Biology subjects

Gross, A.

Publications and source records attributed to Gross, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Spatially coordinated RTK-ERK signaling dynamics shape osteosarcoma single-cell drug response in the lung microenvironment

Purpose: Lung metastases are the primary cause of death in osteosarcoma patients and treatment response often vary due to convergence of genetic and phenotypic influences in the context of a dynamic tumor-host tissue environment. The purpose of this study was to determine how dynamic tumor- and host-driven receptor tyrosine kinase (RTK)-ERK signaling interactions contribute to phenotypic drug response heterogeneity. Experimental Design: Live-cell time-lapse microscopy and data-driven dynamical modeling was used to resolve ERK activity, FOSL1/Fra-1 reporter expression, and spatiotemporal cell fate in living, biosensor-expressing osteosarcoma lung metastases ex vivo following MCL1 inhibitor exposure. RTK inhibitors were then evaluated for their ability to suppress adaptive signaling and enhance MCL1 inhibitor efficacy ex vivo and in vivo. Results: MCL1 inhibition induced extensive tumor-cell death; however, persistent ERKhigh/Fra-1high reporter cells emerged and were enriched at the tumor-lung interface, consistent with adaptive resistance. Experimental and computational approaches revealed that tumor-cell lysis amplified fibroblast growth factor receptor (FGFR)-mediated ERK signaling in neighboring cells, promoting a targetable drug-resistant state marked by adaptive ERK induction, FOSL1/Fra-1 expression, and correlated with upregulation of known drug resistance pathways Nrf2 and HMOX1. Combinatorial inhibition of FGFR with fexagratinib, or broad-spectrum RTK inhibitor, pazopanib, suppressed adaptive ERK activation and enhanced MCL1 inhibitor response resulting in greater efficacy ex vivo and in vivo. Conclusions: Tumor-host and tumor-cell-lysis-induced FGFR-ERK signaling contribute to spatiotemporally heterogeneous adaptive resistance in metastatic osteosarcoma. These data support combinatorial targeting of RTK signaling with cytotoxic or targeted agents as a strategy to block adaptive resistance and improve treatment efficacy.

cancer biology↗

bioRxiv2026

QTrap-Enabled GERD Safety Analysis of Commercial Salsas

Gastroesophageal reflux disease (GERD) is a prevalent chronic disorder where dietary modifications, particularly reducing spicy foods, are a primary management strategy. Salsa, a widely consumed condiment whose spiciness comes from capsaicin, lacks standardized heat labelling, potentially leading to inconsistent capsaicin exposure for consumers. To address this, our study aimed to develop and apply an LC-MS workflow for accurate capsaicin quantification in commercially available salsas. This approach seeks to provide objective "reflux-conscious" spice classification, supporting evidence-based dietary recommendations for individuals with GERD. In the eight commercial brands we examined, we found that products labelled "mild" had significantly lower capsaicin levels as compared to "medium" or "hot", but that there was an almost 15-fold range of capsaicin within this group. Surprisingly, there was no statistical difference in capsaicin content between those groups labelled "medium" or "hot" facilitating unambiguous assignment to either category, revealing that product labelling alone is insufficient to guide consumers seeking to control capsaicin exposure in their food. The results in this study enable improved brand-specific recommendations for GERD symptom management.

pharmacology and toxicology↗

bioRxiv2026

Organizational principles governing synapse types in a whole-brain connectome

Neurons are classically viewed as polarized elements in which dendrites receive synaptic input and axons provide output. However, many neurons contain intermingled presynaptic and postsynaptic sites, enabling non-canonical forms of connectivity beyond axo-dendritic interactions. How such mixed polarity shapes connectivity across an entire nervous system remains unknown. Here, using the complete Drosophila connectome of an adult brain (approximately 140,000 neurons and >80 million synapses), we systematically mapped synapse types across neuronal compartments, cell types, and brain regions. We found that mixed polarity is widespread yet highly structured across neuronal populations. Approximately one third of synapses between polarized neurons are non-canonical, including axo-axonic, dendrodendritic, and dendro-axonic interactions. Remarkably, synapse type can be predicted from a simple axis of neuronal complexity derived from morphology and connectivity. Low-complexity neurons, which dominate early visual circuits, preferentially interact through dendrites, whereas larger and more highly connected neurons enriched in central brain regions preferentially interact through axons. Mixed polarity also strongly promotes reciprocal connectivity, which is dominated by non-canonical motifs. Finally, we identified postsynaptic terminals on presynaptic boutons as a widespread anatomical motif associated with local reciprocal and non-canonical interactions. Together, these findings reveal organizational principles linking neuronal architecture, synapse type, and circuit connectivity across a complete brain.

