Biology subjects

Nijman, H. W.

Publications and source records attributed to Nijman, H. W..

4 recordsLinked to original sources

bioRxiv2025

The landscape of tertiary lymphoid structures in endometrial cancer revealed through harmonized multi-level transcriptomics

Tertiary lymphoid structures (TLSs) are ectopic lymphoid tissues that form within tumors. TLSs are associated with improved prognosis and better responses to immune checkpoint inhibitors (ICI) in cancer. However, the contribution of genetic, immune, and (micro)environmental factors to TLS formation and function remain incompletely understood. Using harmonized bulk and single-cell RNA-sequencing coupled with spatial transcriptomics, we present a comprehensive characterization of tumor-associated TLSs in endometrial cancer (EC). Our integrated datasets reveal the cellular architecture of TLSs, their organizing principles--including chemokine-receptor gradients--and TLS activity compared to paired tumor-draining lymph nodes, as well as spatial preferences in IgA/IgG plasma cell and T cell distribution. We identified a consensus set of transcriptional components that independently predict the presence of TLS in EC. Furthermore, we demonstrate that clinical neoadjuvant ICI in EC patients shifts the cellular balance in favor of immunogenic CXCL13+ PDCD1+ T cells, providing a mechanistic insight into ICI-induced TLSs formation. Our data offers a systems-level understanding of TLSs and a roadmap for their therapeutic exploitation.

immunology↗

bioRxiv2021

Cancer tolerance to chromosomal instability is driven by Stat1 inactivation in vivo

Chromosomal instability is a hallmark of cancer, but also an instigator of aneuploidy-induced stress, reducing cellular fitness. To better understand how cells with CIN adjust to aneuploidy and adopt a malignant fate in vivo, we performed a genome-wide mutagenesis screen in mice. We find that specifically aneuploid tumors inactivate Stat1 signaling in combination with increased Myc activity. By contrast, loss of p53 is common, but not enriched in CIN tumors. Validation in another tissue type confirmed that CIN promotes immune cell infiltration, which is alleviated by Stat1 loss combined with Myc activation, but not with p53 inactivation, or Myc activation alone. Importantly, we find that this mechanism is preserved in human aneuploid cancers. We conclude that aneuploid cancers inactivate Stat1 signaling to circumvent immune surveillance.

cancer biology↗

bioRxiv2021

Rapid and efficient generation of antigen-specific isogenic T cells from cryopreserved blood samples

ObjectivesCRISPR/Cas9-mediated gene editing has been leveraged for the modification of human and mouse T cells. However, limited experience is available on the application of CRISPR/Cas9 electroporation in cryopreserved T cells collected during e.g. clinical trials. MethodsPBMCs from healthy donors were used to generate knockout T cell models for interferon-{gamma} (IFN{gamma}), Cbl Proto-Oncogene B (CBLB), Fas cell surface death receptor (Fas) and T cell receptor (TCR{beta}b) genes. The effect of CRISPR-cas9-mediated gene editing on T cells was evaluated using apoptosis assays, cytokine bead arrays and ex vivo and in vitro stimulation assays. ResultsOur results demonstrate that CRISPR/Cas9-mediated gene editing of ex vivo T cells is efficient and does not overtly affect T cell viability. Cytokine release and T cell proliferation were not affected in gene edited T cells. Interestingly, memory T cells were more susceptible to CRISPR/Cas9 gene editing than naive T cells. Ex vivo and in vitro stimulation with antigens resulted in equivalent antigen-specific T cell responses in gene-edited and untouched control cells; making CRISPR/Cas9-mediated gene editing compatible with clinical antigen-specific T cell activation and expansion assays. ConclusionHere, we report an optimized protocol for rapid, viable and highly efficient genetic modification in ex vivo human antigen specific T cells, for subsequent functional evaluation and/or expansion. Our platform extends CRISPR/Cas9-mediated gene editing for use in gold-standard clinically-used immune-monitoring pipelines and serves as a starting point for development of analogous approaches such as those including transcriptional activators and or epigenetic modifiers.

immunology↗

bioRxiv2018

TGF-β induced CXCL13 in CD8+ T cells is associated with tertiary lymphoid structures in cancer

Coordinated immune responses against human tumors are frequently characterized by tertiary lymphoid structures (TLS) which predict improved prognosis. The development of TLS is dependent on the chemokine CXCL13, reported to be secreted by dendritic cells and follicular helper T cells only. We report the unexpected finding that CXCL13 is also secreted by activated CD8+ T cells following stimulation by transforming growth factor beta (TGF-{beta}). Using single cell RNA sequencing we found that expression of CXCL13 in CD8+ T cells was restricted to the intraepithelial CD103+ population. Accordingly, CD8+ T cells activated in the presence of TGF-{beta} simultaneously upregulated CD103 and secreted CXCL13. CXCL13 expression was strongly correlated with neo-antigen burden and cytolytic gene signatures in bulk tumors. In line with this, TLS were abundant in neo-antigen-high, CD103+ T cell-enriched tumors. TGF-{beta} thus appears to play a role in coordinating immune responses against human tumors through CD8-dependent CXCL13-associated formation of TLS.

immunology↗