Biology subjects

Giri, S.

Publications and source records attributed to Giri, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Neuroendocrine-like/EMT dedifferentiation mediates resistance to EGFR inhibitors via the NRG1/HER3 axis

Patients with non-small cell lung cancer (NSCLC) carrying activating EGFR mutations typically respond favorably to third-generation EGFR tyrosine kinase inhibitors (TKIs) such as osimertinib. Nevertheless, resistance almost inevitably emerges, ultimately limiting the durability of these treatments. We investigated non-genomic mechanisms enabling drug-tolerant persister cells to survive EGFR inhibition, likely co-opting compensatory HER3 activation, whose underlying mechanisms remain unclear. Using a combination of immortalized and patient-derived cellular models, together with single-cell RNA sequencing, we demonstrate that activation of EGFR/HER3 axis constitutes an early adaptive response to TKI exposure enriched in pulmonary alveolar type I and type II cancer cells. This response is driven by neuregulin-1 (NRG1), produced by stromal cells and by cancer cells undergoing NE-like/EMT dedifferentiation. Importantly, in vivo studies demonstrated that combining EGFR inhibition and NRG1 neutralization by monoclonal antibody successfully eradicated tumors. Together, these findings point to a therapeutic strategy to overcome TKI resistance in NSCLC through targeting HER3 signalling, its interplay with EGFR, and tumor microenvironment-derived cues.

cancer biology↗

bioRxiv2026

A decline in skeletal muscle NOX4 abrogates adaptive homeostasis and exacerbates ageing

A decline in NFE2L2-orchestrated adaptive homeostasis and oxidative distress are thought to be key features of ageing. In contracting skeletal muscle, the ROS-producing enzyme NADPH oxidase 4 (NOX4) is a potent inducer of NFE2L2 adaptive homeostasis. Here we report that skeletal muscle NOX4 levels decline in aged mice and humans, resulting in abrogated NFE2L2 adaptive homeostasis, increased protein oxidative damage and decreased muscle function. We show that deleting NOX4 in skeletal muscle exacerbates the physiological decline associated with ageing, resulting in overt sarcopenia and frailty, characterised by physical inactivity, increased adiposity, systemic inflammation, whole-body insulin resistance and advanced liver disease in aged chow-fed mice. The systems-wide physiological decline in aged skeletal muscle NOX4-deficient mice could be corrected by activating NFE2L2 with sulforaphane and reinstating adaptive homeostatic responses otherwise induced by exercise. Our findings provide important insights into the basis for the decline in NFE2L2-orchestrated adaptive homeostasis with age and identify key mechanisms by which exercise may promote healthy ageing.

physiology↗

bioRxiv2026

Proximity labelling of the BAK macropore uncovers a new role for SLC35A4-MP in mitochondrial dynamics

Mitochondrial permeabilization by the apoptotic executioners BAK and BAX represents a critical stage of mitochondrial apoptosis and facilitates the release of pro-inflammatory mitochondrial DNA via herniation of the inner mitochondrial membrane. This study utilises TurboID proximity labelling to investigate the temporal changes of the BAK proximal proteome during mitochondrial herniation and apoptosis. In doing so, we detail a comprehensive BAK proximal proteome, both at steady state and during apoptosis and observe the loss of MICOS complex stability and proximity to the BAK pore as apoptosis proceeds. In addition, we identify the mitochondrial microprotein SLC35A4-MP proximal to the BAK pore and reveal a SLC35A4-MP dependent modulation of OPA1 processing. Furthermore, loss of SLC35A4-MP delays mitochondrial fragmentation in response to a variety of stressors, uncovering a previously unrecognised role for SLC35A4-MP in fine-tuning mitochondrial rearrangement during apoptotic stress.

cell biology↗

bioRxiv2026

Integrated Artificial Intelligence and Quantum Chemistry Approach for the Rational Design of Novel Antibacterial Agents against Ralstonia solanacearum.

Antimicrobial resistance (AMR) in plant pathogenic bacteria poses a serious threat to global agriculture, necessitating the development of novel antibacterial agents targeting virulence mechanisms. This study presents an integrated bioinformatics-driven framework for the rational design and computational validation of Solres, a newly designed small molecule targeting key virulence proteins in phytopathogenic bacteria. Approximately 10,000 active compounds from PubChem BioAssay (AID: 588726) were analyzed using structural clustering and scaffold mining to identify conserved molecular motifs associated with antibacterial activity. Guided by high-frequency substructures, Solres was designed de novo and screened for structural novelty against PubChem, ChEMBL, and WIPO databases. Drug-likeness evaluation using Lipinskis Rule of Five confirmed favorable physicochemical properties. Molecular docking was performed against essential virulence regulators, including PhcA, PhcR, HrpB, PehA, and Egl from Ralstonia solanacearum and Xanthomonas spp., with active sites predicted using CaspFold. Docking analyses revealed strong binding affinities and stable interactions with key catalytic and regulatory residues. Complex stability and conformational integrity were further validated through molecular dynamics simulations. Quantum chemical descriptors, including HOMO-LUMO energy gap and dipole moment, supported the electronic suitability and reactivity profile of Solres. Collectively, this study demonstrates the effective integration of cheminformatics, structural bioinformatics, molecular simulations, and quantum chemical analyses for plant-focused antibacterial discovery. The compound Solres represents a promising lead candidate for mitigating bacterial wilt disease and provides a computational framework for future experimental validation and sustainable crop protection strategies against AMR-driven phytopathogens.

