Biology subjects

Rusten, T. E.

Publications and source records attributed to Rusten, T. E..

7 recordsLinked to original sources

bioRxiv2026

Dredd-mediated cleavage of Kenny uncouples the IKK complex from selective autophagy to enable innate immunity

Selective autophagy restrains innate immune signalling to maintain tissue homeostasis, yet how this repression is rapidly relieved during infection remains unclear. Here, we show that under basal conditions the inhibitor of {kappa}B kinase {gamma} (IKK{gamma}) Kenny is sequestered at autophagosomes through Atg8 and the selective autophagy receptor Ref(2)P, thereby silencing Imd pathway activity. Bacterial infection disrupts this interaction, releasing the IKK complex to enable immune signalling. Mechanistically, we identify the initiator caspase Dredd as a direct interactor of the IKK{gamma} Kenny and show that Dredd binds and cleaves Kenny in a ubiquitination-dependent manner during infection. This cleavage removes an N-terminal LC3-interacting region, uncoupling the IKK complex from autophagosomal degradation. Dredd-mediated processing of Kenny stabilises the IKK complex and is required for activation of the NF-{kappa}B transcription factor Relish, robust antibacterial responses, and host survival following infection. Together, these findings uncover a mechanism by which caspase-mediated cleavage intersects with selective autophagy to dynamically control NF-{kappa}B signalling during bacterial infection. Short summaryBacterial infection activates NF-{kappa}B signalling by triggering caspase-dependent cleavage of the IKK subunit Kenny, releasing the IKK complex from autophagosomal repression to enable effective innate immune responses.

molecular biology↗

bioRxiv2026

Interclonal cooperation and suppression shape early Ras-driven tumour growth

Cancer is generally thought to be caused by expansion of a single mutant cell. However, analyses of human early lesions show that tumours can originate from several genetically distinct cell populations1-5. How neighbouring mutant clones interact to shape tumourigenesis, and which driver genes mediate these effects is largely unexplored. Here, we use an in vivo mosaic Drosophila epithelial model to systematically test interclonal interactions during early Ras-driven tumourigenesis. We screened 88 recurrent RAS co-mutated driver genes in human carcinomas for their ability to modify Ras-clone growth when disrupted in neighbouring epithelial clones. This uncovered two opposing classes of interactions: Interclonal cooperativity, where neighbouring mutant clones promote the overgrowth of Ras mutant tumours, and interclonal suppression, in which neighbours restrain Ras tumours, unexpectedly improving host survival. The strongest suppressive modifiers included canonical cell competition regulators, including Myc, archipelago (ago/FBXW7), and taiman (tai/NCOA1-3). In contrast, the strongest cooperative modifiers were disruptions of XNP/ATRX and SWI/SNF chromatin remodelling subunits (including Osa/ARID1A, Bap170/ARID2, Polybromo/PBRM1, among others), which in neighbouring cells induce a wound-like inflammatory program and drive an anabolic, pro-growth state in Ras tumours. Notably, the disruption of SWI/SNF components cell autonomously within Ras tumours confers no cooperativity. We show that interclonal cooperative Ras tumour growth requires reactive oxidative species and prostaglandin synthesis in SWI/SNF-disrupted clones. Together, this study provides a catalogue and emerging principles of cooperative and suppressive interclonal interactions among recurrent RAS co-mutated drivers, extending the rules of oncogenic cooperation beyond cell intrinsic co-mutation.

cancer biology↗

bioRxiv2024

EyaHOST a modular genetic system for investigation of intercellular and tumor-host interactions in Drosophila melanogaster

Cell biology and genetic analysis of intracellular, intercellular and inter-organ interaction studies in animal models are key for understanding development, physiology, and disease. The MARCM technique can emulate tumor development by simultaneous clonal tumor suppressor loss-of-function generation coupled with GAL4-UAS-driven oncogene and marker expression, but the utility is limited for studying tumor-host interactions due to genetic constraints. To overcome this, we introduce EyaHOST, a novel system that replaces MARCM with the QF2-QUAS binary gene expression system under the eya promoter control, unleashing the fly community genome-wide GAL4-UAS driven tools to manipulate any host cells or tissue at scale. EyaHOST generates epithelial clones in the eye epithelium similar to MARCM. EyaHOST-driven RasV12 oncogene overexpression coupled with scribble tumor suppressor knockdown recapitulates key cancer features, including systemic catabolic switching and organ wasting. We demonstrate effective tissue-specific manipulation of host compartments such as neighbouring epithelial cells, immune cells, fat body, and muscle using fly avatars with tissue-specific GAL4 drivers. Organ-specific inhibition of autophagy or stimulation of growth-signaling through PTEN knockdown in fat body or muscle prevents cachexia-like wasting. Additionally, we show that RasV12, scribRNAi tumors induce caspase-driven apoptosis in the epithelial microenvironment. Inhibition of apoptosis by p35 expression in the microenvironment promotes tumor growth. EyaHOST offers a versatile modular platform for dissecting tumor-host interactions and other mechanisms involving intercellular and inter-organ communication in Drosophila. Highlights*eyes absent, eye disc-specific enhancer drives clonal KD recombinase flip-out activated QF2 expression in the larval eye epithelium for simultaneous QUAS-driven gain and loss-of-function analysis of gene function. *Clones are visualized by QUAS-tagBFP or QUAS-eGFP facilitating analysis of existing fluorescent reporters. *The GAL4-UAS system and existing genome-wide genetic tools are released to independently manipulate any cell population in the animal for cell biology, intercellular or inter-organ analysis for developmental, physiological, or disease model analysis. *Fly avatars for tumor-host interaction studies with multiple organs allow live monitoring and manipulation of tumors and organs in translucent larva.

