Biology subjects

Ochs, M.

Publications and source records attributed to Ochs, M..

9 recordsLinked to original sources

bioRxiv2026

Clear cell renal cell carcinoma consensus transcriptomic programs reveal converging trajectories towards aggressive disease

Clear cell renal cell carcinoma (ccRCC) is characterized by a branching genomic trajectory in which early biallelic VHL inactivation splits into PBRM1- and BAP1-mutant lineages. However, driver mutations alone do not account for the molecular and phenotypic heterogeneity. To dissect this heterogeneity, we developed a non-negative matrix factorization (NMF)-based gene expression analytical framework for identifying recurrent transcriptional programs across factorization dimensionalities and across datasets. We applied it to three curated datasets (IMmotion151, n = 823; JAVELIN Renal 101, n = 726; TCGA, n = 614) to define 17 consensus transcriptomic programs (CTPs). Mapping CTPs onto single-cell RNAseq (scRNAseq) of human ccRCC tumors and patient-derived tumorgraft models linked these programs to their cellular sources, distinguishing RCC-intrinsic, tumor-cell-extrinsic, and mixed programs. RCC-intrinsic CTPs associated with canonical drivers, including VHL (R1), PBRM1 (R2), BAP1 (R4), PTEN/TSC1 (R3), TFE3/TFEB fusions (R5), NF2 (R6), and CDKN2A/TP53 (MP-Prolif). Additional CTPs captured tumor microenvironment (TME) composition (TME-Tcell, TME-Myelo, TME-Endo, TME-Stroma) and biological processes active across multiple cellular compartments, including proliferation, Y-chromosome-linked expression in male tumors, ciliary biology, and translation. Trajectory inference methods revealed PBRM1-like and BAP1-like branches that converged on a shared aggressive late transcriptomic stage (TS) associated with higher nuclear grade, additional driver alterations, myeloid/stromal infiltration, and poor clinical outcomes. Spatial transcriptomics (and multiregional sequencing) of paired conventional ccRCC and sarcomatoid regions linked TS advancement with morphological progression and clonal evolution. After adjusting for stage, grade, and BAP1/PBRM1 status, TS remained independently prognostic. Furthermore, our data suggest that immune checkpoint inhibitor combinations are particularly beneficial for MP-Prolif and not R1 utilizing specimens. In summary, we present an atlas of recurring transcriptomic programs in RCC and an ontological framework bridging genotype, tumor-cell-intrinsic gene expression, and microenvironment remodeling, with implications for risk stratification and treatment selection in ccRCC.

Cancer Biology↗

bioRxiv2024

Overventilation-induced airspace acidification increases susceptibility to Pseudomonas pneumonia

Ventilator-associated pneumonia (VAP) is the most frequent nosocomial infection in critically ill patients. Local pH variations affect bacterial growth. Whether airway acidification contributes to the pathogenesis and pathophysiology of Pseudomonas aeruginosa (PA)-induced VAP is currently unknown. This study was undertaken to investigate the role and mechanisms of airspace acidification by mechanical ventilation (MV) in PA-induced VAP. C57BL/6J mice were subjected to high (HVt: 34 mL/kg) or low (LVt: 9 mL/kg) tidal volume MV for 4 h. PA was instilled via the tracheal tube, and animals were allowed to recover from sedation and breathe spontaneously for 24 h following extubation. Fluorescence microscopy was applied to determine alveolar pH in ex vivo perfused and ventilated murine lungs. Bacterial growth and adhesion on cyclically stretched A549 and human alveolar epithelial cells was examined. Upon PA infection, HVt mice showed increased alveolo-capillary permeability, elevated lung and blood leukocyte counts, and higher bacterial load in lungs and extrapulmonary organs as compared to LVt controls. HVt MV induced acidification of alveolar lining fluid (ALF) in lungs and decreased pulmonary expression of Na+/H+ exchanger 1 (NHE1). Inhibition of NHE1 enhanced PA growth in vitro on alveolar epithelial cells and increased pulmonary bacterial loads in LVt-MV mice in vivo. In a novel murine VAP model, key characteristics of PA-VAP were replicated. HVt MV induced mild VILI with acidification of airway lining fluid, increasing susceptibility to PA pneumonia. NHE1 was identified as critical factor for MV-induced airspace acidification, and thus as potential target to combat PA-VAP.