neuroscience↗

bioRxiv2026

Whole genome-based Characterization of Virulence and Antimicrobial Resistance Determinants in Clinical Campylobacter jejuni Isolates from Minnesota, 2018-2021

Campylobacter jejuni is a leading cause of foodborne gastroenteritis globally and is classified by the CDC as a serious public health threat due to increasing resistance to fluoroquinolones and macrolides. This study used whole-genome sequencing to characterize the virulence and antimicrobial resistance profiles of 2,783 clinical C. jejuni isolates collected from Minnesota residents from 2018 through 2021. More than 90% of the isolates had genes related to stress defense (rpoN and htrB), cytolethal distending toxin (cdtA, cdtB, and cdtC), and cell adhesion and invasion (ciaB, cadF, and flaC). A diverse array of antimicrobial resistance genes was detected, with beta-lactam resistance genes having a particularly high prevalence. The gyrA point mutation associated with quinolone resistance was present in 29% of isolates. To evaluate the correlation between genotypic and phenotypic antimicrobial resistance profiles, the antimicrobial susceptibility testing results from a subset of isolates were compared with genotypic resistance profiles. Results showed a strong overall correlation, particularly for tetracycline and quinolones, though 24 discrepancies were detected. In the majority of discrepancies (n=21), genomic antimicrobial resistance markers were absent in isolates that were phenotypically resistant, suggesting possible unknown resistance mechanisms or limitations in current sequencing methods. The remaining three discrepancies occurred in isolates that had the tet(O) resistance gene but were susceptible to tetracycline phenotypically. These findings highlight the value of whole genome sequencing in improving antimicrobial resistance surveillance and understanding virulence factors in C. jejuni, supporting its integration into routine monitoring practices to better manage and understand antimicrobial resistance in foodborne pathogens.

microbiology↗

bioRxiv2025

Metabolic Rewiring by alpha-Synuclein Enables Mitohormetic Protection

-Synuclein (Syn) is widely associated with Parkinsons disease pathology, yet its physiological impact on cellular metabolism remains unclear. Here we show that stable Syn expression in HEK293 cells induces coordinated metabolic remodeling that enhances mitochondrial resilience. Syn interacts with lactate dehydrogenase A (LDHA) and Syn-expressing clones exhibit elevated LDHA activity. Moreover, these clones exhibit increased lactate secretion, enhanced glycolysis, and reduced mitochondrial-reactive oxygen species, coupling metabolic rewiring to improved mitochondrial adaptation. Strikingly, following chronic low-dose rotenone preconditioning, Syn- expressing clones acquire robust resistance to subsequent respiratory complex I inhibition, revealing a potent Syn-dependent mitohormetic response. These findings identify Syn as a conditional metabolic modulator that supports mitochondrial adaptation under sustained stress.

cell biology↗

bioRxiv2025

Cat brains age like humans: Translating Time shows pet cats live to be natural models for human aging

Translating biological time across species is a powerful tool to identify new models of human aging and disease. Currently, it is not clear whether any animal reaches an age comparable to a human in their 80s. Most species seem to age differently compared with humans. Some preliminary observations suggest that cats may share common patterns of aging with humans. Cats could serve as a promising model for human aging. Here, we find corresponding ages between cats, humans and other species to test whether cats can live to the equivalent of a human in their 80s. We analyzed 3,754 observations across species from sudden and gradual changes in anatomy, physiology, and behavior. Some of these data are from clinical records, whereas others are from brain scans using high-resolution MRI (7T and 3T). We studied pet cats, research colony cats, and wildcats living in zoos to encapsulate species variation in the speed of development and aging. We found that cat and human brains atrophy with age, and that their age-related patterns in brain aging are sufficiently similar that we could use them to generate cross-species age alignments. We also found that human postnatal development is stretched compared with cats and mice. Interestingly, some pet cats that visit clinics are much older than those in colonies. Therefore, cats, and especially pet cats, are natural model systems of human aging. Our findings call for increased integration across veterinary and human medicine to understand aging.

