Biology subjects

Bassermann, F.

Publications and source records attributed to Bassermann, F..

10 recordsLinked to original sources

bioRxiv2025

Single-domain antibodies targeting the pan-T-cell markers CD2 and CD7 as universal immunotherapy T-cell tracers

RationaleDespite significant advancements in immunotherapeutic approaches, such as immune checkpoint modulation and CAR-T cell therapy, reliable and universally applicable surrogate markers to monitor and evaluate the wide variety of therapeutic responses are still missing. This gap of information can lead to delayed assessment of responders versus non-responders and to misinterpretation, potentially resulting in premature or erroneous treatment decisions. Thus, a universal surrogate marker may be of preeminent value in monitoring immune responses, guiding immunotherapies, and ultimately improving patient outcomes. To address this challenge, we developed two immunoPET tracers based on single-domain antibodies (sdAbs) that target the pan T-cell markers CD2 and CD7 to monitor and visualize T cells distribution in vivo. MethodsThis study aimed to establish a comprehensive approach for clinical translation by assessing the feasibility and key characteristics of CD2- and CD7-sdAb for safe, effective clinical application. Binding specificity was confirmed through antigen transduction and knockout in tumor and T-cell leukemia cell lines. In vitro, cytokine secretion and T-cell cytotoxicity were evaluated, while a xenogeneic myeloid sarcoma mouse model was used to analyze T-cell cytotoxicity and visualize TCR-transduced CD8+ T cells at the tumor site using PET/MR imaging. ResultsThis study demonstrates the high specificity, affinity, and thermal stability of CD2- and CD7-sdAb, enabling efficient radiolabeling without impairing T-cell functionality. Specifically, binding to human CD8 T cells did not alter cytokine secretion or cytotoxicity in vitro. Furthermore, in vivo, the cytotoxic ability of transferred TCR-transduced human CD8+ T cells was not compromised upon i.v. application of CD2- and CD7-sdAb. Ultimately, intravenously injected 68Ga-NOTA-CD2-sdAb and 68Ga-NOTA-CD7-sdAb were respectively able to clearly depict and visualize previously administered TCR-transduced CD8+ T cells at the tumor site by PET/MRI. ConclusionsIn this study we have developed two pan T-cell tracers that are able to visualize human T cells and clearly differentiate between responding- and non-responding tumors while not impacting T-cell functionality in vitro and in vivo. The results provide a base for clinical use of these tracers as pan T-cell tracers applicable for any form of immunotherapy, making them a crucial tool in guiding immunotherapeutic decision-making.

immunology↗

bioRxiv2025

A microbial metabolite protects against graft-versus-host disease via mTORC1 and STING-dependent intestinal regeneration

Changes in the intestinal microbiome and microbiota-derived metabolites predict clinical outcomes after allogeneic hematopoietic stem cell transplantation (allo-HSCT). Here, we report that desaminotyrosine (DAT), a product of bacterial flavonoid metabolism, correlates with improved overall survival and reduced relapse rates in allo-HSCT patients. In preclinical mouse models, treatment with synthetic DAT prevents graft-versus-host disease by protecting the intestinal barrier and promoting intestinal regeneration and contributes to graft-vs.-leukemia responses. DATs beneficial effects on intestinal regeneration remain effective despite broad-spectrum antibiotics-induced dysbiosis, also when administered by fecal microbiota transfer with flavonoid-degrading F. plautii. Mechanistically, DAT promotes mTORC1-dependent activation and proliferation of intestinal stem cells, with concomitant engagement of the innate immune receptor STING required to mitigate metabolic stress and maintain an undifferentiated stem cell state independently of type-I interferon responses. Additionally, DAT can skew T cells towards an effector phenotype to modulate graft-versus-leukemia responses. Our data uncover DATs dual, tissue- and immune-modulating properties and underscore its potential in precision microbiome-based therapies to improve tissue regeneration and minimize immune-mediated side effects.

