Biology subjects

Patel, K.

Publications and source records attributed to Patel, K..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Relative phase of membrane potential theta oscillations between individual hippocampal neurons code space

The timing of spikes dictates a neurons impact on downstream circuits and behavior, and spike timing is determined by the membrane potential (Vm). However, due to technical challenges, it has been impossible to analyze the relative timing of Vm dynamics between neurons during behavior. Using large scale membrane voltage imaging, we simultaneously recorded Vm from many individual hippocampal neurons in animals engaged in a virtual spatial task. We found that relative phase of Vm theta oscillations across neurons exhibit gradual or discrete shifts depending on spatial position. This finding extends beyond previous studies showing Vm dynamics in single neurons or spiking activity in multiple neurons, revealing previously unknown evidence for consistent coding of space by spike-independent relative phase of Vm theta dynamics between neurons.

neuroscience↗

bioRxiv2025

Predicting Isoniazid Resistance in Mycobacterium tuberculosis Complex in New York State using Whole Genome Sequencing

Isoniazid (INH) is a critical antibiotic used worldwide for treatment and prophylaxis of tuberculosis. Drug resistance (DR) to INH is the single most common type of DR, mediated by multiple genes/loci including katG, inhA, mabA, mabA-inhA and the oxyR-ahpC intergenic region. Over the course of 6 years, we performed a 2-phase study of 3,696 Mycobacterium tuberculosis complex (MTBC) strains aiming to determine the molecular basis of INH resistance and assess whole genome sequencing (WGS) for predicting resistance. In phase 1, we performed a side-by-side study including 1,767 strains with paired phenotypic drug susceptibility testing (DST) and genotypic DST. We found WGS capable of accurately predicting INH resistance with sensitivity of 90.3%, and specificity of 99.8%. The negative predictive value of WGS for INH susceptibility was 98.8%. Based on these findings, we developed a molecular testing algorithm where phenotypic DST was reduced and applied this new testing algorithm in phase 2 to 1,929 MTBC strains, resulting in streamlined testing, reduced cost and decreasing turnaround time (TAT). The prevalence of INH resistance among MTBC strains in New York was found to be 10.2%. Of the 3,696 isolates tested, 337 were predicted INH resistant by WGS. Of 41 additional strains exhibiting phenotypic INH resistance, 38 were found to have mutations in genes known to be associated with INH resistance. This study demonstrates the utility of WGS as a molecular tool for predicting INH DR and shows that the vast majority of INH resistance in MTBC has a molecular basis in known resistance loci.

microbiology↗

bioRxiv2025

Peptide molecular glues select between BET paralogues by exploiting allosteric sites and conformational dynamics

Achieving selective target inhibition is critical for minimising drug side effects. This can be especially challenging when targeting individual members of protein families with high sequence similarity. A well-recognised example is the Bromodomain and Extraterminal domain (BET) family of proteins. Chemical inhibition of the acetyllysine (AcK)-binding bromodomains (BDs) of BET proteins has shown considerable promise in a range of disease models. However, despite over a decade of medicinal chemistry efforts, it has proven challenging to develop BET BD inhibitors that exhibit high selectivity between BET family paralogues. Cyclic peptides are versatile scaffolds for therapeutic development and often exhibit high selectivity and affinity for their targets. To explore their potential as selective BET BD inhibitors, we have used mRNA display to identify cyclic peptide ligands for the N-terminal BD of BRD2 and BRD4. The structurally diverse cyclic peptides enriched from the selections boast superior selectivity and affinity to previously developed inhibitors. Most strikingly, we isolated cyclic peptides with [~]1000-fold higher affinity for their target BD over the paralogous BDs, far surpassing selectivities reported to date. Our biochemical and structural data suggest that paralogue-selective cyclic peptides act as molecular glues, exploiting both subtle sequence differences at locations far from the AcK-binding pocket and differences in conformational dynamics between BET BD paralogues to achieve this unprecedented level of specificity. This work provides a blueprint for the development of new classes of selective BET inhibitors and, more generally, underscores the potential of exploiting protein dynamics in the design of selective ligands.