neuroscience↗

bioRxiv2025

Spatial Biodiversity Indicators and a Composite Index for Conservation Prioritization in Switzerland

Spatially explicit indicators that quantify to which extent landscapes support biodiversity are essential for guiding evidence-based conservation planning. Here, we present a 25-meter resolution dataset for Switzerland, encompassing three key biodiversity indicators-- Complementarity, Extinction Risk, and Ecological Connectivity--developed across 17 major taxonomic groups, using habitat suitability maps for approximately 7,500 individual species. These three indicators capture (1) the contribution of landscapes to taxonomic, functional, and phylogenetic diversity, (2) species vulnerability to extinction and (3) ecological connectivity. Outputs are provided for both terrestrial and aquatic realms, including versions adjusted for species richness, and integrated into composite indices. In total, 272 spatial layers were produced and made openly accessible. Relationships among the three indicators were analyzed to assess their distinct contributions, and expert-based validations were performed to evaluate their ecological plausibility and relevance for conservation applications. This dataset provides a robust foundation to support spatial planning and conservation decision-making in Switzerland and can be used as a blueprint for analogue integration in other countries.

ecology↗

bioRxiv2025

Non-Invasive Mechanical-Functional Analysis of Individual Liver Mitochondria by Atomic Force Microscopy

Mitochondria play a pivotal role in energy production, signaling, and apoptosis. Yet, probing their functional state at the single-organelle level without invasive labels remains a major challenge. Here, we introduce a novel, label-free approach that leverages Atomic Force Microscopy (AFM) beyond its traditional imaging role, transforming it into a powerful tool for functional analysis of individual, isolated mitochondria. By immobilizing mouse liver mitochondria on polylysine-coated mica, we achieved nanoscale resolution of mitochondrial mechanical properties including height, height fluctuation power spectra, and Youngs modulus, under different respiratory states. Strikingly, fluctuations in mitochondrial height fluctuations below 20 Hz showed robust correlation with the mitochondria membrane potential ({Delta}{Psi}m), a cornerstone of mitochondrial function. This relationship allows AFM to sensitively detect changes in the mitochondria bioenergetic status. Applying this method to mitochondria from liver-specific MTCH2 liver-conditional knockout mice, a model of mitochondrial malfunction, we confirmed AFMs diagnostic potential. The technique reliably distinguished malfunctional mitochondria, mirroring and adding new insights beyond conventional fluorescence assays. By bridging nanomechanics and mitochondrial bioenergetics, this approach paves the way for non-invasive, high-resolution diagnostics at the single-organelle level, holding promise to monitor the actual functional state of mitochondria in clinical settings.

biophysics↗

bioRxiv2025

Differential cell survival outcomes in response to diverseamino acid stress

Amino acid (AA) detection is fundamental for cellular function, balancing translation demands, biochemical pathways, and signaling networks. While the GCN2 and mTORC1 pathways are known to regulate AA sensing, the global cellular response to AA deprivation remains poorly understood, particularly in non-transformed cells, which may exhibit distinct adaptive strategies compared to cancer cells. Here we employed murine pluripotent embryonic stem (ES) cells as a model system to dissect responses to AA stress. Using multi-omics analyses over an extended time course, we examined the effects of arginine (Arg) and leucine (Leu) deprivation and uncovered a broad array of proteomic, phosphoproteomic, transcriptomic, and metabolomic adaptations, including an increase in lysosome production, all occurring without lethality. We found that Arg or Leu starvation induces reversible cell cycle exit, promoting a quiescent state that enhances resistance to cytotoxic stressors. By contrast, cysteine (Cys) and threonine (Thr) deprivation led to cell death via distinct pathways: ferroptosis for Cys starvation, while Thr deprivation triggered a previously uncharacterized form of cell death, which could be entirely suppressed by methionine (Met) co-starvation, mTOR or translational inhibition. These findings suggest that ES cells implement specialized survival strategies in response to different AA limitations, highlighting their ability to reprogram cellular biochemistry under nutrient stress.

cell biology↗

bioRxiv2024

Unveiling novel conserved HIV-1 open reading frames encoding T cell antigens using ribosome profiling.

