Biology subjects

Lenz, G.

Publications and source records attributed to Lenz, G..

12 recordsLinked to original sources

bioRxiv2025

Functional autophagy gene set signature and state classification reveal a link between autophagy induction, lysosomal activity, and poor prognosis in glioblastoma

Autophagy is an essential mechanism for maintaining cell homeostasis and, when dysregulated, is related to various pathologies. In cancer, it functions as a double-edged sword, either as a tumor suppressor or as a tumor promoter. Elevated GFP-LC3 puncta and increased levels of autophagy-related proteins, commonly interpreted as markers of high autophagic activity, are often associated with poor prognosis in tumors. However, current assessments of autophagy largely rely on isolated cellular and protein-level observations. While transcriptomic approaches offer broader insights, they often utilize large gene signatures without adequately accounting for the dynamic nature of autophagic flux. In this study, we propose a functional gene set signature for autophagy based on the rational mapping of flux stages, enabling the inference of distinct autophagy states. Using a supervised machine learning approach, we developed two indices - AutoIndex and LysoIndex - that effectively distinguish between cells treated with autophagy inducers and inhibitors. Applying this framework, we analyzed autophagy states across four cancer types, comparing tumor samples to matched normal tissues and evaluating their association with patient survival. Among these, glioblastoma (GBM) exhibited the strongest correlation between inferred autophagy states and clinical outcomes. GBM samples characterized by high LysoIndex and low AutoIndex--corresponding to a transcriptomic induction state--were linked to significantly poorer survival. Compared to lower-grade gliomas, GBM showed elevated lysosomal activity, which may contribute to its more aggressive behavior. Additionally, GBM cell lines treated with temozolomide displayed signatures consistent with autophagy induction, supporting our models predictive relevance. These results reinforce the understanding and monitoring of autophagy, and suggest that, in the case of GBM, its negative influence may represent a potential target for novel therapeutic interventions.

cell biology↗

bioRxiv2024

Mitochondrial sites of contact with the nucleus aid in chemotherapy evasion of glioblastoma cells

Glioblastoma (GBM) is the most common form of a malignant primary brain tumour in adults for which therapeutic options are minimal. The rapid onset of the resistance mechanisms against the chemotherapeutic agent Temozolomide (TMZ), the first line of pharmacological care for patients, prevents the long-term validity of this approach. The underpinning biology for this remains poorly understood thus compromising the efficacy of this approach. The Translocator Protein (TSPO) is an 18kDa ubiquitous cholesterol-binding molecule on the outer membrane of mitochondria (OMM). Upregulated in cancers TSPO is required to form contacts between mitochondria and the nucleus termed: Nucleus Associated Mitochondria (NAM). In GBM tissues as well as in 2D and 3D cell cultures we assayed patterns of TSPO expression (i), autophagy/mitophagy (ii), transcription factors (iii) and susceptibility to TMZ-induced demise (iv). Confocal and ultrastructural imaging detailed the organization and redistribution of the mitochondrial network (v). Our findings show that TMZ exploits mitochondria via TSPO to aid the formation of NAM which couples the expression of the nuclear transcription factor Sterol regulatory element-binding transcription factor 1 (SREBP1) and the stabilization of YAP/TAZ. Pharmacological modulation of TSPO counteracts all the above and re-instates susceptibility to TMZ-induced demise. NAM is therefore proposed as a variable in the engagement and execution of pro-survival mechanisms in GBM thus offering a means to both insight into the pathophysiology of this disease and offer novel therapeutic strategies. Key PointsO_LITMZ exploits TSPO to curb mitochondrial quality control in glioblastoma cells. C_LIO_LITMZ-mediated MRR is associated with the relocation of mitochondria to the nucleus and modulation of transcriptional factors involved in cholesterol metabolism and adaptation to aggressive growth. C_LIO_LITSPO represents a pharmacological target to revert chemoresistance in glioblastoma cells. C_LI Importance of the StudyThis study elucidates a mitochondrion-driven mechanism of chemoresistance in human glioblastoma cells, which depends on the mitochondrial translocator protein TSPO. The administration of TSPO ligands restores susceptibility to TMZ by influencing the dynamics of transcriptional factors associated with cholesterol metabolism and mechanical transduction.

