Biology subjects

Schaper, S.

Publications and source records attributed to Schaper, S..

7 recordsLinked to original sources

bioRxiv2026

Tumor-versus-non-tumor T cell enrichment supported by single-cell and spatial phenotyping enables antigen-agnostic prioritization of candidate tumor-reactive TCRs

Introduction: Tumor-reactive T cell receptors (TCRs) are promising candidates for the manufacturing of safe and effective adoptive TCR-T cell therapies, but their efficient identification remains a major challenge. We previously established an antigen-agnostic TCR-repertoire analysis workflow that prioritizes candidate TCRs based on intratumoral clonal expansion and high tumor-to-non-tumor (T/N) frequency ratios. Here, we investigated whether T/N-selected clonotypes show independent transcriptional and spatial features consistent with tumor association. Methods: Bulk and single-cell TCR repertoire sequencing of paired tumor and adjacent non-tumor tissues was used to identify clonotypes with high T/N ratios across 15 cancer cases, comprising six non-small cell lung cancers, five pancreatic cancers, two breast cancers, and two colorectal cancers. Candidate clonotypes were further characterized by paired single-cell TCR and gene expression profiling and, in two PDAC cases, by Xenium spatial transcriptomics to assess their cellular phenotype, spatial localization, and proximity to malignant cells. Results: High T/N ratios consistently marked T cell clonotypes with features of tumor reactivity across the studied solid tumor entities. The analysis included Cluster-A, a lead T cell cluster comprising highly similar TCRs shared among 14 HLA-A*02:01-positive patients in the present cohort. Cluster-A clonotypes were consistently enriched in tumor relative to matched non-tumor tissue, and previous functional studies demonstrated tumor recognition by Cluster-A members. In a focused analysis of a pancreatic cancer case, Cluster-A CD8 T cells were selectively detected in tumor tissue, preferentially localized near malignant epithelial cells, and displayed an antigen-experienced effector-memory phenotype with prominent expression of granzymes A and K (GZMA/GZMK). Importantly, in another PDAC case that lacked Cluster-A clonotypes, these features extended to independent clonotypes, revealing a continuous tumor-association axis in which increasing T/N ratios were associated with progressively closer localization to malignant cells and increased GZMA/GZMK expression. Thus, repertoire enrichment, spatial tumor proximity, and effector-associated transcriptional states converged across independent tumor-enriched clonotypes. Outlook: These findings support the T/N ratio as a robust primary criterion for identifying candidate tumor-reactive TCRs. Integration of single-cell and spatial transcriptomics provides supporting biological evidence of tumor association and a framework for prioritizing therapeutic TCR candidates when functional validation is limited.

immunology↗

bioRxiv2025

A new clustering approach identifies tumor-specific common TCRs with pan-cancer reactivity

Tumor-specific T-cells are key in combating cancer as shown in adoptive cell therapy with tumor infiltrating lymphocytes (TILs) and checkpoint inhibitor therapy. Studies in many types of cancer have shown that preexisting tumor reactive T-cells are not only tumor-but typically also patient-specific, requiring personalized treatment options. For viral infections, public T-cell receptors (TCRs) with substantial sequence homologies suggest shared immune-dominant targets in human leucocyte antigen (HLA)-matched individuals. We hypothesized that also in the complex TCR repertoires of tumors subsets of tumor-specific TCRs exist that can be found in different patients with identical or near identical TCRs. This paper presents a TCR-V(D)J-sequence clustering approach identifying clusters of tumor-specific common TCRs mainly from TILs of non-small cell lung cancer (NSCLC) patients. Using two TCR-clusters as examples, we show that T-cells engineered genetically to only express those common TCRs recognized HLA-matched allogeneic tumor cell lines in a cluster typical manner. Recognition of allogeneic tumors was dependent on the HLA allele inferred by the cluster and could be blocked by HLA antibodies. In addition to NSCLC, TCR repertoire analyses in pancreatic ductal adenocarcinoma and a smaller number of breast and colorectal cancer samples revealed TCRs highly homologous or even identical to NSCLC cluster TCRs. TCR-T cells expressing TCRs from these tumors assigned to a specific cluster recognized allogeneic tumor lines in the expected cluster-typical manner. These findings suggest a pan-cancer therapeutic potential of tumor-specific common TCRs.

immunology↗

bioRxiv2024

T-cell receptors identified by a personalized antigen-agnostic screening approach target shared neoantigen KRAS Q61H

Adoptive cell therapy (ACT) with TCR-engineered T-cells represents a promising alternative to TIL- or CAR-T therapies for patients with advanced solid cancers. Currently, selection of therapeutic TCRs critically depends on knowing the target antigens, a condition excluding most patients from treatment. Direct antigen-agnostic identification of tumor-specific T-cell clonotypes and TCR-T manufacturing using their TCRs can advance ACT for patients with aggressive solid cancers. We present a method to identify tumor-specific clonotypes from surgical specimens by comparing TCR{beta}-chain repertoires of TILs and adjacent tissue-resident lymphocytes. In seven NSCLC-patients, tumor-specific clonotypes were selected based on TIL-abundance and high tumor-to-nontumor frequency ratios. In two of the patients, we demonstrate that predicted tumor-specific clonotypes reacted against autologous tumors. In a third patient, we engineered TCR T-cells with four candidate tumor-specific TCRs that showed reactivity against the patients tumor and HLA-matched NSCLC cell lines. The TCR-T cells were then used to screen for candidate neoantigens and aberrantly expressed antigens. Three TCRs recognized recurrent driver-mutation KRAS Q61H-peptide ILDTAGHEEY presented by HLA-A*01:01. The TCRs were also dominant in a tumor relapse, one was found in cell free DNA. The finding of homologous TCRs in independent KRAS Q61H-positive cancers suggests a therapeutic opportunity for HLA-matched patients with KRAS Q61H-expressing tumors.

