Biology subjects

Saur, D.

Publications and source records attributed to Saur, D..

At least 19 recordsLinked to original sources

bioRxiv2026

Changes in Neural Dynamics of Brain Activity and Connectivity Independently Predict Post-Stroke Aphasia Recovery

Post-stroke language recovery involves reorganization of left-hemisphere language and bilateral domain-general multiple-demand networks. Neuroimaging predictors of recovery are widely used, yet, they are often grouped into broad predictor families, limiting clinical translation and the identification of specific therapeutic targets. Here, we assess brain region-specific neural predictors of recovery using task-related activity and connectivity within a multivariate, cross-validated predictive framework. Forty-seven patients with aphasia were examined longitudinally in the acute, subacute, and chronic phases after ischemic stroke using a sentence comprehension paradigm during functional neuroimaging, with regions of interest spanning language and multiple-demand networks. Confound-controlled multivariate regularized regression with feature ablation tested whether predictor families explained language recovery beyond lesion, age, and aphasia severity, and identified the most relevant region-specific predictors. Early recovery was independently predicted by acute and subacute activity and connectivity, whereas later improvement was predicted by activity alone. Subacute connectivity from multiple-demand to language regions predicted early recovery, while acute multiple-demand network activity predicted long-term outcomes. Later subacute-to-chronic recovery was instead predicted by subacute and chronic activity in bilateral inferior frontal regions. These findings identify phase-specific functional biomarkers of aphasia recovery beyond traditional clinical measures, highlighting multiple-demand and inferior frontal regions as candidate targets for phase-adapted neurostimulation approaches.

neuroscience↗

bioRxiv2026

MYC/MIZ1 suppression of lysosomal protein degradation drives immune evasion in pancreatic ductal adenocarcinoma

The MYC oncoprotein promotes immune evasion of pancreatic ductal adenocarcinoma (PDAC), but the underlying molecular mechanisms are not fully understood. Here we show that MYC protects PDAC tumors from CD4+ T cell-dependent elimination. Single cell sequencing shows that MYC suppression in tumor cells increases amino acid availability and broadly activates amino acid-responsive gene expression programs in immune cell populations. This occurs because MYC-driven uptake depletes free amino acids from tumor interstitial fluid and plasma, while MYC compromises macropinocytosis and autophagy, both of which depend on lysosomal protein degradation. MYC engages the POZ/BTB transcription factor MIZ1 to suppress lysosomal genes regulated by the TFE3/TFEB/MITF network or by free MIZ1, thereby inhibiting lysosomal protein degradation. An orthogonal genetic model enabling transient, selective inhibition of amino acid uptake in tumor cells recapitulates the effects of MYC depletion on amino acid levels in the tumor microenvironment and induces complete, CD4+ T cell-dependent tumor eradication with long-term survival. We propose that MYC-mediated, cell-autonomous disruption of lysosome function coupled to non-cell-autonomous protection from immune clearance allows MYC-low cells to benefit from MYC-high neighbors, such that intratumoral heterogeneity in MYC expression confers a selective advantage to the entire tumor. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=141 SRC="FIGDIR/small/740267v1_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@140d2ccorg.highwire.dtl.DTLVardef@cf5f1borg.highwire.dtl.DTLVardef@6d132aorg.highwire.dtl.DTLVardef@10535e6_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2026

Microbial Invasion and Immunosuppression Drives Adenoma Progression in Early Colorectal Cancer Development