biochemistry↗

bioRxiv2025

Hypoxia-induced metastatic heterogeneity in pancreatic cancer

In most solid tumors, hypoxia constitutes a defining microenvironmental feature that reprograms malignant cells into a highly metastatic state by driving cellular plasticity and exacerbating chromosomal instability (CIN). However, the mechanisms by which cancer cells concurrently co-opt these elements of hypoxic adaptation to promote metastasis remains poorly understood. Here, we report that hypoxia promotes metastasis by suppressing the JmjC-containing histone lysine demethylase Kdm8. CRISPR/Cas9-mediated targeting of Kdm8 in a Kras;Trp53-driven mouse model of pancreatic ductal adenocarcinoma (PDA) robustly rewires the malignant cell transcriptomic programs, leading to a profound loss of the epithelial morphology and widespread metastatic disease. In PDA patients, a high KDM8-induced gene signature is associated with reduced metastatic burden and better survival in advanced disease. Notably, Kdm8 suppression in normoxia recapitulates key aspects of the global epigenetic and transcriptomic rewiring, mitotic spindle defects, and CIN induced by hypoxia. Moreover, disruption of Kdm8s demethylase activity phenocopies Kdm8 loss, whereas expression of hypermorphic Kdm8 variants resistant to hypoxic suppression markedly reduces metastasis beyond the levels achieved by the wildtype protein. Through the suppression of Kdm8 demethylase function, hypoxia unleashes a potent metastatic program by simultaneously advancing cellular plasticity and CIN.

cell biology↗

bioRxiv2025

IL-12 Secreting CAR-T Cells Reprogram the Tumor Microenvironment and Improve Efficacy Against Heterogeneous Models of Glioblastoma

BackgroundGlioblastoma (GBM) remains uniformly lethal due to pronounced intratumoral heterogeneity and a highly immunosuppressive microenvironment that limits the efficacy of targeted therapies. MethodsWe engineered chimeric antigen receptor (CAR) T cells targeting EGFRvIII and armored them with a single-chain interleukin-12 (scIL12) payload. These cells were tested in syngeneic, orthotopic GBM mouse models exhibiting heterogeneous EGFRvIII expression. CAR T cells were delivered intracranially without lymphodepletion. ResultsIntracranial administration of of scIL12-secreting CAR-T cells eradicated tumors without requiring lymphodepletion, achieving 50% long-term survival. Survival benefits depended entirely on endogenous CD8 T cells, as efficacy was abolished in CD8-deficient hosts and unaffected by NK cell depletion. Notably, therapeutic efficacy was abrogated by lymphodepletion, underscoring the necessity of an intact endogenous immune response. Mechanistically, scIL12 enhanced CAR-T cell persistence and reprogrammed tumor-associated microglia, indicating potential epitope spreading through polyclonal endogenous CD8+ T-cell responses, which facilitate the elimination of EGFRvIII-negative tumor cells. ConclusionsThis study demonstrates the pleiotropic benefits of IL-12 armored CAR-T cells with improved targeting of antigen-positive tumor cells and simultaneous remodeling of the microenvironment to engage adaptive immunity against antigen-negative clones. This strategy offers a potential clinically actionable approach to improve outcomes in GBM by circumventing the need for toxic lymphodepletion and addressing tumor heterogeneity.

immunology↗

bioRxiv2025

The BRD4-nucleosome interaction is enhanced modestly and non-selectively by histone acetylation

