria.
  • Jose Gomez-Arroyo
    Department of Pulmonary Diseases, VU University Medical Center, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands.
  • Harm-Jan Bogaard
    Department of Pulmonary Diseases, VU University Medical Center, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands.
  • David P Noske
    Department of Neurosurgery, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands; Brain Tumor Center Amsterdam, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands.
  • W Peter Vandertop
    Department of Neurosurgery, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands; Brain Tumor Center Amsterdam, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands.
  • Daan van den Broek
    Department of Clinical Chemistry, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands.
  • Bauke Ylstra
    Department of Pathology, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands.
  • R Jonas A Nilsson
    Department of Neurosurgery, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands; Department of Radiation Sciences, Oncology, Umeå University, 90185 Umeå, Sweden.
  • Pieter Wesseling
    Department of Pathology, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands; Brain Tumor Center Amsterdam, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands; Department of Pathology, Princess Máxima Center for Pediatric Oncology and University Medical Center Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands.
  • Niki Karachaliou
    Translational Research Unit, Dr. Rosell Oncology Institute, Quirón Dexeus University Hospital, Calle Sabine Arana 5-19, 08028 Barcelona, Spain.
  • Rafael Rosell
    Translational Research Unit, Dr. Rosell Oncology Institute, Quirón Dexeus University Hospital, Calle Sabine Arana 5-19, 08028 Barcelona, Spain; Pangaea Biotech SL, Calle Sabine Arana 5-19, 08028 Barcelona, Spain; Catalan Institute of Oncology, Hospital Germans Trias i Pujol, Carretera de Canyet, 08916 Barcelona, Spain; Molecular Oncology Research (MORe) Foundation, Calle Sabine Arana 5-19, 08028 Barcelona, Spain.
  • Elizabeth Lee-Lewandrowski
    Department of Pathology, Massachusetts General Hospital, Harvard Medical School, 149 13(th) Street, Charlestown, MA 02129, USA.
  • Kent B Lewandrowski
    Department of Pathology, Massachusetts General Hospital, Harvard Medical School, 149 13(th) Street, Charlestown, MA 02129, USA.
  • Bakhos A Tannous
    Department of Neurology, Massachusetts General Hospital and Neuroscience Program, Harvard Medical School, 149 13(th) Street, Charlestown, MA 02129, USA.
  • Adrianus J de Langen
    Department of Pulmonary Diseases, VU University Medical Center, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands.
  • Egbert F Smit
    Department of Thoracic Oncology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Department of Pulmonary Diseases, VU University Medical Center, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands.
  • Michel M van den Heuvel
    Department of Thoracic Oncology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Department of Respiratory Diseases, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands.
  • Thomas Wurdinger
    Department of Neurosurgery, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands; Brain Tumor Center Amsterdam, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands; Department of Neurology, Massachusetts General Hospital and Neuroscience Program, Harvard Medical School, 149 13(th) Street, Charlestown, MA 02129, USA. Electronic address: t.wurdinger@vumc.nl.

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