Several inherited predispositions to colorectal cancer exist, most notably familial adenomatous polyposis (FAP), which typically involves a germline loss-of-function mutation in one APC allele. A second hit in APC or related loci leads to aberrant Wnt signalling, triggering adenoma formation with near-complete penetrance. Yet, substantial variability in disease onset and severity, even among siblings with identical APC germline mutations, implicates environmental modifiers. Emerging evidence points to the gut microbiome as a critical regulator of adenoma initiation and progression, particularly in early-onset CRC. Here, we show that bacterial invasion is associated with neutrophil immunosuppression, T-cell exclusion and adenoma progression in a porcine model of FAP. Longitudinal mapping of progressing and regressing polyps using single-cell RNA sequencing, spatial transcriptomics and integrated microbiome profiling resolved the cellular and microbial architecture underlying these divergent lesion states. Single-cell RNA-seq identified 35 cell subpopulations and showed that regressing polyps are enriched for central-memory CD4+ T cells, cytotoxic CD8+ T cells and inflammatory neutrophils, whereas progressing polyps contain immunosuppressive/PD-L1-associated neutrophils, regulatory and dysfunctional T cells. Spatial transcriptomics with a custom host panel and targeted bacterial probes linked bacterial-high adenomatous regions to immunosuppressive neutrophil niches and T cell exclusion, while regressing lesions showed predominantly lumen-adjacent bacterial localization and spatially organized immune surveillance. These results provide a spatially resolved map of cellular and microbial organisation in early colorectal polyp progression and regression and reveal a microbiome-driven, neutrophil-mediated mechanism of early tumour progression with implications for CRC interception. Grant support: This study was funded by the German Research Foundation (DFG) through SFB1371 "Microbiome signature" (Project no. 395357507; TF, DS, FE, DH) and by the German Ministry for Research and Education (BMBF) through Mi-EOCRC consortium project (Project no. 01KD2102D; KF and DH).

cancer biology↗

bioRxiv2026

Distinct colorectal cancer genotypes shape microbial ecosystems and reveal stage-specific microbiota dependencies

The gut microbiota has emerged as an important modifier of colorectal cancer (CRC), yet how tumor genotype influences host-microbiota interactions and whether microbial signals are required throughout tumor progression remain unclear. Here, we combined genetically engineered mouse models, microbial multi-omics and a germ-free-compatible orthotopic transplantation system to define the functional contribution of the microbiota across distinct stages of CRC evolution. Across multiple CRC genotypes, we identified tumor-associated microbial ecosystem states characterized by distinct taxonomic, functional and metabolic configurations. To directly test their contribution to tumor progression, we established the first orthotopic CRC transplantation platform compatible with long-term experimentation in germ-free mice, enabling side-by-side comparison of genetically identical tumors in the presence or absence of microbiota. Using organoids spanning low-grade adenoma, high-grade adenoma and adenocarcinoma states, we found that the dependence on the presence of microbiota progressively decreases during malignant evolution. Whereas adenoma-derived organoids exhibited profound dependence on microbial exposure and failed or were markedly impaired in establishing tumors under germ-free conditions, adenocarcinoma organoids engrafted and metastasized in both germ-free and specific pathogen-free (SPF) hosts. Unexpectedly, comprehensive histological, immunological and transcriptomic analyses revealed highly similar tumor ecosystem states in advanced tumors arising under both microbial conditions, arguing against broad immune or epithelial defects as a primary explanation for the observed phenotype. Together, our findings demonstrate that distinct oncogenic drivers establish specific microbial ecosystem states and reveal a stage-dependent role of the microbiota during colorectal tumorigenesis. Whereas microbial signals are critical during early stages of tumor progression and may promote malignant transformation, advanced tumors progressively acquire microbiota-independent growth programs and increasingly impose genotype-specific ecological signatures on the surrounding microbial ecosystem. More broadly, we establish a versatile framework for the causal dissection of tumor-microbiota interactions in cancer.

cancer biology↗

bioRxiv2026

Modeling pancreatic cancer tumor stroma co-evolution in an in ovo model

Pancreatic ductal adenocarcinoma (PDAC) is characterized by a dense, desmoplastic microenvironment that drives disease progression, yet conventional models fail to capture this complex tumor-stroma coevolution. Here, we utilize the chick chorioallantoic membrane (CAM) platform to investigate tumor-stroma interactions using murine PDAC cell lines and patient-derived organoids (PDOs). Integrating single-cell RNA sequencing and spatial transcriptomics, we show that the CAM microenvironment supports the emergence of complex tumor ecosystems while preserving patient-specific characteristics. Within five days, in ovo tumors faithfully recapitulated the structural and molecular features of parental tumors. Histological analysis revealed the rapid recruitment and spatial organization of heterogeneous host cancer-associated fibroblast (CAF) populations, showcasing distinct myofibroblastic and inflammatory stromal states. Crucially, the model preserved intrinsic tumor heterogeneity and permitted functional interrogation of subtype-specific extracellular matrix remodeling and metastatic dissemination. Together, our findings demonstrate that the CAM provides a highly permissive niche for tumor-stroma coevolution. As a rapid, scalable, and biologically relevant platform, this in ovo model offers a powerful approach for studying stromal composition, metastatic progression, and patient-specific tumor biology in pancreatic cancer.