BRD4 regulates gene transcription in complex eukaryotes, in part through the binding of its tandem bromodomains to acetylated lysine residues found in histones and transcription factors. Despite pharmacological inhibition of these domains showing promise in preclinical studies, clinical trial data have been less encouraging so far. A stronger understanding of BRD4 biochemistry could provide a route to better outcomes. To advance on prior work, which has focused almost entirely on the binding of isolated bromodomains and acetylated peptides, we have sought the preferred nucleosomal binding partner of full-length BRD4. We demonstrate that BRD4 binds with sub-micromolar affinity to both unmodified nucleosomes and to DNA alone. In strong contrast to BRD4-peptide interactions, we also find that the affinity of BRD4 for nucleosomes is increased only 2-4-fold by histone acetylation and that this affinity has little dependence on the acetylation pattern. Despite this modest effect of acetylation, binding of BRD4 to acetyllysine in the nucleosome was more resistant to perturbation by mutation or small-molecule inhibition than BRD4-peptide interactions. Our work helps bridge the gap between cellular and prior in vitro work and provides clues to explain the in vivo chromatin occupancy profile of BRD4 and how it changes upon therapeutic inhibition. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=79 SRC="FIGDIR/small/656505v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@1aa532aorg.highwire.dtl.DTLVardef@13a154forg.highwire.dtl.DTLVardef@4d2039org.highwire.dtl.DTLVardef@17e8377_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2025

Experimental flooding impacts soil biogeochemistry but not aboveground vegetation in a coastal forest

Rising sea levels and intensifying storms increase flooding pressure on coastal forests, triggering tree mortality, ecosystem transitions, and changes to the coastal carbon cycle. However, the mechanisms that drive coastal forest mortality remain elusive due to the complex interplay between belowground and aboveground processes during flooding disturbances and limitations of observations typically reported in coastal forest mortality studies. We used an ecosystem-scale manipulation to simulate hurricane-level flooding of a coastal forest. Monitoring real-time soil conditions and tree physiological responses, we observed consistent impacts on soil biogeochemistry aligned with belowground drivers of tree mortality, but no consistent responses in aboveground vegetation. Our findings provide unprecedented empirically based insight into the earliest stages of a hypothesized forest mortality spiral and offer critical benchmarks for predicting coastal forest resilience in the face of accelerating climate change. Significance StatementChanging sea levels and storms are causing more flooding in coastal forests. This flooding kills trees, changing how coastal ecosystems function, but we do not fully understand what factors determine whether forests survive flooding. We designed an ecosystem-scale experiment to answer this question, with controlled saltwater and freshwater floods equivalent to a hurricane in experimental forest plots. Flooding quickly changed soil conditions, but we have not yet observed consistent tree stress responses. Our study provides the most detailed measurements to date of how coastal forests respond to flooding in real time. These findings will help us better understand the early mechanisms and warning signs of forests threatened by flooding.

systems biology↗

bioRxiv2025

A large global soil carbon sink informed by repeated soil samplings

Partitioning the terrestrial carbon sink between vegetation and soil is crucial for predicting future climate change, but the role of soils remains poorly quantified. Here, we compiled 3,099 soil organic carbon time series spanning five decades. We found a global soil organic carbon sink of 1.83 {+/-} 0.9 (mean {+/-} SE) petagrams per year from 1992 to 2020, driven by extratropical young forests, boreal old forests, and grasslands, while trends in tropical ecosystems remain uncertain. Our findings suggest the net land sink resides almost exclusively belowground as soil carbon, emphasizing the global opportunity of soil conservation and restoration for climate mitigation.

ecology↗

bioRxiv2025

mcDETECT: Decoding 3D Spatial Synaptic Transcriptomes with Subcellular-Resolution Spatial Transcriptomics

Spatial transcriptomics (ST) is a powerful tool for studying the molecular basis of brain diseases. However, most current analyses focus only on nuclear or somatic expression, overlooking distally localized mRNAs, known as the "dark transcriptome." These transcripts, which make up nearly 40% of the brain transcriptome, are packaged into RNA granules and transported to polarized neuronal structures critical for neuronal function. Here, we present mcDETECT, a machine learning framework that leverages in situ ST (iST) data to detect RNA granules and resolve their RNA composition. Applying mcDETECT to simulated and real datasets from multiple iST platforms, we demonstrate robust granule detection and molecular subtyping. Granule-informed downstream analysis further revealed functionally distinct neuronal substates not captured by somatic expression alone. In an Alzheimers disease (AD) mouse model, mcDETECT uncovered alterations in RNA granule distributions and associated neuronal substates prior to measurable neuronal loss, highlighting potential therapeutic targets for early AD pathology.

bioinformatics↗

bioRxiv2025

The Pro- vs. Anti-Angiogenic Capacity of Short Chain Fatty Acids is Dependent on the Bioavailability of FFAR3 in Peripheral Artery Disease.