immunology↗

bioRxiv2025

Illuminating oncogenic KRAS signaling by multi-dimensional chemical proteomics

Mutated KRAS is among the most frequent activating genetic alterations in cancer and drug discovery efforts have led to inhibitors that block its activity. To better understand oncogenic KRAS signaling and the cytostatic effects of drugs, we performed comprehensive dose-dependent proteome-wide target deconvolution, pathway engagement and protein expression characterization of KRAS, MEK, ERK, SHP2 and SOS1 inhibitors in pancreatic (KRAS G12C, G12D) and lung cancer (KRAS G12C) cells. Analysis of the resulting 687,954 dose-response curves available online revealed both common and cell line-specific signaling networks dominated by oncogenic KRAS activity. Time-dose experiments separated early KRAS-MEK-ERK from CDK-mediated signaling that cause cells to exit from the cell cycle. This transition to a quiescent state occurred without substantial proteome re-modelling but extensive changes of protein phosphorylation and ubiquitylation. The collective data highlights the complexity of KRAS signaling in cancer and places a large number of new proteins into this functional context.

cell biology↗

bioRxiv2024

Engineering de novo binder CAR-T cell therapies with generative AI

Chimeric antigen receptor T cell (CAR-T) therapies have revolutionized cancer treatment, with six CAR-T products currently in clinical use1-4. Despite their success, high resistance rates due to antigen escape remain a major challenge5,6. In silico design of de novo binders (DNBs) has the potential to accelerate the development of new binding domains for CAR-T, possibly enabling personalized therapies for cancer resistance7,8. Here, we show that DNBs can be used for CAR-T, targeting clinically relevant cancer antigens. Using a DNB against the epidermal growth factor receptor (EGFR), we demonstrate comparable cytotoxicity, cytokine secretion, long-term proliferation, and lysis of primary patient-derived cancer organoids with single-chain variable fragment (scFv)-based and DNB-based CAR-T cells. Moreover, we use generative artificial intelligence (AI) guided binder design with RFdiffusion9 to target the B cell maturation antigen (BCMA), a key antigen in multiple myeloma treatment10-17. We confirmed the activity of our AI-designed BCMA CAR-T in short- and long-term effector readouts, including a xenograft mouse model of multiple myeloma. Notably, our AI-guided CAR-T approach also successfully targets a mutated BCMA protein variant resistant to the clinically used bispecific antibody teclistamab. In sum, we demonstrate a proof-of-concept for engineering new, bespoke cellular immunotherapies targeting cancer resistance with the help of generative AI. This approach may further accelerate the development of new CAR-T therapies addressing cancer resistance.

bioengineering↗

bioRxiv2024

Tissue-adapted Tregs harness inflammatory signals to promote intestinal repair from therapy-related injury

Intestinal stem cells (ISC) promote tissue repair after genotoxic or immune-mediated injury. However, ISCs are particularly sensitive to various stressors and primary targets of overwhelming immune responses such as interferon-{gamma} (IFN{gamma})-mediated killing. In mouse models of gut damage and biopsies from patients having undergone allo-hematopoietic stem cell transplantation, we observed IFNy expression by intestinal Treg cells. Treg cells leverage combined IFN{gamma} and interleukin 10 (IL-10) stimulation of ISCs to nurture the growth of intestinal organoids through the activation of the mTORC1 and Myc pathways. Similarly, Treg cells or the combined addition of recombinant IFN{gamma} and IL-10 promote the regeneration of organoids after irradiation. Exposure of organoids to Wnt- or EGF-free culture conditions revealed distinct growth factor-like properties of IFN{gamma} and IL-10. While IFN{gamma} induced epithelial proliferation and differentiation, combined addition of IFN{gamma} and IL-10 led to balanced proliferation, ensuring ISC maintenance. Our results uncover a context-dependent role of inflammatory signaling in ISC, through which Treg cells promote epithelial repair.

immunology↗

bioRxiv2024

Limitations of the radiotheranostic concept in neuroendocrine tumors due to lineage-dependent somatostatin receptor expression on hematopoietic stem and progenitor cells