cancer biology↗

bioRxiv2026

Cellpin enables reference-based imputation and denoising of spatial transcriptomes

Spatially resolved transcriptomics enables gene expression profiling within tissue architecture, but targeted panels leave much of the transcriptome unmeasured and spatial artifacts such as RNA diffusion and segmentation errors introduce technical noise. These limitations necessitate computational imputation and denoising, yet existing methods typically incorporate spatial measurements during training, limiting scalability and risking the embedding of technology-specific artifacts into learned representations. To address this, we present cellpin, a variational autoencoder trained exclusively on single-cell RNA sequencing data, using teacher-student latent distillation and noise-simulating augmentations to jointly impute unmeasured genes and denoise spatial profiles without requiring cross-modality alignment. Benchmarked against six methods across multiple paired datasets, cellpin achieves superior held-out gene prediction while scaling efficiently to atlas-size references and multi-sample cohorts. In full-transcriptome Atera data, cellpin reduces residual spatial noise and improves cell-state resolution, providing a scalable and principled foundation for biological discovery from spatial transcriptomics data.

bioinformatics↗

bioRxiv2026

Pan-cancer virtual spatial transcriptomics from routine histology with Phoenix

Spatial transcriptomics links gene expression to tissue architecture, providing a mechanistic view of cellular organization. Yet existing datasets cover few donors and miss the complexity of human disease. Experimental costs remain prohibitive, and large-scale profiling is impractically slow for population-level studies. Accurate computational methods are urgently needed. Predicting gene expression from standard histology, however, remains an open problem, as current approaches transfer poorly to unseen cohorts and diseases. Here, we present Phoenix, a (latent) flow matching generative model that infers pan-cancer spatially resolved single-cell gene expression with high accuracy. Phoenix analyzes treatment response in silico: Applied to 763 head and neck cancer patients, it identified three new spatial biomarkers that we validated across two cancers (breast cancer, n = 84; ovarian cancer, n = 157) and treatment regimens (platinum, trastuzumab). Phoenix generalizes beyond carcinomas: In a large sarcoma cohort (802 tissue microarray cores), it accurately predicted cell-type-specific signatures in held-out samples and captured chemotherapy-induced immune remodeling. Phoenix also extends across species: In a mouse model, it accurately predicted the expression of pancreatic cancer lineage markers and the mutant mKras^G12D allele in silico. In total, we evaluated Phoenix on over 10,000 patients. Our results establish virtual spatial transcriptomics as a scalable framework for studying tissue organization, therapeutic response, and disease mechanisms.

bioinformatics↗

bioRxiv2026

Cross-species single-cell atlases chart progression, therapy-driven remodelling and immune evasion in pancreatic cancer