cancer biology↗

bioRxiv2024

Oriented Cell Dataset: efficient imagery analyses using angular representation

In this work, we propose a new public dataset for cell detection in bright-field microscopy images annotated with Oriented Bounding Boxes (OBBs), named Oriented Cell Dataset (OCD). We show that OBBs provide a more accurate shape representation compared to standard Horizontal Bounding Boxes (HBBs), with slight overhead of one extra click in the annotation process. Our dataset also contains a subset of images with five independent expert annotations, which allows inter-annotation analysis to determine if the results produced by algorithms are within the expected variability of human experts. We investigated how to automate cell biology microscopy images by training seven popular OBB detectors in the proposed dataset, and focused our analyses on two main problems in cancer biology: cell confluence and polarity determination, the latter not possible through HBB representation. All models achieved statistically similar results to the biological applications compared to human annotation, enabling the automation of cell biology and cancer cell biology microscopy image analysis. Our code and dataset are available at https://github.com/LucasKirsten/Deep-Cell-Tracking-EBB.

bioinformatics↗

bioRxiv2024

CloVarS: a simulation of single-cell clonal variability

High-throughput time-lapse microscopy has allowed researchers to monitor individual cells as they grow into colonies and react to treatments, but a deeper understanding of the data obtained after image analysis is still lacking. This is partly due to the biological and computational challenges related to long-running experiments and single-cell tracking. In this work, we present the Clonal Variability Simulator (CloVarS), a Python tool for generating synthetic data of single-cell lineage trees to model time-lapse microscopy experiments. After colony initialization, each individual cell is simulated for a given number of simulation frames. Over the course of the simulation, cells are able to migrate, enter mitosis (divide), and enter apoptosis (die). These events are determined by distributions of cell division and death times, which can be inferred from and fit to experimental data. Colonies have an adjustable fitness memory, meaning cells are able to inherit their parent cells fitness (i.e. their parents time to division/death) to a higher or lesser degree. Arbitrary treatments are able to be delivered to colonies at any time point, modifying their division and death distributions, and fitness memory. CloVarS is an important asset for quickly exploring colony fitness dynamics, testing biological hypotheses, bench-marking cell tracking algorithms, and ultimately improving our understanding of single-cell lineage data.

bioinformatics↗

bioRxiv2022

A new type of transcriptional reprogramming by an IRF4 mutation in lymphoma

SUMMARY PARAGRAPHDisease-causing mutations in genes encoding transcription factors (TFs) are a recurrent finding in hematopoietic malignancies and might involve key regulators of lineage adherence and cellular differentiation1-3. Such mutations can affect TF-interactions with their cognate DNA-binding motifs4, 5. Whether and how TF-mutations impact upon the nature of binding to TF composite elements (CE) and influence their interaction with other TFs is unclear. Here, we report a new mechanism of TF alteration in human lymphomas with perturbed B cell identity. It is caused by a recurrent somatic missense mutation c.295T>C (p.Cys99Arg; p.C99R) targeting the center of the DNA-binding domain of Interferon Regulatory Factor 4 (IRF4), a key TF in immune cell-differentiation and -activation6, 7. IRF4-C99R fundamentally alters IRF4 DNA-binding, with loss-of-binding to canonical IRF motifs and neomorphic gain-of-binding to canonical and non-canonical IRF composite elements (CEs). Furthermore, IRF4-C99R thoroughly modifies IRF4 function, by blocking IRF4-dependent plasma cell induction, and up-regulating disease-specific genes in a non-canonical Activator Protein-1 (AP-1)-IRF-CE (AICE)-dependent manner. Our data explain how a single arginine mutation creates a complex switch of TF specificity and gene regulation. These data open the possibility of designing specific inhibitors to block the neomorphic, disease-causing DNA-binding activities of a mutant transcription factor.

cancer biology↗

bioRxiv2022

Malt1-dependent cleavage of Tensin-3 controls B-cell adhesion and lymphomagenesis

