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Papers by Mireille Toebes

Title Differentiation of cytomegalovirus-specific CD8(+) T cells in healthy and

is published twice each month byThe Journal of Immunology

Nature Chemical Biology, 2021

The functional activity and differentiation potential of cells are determined by their interactio... more The functional activity and differentiation potential of cells are determined by their interactions with surrounding cells. Approaches that allow unbiased characterization of cell states while at the same time providing spatial information are of major value to assess this environmental influence. However, most current techniques are hampered by a tradeoff between spatial resolution and cell profiling depth. Here, we develop a photocage-based technology that allows isolation and in-depth analysis of live cells from regions of interest in complex ex vivo systems, including primary human tissues. The use of a highly sensitive 4-nitrophenyl(benzofuran) cage coupled to a set of nanobodies allows high-resolution photo-uncaging of different cell types in areas of interest. Single-cell RNA-sequencing of spatially defined CD8+ T cells is used to exemplify the feasibility of identifying location-dependent cell states. The technology described here provides a valuable tool for the analysis of spatially defined cells in diverse biological systems, including clinical samples. The development of a photocage-nanobody based technology enabled in-depth analysis of live cells from tissues while retaining their spatial information.

Nature Immunology, 2019

Emerging data show that tissue-resident memory T cells (TRM) play an important protective role at... more Emerging data show that tissue-resident memory T cells (TRM) play an important protective role at murine and human barrier sites. In line with this, prior in vivo data demonstrate that skin-TRM in murine epidermis patrol their surroundings and rapidly respond upon antigen encounter. However, whether a similar migratory behavior is performed by human TRM is unclear, as technology to longitudinally follow these cells in situ has been lacking. To address this issue, we developed an ex vivo culture system that allows the labeling and tracking of T cells in fresh skin samples. We validated this system by comparison of the in vivo and ex vivo properties of murine TRM. Using nanobody labeling, we subsequently demonstrate in human ex vivo skin that CD8 + TRM migrate through the papillary dermis and through the epidermis, below sessile Langerhans cells. Collectively, this work provides a means to study skin resident immune cells in human skin in real-time and demonstrates the existence of tissue patrol by human CD8 + TRM.

Cancer research, Jan 15, 1998

Human papillomavirus (HPV) E6 and E7 oncoproteins are attractive targets for T-cell-based immunot... more Human papillomavirus (HPV) E6 and E7 oncoproteins are attractive targets for T-cell-based immunotherapy of cervical cancer. In this study, we demonstrate that dendritic cells (DCs) pulsed with HPV16 E7 protein are not only recognized in vitro by E7-specific CTLs but also elicit E7-specific CTL responses in vivo, associated with protection against a challenge with syngeneic HPV16-induced tumor cells. Vaccination with soluble E7 protein in incomplete Freund's adjuvant likewise induces E7-specific CTL responses associated with tumor protection. The presence of HPV16 E7-specific CTLs in vivo and the observation that depletion of CD8+ cells completely abolishes tumor protection demonstrate that CTLs are the major effector cells in mediating antitumor activity. The in vivo involvement of DCs in the activation of protective CTLs is suggested by the surface display of E7 peptide-loaded MHC class I molecules on these cells after E7 protein immunization. These data show that HPV16 E7 prot...

claus-online.nl

... choice. Because HLA-bound peptides are critical for the stability of the complex only a pepti... more ... choice. Because HLA-bound peptides are critical for the stability of the complex only a peptide that fits in the HLA binding groove will be able to maintain the integrity of the empty HLA complex. Methods Results Conclusions ...

Dendritic cells (DCs) play a central role in the immune system as they drive activation of T lymp... more Dendritic cells (DCs) play a central role in the immune system as they drive activation of T lymphocytes by cognate interactions. However, as DCs express high levels of major histocompatibility complex class I, this intimate contact may also result in elimination of DCs by activated cytotoxic T lymphocytes (CTLs) and thereby limit induction of immunity. We show here that immature DCs are indeed susceptible to CTL-induced killing, but become resistant upon maturation with anti-CD40 or lipopolysaccharide. Protection is achieved by expression of serine protease inhibitor (SPI)-6, a member of the serpin family that specifically inactivates granzyme B and thereby blocks CTL-induced apoptosis. Anti-CD40 and LPS-induced SPI-6 expression is sustained for long periods of time, suggesting a role for SPI-6 in the longevity of DCs. Importantly, T helper 1 cells, which mature DCs and boost CTL immunity, induce SPI-6 expression and subsequent DC resistance. In contrast, T helper 2 cells neither i...