Pancreatic ductal adenocarcinoma (PDAC) is typically diagnosed at advanced stages, yet single-cell datasets that capture late-stage and treated disease remain sparse, hindering progress in understanding tumour heterogeneity and therapy resistance. Here, we have generated integrated single-cell transcriptomic atlases of human and mouse PDAC to define the cellular and molecular landscape of the disease, from early to advanced and metastatic stages, including post-treatment disease, and to enable direct cross-species comparison. Using scANVI to harmonize 16 human studies comprising 257 donors and representative mouse models (101 tumours), we compiled over 1.6 million cells and established a four-level hierarchical taxonomy of more than 60 distinct cell states spanning malignant, stromal, immune, endothelial, adipose, exocrine and endocrine compartments. We resolve ten malignant programmes linked to progression and uncover rare immune phenotypes, including CD4CD8 double-positive T cells that remain poorly characterized in PDAC. Notably, we show that radiotherapy (RT) exposure is associated with enrichment of an EMT-persistent malignant state and an immunosuppressive microenvironment characterized by expansion of tumour-associated endothelium, depletion of intratumoral T cells and heightened laminin-CD44 signalling, with RT-associated genes linked to adverse prognosis in independent cohorts. Cross-species mapping reveals that orthotopic syngeneic allografts more faithfully recapitulate the cellular diversity and EMT-enriched states of advanced human PDAC, underrepresented in autochthonous genetically engineered models, with differences driven primarily by cell-type composition rather than pathway divergence. Together, these atlases and pretrained models provide a broadly accessible reference for benchmarking PDAC model fidelity and for interrogating mechanisms of tumour progression, microenvironmental remodelling and therapy response and resistance.

cancer biology↗

bioRxiv2026

Spatial Bias in Lesion Network Mapping Is Connectome-Independent

Lesion network mapping (LNM) is increasingly used to link focal brain lesions to distributed functional networks. Recent work has raised concerns that LNM results may be spatially biased by dominant features of the normative connectome. If this were the case, three testable predictions would follow: (i) a consistent spatial pattern of false positives across LNM studies, (ii) that this pattern can be consistently explained by intrinsic connectome organization, and (iii) that symptom-associated LNM findings preferentially occur in regions with high spatial bias. We tested these predictions across three independent LNM datasets (n = 49/101/200), evaluating each prediction in all cohorts. Spatial bias maps derived from 4,000,000 random permutations under the null hypothesis showed minimal correspondence across cohorts (R2 = 0.4-0.8%), indicating strong cohort specificity. Moreover, dominant connectome features--captured by the first 10 principal components of connectivity profiles from 1,000 atlas regions--did not systematically explain these bias maps. Finally, symptom-associated results showed no enrichment in high-bias regions. Together, these findings provide strong evidence that spatial bias in LNM is not driven by dominant connectome features. With appropriate inferential statistics and rigorous study design, LNM remains a valid approach for mapping symptom-related brain networks.

neuroscience↗

bioRxiv2024

Spatial neglect after subcortical stroke: sometimes a cortico-cortical disconnection syndrome

Background and ObjectivesSpatial neglect is commonly attributed to lesions of a predominantly right-hemispheric cortical network. Although spatial neglect was also repeatedly observed after lesions to the basal ganglia and the thalamus, many anatomical network models omit these structures. We investigated if disruption of functional or structural connectivity can explain spatial neglect in subcortical stroke. MethodsWe retrospectively investigated data of first-ever, acute stroke patients with right-sided lesions of the basal ganglia (n = 27) or the thalamus (n = 16). Based on lesion location, we estimated i) functional connectivity via lesion-network mapping with normative resting state fMRI data, ii) structural white matter disconnection and iii) tract-wise disconnection of association fibres based on normative tractography data to investigate the association of spatial neglect and disconnection measures. ResultsApart from very small clusters of functional disconnection observed in inferior/middle frontal regions in lesion-network symptom mapping for basal ganglia lesions, our analyses found no evidence of functional or structural subcortico-cortical disconnection. Instead, the multivariate consideration of lesion load to several association fibres predicted the occurrence of spatial neglect (p = 0.0048; AUC = 0.76), which were the superior longitudinal fasciculus, inferior occipitofrontal fasciculus, superior occipitofrontal fasciculus, and the uncinate fasciculus. ConclusionDisconnection of long (cortico-cortical) association fibres can explain spatial neglect in subcortical stroke. Like the competing theory of remote cortical hypoperfusion, this mechanism does not require the assumption of a genuine role for subcortical grey matter structures in spatial neglect.

neuroscience↗

bioRxiv2023

The pharmacoepigenomic landscape of cancer cell lines reveals the epigenetic component of drug sensitivity

