MPAPASS software enables stitched multiplex, multidimensional EV repertoire analysis and a standard framework for reporting bead-based assays

Joshua A Welsh; Bryce Killingsworth; Julia Kepley; Tim Traynor; Sean Cook; Jason Savage; Jenn Marte; Min-Jung Lee; Hoyoung M Maeng; Michelle L Pleet; Setty Magana; André Gorgens; Cecile L Maire; Katrin Lamszus; Franz L Ricklefs; Maria J Merino; W Marston Linehan; Tim Greten; Tomer Cooks; Curtis C Harris; Andrea Apolo; Asim Abdel-Mageed; Alexander R Ivanov; Jane B Trepel; Matthew Roth; Mercedes Tkach; Aleksandar Milosavljevic; Clotilde Théry; Amy LeBlanc; Jay A Berzofsky; Eytan Ruppin; Kenneth Aldape; Kevin Camphausen; James L Gulley; Ionita Ghiran; Steve Jacobson; Jennifer C Jones

doi:10.1016/j.crmeth.2021.100136

MPA_PASS software enables stitched multiplex, multidimensional EV repertoire analysis and a standard framework for reporting bead-based assays

Cell Rep Methods. 2022 Jan 24;2(1):100136. doi: 10.1016/j.crmeth.2021.100136.

Authors

Joshua A Welsh^{1

2}, Bryce Killingsworth^{1

2}, Julia Kepley¹, Tim Traynor¹, Sean Cook¹, Jason Savage¹, Jenn Marte³, Min-Jung Lee⁴, Hoyoung M Maeng², Michelle L Pleet⁵, Setty Magana⁵, André Gorgens^{6

7}, Cecile L Maire⁸, Katrin Lamszus⁸, Franz L Ricklefs⁸, Maria J Merino⁹, W Marston Linehan¹⁰, Tim Greten¹¹, Tomer Cooks^{12

13}, Curtis C Harris¹³, Andrea Apolo¹⁴, Asim Abdel-Mageed¹⁵, Alexander R Ivanov¹⁶, Jane B Trepel⁴, Matthew Roth¹⁷, Mercedes Tkach¹⁸, Aleksandar Milosavljevic¹⁷, Clotilde Théry¹⁸, Amy LeBlanc¹⁹, Jay A Berzofsky², Eytan Ruppin²⁰, Kenneth Aldape⁹, Kevin Camphausen²¹, James L Gulley³, Ionita Ghiran²², Steve Jacobson⁵, Jennifer C Jones^{1

2}

Affiliations

¹ Translational Nanobiology Section, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
² Vaccine Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
³ Clinical Immunotherapy Section, Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
⁴ Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
⁵ Viral Immunology Section, Neuroimmunology Branch, NINDS/NIH, Bethesda, MD, USA.
⁶ Clinical Research Center, Department for Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden.
⁷ Evox Therapeutics Ltd, Oxford, UK.
⁸ Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany.
⁹ Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
¹⁰ Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
¹¹ Gastrointestinal Malignancy Section, Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
¹² The Shraga Segal Department of Microbiology, Immunology, and Genetics, Ben-Gurion University of the Negev, 84105 Beer-Sheva, Israel.
¹³ Laboratory of Human Carcinogenesis, NCI-CCR, National Institutes of Health, Bethesda, MD 20892-4258, USA.
¹⁴ Bladder Cancer Section, Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institutes of Health, Bethesda, MD, USA.
¹⁵ Department of Urology, Tulane University School of Medicine, 1430 Tulane Avenue, New Orleans, LA, USA.
¹⁶ Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA.
¹⁷ Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
¹⁸ Institut Curie, PSL Research University, INSERM U932, Paris, France.
¹⁹ Comparative Oncology Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
²⁰ Cancer Data Science Lab, National Cancer Institute, Bethesda, MD, USA.
²¹ Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
²² Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.

Abstract

Extracellular vesicles (EVs) of various types are released or shed from all cells. EVs carry proteins and contain additional protein and nucleic acid cargo that relates to their biogenesis and cell of origin. EV cargo in liquid biopsies is of widespread interest owing to its ability to provide a retrospective snapshot of cell state at the time of EV release. For the purposes of EV cargo analysis and repertoire profiling, multiplex assays are an essential tool in multiparametric analyte studies but are still being developed for high-parameter EV protein detection. Although bead-based EV multiplex analyses offer EV profiling capabilities with conventional flow cytometers, the utilization of EV multiplex assays has been limited by the lack of software analysis tools for such assays. To facilitate robust EV repertoire studies, we developed multiplex analysis post-acquisition analysis (MPA_PASS) open-source software for stitched multiplex analysis, EV database-compatible reporting, and visualization of EV repertoires.

Keywords: EV flow cytometry; atlas; liquid biopsy methods; multiplex; standardization.

MPA_PASS software enables stitched multiplex, multidimensional EV repertoire analysis and a standard framework for reporting bead-based assays

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