immunology↗

bioRxiv2024

Cell surface RNA expression modulates alveolar epithelial function

Glycosylated RNA (glycoRNA) has recently emerged as a novel constituent of the glycocalyx on cell surfaces, yet its biological functions remain largely unexplored. In this report, we present the first analysis of glycoRNA expression and functionality in alveolar epithelial cells. To this end, we optimized new techniques for the detection of glycoRNA on living cell surfaces and in cell membrane-associated RNA samples through in-gel imaging after labeling with fluorescent dye conjugates. Specifically, we used conjugation of Cy5-hydrazide following mild oxidation with sodium periodate for detection of the entire cell surface sialoglycoRNA pool. Conjugation of dibenzocyclooctyne-sulfo-Cy5 (DBCO-Sulfo-Cy5) in cells fed with tetraacetylated N-azidoacetyl-mannosamine (Ac4ManNAz) or 6-azido-L-fucose (FucAz) detected de novo formed sialoglycoRNA or fucoglycoRNA. Finally, biotinylated lectins in combination with infrared dye-conjugated streptavidin was used to differentiate between specific glycosidic linkages. Comparisons across primary alveolar epithelial cells and different alveolar-epithelial like cell lines revealed a cell-type specific variation in glycoRNA abundance. Treatment of primary alveolar epithelial cells with an RNAse cocktail reduced epithelial surface glycoRNA and was associated with a reduction in trans-epithelial electrical resistance and influenza A viral particle abundance. As such, the present work identifies glycoRNA as a novel component of the alveolar epithelial glycocalyx, suggesting its potential relevance in epithelial barrier regulation and viral infection.

physiology↗

bioRxiv2024

Inference of alveolar capillary network connectivity from blood flow dynamics

The intricate structure of the lungs is essential for the gas exchange within the alveolar region. Despite extensive research on the pulmonary vasculature, there are still unresolved questions regarding the connection between capillaries and the vascular tree. A major challenge is obtaining comprehensive experimental data that integrates morphological and physiological aspects. We propose a computational approach that combines data-driven 3D morphological modeling with computational fluid dynamics simulations. This method enables investigating the connectivity of the alveolar capillary network with the vascular tree based on the dynamics of blood flow. We developed 3D sheet-flow models to accurately represent the morphology of the alveolar capillary network and conducted computational fluid dynamics simulations to predict flow velocities and pressure distributions. Our approach focuses on leveraging functional features to identify the most plausible architecture of the system. For given capillary flow velocities and arteriole-to-venule pressure drops, we deduce details about arteriole connectivity. Preliminary connectivity analyses for non-human species indicate that their alveolar capillary network of a single alveolus is linked to at least two arterioles with diameters of 20 {micro}m or a single arteriole with a minimum diameter of 30 {micro}m. Our study provides insights into the structure of the pulmonary microvasculature by evaluating blood flow dynamics. This inverse approach represents a new strategy to exploit the intricate relationship between morphology and physiology, applicable to other tissues and organs. In the future, the availability of experimental data will play a pivotal role in validating and refining the hypotheses analyzed with our computational models. New and noteworthyThe alveolus is pivotal for gas exchange. Due to its complex morphology and dynamic nature, structural experimental studies are challenging. Computational modeling offers an alternative. We developed a databased 3D model of the alveolar capillary network and performed blood flow simulations within it. Choosing a novel perspective, we inferred structure from function. We systematically varied properties of vessels connected to our capillary network and compared simulation results with experimental data to obtain plausible vessel configurations.

physiology↗

bioRxiv2024

Enzymatic modulation of the pulmonary glycocalyx alters susceptibility to Streptococcus pneumoniae

The pulmonary epithelial glycocalyx is rich in glycosaminoglycans such as hyaluronan and heparan sulfate. Despite their presence, the precise role of these glycosaminoglycans in bacterial lung infections remains elusive. To address this, we intranasally inoculated mice with Streptococcus pneumoniae in the presence or absence of enzymes targeting pulmonary hyaluronan and heparan sulfate, followed by characterization of subsequent disease pathology, pulmonary inflammation, and lung barrier dysfunction. Enzymatic degradation of hyaluronan and heparan sulfate exacerbated pneumonia in mice, as evidenced by increased disease scores and alveolar neutrophil recruitment. However, targeting epithelial hyaluronan further exacerbated systemic disease, indicated by elevated splenic bacterial load and plasma levels of pro-inflammatory cytokines. In contrast, enzymatic cleavage of heparan sulfate resulted in increased bronchoalveolar bacterial burden, lung damage and pulmonary inflammation in mice infected with Streptococcus pneumoniae. Accordingly, heparinase-treated mice also exhibited disrupted lung barrier integrity as evidenced by higher alveolar edema scores and vascular protein leakage into the airways. This finding was corroborated in a human alveolus-on-a-chip platform, confirming that heparinase treatment also disrupts the human lung barrier. Notably, enzymatic pre-treatment with either hyaluronidase or heparinase also rendered human epithelial cells more sensitive to pneumococcal-induced barrier disruption, as determined by transepithelial electrical resistance measurements, consistent with our findings in murine pneumonia. Taken together, these findings demonstrate the importance of intact hyaluronan and heparan sulfate in controlling pneumococcal virulence, pulmonary inflammation, and epithelial barrier function.

