Biology subjects

Kobold, S.

Publications and source records attributed to Kobold, S..

8 recordsLinked to original sources

bioRxiv2026

Multi-Lab Testing of Early Preclinical Discoveries Identifies Promising Treatments

A fundamental challenge in drug development is the frequent failure of early laboratory research to translate into clinical benefit. One promising solution is to confirm findings from exploratory single-laboratory studies across multiple laboratories before clinical testing. We investigated this approach following the conduct of preclinical multi-laboratory studies across different fields of medicine. For this, we evaluated effect sizes, experimental rigor, and a set of criteria to identify determinants of confirmation success. When tested under increased rigor, only a fraction of multi-laboratory studies confirmed the initial results. The underlying effect size reduction was associated with outcome-relevant experimental differences between exploratory and confirmatory stages. In summary, multi-laboratory studies proved highly informative and served as an effective filter for promising treatments.

scientific communication and education↗

bioRxiv2026

Multicenter preclinical validation of next-generation CAR T cells: a strategy for harmonization, reproducibility, and its feasibility in clinical translation

PurposeClinical translation of CAR T cell therapies has accelerated, yet preclinical evidence still often originates from single-center studies lacking sufficient robustness. Preclinical confirmatory multicenter studies have been proposed to improve the translational success, but their feasibility in cellular therapies remains unexplored. MethodsWe performed a confirmatory multicenter study validating C-C-motive-receptor-8 (CCR8) overexpression in CAR T cells--a strategy previously shown to enhance solid tumor infiltration. In vitro experiments covering activation, cytotoxicity, and migration using three CAR constructs were conducted across two centers with harmonized materials, preregistered protocols, randomization, and blinding. ResultsThe data from the two centers confirmed key findings of the exploratory study: CCR8 overexpression in anti-EpCAM and anti-mesothelin CAR T cells leads to enhanced selective migration towards a CCL1-gradient, while not compromising antigen-specific T cell activatory capacity and cytotoxicity in vitro. The study furthermore broadened the applicability of CCR8 overexpression to anti-CEA CAR T cells. ConclusionsThis first-of-its-kind preclinical confirmatory CAR T study demonstrates the feasibility of a multicenter confirmation in cellular therapy, with technical and logistical challenges resolved through transparent communication between all parties involved. Both exploratory and confirmatory studies aim to downselect CAR candidates with the highest clinical success potential, as they compete for limited resources in preclinical research. It is therefore mandatory to clarify the extent of replications required to validate the experimental methodology and identify CAR candidates with most likelihood of success. TRANSLATIONAL RELEVANCEPreclinical evidence for novel CAR T cell therapeutic strategies relies mostly on exploratory single-center studies lacking robustness, with recent findings substantiating their limited predictive value for cellular therapies tested outside hematology. Here, the function of CCR8-armored CARs in vitro was confirmed in a preclinical confirmatory multicenter study, demonstrating the feasibility of such studies in adding value to the transition of preclinical concepts to clinical development. Our first-of-its-kind study may contribute to define new routes for preclinical testing and further raises the general question of what level of preclinical evidence is reasonably achievable in an academic context. It indicates the need for strong collaborative efforts to realize dedicated preclinical infrastructure for clinical translation of reprogrammed immune cellular therapeutics.

synthetic biology↗

bioRxiv2025

Development of AI-designed protein binders for detection and targeting of cancer cell surface proteins