cancer biology↗

bioRxiv2024

Oncogenic Ras-driven Dorsal/NF-κB signaling contributes to tumorigenesis in a Drosophila carcinoma model

Cancer-driving mutations synergize with inflammatory stress signaling pathways during carcinogenesis. Drosophila melanogaster tumour models are increasingly recognized as models to inform conserved molecular mechanisms of tumorigenesis with both local and systemic effects of cancer. Although initial discoveries of the Toll-NF{kappa}B signaling pathway in development and immunity was pioneered in Drosophila, limited information is available for its role in cancer progression. Using a well-studied cooperative RasV12 -driven epithelial-derived tumour model, we here describe functions of Toll-NF-{kappa}B signaling in malignant RasV12, scrib- tumors. The extracellular Toll pathway components ModSP and PGRP-SA and intracellular signaling Kinase, Pelle/IRAK, are rate-limiting for tumor growth. The Toll pathway NF{kappa}B protein Dorsal, as well as cactus/I{kappa}B show elevated expression in tumors with highest expression in invasive cell populations. Oncogenic RasV12, and not loss of scribble, confers increased expression and heterogenous distribution of two Dorsal isoforms, DorsalA and DorsalB in different tumour cell populations. Mechanistic analyses demonstrates that Dorsal drives growth and malignancy by suppressing differentiation, counteracting apoptosis and promoting invasion of RasV12, scrib- tumors genetically dependent on twist and snail.

cancer biology↗

bioRxiv2024

Genome-wide profiling of the hierarchical control of autophagy dynamics using deep learning

Recycling of cellular components through autophagy maintains homeostasis in dynamic nutrient environments, and its dysregulation is linked to several human disorders. Although extensive research has characterized the core mechanisms of autophagy, limited insight into its systems-wide dynamic control has hampered predictive modeling and effective in vivo manipulation. In this study, we mapped the genetic network that controls both the dynamic activation and inactivation of autophagy during nitrogen changes, using a combination of time-resolved high-content imaging, deep learning, and latent feature analysis. This approach generated a comprehensive genome-wide profiling repository, termed AutoDRY, categorizing 5919 mutants based on their nutrient response kinetics and differential contributions to autophagosome formation and clearance. Integrating these profiles with functional and genetic network data unveiled a hierarchical and multi-layered control of autophagy, identifying new regulatory aspects of the core machinery and established nutrient-sensing pathways. By leveraging multi-omics resources and explainable machine learning to predict genetic perturbation effects and infer new regulatory mechanisms, we identified the retrograde pathway as a pivotal, time-varying autophagy modulator through transcriptional tuning of core genes. By charting the systems-wide dynamical control of autophagy, we have laid the groundwork for connecting the complexity of genome-wide influences with specific core mechanisms. This represents a significant advancement in studying complex genetic phenotypes, guides functional genomics of dynamic cellular processes in any organism, and provides a powerful starting point for hypothesis-based research on autophagy.

systems biology↗

bioRxiv2020

Host autophagy mediates organ wasting and nutrient mobilization for tumor growth

During tumor growth - when nutrient and anabolic demands are high - autophagy supports tumor metabolism and growth through lysosomal organelle turnover and nutrient recycling1. Ras-driven tumors additionally invoke non-autonomous autophagy in the microenvironment to support tumor growth, in part through transfer of amino acids2-4. Here we uncover a third critical role of autophagy in mediating systemic organ wasting and nutrient mobilization for tumor growth using a well-characterized malignant tumor model in Drosophila melanogaster. Micro-computed X-ray tomography and metabolic profiling reveal that RasV12; scrib-/- tumors grow 10-fold in volume, while systemic organ wasting unfolds with progressive muscle atrophy, loss of body mass, -motility, -feeding and eventually death. Tissue wasting is found to be mediated by autophagy and results in host mobilization of amino acids and sugars into circulation. Natural abundance Carbon 13 tracing demonstrates that tumor biomass is increasingly derived from host tissues as a nutrient source as wasting progresses. We conclude that host autophagy mediates organ wasting and nutrient mobilization that is utilized for tumor growth.

cell biology↗

bioRxiv2020

Natural abundance isotope ratios to differentiate sources of carbon used during tumor growth in vivo

BackgroundRadioactive or stable isotopic labeling of metabolites is a strategy that is routinely used to map the cellular fate of a selected labeled metabolite after it is added to cell culture or to the circulation of an animal. However, the transformation of the labeled metabolite by cellular metabolism within organs complicates the use of this experimental strategy to quantify and understand metabolite transfer between organs. These methods are also technically demanding, expensive and potentially toxic. To allow quantification of the bulk movement of metabolites between organs, we have developed a novel application of stable isotope ratio mass spectrometry (SIRMS). ResultsWe exploit natural differences in 13C/12C ratios of plant nutrients for a low-cost and non-toxic carbon labeling, allowing a measurement of bulk carbon transfer between organs in vivo. SIRMS measurements were found to be sufficiently sensitive to measure organs from individual Drosophila melanogaster larvae, giving robust measurements down to 2.5 {micro}g per sample. We apply the method to determine if carbon incorporated into a growing solid tumor is ultimately derived from food or host tissues. ConclusionMeasuring tumor growth in a D.melanogaster larvae tumor model reveals that these tumors derive a majority of carbon from host sources. We believe the low cost and non-toxic nature of this methodology gives it broad applicability to study carbon flows between organs also in other animals and for a range of other biological questions.

cancer biology↗