Biology subjects

Schmid, R. M.

Publications and source records attributed to Schmid, R. M..

9 recordsLinked to original sources

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

Prolonged TGF-β locks NK cells in a dysfunctional state through persistent epigenetic remodeling of IRF, T-bet and EOMES binding sites

TGF-{beta} signaling is a major regulator of immune cell differentiation and function, yet whether prolonged signaling can durably imprint dysfunctional immune states independently of continued pathway engagement remains unclear. Here, we identify signal duration as a critical determinant of human natural killer (NK) cell fate: short-term TGF-{beta} exposure induces largely reversible transcriptional, chromatin and functional changes, whereas prolonged exposure establishes persistent effector dysfunction independent of continued signaling. Mechanistically, prolonged TGF-{beta} drives durable loss of chromatin accessibility at effector-associated regulatory elements, particularly those enriched for IRF, EOMES, and T-bet binding motifs, resulting in stable restriction of NK cell effector programs despite reversibility of active histone marks. In contrast, tissue residency-associated programs remain largely reversible, revealing that distinct NK cell fate programs differ fundamentally in their susceptibility to epigenetic fixation downstream of the same cytokine signal. SMAD4 CUT&RUN and knockout experiments further demonstrate that canonical TGF-{beta} signaling acts primarily through rewiring of upstream transcriptional regulatory networks rather than direct targeting of effector loci. Finally, NK cells from patients with hepatocellular carcinoma recapitulate key functional and epigenetic features of the persistent TGF-{beta}-associated state defined in vitro. Together, these findings identify signal duration as a critical determinant of TGF-{beta}-driven cell fate and demonstrate that prolonged TGF-{beta} exposure can induce epigenetically stabilized dysfunctional states that persist after signal withdrawal, with important implications for therapeutic strategies aimed at reversing chronic TGF-{beta}-mediated dysfunction.

immunology↗

bioRxiv2025

Chronic stress facilitates behavioral engagement and alters lateral habenula activity during flexible decision making in a sex-dependent manner

The ability to integrate feedback and flexibly adjust behavior under shifting environmental demands is required to optimize decision-making strategies. Clinical and preclinical data indicate that individuals with stress-related disorders and rodents exposed to chronic stress exhibit impaired behavioral flexibility. The lateral habenula (LHb) has emerged as a key brain region contributing to the effects of stress on cognitive performance. However, the extent to which the LHb is recruited to fine-tune decision-making strategies, as well as the impacts of chronic stress on LHb recruitment during task performance, remain largely unknown. To this end, we used a three-week model of chronic unpredictable stress (CUS) and performed in vivo fiber photometry to investigate Ca2+ transients in LHb neurons during an attentional set-shifting task in adult male and female Sprague Dawley rats (n=7-12/sex/group). We found that CUS exposure did not significantly impair behavioral flexibility. Rather, CUS-exposed rats made fewer omissions and exhibited shorter response latencies compared to controls, suggesting enhanced task engagement. We also observed sex differences in LHb Ca2+ activity. In control animals, we found that male rats showed stronger LHb signal prior to decision making, and greater activation following trial outcome than females. These differences were normalized by CUS, resulting in similar signaling patterns across sexes. Altogether, these findings reveal that chronic stress alters LHb activity in a sex-dependent manner without overtly impairing behavioral flexibility, thereby underscoring the importance of the LHb in decision making under stressful conditions. HighlightsO_LIChronic stress decreased response latency without impairing behavioral flexibility C_LIO_LIMale rats displayed greater inhibition of LHb activity prior to decision making C_LIO_LIChronic stress abolished sex differences in LHb activity during decision making C_LI

neuroscience↗

bioRxiv2025

c-Rel drives pancreatic cancer metastasis through Fibronectin-Integrin signaling-induced isolation stress resistance and EMT activation