Aberrant DNA methylation accompanies genetic alterations during oncogenesis and tumour homeostasis and contributes to the transcriptional deregulation of key signalling pathways in cancer. Despite increasing efforts in DNA methylation profiling of cancer patients, there is still a lack of epigenetic biomarkers to predict treatment efficacy. To address this, we analysed 721 cancer cell lines across 22 cancer types treated with 453 anti-cancer compounds. We systematically detected the predictive component of DNA methylation in the context of transcriptional and mutational patterns, i.e., in total 19 DNA methylation biomarkers across 17 drugs and five cancer types. DNA methylation constituted drug sensitivity biomarkers by mediating the expression of proximal genes, thereby enhancing biological signals across multi-omics data modalities. Our method reproduced anticipated associations, and in addition, we found that the NEK9 promoter hypermethylation may confer sensitivity to the NEDD8-activating enzyme (NAE) inhibitor pevonedistat in melanoma through downregulation of NEK9. In summary, we envision that epigenomics will refine existing patient stratification, thus empowering the next generation of precision oncology.

cancer biology↗

bioRxiv2023

ZEB1-dependent modulation of fibroblast polarization governs inflammation and immune checkpoint blockade sensitivity in colorectal cancer

The EMT-transcription factor ZEB1 is heterogeneously expressed in tumor cells and in cancer-associated fibroblasts (CAFs) in colorectal cancer (CRC). While ZEB1 in tumor cells regulates metastasis and therapy resistance, its role in CAFs is largely unknown. Combining fibroblast-specific Zeb1 deletion with immunocompetent mouse models of CRC, we observe that inflammation-driven tumorigenesis is accelerated, whereas invasion and metastasis in sporadic cancers is reduced upon fibroblast-specific loss of Zeb1. Single-cell transcriptomics, histological and in vitro characterization reveal a crucial role in CAF polarization, promoting myofibroblastic features whilst restricting inflammatory activation. Zeb1 deficiency impairs collagen deposition and CAF barrier function but increases cytokine production, jointly promoting lymphocyte recruitment and immune checkpoint activation. Strikingly, the Zeb1-deficient CAF repertoire sensitizes to immune checkpoint inhibition, pointing to a therapeutic opportunity of targeting ZEB1 in CAFs and its usage as a prognostic biomarker. Collectively, we demonstrate that ZEB1-dependent plasticity of CAFs suppresses anti-tumor immunity and promotes metastasis.

cancer biology↗

bioRxiv2022

Facilitatory stimulation of the pre-SMA in healthy aging has distinct effects on task-based activity and connectivity

BackgroundThe continuous decline of executive abilities with age is mirrored by increased neural activity of domain-general networks during task processing. So far, it remains unclear how much domain-general networks contribute to domain-specific processes such as language when cognitive demands increase. The current neuroimaging study explored the potential of intermittent theta-burst stimulation (iTBS) over a domain-general hub to enhance executive and semantic processing in healthy middle-aged to older adults. MethodsWe implemented a cross-over within-subject study design with three task-based neuroimaging sessions per participant. Using an individualized stimulation approach, we stimulated each participant once with effective and once with sham iTBS over the pre-supplementary motor area (pre-SMA), a region of domain-general control. Subsequently, task-specific stimulation effects were assessed in functional MRI using a semantic and a non-verbal executive task with varying cognitive demand. ResultsEffective stimulation increased activation relative to sham stimulation only during semantic processing in visual and dorsal attention networks. Further, iTBS induced increased functional connectivity in task-specific networks for semantic and executive conditions with high cognitive load. Notably, stimulation-induced changes in activation and connectivity related differently to behavior: While increased activation of the parietal dorsal attention network was linked to poorer semantic performance, its enhanced coupling with the pre-SMA was associated with more efficient semantic processing. ConclusionsiTBS modulates networks in a task-dependent manner and generates effects at regions remote to the stimulation site. These neural changes are linked to more efficient semantic processing, which underlines the general potential of network stimulation approaches in cognitive aging.