BackgroundOur current study builds on our recent report that showed Palmitate aggravates ischemic endothelial (EC) dysfunction in vitro and aims to determine whether Palmitate is a critical determinant of PAD severity. In contrast to Palmitate, we studied the role of short-chain fatty acids (SCFAs) in regulating ischemic revascularization in PAD. MethodsFemoral artery ligation and resection was used as preclinical-PAD model. Hypoxia serum starvation was used as in vitro PAD model. ResultsPalmitate dramatically decreased ischemic-EC survival and angiogenic capacity in vitro, whereas SCFAs significantly induced their angiogenic capacity. LC-MRM MS analysis showed decreased SCFA content in ischemic-muscle. Laser Speckle perfusion imaging showed that intramuscular SCFA treatment significantly induced perfusion recovery, whereas Palmitate showed a modest but significant impairment in perfusion recovery. Immunoblot analysis showed that SCFAs preferentially induce Free fatty acid receptor (FFAR)-3, but not FFAR2. Accordingly, silencing FFAR3 decreased ischemic-EC angiogenic capacity, whereas inhibiting FFAR2 induced ischemic angiogenesis. Pharmacological inhibition of FFAR3 by beta-hydroxybutyrate (BHB) significantly decreased perfusion recovery. SCFA treatment further decreased perfusion recovery in BHB-treated ischemic-muscle. Mechanistically, inhibiting FFAR3-induced FFAR2-levels that inhibited ischemic-EC angiogenic capacity by decreasing NO and inducing ROS levels in SCFA-treated ischemic-ECs. ConclusionsOur data shows that Palmitate alone is not sufficient to drive the PAD severity. Increased FFAR3 levels in ischemic-muscle allow SCFAs to activate the AKT-NO axis to induce ischemic angiogenesis and perfusion recovery. However, loss of FFAR3 in ischemic-muscle promotes FFAR2 activation that blocks SCFA-induced NO-production and redox balance thereby inhibiting perfusion recovery in preclinical-PAD.

pathology↗

bioRxiv2025

Whole-genome sequencing analysis of anthropometric traits in 672,976 individuals reveals convergence between rare and common genetic associations

Genetic association studies have mostly focussed on common variants from genotyping arrays or rare protein-coding variants from exome sequencing. Here, we used whole-genome sequence (WGS) data in 672,976 individuals of diverse ancestry to evaluate the contribution and architecture of rare non-coding variants to three commonly studied anthropometric traits: height, body mass index (BMI) and waist-hip ratio adjusted for BMI (WHRadjBMI). Analysing 447,461 individuals in UK Biobank for discovery and 225,515 individuals in All of Us for replication, we identified 90 novel rare and low-frequency single variant associations. This includes two independent rare variants upstream of IGF2BP2 that both substantially reduce WHRadjBMI, but have distinct effects on other adiposity traits. We identified 135 coding variant aggregates, several of which were missed by exome sequencing studies. For example, UBR3 protein-truncating variants were associated with a 2.7kg/m2 increase in BMI. We additionally identified 51 non-coding variant aggregate associations, including in the 5UTR of FGF18 (a highly constrained gene with no previously reported coding associations) associated with up to 6cm effects on height. We show that 97% of rare variant associations occur near GWAS loci demonstrating convergence of rare and common variant associations. Finally, we show that ultra rare variants (MAF<0.01%) explain a small fraction of heritability (<10%) compared to common variants for these traits, that heritability is largely shared across ancestries, and that this heritability is concentrated at or near common variant loci. Our work demonstrates the importance of large-scale WGS for fully understanding the genetic architecture of complex traits.

