Biology subjects

Herbst, H.

Publications and source records attributed to Herbst, H..

5 recordsLinked to original sources

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

Impacts of urbanization on the health of American Robins (Turdus migratorus) in Chicagoland

Wild animals in urbanized environments face several unique challenges, including increased anthropogenic stressors, decreased natural food availability and quality, and increased pollutant exposure. While some work has shown that individual urbanization stressors can have negative impacts on aspects of wild bird physiology, other studies have demonstrated ambiguous or sometimes positive interactions. As such, the impact of multiple, coincident urban stressors on avian health still needs to be fully understood. Here, we addressed this knowledge gap by holistically measuring multiple physiological markers of American robin (Turdus migratorius) health across a gradient of urbanization throughout Chicagoland. We predicted that birds using highly urbanized habitats would experience higher heavy metal contamination, higher oxidative stress, lower body condition, higher avian malaria burden, and decreased measures of immune response compared to exurban birds in the Chicagoland area. Multiple linear models revealed that robins in more urbanized areas exhibited higher levels of heavy metal contamination and slightly elevated levels of associated physiological impairments compared to their counterparts in exurban sites. Additionally, noise and light pollution were significantly associated with oxidative stress and infection status, respectively, albeit in different directions. Overall, our findings underscore how the complex environmental changes that accompany urbanization can impact the health of urban bird populations.

ecology↗

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

A multi-omics integrative approach unravels novel genes and pathways associated with senescence escape after targeted therapy in NRAS mutant melanoma

Therapy Induced Senescence (TIS) leads to sustained growth arrest of cancer cells. The associated cytostasis has been shown to be reversible and cells escaping senescence further enhance the aggressiveness of cancers. Together with targeted therapeutics, senolytics, specifically targeting senescent cancer cells, constitute a promising avenue for improved cancer treatments. Understanding how cancer cells evade senescence is needed to optimise the clinical benefits of this therapeutic approach. Here we characterised the response of three different NRAS mutant melanoma cell lines to a combination of CDK4/6 and MEK inhibitors over 33 days. Transcriptomic data show that all cell lines trigger a senescence programme coupled with strong induction of interferons. Kinome profiling revealed the activation of Receptor Tyrosine Kinases (RTKs) and enriched downstream signaling of neurotrophin, ErbB and insulin pathways. Characterisation of the miRNA interactome associates miR-211-5p with resistant phenotypes. Finally, iCELL-based integration of bulk and single-cell RNA-seq data identified biological processes perturbed during senescence, and predicts new genes involved in its escape. Overall, our data associate insulin signaling with persistence of a senescent phenotype and suggest a new role for interferon gamma in senescence escape through the induction of EMT and the activation of ERK5 signaling.

cancer biology↗

bioRxiv2018

Transition of Wnt signaling microenvironment delineates the squamo-columnar junction and emergence of squamous metaplasia of the cervix

The transition zones (TZ) between squamous and columnar epithelium constitute hotspots for the emergence of cancers. Carcinogenesis at these sites is often preceded by the development of metaplasia, where one epithelial type invades the neighboring one. It remains unclear how these niches are restrained at the boundary between the two epithelial types and what factors contribute to metaplasia. Here we show that the cervical squamo-columnar junction derives from two distinct stem cell lineages that meet at the TZ. In contrast to the prevailing notion, our analysis of cervical tissue showed that the TZ is devoid of any locally restricted, specialized stem cell population, which has been implicated as precursor of both cervical squamous cell carcinoma and adenocarcinoma. Instead, we reveal that these cancers originate from two separate stem cell lineages. We show that the switch in the underlying Wnt signaling milieu of the stroma is a key determinant of proliferation or quiescence of epithelial stem cell lineages at the TZ. Strikingly, while the columnar lineage of the endocervix is driven by Wnt signaling, the maintenance of squamous stratified epithelium of the ectocervix and emergence of squamous metaplasia requires inhibition of Wnt signaling via expression of Dickkopf2 (Dkk2) in the underlying stroma. Moreover, Notch signaling is required for squamous cell stratification. Thus, our results indicate that homeostasis at the TZ is not maintained by a transition from one epithelial type to another but rather results from alternative signals from the stromal compartment driving the differential proliferation of the respective cell lineages at the squamo-columnar junction.

cancer biology↗