Biology subjects

Froehlich, J.

Publications and source records attributed to Froehlich, J..

7 recordsLinked to original sources

bioRxiv2026

Integrated transcriptomic and proteomic analyses identify novel biomarkers of bladder outlet obstruction

Bladder outlet obstruction leads to pathological remodeling and emergence of lower urinary tract symptoms. Although relief of obstruction is associated with symptomatic improvement, it is not universally successful, reflecting persistent alterations in the bladder. Reliable surrogate biomarkers of obstruction are lacking, particularly early in the disease course before irreversible damage to the bladder may have occurred. In this study, re-analysis of publicly available transcriptomic datasets from diverse rodent models of obstruction identified tissue transcripts including Cthrc1, Grem1, Ltbp2 and Msn that were induced in response to injury. Candidate markers were validated experimentally in an independent model of neurogenic obstruction demonstrating time-dependent changes. Candidate markers were also attenuated with either surgical removal of obstruction or treatment with anticholinergic medication or inosine. Integrated analysis of tissue transcriptomics data and tissue and urine proteomics data from a model of neurogenic obstruction revealed significant concordance between markers observed in tissue and urine. Urinary proteomics analysis identified a statistically significant increase in MSN in patients with neurogenic bladder compared to unaffected controls. These findings identify tissue and urine biomarkers of both non-neurogenic and neurogenic obstruction that may reflect early changes in obstructive uropathy that could be monitored in a non-invasive manner.

bioinformatics↗

bioRxiv2025

Metabolic Crossroads: AMDHD2 Couples the Hexosamine Biosynthetic Pathway to Acetyl-CoA Homeostasis in Pluripotent Stem Cells

Pluripotent stem cells (SCs) rely on metabolic rewiring to regulate self-renewal and differentiation. The hexosamine biosynthetic pathway (HBP) integrates multiple metabolic inputs to produce uridine diphosphate-N-acetylglucosamine (UDP-GlcNAc), a central substrate for protein and lipid glycoconjugates. While UDP-GlcNAc levels influence pluripotency, the broader metabolic roles of the HBP in stem cell maintenance and differentiation remain largely unexplored. Using proteomic and metabolomic analyses, we uncovered extensive enzymatic remodelling of the HBP during early mouse embryonic stem cell (mESC) differentiation, including a significant decrease in N-acetylglucosamine-6-phosphate (GlcNAc6P) levels, despite stable UDP-GlcNAc levels. Isotope labelling experiments revealed that pluripotent stem cells maintain UDP-GlcNAc biosynthesis through a combination of glucose-driven de novo synthesis and the N-Acetylglucosamine (GlcNAc) salvage pathway, both of which are downregulated during differentiation. Functionally, we identified GlcNAc6P--a point of convergence of the de novo synthesis and the salvage pathways--as a pivotal metabolite of stem cell fate. Preventing GlcNAc6Ps deacetylation by deleting or depleting AMDHD2 impaired mESC differentiation. Mechanistically, we demonstrated that GlcNAc6P catabolism is essential for sustaining cytosolic acetate and in turn acetyl-CoA levels, which are critical for lipid synthesis and histone modifications required for pluripotency exit. These findings establish AMDHD2 as a key supplier of cellular acetate and reveal an essential metabolic link between HBP activity and acetyl-CoA homeostasis. By expanding the role of the HBP beyond UDP-GlcNAc production, this study reveals an unrecognised metabolic vulnerability that can be exploited to manipulate stem cell identity.

molecular biology↗

bioRxiv2024

Arabidopsis thaliana RHAMNOSE 1 condensate formation drives UDP-rhamnose synthesis

Rhamnose is an essential component of the plant cell wall and is synthesized from uridine diphosphate (UDP)-glucose by the RHAMNOSE1 (RHM1) enzyme. RHM1 localizes to biomolecular condensates in plants, but their identity, formation, and function remain elusive. Combining live imaging, genetics, and biochemical approaches in Arabidopsis and heterologous systems, we show that RHM1 alone is sufficient to form enzymatically active condensates, which we name rhamnosomes. Rhamnosome formation is required for UDP-rhamnose synthesis and organ development. Overall, our study demonstrates a novel role for biomolecular condensation in metabolism and organismal development, and provides further support for how organisms have harnessed this biophysical process to regulate small molecule metabolism. One-Sentence SummaryCondensation of RHM1 drives UDP-rhamnose synthesis during plant development.