genetics↗

bioRxiv2025

Desmoplakin tail domain position in the desmosomal plaque is isoform dependent

Desmoplakin (DP) is the anchoring subunit of desmosomes, macromolecular junctions that provide mechanical integrity to the skin and heart. DP has three isoforms, DPI, DPIa, and DPII that arise from alternative splicing. The isoforms are structurally identical excluding the length of their central rod domain. As desmosomes are macromolecular complexes, the precise arrangement of their component proteins, or architecture, is essential to maintain physiological function. Alterations of the tissue-specific expression of DP isoforms underlies rare human diseases impacting the skin and heart. Overall DP is oriented with its head domain closest to the plasma membrane and tail domain extending into the cytosol. However, the differences in the architecture of the DP isoforms within the desmosomal plaque remains unknown. Here, we sought to define the architectural arrangement of each DP isoform. To address this, we utilized direct stochastic optical reconstruction microscopy (dSTORM) and analysis of DP KO HaCaT cells stably expressing DPI, DPIa, or DPII with a C-terminal mEGFP tag. Our results show the DP head domain position in the desmosomal plaque is isoform independent and the DP tail domain position correlates with rod length. The tail domain of DPI, the isoform with the longest rod, is furthest from the plasma membrane and that of DPII, the isoform with the shortest rod, is closest. We propose a variable tail location model to describe the architectural arrangement of each isoform. In this model, the DP isoforms are arranged with their rod domains parallel at an angle between 21{degrees} to 25{degrees} from the plasma membrane. These results provide valuable insight into the role of DP isoforms in desmosomal architecture and function.

cell biology↗

bioRxiv2025

Derivation of cardiac reference ranges for Mus musculus using the Collaborative Cross and identification of new cardiac models

Contemporary approaches for developing interventions and assessing pre-clinical cardiovascular risk frequently utilize animal and in vitro models. However, these models currently lack normal species-specific reference ranges similar to what exists for humans. The genetically diverse Collaborative Cross (CC) population that models human genetic heterogenetiety was characterized to develop mouse-specific cardiac reference ranges for Mus muscuslus, the most commonly used pre-clincial model. Heart function was analyzed in males and females from 58 CC strains and C57BL/6J using high-frequency ultrasound under both conscious and anesthetized conditions, as well as conscious electrocardiography to develop two standard deviation-based reference ranges. The sources and magnitude of measurement variability were identified, and inter-laboratory comparisons determined to quantify phenotypic robustness and heritability. Strain was the largest source of variability, while laboratory where data were collected was also significant but sex was not. Additionally, strains were identified that have characteristics of disease-associated phenotypes in cardiac function and electrophysiology similar to human cases including dilated cardiomyopathy, systolic cardiomyopathy, cancer therapy-related cardiac dysfunction, and long QT. These new models allow a more natural, and therefore more translatable progession to a cardiac disease state, supporting development of strain-specific models for cardiac pathologies, ultimately allowing more accurate diagnoses and informative safety assessments in humans. Article SummaryThe Collaborative Cross (CC) mouse reference population, modeling human genetic diversity, was utilized to derive cardiac reference values for Mus musculus. Strain was the primary source of variability, with the laboratory also playing a significant role, while sex had no impact. Despite inter-laboratory reproducibility challenges, the study identified strains resembling disease-associated phenotypes that offer a more natural progression to cardiac disease and provide crucial data for early disease identification and accurate safety assessments in humans.

genetics↗

bioRxiv2025

A Class 1 OLD family nuclease encoded by Vibrio cholerae is countered by a vibriophage-encoded direct inhibitor