The protease Malt1 controls the development and function of lymphocytes and promotes lymphomagenesis by cleaving a limited set of cellular substrates, many of which regulate gene transcription. Here, we report the identification of the integrin-binding scaffold protein Tensin-3 as a Malt1 substrate in activated B cells. B cells expressing a non-cleavable form of Tensin-3 (TNS3-nc) showed normal NF-{kappa}B and JNK transcriptional responses but increased and prolonged integrin-dependent adhesion upon activation. Moreover, mice expressing a non-cleavable form of Tensin-3 displayed reduced antibody production in response to immunization with a T-cell dependent antigen. We also explored the role of Tensin-3 in diffuse large B cell lymphomas and mantle cell lymphomas characterized by constitutive Malt1 activity, which showed strong constitutive Tensin-3 cleavage and a correlating reduction in total Tensin-3 levels. Silencing of Tensin-3 expression in Malt1-driven lymphoma models did not affect cellular proliferation but enhanced the dissemination of xenografted lymphoma cells. Thus, Malt1-dependent Tensin-3 cleavage limits integrin-dependent B-cell adhesion and promotes humoral immune responses and metastatic spreading of B cell lymphomas in a transcription-independent manner.

immunology↗

bioRxiv2021

A DNA repair-independent role for alkyladenine DNA glycosylase in alkylation-induced unfolded protein response

Alkylating agents damage DNA and proteins and are widely used in cancer chemotherapy. While the cellular responses to alkylation-induced DNA damage have been explored, knowledge of how alkylation damage affects global cellular stress responses is still sparse. Here, we examined the effects of the alkylating agent methylmethane sulfonate (MMS) on gene expression in mouse liver taking advantage of mice deficient in alkyladenine DNA glycosylase (Aag), the enzyme that initiates the repair of alkylated DNA bases. MMS induced a robust transcriptional response in wild-type liver that included markers of the endoplasmic reticulum (ER) stress/unfolded protein response (UPR) known to be controlled by the transcription factor XBP1, a key UPR effector. Importantly, this response is significantly reduced in the Aag knockout. To investigate a potential role for AAG in alkylation-induced UPR, the expression of UPR markers after MMS treatment was interrogated in human glioblastoma cell lines expressing different AAG levels. Alkylation induced the UPR in cells expressing AAG; conversely, AAG knock-down compromised UPR induction and led to a defect in XBP1 activation plus a decrease in the expression of the ER chaperone BiP. To verify that the DNA repair activity of AAG is required for this response, AAG knockdown cells were complemented with wild-type Aag or with a mutant version of the Aag gene producing a glycosylase-deficient AAG protein. As expected, the glycosylase-defective mutant Aag does not fully protect AAG knockdown cells against MMS-induced cytotoxicity. Remarkably, however, alkylation-induced XBP1 activation is fully complemented by the catalytically inactive AAG enzyme. This work establishes that, in addition to its enzymatic activity, AAG has non-canonical functions in alkylation-induced UPR that contribute to the overall cellular response to alkylation. Significance StatementStress response pathways, such as the DNA damage response (DDR) and the UPR, are critical in both the etiology and treatment of cancer and other chronic diseases. Knowledge of an interplay between ER stress and genome damage repair is emerging, but evidence linking defective DNA repair and impaired ER stress response is lacking. Here, we show that AAG is necessary for UPR activation in response to alkylating agents. AAG-deficient mice and human cancer cells are impaired in alkylation-induced UPR. Strikingly, this defect can be complemented by an AAG variant defective in glycosylase activity. Our studies suggest AAG has non-canonical functions and identify AAG as a point of convergence for stress response pathways. This knowledge could be explored to improve cancer treatment.

cell biology↗

bioRxiv2020

SCOUT: Single-cell outlier analysis in cancer

Outliers are often ignored or even removed from data analysis. In cancer, however, single outlier cells can be of major importance, since they have uncommon characteristics that may confer capacity to invade, metastasize, or resist to therapy. Here we present the Single-Cell OUTlier analysis (SCOUT), a resource for single-cell data analysis focusing on outlier cells, and the SCOUT Selector (SCOUTS), an application to systematically apply SCOUT on a dataset over a wide range of biological markers. Using publicly available datasets of cancer samples obtained from mass cytometry and single-cell RNA-seq platforms, outlier cells for the expression of proteins or RNAs were identified and compared to their non-outlier counterparts among different samples. Our results show that analyzing single-cell data using SCOUT can uncover key information not easily observed in the analysis of the whole population.

bioinformatics↗

bioRxiv2019

Prospective, brain-wide labeling of neuronal subclasses with enhancer-driven AAVs