plant biology↗

bioRxiv2023

Integrated omics analysis unveils a DNA damage response to neurogenic injury

Spinal cord injury (SCI) evokes profound bladder dysfunction. Current treatments are limited by a lack of molecular data to inform novel therapeutic avenues. Previously, we showed systemic inosine treatment improved bladder function following SCI in rats. Here, we applied multi-omics analysis to explore molecular alterations in the bladder and their sensitivity to inosine following SCI. Canonical pathways regulated by SCI included those associated with protein synthesis, neuroplasticity, wound healing, and neurotransmitter degradation. Upstream regulator analysis identified MYC as a key regulator, whereas causal network analysis predicted multiple regulators of DNA damage response signaling following injury, including PARP-1. Staining for both DNA damage ({gamma}H2AX) and PARP activity (poly-ADP-ribose) markers in the bladder was increased following SCI, and attenuated in inosine-treated tissues. Proteomics analysis suggested that SCI induced changes in protein synthesis-, neuroplasticity-, and oxidative stress-associated pathways, a subset of which were shown in transcriptomics data to be inosine-sensitive. These findings provide novel insights into the molecular landscape of the bladder following SCI, and highlight a potential role for PARP inhibition to treat neurogenic bladder dysfunction. Synopsis O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=100 SRC="FIGDIR/small/571015v1_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@7c3e79org.highwire.dtl.DTLVardef@e998f5org.highwire.dtl.DTLVardef@38fd4aorg.highwire.dtl.DTLVardef@17d3aba_HPS_FORMAT_FIGEXP M_FIG C_FIG O_LIEmployed a multi-omics approach, integrating both transcriptomic and proteomic analyses, to investigate the molecular response in a rat model of spinal cord injury (SCI) and the therapeutic effect of inosine. C_LIO_LIDiscovered multiple regulators of the DNA damage response, including PARP-1, using causal network analysis. C_LIO_LIObserved decreased markers of DNA damage and PARP activity in inosine-treated tissues, indicating the therapeutic potential of inosine in neurogenic dysfunction. C_LIO_LIIdentified significant alterations in molecular pathways associated with protein synthesis, neuroplasticity, wound healing, and neurotransmitter degradation after SCI, and their modulation by inosine, highlighting its neuroprotective effects beyond DNA damage repair. C_LI

cell biology↗

bioRxiv2022

Transcriptional activity mediated by beta-CATENIN and TCF/LEF family members is completely dispensable for survival of multiple human colorectal cancer cell lines

Unrestrained transcriptional activity of {beta}-CATENIN and its binding partner TCF7L2 frequently underlies colorectal tumor initiation and is considered an obligatory oncogenic driver throughout intestinal carcinogenesis. Yet, the TCF7L2 gene carries inactivating mutations in about 10 % of colorectal tumors and is non-essential in colorectal cancer (CRC) cell lines. To determine whether CRC cells acquire TCF7L2-independence through cancer-specific compensation by other T-cell factor (TCF)/lymphoid enhancer-binding factor (LEF) family members, or rather lose addiction to {beta}-CATENIN/TCF7L2-driven gene expression altogether, we generated multiple CRC cell lines entirely negative for TCF/LEF or {beta}-CATENIN expression. Viability of these cells demonstrates complete {beta}-CATENIN- and TCF/LEF-independence, albeit one {beta}-CATENIN-deficient cell line eventually became senescent. Absence of TCF/LEF proteins and {beta}-CATENIN consistently impaired CRC cell proliferation, reminiscent of mitogenic effects of WNT/{beta}-CATENIN signaling in the healthy intestine. Despite this common phenotype, {beta}-CATENIN-deficient cells exhibited highly cell-line-specific gene expression changes with little overlap between {beta}-CATENIN- and TCF7L2-dependent transcriptomes. Apparently, {beta}-CATENIN and TCF7L2 control sizeable fractions of their target genes independently from each other. The observed divergence of {beta}-CATENIN and TCF7L2 transcriptional programs, and the finding that neither {beta}-CATENIN nor TCF/LEF activity is strictly required for CRC cell survival has important implications when evaluating these factors as potential drug targets.

cell biology↗

bioRxiv2021

Emergent Diversity and Persistent Turnover in Evolving Microbial Cross-Feeding Networks

A distinguishing feature of many ecological networks in the microbial realm is the diversity of substrates that could potentially serve as energy sources for microbial consumers. The microorganisms are themselves the agents of compound diversification via metabolite excretion or overflow metabolism. It has been suggested that the emerging richness of different substrates is an important condition for the immense biological diversity in microbial ecosystems. In this work, we study how complex cross-feeding networks (CFN) of microbial species may develop from a simple initial community given some elemental evolutionary mechanisms of resource-dependent speciation and extinctions using a network flow model. We report results of several numerical experiments and report an in-depth analysis of the evolutionary dynamics. We find that even in stable environments, the system is subject to persisting turnover, indicating an ongoing co-evolution. Further, we compare the impact of different parameters, such as the ratio of mineralization, as well as the metabolic versatility and variability on the evolving community structure. The results imply that high microbial and molecular diversity is an emergent property of evolution in cross-feeding networks, which affects transformation and accumulation of substrates in natural systems, such as soils and oceans, with potential relevance to biotechnological applications.

systems biology↗

bioRxiv2020

Parallel genetics of regulatory sequences in vivo

Understanding how regulatory sequences control gene expression is fundamental to explain how phenotypes arise in health and disease. Traditional reporter assays inform about function of individual regulatory elements, typically in isolation. However, regulatory elements must ultimately be understood by perturbing them within their genomic environment and developmental- or tissue-specific contexts. This is technically challenging; therefore, few regulatory elements have been characterized in vivo. Here, we used inducible Cas9 and multiplexed guide RNAs to create hundreds of mutations in enhancers/promoters and 3' UTRs of 16 genes in C. elegans. To quantify the consequences of mutations on expression, we developed a targeted RNA sequencing strategy across hundreds of mutant animals. We were also able to systematically and quantitatively assign fitness cost to mutations. Finally, we identified and characterized sequence elements that strongly regulate phenotypic traits. Our approach enables highly parallelized, functional analysis of regulatory sequences in vivo.

genetics↗