Artificial intelligence (AI)-based protein design opens new avenues for the rapid generation of new research tools and therapeutics, but experimental validation lags behind the computational design throughput. Here, we present a scalable workflow for the discovery and validation of AI-designed protein binders. Leveraging the RFdiffusion protein design pipeline with a custom filter for stable alpha-helical bundle folds, we construct libraries of thousands of AI-binders against cancer-associated surface proteins. Mammalian cell-surface and phage display screening yield multiple high-affinity PD-L1 binders but fewer hits for CD276 (B7-H3) and VTCN1 (B7-H4), reflecting the target-dependent efficiency of RFdiffusion in generating high-quality designs. Using our experimentally validated AI-designed binder libraries, we benchmark freely available structure prediction models. We find that interface predicted template modelling (ipTM) scores by Chai-1 with ESM embedding correlate well with experimental success and even predict deleterious effects of binding interface mutations. To demonstrate the versatility of AI-binders as research tools, we deploy them in CAR-T cells and also assemble them with fluorophore-labeled streptavidin into tetravalent quattrobinders, which achieve antibody-comparable staining of endogenous PD-L1 by flow cytometry. With high production yields and accessible structural models, AI-designed quattrobinders are versatile and cost-effective research tools amenable to community-driven validation and optimization.

bioengineering↗

bioRxiv2025

IGLV3-21-R110-directed bispecific antibodies activate T cells and promote killing in a high-risk subset of chronic lymphocytic leukemia

We previously used a disease-specific B cell receptor (BCR) point mutation (IGLV3-21R110) for selective targeting of a poor-risk subset of chronic lymphocytic leukemia (CLL) with chimeric antigen receptor (CAR) T cells. Since CLL is a disease of the elderly and a significant fraction of patients is not able to physically tolerate CAR T cell treatment, we explored bispecific antibodies as an alternative for precision targeting of this tumor mutation. Heterodimeric IgG1-based antibodies consisting of a fragment crystallizable region (Fc) attached to either an anti-IGLV3-21R110 Fab or an anti-CD3 (UCHT1) single chain variable fragment (R110-bsAb) selectively killed cell lines engineered to express high levels of the neoepitope as well as primary CLL cells using healthy donor and CLL patient-derived T cells as effectors. R110-bsAb spared polyclonal human B cells (as opposed to CD19-targeting Blinatumomab) as well as CD34+ human stem cells. Yet, R110-bsAb induced lower T cell activation than Blinatumomab with primary CLL cells likely due to lower expression of target antigen. In vivo, R110-bsAb specifically killed IGLV3-21R110-expressing cell lines and CLL cells while sparing peripheral blood mononuclear cells. These findings highlight bispecific antibodies as a promising, off-the-shelf immunotherapy for high-risk CLL patients, offering selective targeting while preserving healthy B cells.

cancer biology↗

bioRxiv2024

Predictive value of preclinical models for CAR-T cell therapy clinical trials: a systematic review and meta-analysis

Experimental mouse models are indispensable for the preclinical development of cancer immunotherapies, whereby complex interactions in the tumor microenvironment (TME) can be somewhat replicated. Despite the availability of diverse models, their predictive capacity for clinical outcomes remains largely unknown, posing a hurdle in the translation from preclinical to clinical success. This study systematically reviews and meta-analyzes clinical trials of chimeric antigen receptor (CAR-) T cell monotherapies with their corresponding preclinical studies. Adhering to PRISMA guidelines, a comprehensive search of PubMed and ClinicalTrials.gov was conducted, identifying 422 clinical trials and 3157 preclinical studies. From these, 105 clinical trials and 180 preclinical studies, accounting for 44 and 131 distinct CAR constructs, respectively, were included. Patient[s] responses varied based on the target antigen, expectedly with higher efficacy and toxicity rates in hematological cancers. Preclinical data analysis revealed homogenous and antigen-independent efficacy rates. Our analysis revealed that only 4 % (n = 12) of mouse studies used syngeneic models, highlighting their scarcity in research. Three logistic regression models were trained on CAR structures, tumor entities, and experimental settings to predict treatment outcomes. While the logistic regression model accurately predicted clinical outcomes based on clinical or preclinical features (Macro F1 and AUC > 0.8), it failed in predicting preclinical outcomes from preclinical features (Macro F1 < 0.5, AUC < 0.6), indicating that preclinical studies may be influenced by experimental factors not accounted for in the model. These findings underscore the need for better understanding the experimental factors enhancing the predictive accuracy of mouse models in preclinical settings.