neuroscience↗

bioRxiv2022

Thalamocortical networks involved in Pusher Syndrome

Indirect quantification of functional and structural disconnection increases the knowledge derived from focal brain lesions by inferring subsequent brain network damage from the respective lesion. We applied both measures to a sample of 124 stroke patients to investigate brain disconnection in pusher syndrome - a disorder characterized by a disturbed perception of ones own upright body posture. Our results suggest a hub-like function of the posterior and lateral portions of the thalamus in the perception of ones own postural upright and identified dysfunction in a thalamo-cortical network as one likely cause of pusher syndrome. Lesion network-symptom-mapping investigating functional disconnection indicated cortical diaschisis in cerebellar, frontal, parietal, occipital, and temporal areas in patients with thalamic lesions suffering from pusher syndrome, but there was no evidence for functional diaschisis in cortical stroke and no evidence for the convergence of thalamic and cortical lesions onto a common functional network. Structural disconnectivity mapping identified several thalamo-cortical disconnections. Many of the thalamic and cortical regions disconnected by lesions that lead to pusher behavior correspond to previously reported lesion sites associated with pusher syndrome. Thus, while the presence of both, isolated thalamic and cortical lesions in context with pusher behavior has been reported previously and led to the conclusion that the correct estimation of ones own postural upright might depend on a thalamo-cortical network, our analyses offer the first evidence for a direct thalamo-cortical (or cortico-thalamic) interconnection and, more importantly, shed light on the location of the respective thalamo-cortical disconnections.

neuroscience↗

bioRxiv2022

Age-related reorganization of functional network architecture for language processing

Semantic memory is a fundamental human ability which is central to communication. Although it is usually well preserved in healthy aging, memory problems in verbal communication due to slowed access and retrieval processes are a common complaint with increasing age. So far, the neural bases of this paradox remain poorly understood. The current neuroimaging study investigated age differences in the functional network architecture during semantic word retrieval in young and older adults. Using group spatial independent component analysis, we defined functional networks for verbal semantic fluency. Combining task-based functional connectivity, graph theory and cognitive measures of fluid and crystallized intelligence, our findings show age-accompanied large-scale network reorganization even when older adults have intact word retrieval abilities. In particular, functional networks of older adults were characterized by reduced decoupling between systems, reduced segregation and efficiency, and a larger number of hub regions relative to young adults. Exploring the predictive utility of these age-related changes in network topology revealed high, albeit less efficient, performance for older adults whose brain graphs showed stronger dedifferentiation and reduced distinctiveness. Our results extend theoretical accounts on neurocognitive aging by revealing the compensational potential of the commonly reported pattern of network dedifferentiation when older adults can rely on their prior knowledge for successful task processing. However, we also demonstrate the limitations of such compensatory reorganization processes and demonstrate that a youth-like network architecture in terms of balanced integration and segregation is associated with more economical processing. Significance StatementCognitive aging is associated with widespread neural reorganization processes in the human brain. However, the behavioral impact of such reorganization is not well understood. Here, we used taskbased fMRI to demonstrate a large-scale reorganization of brain networks in older adults even when their semantic abilities are intact. In particular, functional networks of older adults were characterized by increased coupling between different systems, reduced segregation and efficiency, and a larger number of hub regions relative to young adults. Associating these changes with behavior revealed high, albeit less efficient, performance for networks in older adults showing stronger dedifferentiation and reduced distinctiveness. Our results highlight the compensatory potential of network reconfiguration with age, but also reveal the limitations of such reorganization processes.

neuroscience↗

bioRxiv2022

spongEffects: ceRNA modules offer patient-specific insights into the miRNA regulatory landscape

