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Simultaneous selection of nanobodies for accessible epitopes on immune cells in the tumor microenvironment

Author

Listed:
  • Thillai V. Sekar

    (the University of Texas Southwestern Medical Center
    Pondicherry University)

  • Eslam A. Elghonaimy

    (the University of Texas Southwestern Medical Center)

  • Katy L. Swancutt

    (the University of Texas Southwestern Medical Center)

  • Sebastian Diegeler

    (the University of Texas Southwestern Medical Center)

  • Isaac Gonzalez

    (the University of Texas Southwestern Medical Center)

  • Cassandra Hamilton

    (the University of Texas Southwestern Medical Center)

  • Peter Q. Leung

    (the University of Texas Southwestern Medical Center)

  • Jens Meiler

    (Vanderbilt University
    Leipzig University Medical School)

  • Cristina E. Martina

    (Vanderbilt University)

  • Michael Whitney

    (University of California San Diego)

  • Todd A. Aguilera

    (the University of Texas Southwestern Medical Center)

Abstract

In the rapidly advancing field of synthetic biology, there exists a critical need for technology to discover targeting moieties for therapeutic biologics. Here we present INSPIRE-seq, an approach that utilizes a nanobody library and next-generation sequencing to identify nanobodies selected for complex environments. INSPIRE-seq enables the parallel enrichment of immune cell-binding nanobodies that penetrate the tumor microenvironment. Clone enrichment and specificity vary across immune cell subtypes in the tumor, lymph node, and spleen. INSPIRE-seq identifies a dendritic cell binding clone that binds PHB2. Single-cell RNA sequencing reveals a connection with cDC1s, and immunofluorescence confirms nanobody-PHB2 colocalization along cell membranes. Structural modeling and docking studies assist binding predictions and will guide nanobody selection. In this work, we demonstrate that INSPIRE-seq offers an unbiased approach to examine complex microenvironments and assist in the development of nanobodies, which could serve as active drugs, modified to become drugs, or used as targeting moieties.

Suggested Citation

  • Thillai V. Sekar & Eslam A. Elghonaimy & Katy L. Swancutt & Sebastian Diegeler & Isaac Gonzalez & Cassandra Hamilton & Peter Q. Leung & Jens Meiler & Cristina E. Martina & Michael Whitney & Todd A. Ag, 2023. "Simultaneous selection of nanobodies for accessible epitopes on immune cells in the tumor microenvironment," Nature Communications, Nature, vol. 14(1), pages 1-20, December.
  • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-43038-z
    DOI: 10.1038/s41467-023-43038-z
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    1. Barbara Maier & Andrew M. Leader & Steven T. Chen & Navpreet Tung & Christie Chang & Jessica LeBerichel & Aleksey Chudnovskiy & Shrisha Maskey & Laura Walker & John P. Finnigan & Margaret E. Kirkling , 2020. "A conserved dendritic-cell regulatory program limits antitumour immunity," Nature, Nature, vol. 580(7802), pages 257-262, April.
    2. Kathryn Tunyasuvunakool & Jonas Adler & Zachary Wu & Tim Green & Michal Zielinski & Augustin Žídek & Alex Bridgland & Andrew Cowie & Clemens Meyer & Agata Laydon & Sameer Velankar & Gerard J. Kleywegt, 2021. "Highly accurate protein structure prediction for the human proteome," Nature, Nature, vol. 596(7873), pages 590-596, August.
    3. Aroop Sircar & Jeffrey J Gray, 2010. "SnugDock: Paratope Structural Optimization during Antibody-Antigen Docking Compensates for Errors in Antibody Homology Models," PLOS Computational Biology, Public Library of Science, vol. 6(1), pages 1-13, January.
    4. Barbara Maier & Andrew M. Leader & Steven T. Chen & Navpreet Tung & Christie Chang & Jessica LeBerichel & Aleksey Chudnovskiy & Shrisha Maskey & Laura Walker & John P. Finnigan & Margaret E. Kirkling , 2020. "Author Correction: A conserved dendritic-cell regulatory program limits antitumour immunity," Nature, Nature, vol. 582(7813), pages 17-17, June.
    5. Mikhail Shugay & Dmitriy V Bagaev & Maria A Turchaninova & Dmitriy A Bolotin & Olga V Britanova & Ekaterina V Putintseva & Mikhail V Pogorelyy & Vadim I Nazarov & Ivan V Zvyagin & Vitalina I Kirgizova, 2015. "VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires," PLOS Computational Biology, Public Library of Science, vol. 11(11), pages 1-16, November.
    6. Yaron Carmi & Matthew H. Spitzer & Ian L. Linde & Bryan M. Burt & Tyler R. Prestwood & Nicola Perlman & Matthew G. Davidson & Justin A. Kenkel & Ehud Segal & Ganesh V. Pusapati & Nupur Bhattacharya & , 2015. "Allogeneic IgG combined with dendritic cell stimuli induce antitumour T-cell immunity," Nature, Nature, vol. 521(7550), pages 99-104, May.
    7. Julia Koehler Leman & Sergey Lyskov & Steven M. Lewis & Jared Adolf-Bryfogle & Rebecca F. Alford & Kyle Barlow & Ziv Ben-Aharon & Daniel Farrell & Jason Fell & William A. Hansen & Ameya Harmalkar & Je, 2021. "Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks," Nature Communications, Nature, vol. 12(1), pages 1-15, December.
    8. Todd A. Aguilera & Marjan Rafat & Laura Castellini & Hussein Shehade & Mihalis S. Kariolis & Angela Bik-Yu Hui & Henning Stehr & Rie von Eyben & Dadi Jiang & Lesley G. Ellies & Albert C. Koong & Maxim, 2016. "Reprogramming the immunological microenvironment through radiation and targeting Axl," Nature Communications, Nature, vol. 7(1), pages 1-14, December.
    9. John Jumper & Richard Evans & Alexander Pritzel & Tim Green & Michael Figurnov & Olaf Ronneberger & Kathryn Tunyasuvunakool & Russ Bates & Augustin Žídek & Anna Potapenko & Alex Bridgland & Clemens Me, 2021. "Highly accurate protein structure prediction with AlphaFold," Nature, Nature, vol. 596(7873), pages 583-589, August.
    10. Jared Adolf-Bryfogle & Oleks Kalyuzhniy & Michael Kubitz & Brian D Weitzner & Xiaozhen Hu & Yumiko Adachi & William R Schief & Roland L Dunbrack Jr., 2018. "RosettaAntibodyDesign (RAbD): A general framework for computational antibody design," PLOS Computational Biology, Public Library of Science, vol. 14(4), pages 1-38, April.
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