cancer biology↗

bioRxiv2023

Mutation-specific CAR T cells as precision therapy for IGLV3-21R110 expressing high-risk chronic lymphocytic leukemia

The concept of precision cell therapy targeting tumor-specific mutations is appealing but requires surface-exposed neoepitopes, which is a rarity in cancer. B cell receptors (BCR) of mature lymphoid malignancies are exceptional in that they harbor tumor-specific-stereotyped sequences in the form of point mutations that drive self-engagement of the BCR and autologous signaling. Here, we used a BCR light chain neoepitope defined by a characteristic point mutation (IGLV3-21R110) for selective targeting of a poor-risk subset of chronic lymphocytic leukemia (CLL) with chimeric antigen receptor (CAR) T cells. We developed murine and humanized CAR constructs expressed in T cells from healthy donors and CLL patients that eradicated IGLV3-21R110 expressing cell lines and primary CLL cells, but not polyclonal healthy B cells. In vivo experiments confirmed epitope-selective cytolysis in xenograft models using engrafted IGLV3-21R110 expressing cell lines or primary CLL cells. We further demonstrate in two humanized mouse models lack of cytotoxicity towards human B cells. These data provide the basis for novel avenues of resistance-preventive and biomarker-guided cellular targeting of functionally relevant lymphoma driver mutations sparing normal B cells.

cancer biology↗

bioRxiv2023

HIF-1α-mediated mitochondrial-glycolytic reprogramming controls the transition of precursor to terminally exhausted T cells

Functional exhaustion of T cells in cancer and persistent infections is characterized by the upregulation of inhibitory receptors, the progressive decline in cytokine secretion and impaired cytolytic activity. Terminally exhausted T cells are steadily replenished by a precursor population (Tpex) with phenotypic features of memory T cells and a stem-like capacity to self-renew. However, the metabolic principles of Tpex maintenance and the regulatory circuits that control the exhaustion of their progeny remain incompletely understood. Using a combination of gene-deficient mice, single-cell transcriptomics and metabolomic analyses, we here show that mitochondrial insufficiency is a cell-intrinsic trigger that initiates the T cell exhaustion program. At the molecular level, we found that diminished mitochondrial respiration and metabolic remodeling cause oxidative stress, which inhibits the proteasomal degradation of hypoxia inducible factor 1 alpha (HIF-1) in Tpex cells. HIF-1 mediates the transcriptional-glycolytic reprogramming of Tpex cells as an initial step towards terminal differentiation and functional exhaustion. Finally, we show that enhancing respiration by limiting the glycolytic activity of CAR T cells is a feasible metabolic intervention strategy to preserve the stemness of Tpex cells during chronic viral infection and cancer immunotherapy.

immunology↗

bioRxiv2019

An in vivo inflammatory loop potentiates KRAS blockade

KRAS inhibitors perform inferior to other targeted drugs. To investigate a possible reason for this, we treated cancer cells with KRAS inhibitors deltarasin (targeting phosphodiesterase-{delta}), cysmethynil (targeting isoprenylcysteine carboxylmethyltransferase), and AA12 (targeting KRASG12C), and silenced/overexpressed mutant KRAS using custom vectors. We show that KRAS-mutant tumor cells exclusively respond to KRAS blockade in vivo, because the oncogene co-opts host myeloid cells via a C-C-motif chemokine ligand 2/interleukin-1{beta} signaling loop for sustained tumorigenicity. Indeed, KRAS-mutant tumors did not respond to deltarasin in Ccr2 and Il1b gene-deficient mice, but were deltarasin-sensitive in wild-type and Ccr2-deficient mice adoptively transplanted with wild-type murine bone marrow. A KRAS-dependent pro-inflammatory transcriptome was prominent in human cancers with high KRAS mutation prevalence and predicted poor survival. Hence the findings support that in vitro systems are suboptimal for anti-KRAS drug screens, and suggest that interleukin-1{beta} blockade might be specific for KRAS-mutant cancers.

cancer biology↗