The development of ribosomal profiling (Riboseq) revealed the immense coding capacity of human and viral genomes. Here, we used Riboseq to delineate the first translatome of HIV-1 in infected CD4+ T cells. In addition to canonical viral protein coding sequences (CDSs), we identify 98 alternative open reading frames (ARFs), corresponding to small Open Reading Frames (sORFs) that are distributed across the HIV genome including the UTR regions. Using a database of HIV genomes, we observed that most ARF amino-acid sequences are likely conserved among clade B and C of HIV-1, with 8 ARF-encoded amino-acid sequences being more conserved than the overlapping CDSs. Using T cell-based assays and mass spectrometry-based immunopeptidomics, we demonstrate that ARFs encode viral polypeptides. In the blood of HIV-infected individuals, ARF-derived peptides elicit potent poly-functional T cell responses mediated by both CD4+ and CD8+ T cells. Our discovery expands the list of conserved viral polypeptides that are targets for vaccination strategies and might reveal the existence of viral microproteins or pseudogenes.

immunology↗

bioRxiv2024

Up-regulated transcriptional regulators in mutant RAS gene signatures: a time-resolved multi-omics study in generic epithelial cell models

The expression of mutated RAS genes drives extensive transcriptome alterations. Perturbation experiments have shown that the transcriptional responses to downstream effector pathways are partially unique and non-overlapping, suggesting a modular organization of the RAS-driven expression program. However, the relationship between individual deregulated transcription factors and the entire cancer cell-specific genetic program is poorly understood. To identify potential regulators of the RAS/MAPK-dependent fraction of the genetic program, we monitored transcriptome and proteome changes following conditional, time-resolved expression of mutant HRASG12V in human epithelial cells during neoplastic conversion. High mobility group AT hook2 (HMGA2), an architectural chromatin modulating protein and oncofetal tumour marker, was recovered as the earliest upregulated transcription factor. Knock-down of HMGA2 reverted anchorage-independent growth and epithelial-mesenchymal transition not only in HRAS-transformed cells but also in an independent, KRASG12V-driven rat epithelial model. Moreover, HMGA2 silencing reverted the deregulated expression of 60% of RAS-responsive target genes. These features qualify HMGA2 as a master regulator of mutant RAS-driven expression patterns. The delayed deregulation of FOSL1, ZEB1 and other transcription factors with known oncogenic activity suggests that HMGA2 acts in concert with a network of regulatory factors to trigger full neoplastic conversion. Although transcription factors are considered difficult to drug, the central role of HMGA2 in the transcription factor network as well as its relevance for cancer prognosis has motivated attempts to block its function using small molecular weight compounds. The further development of direct HMGA2 antagonists may prove useful in cancer cells that have developed resistance to signalling chain inhibition.

cancer biology↗

bioRxiv2023

High-energy demand and nutrient exhaustion in MTCH2 knockout cells

Mitochondrial carrier homolog 2 (MTCH2) is a regulator of apoptosis, mitochondrial dynamics, and metabolism. Loss of MTCH2 results in mitochondrial fragmentation, an increase in whole-body energy utilization, and protection from diet-induced obesity. We now show using temporal metabolomics that MTCH2 deletion results in a high ATP demand, an oxidized environment, a high lipid/amino acid/carbohydrate metabolism, and in the decrease of many metabolites. Lipidomics analyses show a strategic adaptive decrease in membrane lipids and an increase in storage lipids in MTCH2 knockout cells. Importantly, all the metabolic changes in the MTCH2 knockout cells were rescued by MTCH2 re-expression. Interestingly, this imbalance in energy metabolism and reductive potential triggered by MTCH2-deletion inhibits adipocyte differentiation, an energy consuming reductive biosynthetic process. In summary, loss of MTCH2 results in an increase in energy demand that triggers a catabolic and oxidizing environment, which fails to fuel the anabolic processes during adipocyte differentiation.

