Denis Wirtz

Reprogramming CAR-T cell function through synthetic cytokine receptors suppresses metastatic progression of TNBC

This study enhances CAR-T cell migration through synthetic cytokine receptors, reducing metastasis in TNBC mouse models.

TiSAM: fusing spatial and histopathology foundation models for whole-slide image segmentation

TiSAM improves whole-slide image segmentation by fusing spatial and histopathology features, achieving high accuracy across diverse datasets and scanners.

VITAL-3D: Volumetric Single-Cell Quantification Reveals Microenvironment-Dependent Drug Responses in Breast Cancer

VITAL-3D quantifies single-cell drug responses in 2D and 3D cultures, revealing microenvironment-dependent efficacy differences in breast cancer.

CODAvision: best practices and a user-friendly interface for rapid, customizable segmentation of medical images

CODAvision provides a user-friendly interface for rapid, customizable medical image segmentation using deep learning, enabling non-experts to train and evaluate models across diverse imaging modalities.

Distinct senescent β-cell senotypes differentially drive islet aging and dysfunction

The paper identifies two distinct senescent β-cell subpopulations with different functional roles in islet aging and dysfunction using single-cell proteomics and transcriptomics.

Spatial Regulation of CAR Signaling Enables Logic-Gated Activity

The paper designs an AND-gated CAR T cell receptor called MANTIS that uses extracellular size differences to spatially regulate signaling for precise antigen recognition.

Virtual multiplex staining of the pancreatic islets across type 1 diabetes progression using a Schroedinger bridge

This paper introduces SMILE, a diffusion model for converting H&E stains to multiplex IHC images, showing superior performance in pancreatic islet analysis and breast cancer stain conversion.

Whole organism 3D mapping reveals universal branching topology and biophysical optimization governs vascular and nervous system development

The paper uses 3D imaging to analyze vascular and nervous systems in embryos, finding shared structural principles but distinct architectures shaped by biophysical constraints.

Accelerated Discovery of Cell Migration Regulators Using Label-Free Deep Learning-Based Automated Tracking

This paper introduces DeepBIT, a deep learning method for automated cell migration tracking, enabling high-throughput analysis of cancer cell motility under various conditions and identifying new regulators of migration.

Deep Learning Enabled 3D Multi-Omic Analysis Reveals Molecular Signatures of Heterogeneous Response to Chemotherapy in Pancreatic Cancer

The paper develops a 3D multi-omic pipeline using deep learning to analyze chemotherapy response in pancreatic cancer, identifying molecular signatures of resistance and fibroblast-cancer interactions.

3D, multi-omic imaging reveals molecular biomarkers of the pre-metastatic niche in lung cancer

This study uses 3D multi-omic imaging to identify biomarkers of the pre-metastatic niche in lung cancer, revealing myeloid and senescent cell signatures associated with metastasis risk.

A 3D in vitro assay to study combined immune cell infiltration and cytotoxicity

This paper introduces a 3D in vitro assay to study immune cell infiltration and cytotoxicity in solid tumors, showing it captures key steps of immune cell interaction with the tumor microenvironment.

A disrupted compartment boundary underlies abnormal cardiac patterning and congenital heart defects

The paper identifies Tbx5 as a gene critical for forming a compartment boundary in the interventricular septum, and shows its disruption leads to congenital heart defects.

Senescence-Linked Fibrosis in the Aging Human Ovary Revealed by p16-Based Histological Profiling and Spatial Transcriptomics

The paper identifies and maps senescent cells in postmenopausal ovaries using p16 expression and spatial transcriptomics, revealing a fibro-inflammatory signature associated with aging.

Precision targeting of autoreactive B cells in systemic lupus erythematosus using anti-9G4 idiotope synthetic immune receptor T cells

This study develops anti-9G4 CAR-T and TCR-T cells to selectively target autoreactive B cells in SLE, reducing immunosuppression and cytokine toxicity.

Optimization of velocity receptor transduction in CAR T cells

This study optimizes velocity receptor (VR) transduction in CAR T cells by evaluating vector modifications and transduction efficiency, finding that VR5IL8 and VR5TNF perform best.

NLTD 2.0: A Nonlinear Framework for Robust and Customizable Color Deconvolution in Histopathology

NLTD 2.0 improves color deconvolution in histopathology by handling more than three stains without requiring optimal color vectors, enhancing reliability and accessibility through an ImageJ plugin.

Hyper-migratory CAR T cells alleviate ovarian cancer metastatic burden and improve prognosis

This study shows hyper-migratory CAR T cells reduce ovarian cancer metastasis and improve survival in mice.

3D multi-omic mapping of whole nondiseased human fallopian tubes at cellular resolution reveals a large incidence of ovarian cancer precursors

The paper presents a 3D multi-omic framework to detect and characterize ovarian cancer precursors in fallopian tubes, identifying TP53 mutations in microscopic lesions.

3D map-guided modeling of functional endometrial tissue using multi-compartment assembloids

This paper develops a 3D multi-compartment assembloid that mimics human endometrial tissue and its menstrual cycle phases, enabling study of compartment-specific hormonal responses and paracrine signaling.

Senescent cell heterogeneity and responses to senolytic treatment are related to cell cycle status during cell growth arrest.

This study identifies functionally distinct senescent cell subpopulations based on cell cycle status, showing G2-arrested cells secrete more IL-6 and are more sensitive to senolytic treatment.

Digitize your Biology! Modeling multicellular systems through interpretable cell behavior

The paper introduces a framework for mathematical modeling of multicellular systems using interpretable cell behavior rules derived from biological knowledge and multi-omics data.

PIVOT: an open-source tool for multi-omic spatial data registration

PIVOT is an open-source tool for nonlinear registration of multi-omic spatial data, demonstrating improved throughput compared to existing workflows.

Integration of nuclear morphology and 3D imaging to profile cellular neighborhoods

The paper integrates 3D imaging with nuclear segmentation to analyze nuclear morphology in human tissue, revealing spatial patterns and interactions in disease progression.

Solving the "Blind men and the elephant problem": Additive deep learning of complex high dimensional models from partial faceted datasets

The paper develops a machine learning approach to reconstruct complex biological systems from partial faceted datasets, showing successful reconstruction in both mechanical and biological examples.

3D histology reveals that immune response to pancreatic precancers is heterogeneous and depends on global pancreas structure

The paper profiles the immune microenvironment of PanINs in 3D at single-cell resolution to understand inflammation's role in cancer progression and finds immune heterogeneity and correlations with PanIN grade.

High-motility pro-tumorigenic monocytes drive macrophage enrichment in the tumor microenvironment

This study identifies high-motility tumor-associated monocytes (TAMos) that drive macrophage infiltration and cancer cell proliferation via IL-6 and MAPK pathways, suggesting IL-6 as a therapeutic target.

qMAP Enabled Microanatomical Mapping of Human Skin Aging

This study introduces qMAP, a deep learning-based workflow for microanatomical mapping of human skin, identifying 10 core processes strongly associated with aging and achieving age prediction accuracy comparable to epigenetic clocks.

Generative interpolation and restoration of images using deep learning for improved 3D tissue mapping

This paper uses a generative AI model to improve 3D tissue imaging by interpolating and restoring images, enhancing resolution and reducing artifacts across multiple modalities and species.

Substrate stiffness modulates the emergence and magnitude of senescence phenotypes in dermal fibroblasts

This study shows that substrate stiffness affects the development and strength of senescence features in fibroblasts, with mechanosensitive regulation of key biomarkers.