Radiopharmaceutical therapy (RPT) has become an effective treatment option for neuroendocrine tumors (NETs) and castration-resistant prostate cancer and is in clinical development for a growing number of indications. One of the major advantages of theranostic RPT is that the distribution of radiopharmaceuticals in the human body can be imaged, and radiation doses to the patients organs can be calculated. However, accurate dosimetry may be fundamentally limited by microscopic heterogeneity of radiopharmaceutical distribution. We developed fluorescent analogs of somatostatin-receptor-subtype 2 (SSTR2) targeting Lutetium-177 labelled radiopharmaceuticals that are clinically used in patients with neuroendocrine tumors (NETs) and studied their uptake by hematopoietic stem and progenitor cells (HSPC). Hematopoietic stem cells (HSCs) and multipotent progenitor cells (MPPs) showed high and specific SSTR2-ligand uptake, which was at similar levels as neuroendocrine tumor cells. Furthermore, they displayed a several-fold higher uptake of SSTR2-antagonists than of SSTR2-agonists. HSPC treatment with a 177Lu-labelled antagonist and agonist showed a stronger reduction of HSC proliferation by the antagonist. Due to the scarcity of HSCs and MPPs, their contribution to total bone marrow uptake of SSTR2-ligands is not detectable in imaging-based dosimetry studies. This likely explains why SSTR2-antagonists caused pancytopenia in clinical trials despite safe dosimetry estimates. In conclusion, target expression heterogeneity can lead to underestimation of radiopharmaceutical toxicity and should be considered when designing clinical trials for new radiopharmaceuticals. The implications of our findings go beyond somatostatin receptor-targeted radiopharmaceuticals and suggest more generally that first-in-human studies should not only be guided by radiation dosimetry from imaging studies but should also include careful escalation of the administered therapeutic activity. The MMC technology is modular and can be applied to other peptide or protein-based radiopharmaceuticals to study cellular distribution and potential bone marrow uptake prior to clinical testing.

cancer biology↗

bioRxiv2024

The USP12/46 deubiquitinases protect integrins from ESCRT-mediated lysosomal degradation

The functions of integrins are tightly regulated via multiple mechanisms including trafficking and degradation. Integrins are repeatedly internalized, routed into the endosomal system and either degraded by the lysosome or recycled back to the plasma membrane. The ubiquitin system dictates whether internalized proteins are degraded or recycled. Here, we used a genetic screen and proximity-dependent biotin identification to identify deubiquitinase(s) that control integrin surface levels. We found that a ternary deubiquitinating complex, comprised of USP12 (or the homologous USP46), WDR48 and WDR20, stabilizes {beta}1 integrin (Itgb1) by preventing ESCRT-mediated lysosomal degradation. Mechanistically, the USP12/46-WDR48-WDR20 complex removes ubiquitin from the cytoplasmic tail of internalized Itgb1 in early endosomes, which in turn prevents ESCRT-mediated sorting and Itgb1 degradation.

cell biology↗

bioRxiv2024

Protein-structure-sensitive mid-infrared optoacoustic microscopy enables label-free assessment of drug therapy in myeloma cells

Conventional live-cell optical microscopy lacks sensitivity and specificity for label-free detection of intracellular protein-structure dynamics, such as conformational transition from -helix to {beta}-sheet. Detecting intermolecular {beta}-sheet formation, for instance, is important because it is a hallmark of misfolded proteins and aggresome formation--which are intrinsic indicators of cell apoptosis in myeloma therapy. Going beyond conventional optical microscopy, we introduce a single-cell imaging technology with label-free sensitivity to intracellular intermolecular {beta}-sheet formation in living cells. This unique ability was attained by exploiting the spectral specificity of the mid-infrared amide I region (1700 - 1600 cm-1) to protein structure and the positive-contrast nature of optoacoustic microscopy. By means of this technology, we were able to monitor the efficiency of proteasome inhibition in a myeloma cell line and--as a first demonstration towards clinical translation--in biopsied myeloma cells from patients. Achieving label-free monitoring of treatment at a single-cell level allows longitudinal assessment of response heterogeneity, which could provide crucial therapeutic information, such as patient-specific sensitivity to treatment, thus facilitating personalized medicine in myeloma therapy.