cell biology↗

bioRxiv2023

A Graph Matching Approach to Tracking Neurons in Freely-Moving C. elegans

MotivationRecent advances in 3D microscopy allow for recording the neurons in freely-moving C. elegans at high frame rates. In order to read out calcium activity, it is necessary to track individual neurons from frame to frame. However, doing this by hand for tens of neurons in a single ten-minute recording requires more than a hundred hours. Moreover, most methods proposed in the literature for tracking neurons focus on immobilized or partially-immobilized worms and fail with freely-behaving worms. ResultsIn this paper we present an approach based on graph matching for tracking fluorescently-marked neurons in freely-moving C. elegans. Neurites (and sometimes neurons) can be oversegmented into pieces at the preprocessing phase; our algorithm allows several segments to match the same reference neuron or neurite. We demon-strate our method on three recordings. We find that with five labeled frames we can typically track the neurons and pieces of neurites with over 75% accuracy, with more reliable annotations for the most distinctive neurons. Availability and ImplementationThe code and preprocessed data will be made available upon publication. Contactcorinne.jones@epfl.ch

neuroscience↗

bioRxiv2023

Deciphering Cell-types and Gene Signatures Associated with Disease Activity in Rheumatoid Arthritis using Single Cell RNA-sequencing

ObjectiveSingle cell profiling of synovial tissue has previously identified gene signatures associated with rheumatoid arthritis (RA) pathophysiology, but synovial tissue is difficult to obtain. This study leverages single cell sequencing of peripheral blood mononuclear cells (PBMCs) from patients with RA and matched healthy controls to identify disease relevant cell subsets and cell type specific signatures of disease. MethodsSingle-cell RNA sequencing (scRNAseq) was performed on peripheral blood mononuclear cells (PBMCs) from 18 RA patients and 18 matched controls, accounting for age, gender, race, and ethnicity). Samples were processed using standard CellRanger and Scanpy pipelines, pseudobulk differential gene expression analysis was performed using DESeq2, and cell-cell communication analysis using CellChat. ResultsWe identified 18 distinct PBMC subsets, including a novel IFITM3+ monocyte subset. CD4+ T effector memory cells were increased in patients with moderate to high disease activity (DAS28-CRP [≥] 3.2), while non-classical monocytes were decreased in patients with low disease activity or remission (DAS28-CRP < 3.2). Differential gene expression analysis identified RA-associated genes in IFITM3+ and non-classical monocyte subsets, and downregulation of pro-inflammatory genes in the V{delta} subset. Additionally, we identified gene signatures associated with disease activity, characterized by upregulation of pro-inflammatory genes TNF, JUN, EGR1, IFIT2, MAFB, G0S2, and downregulation of HLA-DQB1, HLA-DRB5, TNFSF13B. Notably, cell-cell communication analysis revealed upregulation of immune-associated signaling pathways, including VISTA, in patients with RA. ConclusionsWe provide a novel single-cell transcriptomics dataset of PBMCs from patients with RA, and identify insights into the systemic cellular and molecular mechanisms underlying RA disease activity.

immunology↗

bioRxiv2023

Diversity loss in microbial ecosystems undergoing gradual environmental changes

Microbial ecosystems in soils, oceans, and other environments are essential for global ecological stability. Environmental shifts are anticipated to trigger destabilizing events across the planet. In this study, we model how gradual environmental changes impact ecosystems, specifically when leading to a loss of diversity. We investigate how an ecosystem, within a serial-dilution setup, relaxes to a stable steady state. Our results reveal that as an ecosystem approaches its loss of diversity transition, its dynamics slow down. Consequently, diverse ecosystems, such as tropical rainforest soils, gradually driven past their transition point may exhibit a significant response lag. This suggests that some ecosystems may be closer to a collapse in diversity than current observations indicate. Although our model does not capture the full complexity of real-world ecosystems, it highlights critical aspects underlying the loss of biodiversity in changing environments. This has potential implications for empirical studies and when planning interventions.