Pancreatic ductal adenocarcinoma remains one of the deadliest malignancies, with limited treatment options and a high recurrence rate. Recurrence happens often with metastasis, for which cancer cells must adapt to isolation stress to successfully colonize distant organs. While the fibronectin-integrin axis has been implicated in this adaptation, its regulatory mechanisms require further elaboration. Here, we identify c-Rel as an oncogenic driver in PDAC, promoting epithelial-to-mesenchymal transition (EMT) plasticity, extracellular matrix (ECM) remodeling, and resistance to isolation stress. Mechanistically, c-Rel directly regulates fibronectin (Fn1) and CD61 (itgb3) transcription, enhancing cellular plasticity and survival under anchorage-independent conditions. Fibronectin is not essential for EMT, but its absence significantly impairs metastatic colonization, highlighting a tumor-autonomous role for FN1 in isolation stress adaptation. These findings establish c-Rel as a key regulator of PDAC metastasis by controlling circulating tumor cell (CTC) niche and survival, suggesting that targeting the c-Rel-fibronectin-integrin axis could provide new therapeutic strategies to mitigate disease progression and recurrence.

cancer biology↗

bioRxiv2023

Ras-dependent activation of BMAL2 regulates hypoxic metabolism in pancreatic cancer

KRAS is the archetypal oncogenic driver of pancreatic cancer. To identify new modulators of KRAS activity in human pancreatic ductal adenocarcinoma (PDAC), we performed regulatory network analysis on a large collection of expression profiles from laser capture microdissected samples of PDAC and benign controls. We discovered that BMAL2, a member of the PAS family of transcription factors, promotes tumor initiation, progression, and post-resection survival, and is highly correlated with KRAS activity. Functional analysis of BMAL2 target genes suggested a role in regulating the hypoxia response, a hallmark of PDAC. Knockout of BMAL2 in multiple human PDAC cell lines reduced cancer cell viability, invasion, and glycolysis, leading to broad dysregulation of cellular metabolism, particularly under hypoxic conditions. We find that BMAL2 directly regulates hypoxia-responsive target genes and is necessary for the stabilization of HIF1A under low oxygen conditions, while simultaneously destabilizing HIF2A. Notably, in vivo xenograft studies demonstrated that BMAL2 loss significantly impairs tumor growth and reduces tumor volume, underscoring its functional importance in tumor progression. We conclude that BMAL2 is a master transcriptional regulator of hypoxia responses in PDAC that works downstream of KRAS signaling, possibly serving as a long-sought molecular switch that distinguishes HIF1A- and HIF2A-dependent modes of hypoxic metabolism. Statement of SignificanceWe annotate the landscape of KRAS-associated transcriptional drivers of pancreatic cancer initiation, progression, and overall survival, leading to the identification of BMAL2 as a novel regulator of hypoxic metabolism. BMAL2 helps execute the oncogenic transcriptional programs of KRAS and serves as a long-sought switch between HIF1A- and HIF2A-dependent modes of hypoxic metabolism.

cancer biology↗

bioRxiv2022

Intestinal myofibroblasts regulate intestinal epithelial cell plasticity via YAP/TAZ

Intestinal stromal cells play a key role as the crypt niche cells during epithelial homeostasis and tumor initiation. However, the underlying cellular and molecular mechanisms remain unclear. We developed various types of three-dimensional (3D) tissue culture models to culture small intestinal myofibroblasts (SI MFs) together with enteroids. SI MFs significantly enhanced self-renewal, lumen formation and survival of enteroids, that was mediated via a paracrine mechanism in a Wnt-independent manner. Such co-cultured enteroids resembled SI organoids derived from Apc+/1638N tumors. Microarray analysis showed upregulation of genes associated with YAP signaling in enteroids co-cultured with SI MFs, which was confirmed by protein quantification by mass spectrometry and could be correlated with findings from human colorectal tumor specimens. Mass spectrometric analysis of conditioned media and inhibitor studies pointed to a role for TGF-{beta} in the SI MF-SI epithelium cross-talk. Altogether, utilizing different 3D stroma-epithelium co-culture models, we demonstrate here that SI MFs have the potential to induce a tumor-like phenotype in the intestinal crypts via a paracrine mechanism, that involves YAP and TGF-{beta}, but not canonical Wnt signaling.

cell biology↗

bioRxiv2022

Gut microbial disruption in critically ill patients with COVID-19 associated pulmonary aspergillosis