biophysics↗

bioRxiv2022

Proteogenomic analysis reveals RNA as an important source for tumor-agnostic neoantigen identification correlating with T-cell infiltration

Systemic pan-tumor analyses may reveal the significance of common features implicated in cancer immunogenicity and patient survival. Here, we provide a comprehensive multi-omics data set for 32 patients across 25 tumor types by combining proteogenomics with phenotypic and functional analyses. By using an optimized computational approach, we discovered a large number of novel tumor-specific and tumor-associated antigens including shared common target candidates. To create a pipeline for the identification of neoantigens in our cohort, we combined deep DNA and RNA sequencing with MS- based immunopeptidomics of tumor specimens, followed by the assessment of their immunogenicity. In fact, we could detect a broad variety of non-wild type HLA-binding peptides in the majority of patients and confirmed the immunogenicity of 24 neoantigens. Most interestingly, the majority of total and immunogenic neoantigens originated from variants identified in the RNA dataset, illustrating the importance of RNA as a still understudied source of cancer antigens. Moreover, the amount of these mainly RNA-based immunogenic neoantigens correlated positively with overall CD8+ tumor-infiltrating T cells. This study therefore underlines the importance of RNA-centered variant detection for the identification of shared biomarkers and potentially relevant neoantigen candidates. Statement of significanceThe significance of this study lies not only in the potential of our optimized proteogenomic workflow for the discovery of neoantigens (in particular RNA-derived neoantigens) for clinical application, but sheds light on the entity-agnostic prevalence of HLA class I peptide presentation of RNA processing events to be used for tumor targeting.

cancer biology↗

bioRxiv2021

Spatial and temporal plasticity of neoantigen-specific T-cell responses bases on characteristics associated to antigen and TCR

Neoantigens derived from somatic mutations have been demonstrated to correlate with therapeutic responses mediated by treatment with immune checkpoint inhibitors. Neoantigens are therefore highly attractive targets for the development of personalized medicine approaches although their quality and associated immune responses is not yet well understood. In a case study of metastatic malignant melanoma, we performed an in-depth characterization of neoantigens and respective T-cell responses in the context of immunotherapy with Ipilimumab. Three neoantigens identified either by immunopeptidomics or in silico prediction were investigated using binding affinity analyses and structural simulations. We isolated seven T-cell receptors (TCRs) from the patient immune repertoire recognizing these antigens. TCRs were compared in-vitro and in-vivo with multi-parametric analyses. Identified immunogenic peptides showed similar binding affinities to the human leukocyte antigen (HLA) complex and comparable differences to their wildtype counterparts in molecular dynamic simulations. Nevertheless, isolated TCRs differed substantially in functionality and frequency. In fact, TCRs with comparably lower functional avidity and higher potential for cross-reactivity provided at least equal anti-tumor immune responses in vivo. Of note, these TCRs showed a reduced activation pattern upon primary in vitro stimulation. Exploration of the TCR-{beta} repertoire in blood and in different tumor-related tissues over three years, offered insights on the high frequency and particular long-term persistence of low-avidity TCRs. These data indicate that qualitative differences of neoantigen-specific TCRs and their impact on function and longevity need to be considered for neoantigen targeting by adoptive T-cell therapy using TCR-transgenic T cells. Statement of translational relevanceImmunotherapy has demonstrated high efficacy in diverse malignancies. Neoantigens derived from mutations provide promising targets for safe and highly tumor-specific therapeutic approaches. Yet, single determinants of an effective and enduring T-cell mediated tumor rejection are still not well understood. We analyzed in detail seven neoantigen-specific T-cell receptors (TCRs) derived from a melanoma patient targeting three different altered peptide ligands identified by mass spectrometry and prediction analyses. Functional characterization of these TCRs revealed potent anti-tumor reactivity of all TCRs. Of special interest, TCRs with comparably lower affinity demonstrated effective in vivo activity as well as dominant spatial and temporal distribution in blood and tissue. Functional differences of TCR may require further T-cell and/or TCR engineering and should be considered for future clinical trial designs.

immunology↗