The rapid pace of cell type identification by new single-cell analysis methods has not been met with efficient experimental access to the newly discovered types. To enable flexible and efficient access to specific neural populations in the mouse cortex, we collected chromatin accessibility data from individual cells and clustered the single-cell data to identify enhancers specific for cell classes and subclasses. When cloned into adeno-associated viruses (AAVs) and delivered to the brain by retro-orbital injections, these enhancers drive transgene expression in specific cell subclasses in the cortex. We characterize several enhancer viruses in detail to show that they result in labeling of different projection neuron subclasses in mouse cortex, and that one of them can be used to label the homologous projection neuron subclass in human cortical slices. To enable the combinatorial labeling of more than one cell type by enhancer viruses, we developed a three-color Cre-, Flp- and Nigri-recombinase dependent reporter mouse line, Ai213. The delivery of three enhancer viruses driving these recombinases via a single retroorbital injection into a single Ai213 transgenic mouse results in labeling of three different neuronal classes/subclasses in the same brain tissue. This approach combines unprecedented flexibility with specificity for investigation of cell types in the mouse brain and beyond.

neuroscience↗

bioRxiv2018

Chromatin conformation analysis of primary patient tissue using a low input Hi-C method

Chromatin conformation constitutes a fundamental level of eukaryotic genome regulation. However, our ability to examine its biological function and role in disease is limited by the large amounts of starting material required to perform current experimental approaches. Here, we present Low-C, a Hi-C method for low amounts of input material. By systematically comparing Hi-C libraries made with decreasing amounts of starting material we show that Low-C is highly reproducible and robust to experimental noise. To demonstrate the suitability of Low-C to analyse rare cell populations, we produce Low-C maps from primary B-cells of a diffuse large B-cell lymphoma patient. We detect a common reciprocal translocation t (3;14) (q27;q32) affecting the BCL6 and IGH loci and abundant local structural variation between the patient and healthy B-cells. The ability to study chromatin conformation in primary tissue will be fundamental to fully understand the molecular pathogenesis of diseases and to eventually guide personalised therapeutic strategies.

genomics↗

bioRxiv2017

A suite of transgenic driver and reporter mouse lines with enhanced brain cell type targeting and functionality

Modern genetic approaches are powerful in providing access to diverse types of neurons within the mammalian brain and greatly facilitating the study of their function. We here report a large set of driver and reporter transgenic mouse lines, including 23 new driver lines targeting a variety of cortical and subcortical cell populations and 26 new reporter lines expressing an array of molecular tools. In particular, we describe the TIGRE2.0 transgenic platform and introduce Cre-dependent reporter lines that enable optical physiology, optogenetics, and sparse labeling of genetically-defined cell populations. TIGRE2.0 reporters broke the barrier in transgene expression level of single-copy targeted-insertion transgenesis in a wide range of neuronal types, along with additional advantage of a simplified breeding strategy compared to our first-generation TIGRE lines. These novel transgenic lines greatly expand the repertoire of high-precision genetic tools available to effectively identify, monitor, and manipulate distinct cell types in the mouse brain.

neuroscience↗

bioRxiv2017

The Developing Human Connectome Project: a Minimal Processing Pipeline for Neonatal Cortical Surface Reconstruction

The Developing Human Connectome Project (dHCP) seeks to create the first 4-dimensional connectome of early life. Understanding this connectome in detail may provide insights into normal as well as abnormal patterns of brain development. Following established best practices adopted by the WU-MINN Human Connectome Project (HCP), and pioneered by FreeSurfer, the project utilises cortical surface-based processing pipelines. In this paper, we propose a fully automated processing pipeline for the structural Magnetic Resonance Imaging (MRI) of the developing neonatal brain. This proposed pipeline consists of a refined framework for cortical and sub-cortical volume segmentation, cortical surface extraction, and cortical surface inflation, which has been specifically designed to address considerable differences between adult and neonatal brains, as imaged using MRI. Using the proposed pipeline our results demonstrate that images collected from 465 subjects ranging from 28 to 45 weeks post-menstrual age (PMA) can be processed fully automatically; generating cortical surface models that are topologically correct, and correspond well with manual evaluations of tissue boundaries in 85% of cases. Results improve on state-of-the-art neonatal tissue segmentation models and significant errors were found in only 2% of cases, where these corresponded to subjects with high motion. Downstream, these surfaces will enhance comparisons of functional and diffusion MRI datasets, supporting the modelling of emerging patterns of brain connectivity.

neuroscience↗