MotivationCancer is one of the leading causes of death worldwide. Despite significant improvements in prevention and treatment, mortality remains high for many cancer types. Hence, innovative methods that use molecular data to stratify patients and identify biomarkers are needed. Promising biomarkers can also be inferred from competing endogenous RNA (ceRNA) networks that capture the gene-miRNA gene regulatory landscape. Thus far, the role of these biomarkers could only be studied globally but not in a sample-specific manner. To mitigate this, we introduce spongEffects, a novel method that infers subnetworks (or modules) from ceRNA networks and calculates patient- or sample-specific scores related to their regulatory activity. ResultsWe show how spongEffects can be used for downstream interpretation and machine learning tasks such as tumor classification and for identifying subtype-specific regulatory interactions. In a concrete example of breast cancer subtype classification, we prioritize modules impacting the biology of the different subtypes. In summary, spongEffects prioritizes ceRNA modules as biomarkers and offers insights into the miRNA regulatory landscape. Notably, these module scores can be inferred from gene expression data alone and can thus be applied to cohorts where miRNA expression information is lacking. Availabilityhttps://bioconductor.org/packages/devel/bioc/html/SPONGE.html Contactmarkus.daniel.hoffmann@tum.de; markus.list@tum.de Supplementary informationSupplementary data are available at Bioinformatics online.

systems biology↗

bioRxiv2021

Stromal HIF2 Regulates Immune Suppression in the Pancreatic Cancer Microenvironment

Background & AimsPancreatic ductal adenocarcinoma (PDAC) has a hypoxic, immunosuppressive stroma, which contributes to its resistance to immune checkpoint blockade therapies. The hypoxia-inducible factors (HIFs) mediate the cellular response to hypoxia, but their role within the PDAC tumor microenvironment remains unknown. MethodsWe used a dual recombinase mouse model to delete Hif1 or Hif2 in -smooth muscle actin (SMA)-expressing cancer-associated fibroblasts (CAFs) arising within spontaneous pancreatic tumors. The effects of CAF-Hif2 expression on tumor progression and composition of the tumor microenvironment were evaluated by Kaplan-Meier analysis, quantitative real-time polymerase chain reaction, histology, immunostaining, and by both bulk and single-cell RNA sequencing. CAF-macrophage crosstalk was modeled ex vivo using conditioned media from CAFs after treatment with hypoxia and PT2399, a HIF2 inhibitor currently in clinical trials. Syngeneic flank and orthotopic PDAC models were used to assess whether HIF2 inhibition improves response to immune checkpoint blockade. ResultsCAF-specific deletion of HIF2, but not HIF1, suppressed PDAC tumor progression and growth, and improved survival of mice by 50% (n = 21-23 mice/group, Log-rank P = 0.0009). Deletion of CAF-HIF2 modestly reduced tumor fibrosis and significantly decreased the intratumoral recruitment of immunosuppressive M2 macrophages and regulatory T cells. Treatment with the clinical HIF2 inhibitor PT2399 significantly reduced in vitro macrophage chemotaxis and M2 polarization, and improved tumor responses to immunotherapy in both syngeneic PDAC mouse models. ConclusionsTogether, these data suggest that stromal HIF2 is an essential component of PDAC pathobiology and is a druggable therapeutic target that could relieve tumor microenvironment immunosuppression and enhance immune responses in this disease.

cancer biology↗

bioRxiv2021

ExoBow: A transgenic strategy to study CD63 exosomes in vivo

Exosomes are described as central players in a myriad of biological processes. However, the available methodologies to study their function in complex biological systems in vivo are still very limited. The biodistribution of endogenously produced exosomes, the ability to trace their spontaneous flow in order to identify the cell types they interact with, remains a major challenge. New tools to identify comprehensive networks of communication established by exosomes originated in distinct cell types in vivo, are fundamental for a better understanding of their biology. Here, we describe the development of a genetically engineered mouse model that allows the expression of the mouse CD63 exosomal marker fused with one (monocolor) or up to four fluorescent proteins (multireporter), the ExoBow. The genetic design of the ExoBow transgene allows the conditional expression of the reporters in any tissue/cell-type in an inducible or non-inducible fashion. In addition, communication mediated by CD63 positive (CD63+) exosomes can be identified amongst the same tissue/cell types using the multireporter version of the model, in order to map intra-organ/tissue communication. We demonstrate the applicability of the ExoBow transgene in normal physiological conditions and in the context of cancer, using pancreas as a working model. The ExoBow comprises a unique strategy to identify intra- and inter-organ/cell-type communication mediated by CD63+ exosomes. We believe this tool will contribute for a better understanding of the complex interactions occurring in vivo that underly the biology of exosomes in health and disease.

cell biology↗