immunology↗

bioRxiv2023

Non-Poissonian bursts in the arrival of phenotypic variation can strongly affect the dynamics of adaptation

The introduction of novel phenotypic variation in a population through random mutations plays a crucial role in evolutionary dynamics. Here we show that, when the probability that a sequence has a particular phenotype in its 1-mutational neighbourhood is low, statistical fluctuations imply that in the weak-mutation or monomorphic regime, novel phenotypic variation is not introduced at a constant rate, but rather in non-Poissonian "bursts". In other words, a novel phenotype appears multiple times in quick succession, or not at all for many generations. We use the RNA secondary-structure genotype-phenotype map to explore how increasing levels of heterogeneity in mutational neighbourhoods strengthen the bursts. Similar results are obtained for the HP model for protein tertiary structure and the Biomorphs model for morphological development. Burst can profoundly affect adaptive dynamics. Most notably, they imply that differences in arrival rates of novel variation can influence fixation rates more than fitness differences do.

evolutionary biology↗

bioRxiv2023

The role of GpsB in cell morphogenesis of Staphylococcus aureus

For decades, cells of the gram-positive bacterial pathogen Staphylococcus aureus were thought to lack a dedicated elongation machinery. However, S. aureus cells were recently shown to elongate before division, in a process that requires a SEDS (Shape Elongation Division and Sporulation) / PBP (Penicillin Binding Protein) pair for peptidoglycan synthesis, consisting of the glycosyltransferase RodA and the transpeptidase PBP3. In ovococci and rod-shaped bacteria the elongation machinery, known as elongasome, is composed of various proteins besides a dedicated SEDS/PBP pair. To identify proteins involved in the elongation of S. aureus, we screened the Nebraska Transposon Mutant Library, which contains transposon mutants in virtually all non-essential staphylococcal genes, for mutants with modified cell shape. We confirmed the roles of RodA/PBP3 in S. aureus elongation and identified GpsB, SsaA, and RodZ as additional proteins involved in this process. The gpsB mutant showed the strongest phenotype, mediated by the partial delocalization from the division septum of PBP2, the only bifunctional PBP in S. aureus, with both glycosyltransferase and transpeptidase activity, and of the PBP4 transpeptidase. Increased levels of these PBPs at the cell periphery result in higher levels of peptidoglycan insertion throughout the entire cell, overriding the RodA/PBP3-mediated peptidoglycan synthesis at the outer edge of the septum, which leads to cell elongation. As a consequence, in the absence of GpsB, S. aureus cells become more spherical.

microbiology↗

bioRxiv2022

Twist1 and balanced retinoic acid signaling act to suppress cortical folding in mice

Evolution of cortical folding in gyrencephalic animals enabled higher cognitive functions and complex behaviors. Gene expression patterns and signaling molecules that control cortical folding have only recently been described and thus are still not well understood. In transgenic mouse models with induced cortical folding, amplification of neuroprogenitor cells or loss of their adhesion from the apical ventricular surface leads to gyri formation, whereas decreased cell adhesion in migrating projection neurons causes abnormal neuronal clustering and development of cortical fissures that resemble sulci. We now report that loss of Twist1 expression in the primitive meninx results in cortical folding and sulci formation in the dorsolateral telencephalon. In developing sulcal regions, generation of apical and basal neuroprogenitor cells is normal. Instead, cell proliferation in the developing meninges is reduced, leading to loss of arachnoid fibroblasts that express Raldh2, an enzyme required for retinoic acid synthesis. Maternal retinoic acid supplementation rescues cortical folding and sulci formation. Our results suggest that balanced retinoic acid signaling from the meninges is required to maintain lissencephaly in mice, and in a manner independent from neuroprogenitor cell amplification.

neuroscience↗

bioRxiv2022

A cadherin mutation in Celsr3 linked to Tourette Disorder affects dendritic patterning and excitability of cholinergic interneurons

CELSR3 encodes an atypical protocadherin cell adhesion receptor that was recently identified as a high-risk gene for Tourette disorder. A putative damaging de novo variant was inserted into the mouse genome to generate an amino acid substitution within the fifth cadherin repeat. By contrast to Celsr3 constitutive null animals, mice homozygous for the R774H amino acid substitution are viable and have grossly normal forebrain development. The density of cortical and striatal interneuron subpopulations is normal, but 3D geometric analysis of cortical pyramidal neurons and striatal cholinergic interneurons revealed changes to dendritic patterning and types and distributions of spines. Furthermore, patch clamp recordings in cholinergic interneurons located within the sensorimotor striatum uncovered mild intrinsic hyperexcitability. Despite these changes, Celsr3R774H homozygous mice do not show obvious tic-like stereotypies at baseline nor motor learning impairments, but females exhibited perseverative digging behavior. Our findings show that a human mutation in CELSR3 linked to Tourette disorder is sufficient to alter dendritic patterning in the cortex and striatum and also the intrinsic excitability of cholinergic interneurons.

neuroscience↗