Bacteria are constantly threatened by their viral predators (phages), which has resulted in the development of defense systems for bacterial survival. One family of defense systems found widely across bacteria are OLD (for overcoming lysogeny defect) family nucleases. Despite recent discoveries regarding Class 2 and 4 OLD family nucleases and how phages overcome them, Class 1 OLD family nucleases warrant further study as there has only been one anti-phage Class 1 OLD family nuclease described to date. Here, we identify the Vibrio cholerae-encoded Class 1 OLD family nuclease Vc OLD and describe its disruption of genome replication of the lytic vibriophage ICP1. Furthermore, we examine its in vitro activity, identifying Vc OLD as a DNA nickase. Finally, we identify the first direct inhibitor of a Class 1 OLD family nuclease, the ICP1-encoded Oad1. Our research further illuminates Class 1 OLD family nucleases role in phage defense and explores the dynamic arms race between V. cholerae and its predatory phage ICP1.

microbiology↗

bioRxiv2024

Cytosolic Carboxypeptidase 5 maintains mammalian ependymal multicilia to ensure proper homeostasis and functions of the brain

Ependymal multicilia position at one-side on the cell surface and beat synchronously across tissue to propel the flow of cerebrospinal fluid. Loss of ependymal cilia often causes hydrocephalus. However, molecules contributing to their maintenance remain yet fully revealed. Cytosolic carboxypeptidase (CCP) family are erasers of polyglutamylation, a conserved posttranslational modification of ciliary-axoneme microtubules. CCPs possess a unique domain (N-domain) N-terminal to their carboxypeptidase (CP) domain with unclear function. Here, we show that a novel mutant mouse of Agbl5, the gene encoding CCP5, with deletion of its N-terminus and partial CP domain (designated Agbl5M1/M1), developed lethal hydrocephalus due to degeneration of ependymal multicilia. Interestingly, multiciliogenesis was not impaired in Agbl5M1/M1 ependyma, but the initially formed multicilia beat in intercellularly diverse directions, indicative of aberrant tissue-level coordination. Moreover, actin networks are severely disrupted and basal body patches are improperly displaced in mutant cells, suggesting impaired cell level polarity. In contrast, Agbl5 mutants with disruption solely in the CP domain of CCP5 (Agbl5M2/M2) do not develop hydrocephalus despite increased glutamylation levels in ependymal cilia as similarly seen in Agbl5M1/M1. This study revealed an unappreciated role of CCP5, particularly its N-domain, in ependymal multicilia stability associated with their polarization and coordination.

cell biology↗

bioRxiv2024

Asynchronous Transitions from Hepatoblastoma to Carcinoma in High-Risk Pediatric Tumors

BackgroundPediatric hepatocellular tumors are most commonly classified as hepatoblastoma (HB) or hepatocellular carcinoma (HCC), yet a subset exhibits mixed histological and molecular features of both. These tumors, previously described as hepatoblastomas with carcinoma features (HBCs), include cases provisionally designated by the World Health Organization as hepatocellular neoplasm-not otherwise specified (HCN-NOS). Their biology remains poorly understood, with unresolved questions about their cellular composition and outcomes. In particular, it is unclear whether HBCs comprise hybrid cell populations with combined HB and HCC characteristics (HBC cells) or admixtures of distinct HB and HCC cells. MethodsWe performed multi-omics profiling--including snRNA-seq, snDNA-seq, and multi-region longitudinal bulk RNA and DNA sequencing--to characterize HBC composition, evolution, and treatment response. ResultsHBCs comprise heterogeneous mixtures of HB-like, HBC-like, and HCC-like molecular cell types. HBC outcomes are significantly worse than HB, and HBC cells are more chemoresistant than HB cells, with resistance shaped by their cell identity, genetic alterations, and embryonic differentiation stage. HBC cells originate from HB cells that were arrested at early hepatic stem cell development stages because of aberrant WNT signaling activation. Inhibition of WNT signaling promoted differentiation and enhanced sensitivity to chemotherapy. Furthermore, each analyzed HBC reflected a dynamic process of multiple HB-to-HBC and HBC-to-HCC transitions, underscoring their evolutionary complexity. ConclusionsMulti-omics profiling of HBCs revealed key findings about their biology and composition, demonstrating that they originate from HB precursors at early hepatic stem cell development stages and that their differentiation arrest depends on sustained aberrant WNT-signaling activity.

