Integrative analysis of neuroblastoma by single-cell RNA sequencing identifies the NECTIN2-TIGIT axis as a target for immunotherapy

Judith Wienke*, Lindy L Visser, Waleed M Kholosy, Kaylee M Keller, Marta Barisa, Evon Poon, Sophie Munnings-Tomes, Courtney Himsworth, Elizabeth Calton, Ana Rodriguez, Ronald Bernardi, Femke van den Ham, Sander R van Hooff, Yvette A H Matser, Michelle L Tas, Karin P S Langenberg, Philip Lijnzaad, Anne L Borst, Elisa Zappa, Francisca J BergsmaJosephine G M Strijker, Bronte M Verhoeven, Shenglin Mei, Amira Kramdi, Restuadi Restuadi, Alvaro Sanchez-Bernabeu, Annelisa M Cornel, Frank C P Holstege, Juliet C Gray, Godelieve A M Tytgat, Marijn A Scheijde-Vermeulen, Marc H W A Wijnen, Miranda P Dierselhuis, Karin Straathof, Sam Behjati, Wei Wu, Albert J R Heck, Jan Koster, Stefan Nierkens, Isabelle Janoueix-Lerosey, Ronald R de Krijger, Ninib Baryawno, Louis Chesler, John Anderson, Hubert N Caron, Thanasis Margaritis, Max M van Noesel, Jan J Molenaar

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

Abstract

Pediatric patients with high-risk neuroblastoma have poor survival rates and urgently need more effective treatment options with less side effects. Since novel and improved immunotherapies may fill this need, we dissect the immunoregulatory interactions in neuroblastoma by single-cell RNA-sequencing of 24 tumors (10 pre- and 14 post-chemotherapy, including 5 pairs) to identify strategies for optimizing immunotherapy efficacy. Neuroblastomas are infiltrated by natural killer (NK), T and B cells, and immunosuppressive myeloid populations. NK cells show reduced cytotoxicity and T cells have a dysfunctional profile. Interaction analysis reveals a vast immunoregulatory network and identifies NECTIN2-TIGIT as a crucial immune checkpoint. Combined blockade of TIGIT and PD-L1 significantly reduces neuroblastoma growth, with complete responses (CR) in vivo. Moreover, addition of TIGIT+PD-L1 blockade to standard relapse treatment in a chemotherapy-resistant Th-ALK F1174L/MYCN 129/SvJ syngeneic model induces CR. In conclusion, our integrative analysis provides promising targets and a rationale for immunotherapeutic combination strategies.

Original languageEnglish
Pages (from-to)283-300.e8
JournalCancer Cell
Volume42
Issue number2
Early online date4 Jan 2024
DOIs
Publication statusPublished - 12 Feb 2024

Bibliographical note

Publisher Copyright:
© 2023 The Authors

Funding

We would like to acknowledge our FACS facility, particularly Tomasz Poplonski and Tom O'Toole, and the Multiplex facility of the UMC Utrecht, particularly Edward Knol and Rianne Scholman. This work received funding from the European Union's Horizon 2020 research and innovation program under MarieSk1odowska-Curie grant agreement, No. 956285 (VAGABOND), and grant agreement H2020-iPC-826121, European Research Council (ERC), No.716079 (Predict), KiKa (Kika404 ''Toward TIL therapy in neuroblastoma''), Villa Joep, the Alexander von Humboldt Foundation, and is part of research program Vernieuwingsimpuls Vidi (Combining targeted compounds in neuroblastoma tumors; is two better than one?), project 91716482, and Veni (Release the beast: Boosting CAR-T cell immunotherapy for neuroblastoma), project 09150162010022, which are partly financed by the Dutch Research Council (NWO) and by ZonMW. The first threein vivostudies were funded by Hoffman-La Roche. L.C. and E.P. received support from Cancer Research UK (CRUK) (C34648/A18339 and C34648/A28278). E.C. received funding from Children with Cancer UK. In vivo work at ICH was funded by Hoffman-La Roche and by Stand up to Cancer/CRUK grant RT6188. JA is further supported by GOSH NIHR BRC. TM and LV (single cell genomics facility of Maxima) are funded by KiKa. AK and II-L were supported by grants fromInstitut Curie, Inserm, the Institut National Du Cancer (PEDIAC program, INCA_15670, IJ-L), ERC (ERC-2019-SyG, KILL or DIFFERENTIATE, Olivier Delattre) and the Association Hubert Gouin Enfance et Cancer. We sincerelythank Leonard Didelet, Cecile Thirant and Olivier Delattre for their helpful contributions. S.B. acknowledges funding for this research from the Wellcome Trust (grants 206194 and 223135/Z/21/Z). W.W. is supported by SingaporeImmunology Network (SIgN), Agency for Science, Technology and Research (A*STAR); Biomedical Research Council (BMRC) Core Research Fund foruse-inspired basic research (UIBR) and IAF-PP project H22J2a0043, and Singapore National Medical Research Council (NMRC) project MOH-001401-00.r 09150162010022, which are partly financed by the Dutch Research Council (NWO) and by ZonMW. The first three in vivo studies were funded by Hoffman-La Roche. L.C. and E.P. received support from Cancer Research UK (CRUK) (C34648/A18339 and C34648/A28278) . E.C. received funding from Children with Cancer UK. In vivo work at ICH was funded by Hoffman-La Roche and by Stand up to Cancer/CRUK grant RT6188. JA is further sup-ported by GOSH NIHR BRC. TM and LV (single cell genomics facility of Ma<acute accent>xima) are funded by KiKa. AK and II-L were supported by grants from Institut Curie, Inserm, the Institut National Du Cancer (PEDIAC program, INCA_15670, IJ-L) , ERC (ERC-2019-SyG, KILL or DIFFERENTIATE, Olivier De-lattre) and the Association Hubert Gouin Enfance et Cancer. We sincerely thank Le<acute accent>onard Didelet, Ce<acute accent>cile Thirant and Olivier Delattre for their helpful con-tributions. S.B. acknowledges funding for this research from the Wellcome Trust (grants 206194 and 223135/Z/21/Z) . W.W. is supported by Singapore Immunology Network (SIgN) , Agency for Science, Technology and Research (A*STAR) ; Biomedical Research Council (BMRC) Core Research Fund for use-inspired basic research (UIBR) and IAF-PP project H22J2a0043, and Singapore National Medical Research Council (NMRC) project MOH-001401-00.

FundersFunder number
Dutch Research Council (NWO)09150162010022
ZonMW - Hoffman-La Roche
Cancer Research UK (CRUK)C34648/A18339, C34648/A28278
Children with Cancer UK - Hoffman-La Roche
GOSH NIHR BRC - KiKaRT6188
Institut Curie, Inserm
Institut National Du CancerINCA_15670
ERC
Association Hubert Gouin Enfance et Cancer
Wellcome Trust206194, 223135/Z/21/Z
Singapore Immunology Network (SIgN) , Agency for Science, Technology and Research (A*STAR)
Biomedical Research Council (BMRC) Core Research Fund for use-inspired basic research (UIBR)H22J2a0043
Singapore National Medical Research Council (NMRC)
Not addedMOH-001401-00

    Keywords

    • Immune checkpoint inhibition
    • NECTIN2
    • Neuroblastoma
    • PD-1
    • PD-L1
    • Pediatric oncology
    • TIGIT
    • immune evasion
    • immunotherapy
    • tumor microenvironment

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