molecular biology↗

bioRxiv2024

Ileal mucus viscoelastic properties differ in Crohns disease

Crohns disease (CD) is an inflammatory bowel disease (IBD) that can affect any part of the gastrointestinal tract, frequently involving the terminal ileum. While colonic mucus alterations in CD patients have been described, terminal ileal mucus and its mechanobiological properties have been neglected. Our study is the first of its kind to decipher the viscoelastic and network properties of ileal mucus. With that aim, oscillatory rheological shear measurements based on an airway mucus protocol that was thoroughly validated for ileal mucus were performed. Our pilot study analyzed terminal ileum mucus from controls (n=11) and CD patients (n=11). Mucus network structure was visualized by scanning electron microscopy (SEM). Interestingly, a statistically significant increase in viscoelasticity as well as a decrease in mesh size was observed in ileal mucus from CD patients compared to controls. Furthermore, rheological data were analyzed in relation to study participants clinical characteristics, such as inflammatory status, revealing noteworthy trends. In conclusion, this study provides the first data on the viscoelastic properties and structure of human ileal mucus in the healthy state and in CD, demonstrating significant alterations between groups and highlighting the need for further research on mucus and its effect on the underlying epithelial barrier.

biophysics↗

bioRxiv2021

Microstructured hydrogels to guide self-assembly and function of lung alveolospheres

Epithelial cell organoids have increased opportunities to probe questions on tissue development and disease in vitro and for therapeutic cell transplantation. Despite their potential, current protocols to grow these organoids almost exclusively depend on culture within three-dimensional (3D) Matrigel, which limits defined culture conditions, introduces animal components, and results in heterogenous organoids (i.e., shape, size, composition). Here, we describe a method that relies on polymeric hydrogel substrates for the generation and expansion of lung alveolar organoids (alveolospheres). Using synthetic hydrogels with defined chemical and physical properties, human induced pluripotent stem cell (iPSC)-derived alveolar type 2 cells (iAT2s) self-assemble into alveolospheres and propagate in Matrigel-free conditions. By engineering pre-defined microcavities within these hydrogels, the heterogeneity of alveolosphere size and structure was reduced when compared to 3D culture while maintaining alveolar type 2 cell fate of human iAT2 and primary mouse tissue-derived progenitor cells. This hydrogel system is a facile and accessible culture system for the culture of primary and iPSC-derived lung progenitors and the method could be expanded to the culture of other epithelial progenitor and stem cell aggregates.

bioengineering↗

bioRxiv2021

LAMP3 is critical for surfactant homeostasis in mice

Lysosome-associated membrane glycoprotein 3 (LAMP3) is a type I transmembrane protein of the LAMP protein family with a cell-type-specific expression in alveolar type II cells in mice and hitherto unknown function. In type II pneumocytes, LAMP3 is localized in lamellar bodies, secretory organelles releasing pulmonary surfactant into the extracellular space to lower surface tension at the air/liquid interface. The physiological function of LAMP3, however, remains enigmatic. We generated Lamp3 knockout mice by CRISPR/Cas9. LAMP3 deficient mice are viable with an average life span and display regular lung function under basal conditions. The levels of a major hydrophobic protein component of pulmonary surfactant, SP-C, are strongly increased in the lung of Lamp3 knockout mice, and the lipid composition of the bronchoalveolar lavage shows mild but significant changes, resulting in alterations in surfactant functionality. In ovalbumin-induced experimental allergic asthma, the changes in lipid composition are aggravated, and LAMP3-deficient mice exert an increased airway resistance. Our data suggest a critical role of LAMP3 in the regulation of pulmonary surfactant homeostasis and normal lung function.

biochemistry↗

bioRxiv2016

PatternMarkers and Genome-Wide CoGAPS Analysis in Parallel Sets (GWCoGAPS) for data-driven detection of novel biomarkers via whole transcriptome Non-negative matrix factorization (NMF)

SummaryNon-negative Matrix Factorization (NMF) algorithms associate gene expression with biological processes (e.g., time-course dynamics or disease subtypes). Compared with univariate associations, the relative weights of NMF solutions can obscure biomarkers. Therefore, we developed a novel PatternMarkers statistic to extract genes for biological validation and enhanced visualization of NMF results. Finding novel and unbiased gene markers with PatternMarkers requires whole-genome data. However, NMF algorithms typically do not converge for the tens of thousands of genes in genome-wide profiling. Therefore, we also developed Genome-Wide CoGAPS Analysis in Parallel Sets (GWCoGAPS), the first robust whole genome Bayesian NMF using the sparse, MCMC algorithm, CoGAPS. This software contains analytic and visualization tools including a Shiny web application, patternMatcher, which are generalized for any NMF. Using these tools, we find granular brain-region and cell-type specific signatures with corresponding biomarkers in GTex data, illustrating GWCoGAPS and patternMarkers ascertainment of data-driven biomarkers from whole-genome data.\n\nAvailabilityPatternMarkers & GWCoGAPS are in the CoGAPS Bioconductor package (3.5) under the GPL license.\n\nContactgsteinobrien@jhmi.edu; ccolantu@jhmi.edu; ejfertig@jhmi.edu

bioinformatics↗