ecology↗

bioRxiv2022

A metabolite sensor subunit of the Atg1/ULK complex regulates selective autophagy

Cells convert complex metabolic information into stress-adapted autophagy responses. Canonically, multilayered protein kinase networks converge on the conserved Atg1/ULK kinase complex (AKC) to induce non-selective and selective forms of autophagy in response to metabolic changes. Here, we show that, upon phosphate starvation, the metabolite sensor Pho81 interacts with the adaptor subunit Atg11 at the AKC via an Atg11/FIP200 interaction motif to modulate pexophagy by virtue of its conserved phospho-metabolite sensing SPX domain. Notably, we find core AKC components Atg13 and Atg17 are dispensable for phosphate starvation-induced autophagy revealing significant compositional and functional plasticity of the AKC. Our data indicate that, instead of functioning as a selective autophagy receptor, Pho81 compensates for partially inactive Atg13 during pexophagy when TORC1 remains active under phosphate starvation. Our work shows Atg11/FIP200 adaptor subunits not only bind selective autophagy receptors but also modulator subunits that convey metabolic information directly to the AKC for autophagy regulation.

cell biology↗

bioRxiv2022

MTCH2 cooperates with MFN2 and lysophosphatidic acid synthesis to sustain mitochondrial fusion

Mitochondrial dynamics is critical to sustain normal mitochondrial function and is linked to the response of cells to stressful conditions. Fusion of the outer mitochondrial membrane (OMM) is regulated by mitofusin 1 (MFN1) and 2 (MFN2), yet the differential contribution of each of these proteins to this process is less understood. Mitochondrial carrier homolog 2 (MTCH2) was shown to compensate for MFN2s loss, however its exact function in mitochondrial fusion remains poorly understood. Here we determined the mitochondrial fusion-interplay between MFN1, MFN2 and MTCH2 and demonstrate that MFN2 and MTCH2 play separate, but redundant, roles required for mitochondrial fusion. Loss of either MFN2 or MTCH2 elicits mitochondrial fragmentation that retains mitochondrial plasticity, while loss of both proteins completely impairs mitochondrial fusion. We also show that expression of an MFN2 mutant targeted to the endoplasmic reticulum (ER) is sufficient to restore mitochondrial elongation in MTCH2 KO cells and that this restoration depends on the synthesis of the pro-mitochondrial fusion lipid lysophosphatidic acid (LPA). Moreover, silencing of MFN2 or inhibition of de novo LPA synthesis, revealed the requirement of MTCH2 to sustain mitochondrial plasticity in response to stress. Thus, we unmask two cooperative mechanisms that sustain mitochondrial fusion: one in the OMM, dependent on MTCH2 and MFN1, and independent of MFN2; and a second mechanism in the ER that relies on MFN2 and LPA synthesis.

cell biology↗

bioRxiv2022

Differential UBE2H-CTLH E2-E3 ubiquitylation modules regulate erythroid maturation

The development of haematopoietic stem cells into mature erythrocytes - erythropoiesis - is a controlled process characterized by cellular reorganisation and drastic reshaping of the proteome landscape. Failure of ordered erythropoiesis is associated with anaemias and haematological malignancies. Although the ubiquitin (UB) system is a known crucial post-translational regulator in erythropoiesis, how the erythrocyte is reshaped by the UB system is poorly understood. By measuring the proteomic landscape of in vitro human erythropoiesis models, we found dynamic differential expression of subunits of the CTLH E3 ubiquitin ligase complex that formed distinct maturation stage-dependent assemblies of structurally homologous RANBP9-and RANBP10-CTLH complexes. Moreover, protein abundance of CTLHs cognate E2-conjugating enzyme UBE2H increased during terminal differentiation, which depended on catalytically active CTLH E3 complexes. CRISPR-Cas9 mediated inactivation of all CTLH E3 assemblies by targeting the catalytic subunit MAEA, or UBE2H, triggered spontaneous and accelerated maturation of erythroid progenitor cells including increased heme and haemoglobin synthesis. Thus, the orderly progression of human erythropoiesis is controlled by the assembly of distinct UBE2H-CTLH modules functioning at different developmental stages.

cell biology↗