A large global effort is currently ongoing to develop vaccines against SARS-CoV-2, the causative ... more A large global effort is currently ongoing to develop vaccines against SARS-CoV-2, the causative agent of COVID-19. While there is accumulating evidence on the antibody response against SARS-CoV-2, little is known about the SARS-CoV-2 antigens that are targeted by CD8 T cells. To address this issue, we have analyzed samples from 20 COVID-19 patients for T cell recognition of 500 predicted MHC class I epitopes. CD8 T cell reactivity against SARS-CoV- 2 was common. Remarkably, a substantial fraction of the observed CD8 T cell responses were directed towards the ORF1ab polyprotein 1ab, and these CD8 T cell responses were frequently of a very high magnitude. The fact that a major part of the SARS-CoV-2 specific CD8 T cell response is directed against a part of the viral genome that is not included in the majority of vaccine candidates currently in development may potentially influence their clinical activity and toxicity profile.

Nature Communications

The COVID-19 pandemic caused by SARS-CoV-2 is a continuous challenge worldwide, and there is an u... more The COVID-19 pandemic caused by SARS-CoV-2 is a continuous challenge worldwide, and there is an urgent need to map the landscape of immunogenic and immunodominant epitopes recognized by CD8+ T cells. Here, we analyze samples from 31 patients with COVID-19 for CD8+ T cell recognition of 500 peptide-HLA class I complexes, restricted by 10 common HLA alleles. We identify 18 CD8+ T cell recognized SARS-CoV-2 epitopes, including an epitope with immunodominant features derived from ORF1ab and restricted by HLA-A*01:01. In-depth characterization of SARS-CoV-2-specific CD8+ T cell responses of patients with acute critical and severe disease reveals high expression of NKG2A, lack of cytokine production and a gene expression profile inhibiting T cell re-activation and migration while sustaining survival. SARS-CoV-2-specific CD8+ T cell responses are detectable up to 5 months after recovery from critical and severe disease, and these responses convert from dysfunctional effector to functional ...

Nature Cancer

In the version of this article initially published, the label ' Ag-IGS' is incorrect along the ve... more In the version of this article initially published, the label ' Ag-IGS' is incorrect along the vertical axes of Figs. 1b, 2c, 2d, 2e, 3c and 5a. The correct label is ' Ag-IGS'. The error has been corrected in the HTML and PDF versions of the article.

Nature Medicine

†, # These authors contributed equally Ethical Compliance Animal experiments were in compliance w... more †, # These authors contributed equally Ethical Compliance Animal experiments were in compliance with all relevant ethical regulations approved by the IVD committee (Utrecht, the Netherlands). Blood samples from healthy donors was collected after informed consent. The use of human blood samples was in compliance with all relevant ethical regulations approved by the Sanquin Ethics Advisory Council of Sanquin Blood Supply (Amsterdam, the Netherlands). Reporting summary. Further information on experimental design is available in the Nature Research Reporting Summary linked to this article. Data availability All sequencing datasets have been deposited in the NCBI Sequence Read Archive under accession number SRP144590. In addition, all processed screen results are accessible in an interactive database (https://phenosaurus.nki.nl/). All data presented in this manuscript are available from the corresponding authors upon reasonable request Author contributions M.E.W.L. conceived the project, designed and performed experiments, interpreted data and co-wrote the manuscript. M.R., A.F. an T.R.B. designed, performed and interpreted the haploid genetic screens. M.T. and J.N. designed, performed and interpreted biochemical data. J.H.M.J., A.M.B. and J.H.W.L. designed, performed and interpreted anti-Her2 in vitro and in vivo data, and J.H.W.L. co-wrote the manuscript. K.F., H.L.M. and T.K.v.d.B. designed, performed and interpreted in vitro data with human effector cells. S.v.d.S. supported and performed flow cytometry analyses. R.G.-E. and N.A.M.B. designed, performed and interpreted in vitro studies with human T cells. J.H.v.d.B. and J.B.A.G.H. supervised analyses of T cell reactivity. K.A.M. performed and interpreted experiments. M.V. designed experiments and provided reagents. F.A.S. and T.N.S. conceived the project, designed experiments, interpreted data and co-wrote the manuscript.

The functional activity and differentiation potential of cells is determined by their interaction... more The functional activity and differentiation potential of cells is determined by their interaction with surrounding cells. Approaches that allow the unbiased characterization of cell states while at the same time providing spatial information are of major value to assess this environmental influence. However, most current techniques are hampered by a trade-off between spatial resolution and cell profiling depth. Here, we developed a photoswitch-based technology that allows the isolation and in-depth analysis of live cells from regions of interest in complex ex vivo systems, including human tissues. The use of a highly sensitive 4-nitrophenyl(benzofuran)-cage coupled to nanobodies allowed photoswitching of cells in areas of interest with low-intensity violet light and without detectable phototoxicity. Single cell RNA sequencing of spatially defined CD8+ T cells was used to exemplify the feasibility of identifying location-dependent cell states at the single cell level. Finally, we dem...