ObjectivesCOVID-19 disease can be exacerbated by Aspergillus superinfection (CAPA). The causes of CAPA are not yet fully understood. Recently, alterations in the gut microbiome have been associated with a complicating course and increasing severity of COVID-19 disease, most likely via immunological mechanisms. Aim of this study was to investigate a potential association between severe CAPA and alterations in the gut and bronchial microbiota. MethodsWe performed 16S rRNA gene amplicon sequencing of stool and bronchial samples from a total of 16 COVID-19 patients with CAPA and 26 patients without CAPA. All patients were admitted to the intensive care unit. Results were carefully tested for potential influences on the microbiome during hospitalization. ResultsWe found that late in COVID-19 disease, CAPA patients exhibited a trend towards reduced gut microbial diversity. Furthermore, late stage CAPA disease showed an increased presence of Staphylococcus epidermidis in the gut. This is not found in late non-CAPA cases or early disease. The analysis of bronchial samples did not show significant results. ConclusionsThis is the first study showing alterations in the gut microbiome accompany severe CAPA and possibly influence the hosts immunological response. In particular, an increase of Staphylococcus epidermidis in the intestine could be of importance. SummaryThe composition of intestinal bacteria in severe CAPA disease is altered with an increase in Staphylococcus epidermidis in the gut. Alterations in the composition of intestinal bacteria in severe CAPA may indicate immunologic involvement of the gut in the disease.

microbiology↗

bioRxiv2022

Increased glycolysis and functional mitochondria fuel acinar-ductal metaplasia in the pancreas

Reprogramming of the cellular metabolism is a hallmark of pancreatic cancer, yet it remains unclear at what stage during carcinogenesis it occurs. Here, we investigated the metabolic requirements for acinar-to-ductal metaplasia (ADM), the first step in pancreatic carcinogenesis. We detected increased glycolytic marker expression in human ADM suggesting that a metabolic switch occurs during ADM formation. We report that this switch was similarly required for ADM formation in different oncogenic mouse models (KRAS, PI3K, and MEK1) and in ligand-induced ADM in mouse wild-type acini. In addition, we show that a functional electron transport chain (ETC), but not mitochondrial ATP production, was essential to ADM formation. We conclude that the ETC provides NAD+ for the de novo synthesis of serine from glycolysis intermediates. Our findings demonstrate that metabolic programming is essential for the initiation of pancreatic carcinogenesis and thus identifies potential targets for metabolic intervention.

cancer biology↗

bioRxiv2021

Gut Bacterial Dysbiosis and Instability is Associated with the Onset of Complications and Mortality in COVID-19

ObjectiveThere is a growing debate about the involvement of the gut microbiome in COVID-19, although it is not conclusively understood whether the microbiome has an impact on COVID-19, or vice versa, especially as analysis of amplicon data in hospitalized patients requires sophisticated cohort recruitment and integration of clinical parameters. Here, we analyzed fecal and saliva samples from SARS-CoV-2 infected and post COVID-19 patients and controls considering multiple influencing factors during hospitalization. Design16S rRNA gene sequencing was performed on fecal and saliva samples from 108 COVID-19 and 22 post COVID-19 patients, 20 pneumonia controls and 26 asymptomatic controls. Patients were recruited over the first and second corona wave in Germany and detailed clinical parameters were considered. Serial samples per individual allowed intra-individual analysis. ResultsWe found the gut and oral microbiota to be altered depending on number and type of COVID-19-associated complications and disease severity. The occurrence of individual complications was correlated with low-risk (e.g., Faecalibacterium prausznitzii) and high-risk bacteria (e.g., Parabacteroides). We demonstrated that a stable gut bacterial composition was associated with a favorable disease progression. Based on gut microbial profiles, we identified a model to estimate mortality in COVID-19. ConclusionGut microbiota are associated with the occurrence of complications in COVID-19 and may thereby influencing disease severity. A stable gut microbial composition may contribute to a favorable disease progression and using bacterial signatures to estimate mortality could contribute to diagnostic approaches. Importantly, we highlight challenges in the analysis of microbial data in the context of hospitalization.

microbiology↗