genomics↗

bioRxiv2024

Scalable Fabrication of a Tough and Recyclable Spore-Bearing Biocomposite Thermoplastic Polyurethane

Thermoplastic polyurethanes (TPUs) are a class of versatile thermoplastic elastomers where most of their products lack a proper recycling strategy or have no end-of-life solutions. To pursue a sustainable end-of-life solution for TPU based products, self-disintegrating biocomposite TPUs have recently been developed by embedding spores of TPU-degrading bacteria into TPUs using melt extrusion. Herein, we improve upon spore-bearing biocomposites and demonstrate industrially-relevant manufacturing conditions for the fabrication of biocomposite TPUs. Spore production was modified to reduce the innate brown color of the resulting materials and, effectively minimize the coloration of biocomposite TPUs. Reduction of FeSO4 in a sporulation media generated white spores without compromising spore productivity, viability, morphology or heat-shock tolerance. Biocomposite TPUs containing white spores displayed a 45% increase in toughness compared to TPUs without spores, while retaining [~]90% spore viability post processing. Furthermore, biocomposite TPU fabrication was demonstrated using a scalable continuous extruder followed by injection molding. Biocomposite TPUs generated by these industry-relevant processes exhibited comparable toughness improvement and spore viability to biocomposite TPU prepared using a lab scale microcompounder, while enhancing productivity by 30-fold. Finally, spore addition improved biocomposite TPUs recyclability, enabling 80% toughness retention after 5 rounds of iterative melt processing. Additionally, no negative effect on the lifespan of the generated TPUs was observed over a duration of 1 year of storage. Overall, this study confirmed that spore-bearing biocomposite TPUs are promising for practical applications, offering an accessible method to enhance toughness and sustainability of commercial TPUs through the incorporation of spore-based living fillers.

bioengineering↗

bioRxiv2024

KRAS G12 mutant alleles differentially control glutamine metabolism via FOXO1

Mutations in KRAS, particularly at codon 12, are frequent in adenocarcinomas of the colon, lungs and pancreas, driving carcinogenesis by altering cell signalling and reprogramming metabolism. However, the specific mechanisms by which different KRAS G12 alleles initiate distinctive patterns of metabolic reprogramming is unclear. Using isogenic panels of colorectal cell lines harbouring the G12A, G12C, G12D and G12V heterozygous mutations and employing transcriptomics, metabolomics, and extensive biochemical validation, we demonstrate distinctive features of each allele. We also demonstrate that cells harbouring the common G12D and G12V oncogenic mutations significantly alter glutamine metabolism and nitrogen recycling through FOXO1-mediated regulation compared to parental lines. Moreover, with a combination of small molecule inhibitors targeting glutamine and glutamate metabolism, we also identify a common vulnerability that eliminates mutant cells selectively. These results highlight a previously unreported mutant-specific effect of KRAS alleles on metabolism and signalling that could be potentially harnessed for cancer therapy. In briefBer et al. reveal common and distinct features of oncogenic KRAS mutant isogenic cell lines. Mutant lines upregulate different nitrogen-recycling metabolic pathways and show sensitivity to combinatorial drugging of glutamine metabolism. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/618135v1_ufig1.gif" ALT="Figure 1"> View larger version (101K): org.highwire.dtl.DTLVardef@1459558org.highwire.dtl.DTLVardef@14fcd43org.highwire.dtl.DTLVardef@2d22ccorg.highwire.dtl.DTLVardef@147b068_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIDifferent KRAS mutations trigger distinct metabolic phenotypes in colorectal cell lines C_LIO_LIGlutamine metabolism and nitrogen recycling are upregulated in KRAS mutant cells C_LIO_LIFOXO1 is a key regulator of KRAS-induced rewiring of glutamine and nitrogen metabolism C_LIO_LIInhibition of glutamine synthetase and glutaminase selectively kills mutant KRAS lines C_LI

cancer biology↗