bioinformatics↗

bioRxiv2026

Formate-driven isoprene reduction enables energetic independence in Pelotomaculum schinkii: Evidence from metatranscriptomic and functional analyses

Isoprene, a volatile hydrocarbon emitted in vast quantities by terrestrial vegetation, can serve as a terminal electron acceptor in anoxic environments. Here, we investigated the molecular and physiological basis of isoprene reduction in an anaerobic enrichment culture highly enriched in Pelotomaculum. Substrate-exclusion assays revealed that formate is indispensable for isoprene reduction: cultures lacking formate showed no isoprene reduction, whereas formate alone sustained both reduction activity and the highest enrichment of Pelotomaculum. Metatranscriptomic analyses confirmed that Pelotomaculum schinkii was the most transcriptionally active species under isoprene-amended conditions, whereas Sedimentibacter saalensis was most enriched in unamended controls. Isoprene-treated cultures exhibited strong upregulation of [NiFe]-hydrogenase maturation factors (hypA/hybF, hypB), energy-conserving complexes (ATP synthase, H /Na - translocating pyrophosphatases), and transport systems (FeoB, ModBC), consistent with a formate-driven respiratory pathway. In contrast, genes for oxidative stress and metal detoxification were enriched in controls, suggesting physiological stress in the absence of isoprene. Thermodynamic calculations further supported this mechanism, showing that formate oxidation coupled to isoprene reduction is highly favorable ({Delta}G{degrees}' {approx} -135 kJ/mol), with an energy yield far exceeding that of formate-driven hydrogen production. Together, these findings support two mechanistic models: (i) direct isoprene reduction by group 4b [NiFe]-hydrogenase or (ii) indirect reduction via hydrogen transfer to an isrA-like oxidoreductase, analogous to Acetobacterium wieringae ISORED-2. Our results demonstrate that P. schinkii, a metabolically versatile bacterium, couples formate oxidation to isoprene respiration, indicating that isoprene can serve as an alternative electron sink. This allows P. schinkii to escape obligate syntropy with methanogens and alters microbial activity and energy conservation in anoxic ecosystems.

microbiology↗

bioRxiv2026

Anaerobic isoprene reduction by Pelotomaculum sp. from Eucalyptus-leaf sediments and its impacts on methanogenesis

Isoprene is a ubiquitous biogenic volatile organic compound (VOC) with atmospheric concentrations comparable to those of methane. Its high reactivity in the atmosphere significantly influences methane concentrations, contributing to adverse effects on the climate. Understanding the role of isoprene and its link to methane metabolism is crucial to addressing climate change. The fate of isoprene and its potential microbial degraders in soil, particularly in anaerobic environments, remains poorly investigated, underscoring the need for comprehensive studies. Our study provides physiological evidence for anaerobic microbial isoprene reduction and its influence on methanogenesis in Eucalyptus-leaf sediment. In our anaerobic culture-based studies, we have demonstrated that isoprene is reduced to three products, 3-methyl-1-butene, 2-methyl-1-butene, and 2-methyl-2-butene. Our findings suggest that Pelotomaculum sp. is capable of anaerobic isoprene reduction, as indicated by 16S rRNA analysis and dilution-to-extinction studies. Anaerobic microbial isoprene reduction simultaneously inhibited methane formation. Methanogenesis was completely inhibited in microcosm cultures amended solely with isoprene. In cultures supplemented with isoprene and carbon sources, only hydrogenotrophic methanogenesis was inhibited, indicating competition for hydrogen between the methanogens and isoprene degraders. Using a culture-based approach and molecular analysis, this study provides novel insights into the microbial dynamics of anaerobic isoprene reduction and the interplay between isoprene reducers and methanogens. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=118 SRC="FIGDIR/small/706888v1_ufig1.gif" ALT="Figure 1"> View larger version (62K): org.highwire.dtl.DTLVardef@9b559corg.highwire.dtl.DTLVardef@11ab71org.highwire.dtl.DTLVardef@ec759org.highwire.dtl.DTLVardef@41db7b_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2026

Discovering Novel PETase Enzymes for Enhanced PET Plastic Degradation Using in Silico Approaches

Accounting for 12% of global solid waste, Poly (ethylene terephthalate) (PET) is one of the most abundantly produced synthetic polymers. While PET offers substantial commercial benefits, its widespread use has led to disproportionate environmental hazards due to its resistance to degradation. To address this problem, several solutions have been proposed, including enzymatic degradation via PETase, MHETase, and Cutinase. Among these, PETase exhibited significant PET-degrading activity. However, the application of PETase has been hampered by its lack of robustness to pH, temperature ranges, and slow reaction rates. Hence, it has become novel enzymes that can overcome these limitations and function efficiently. In this study, we utilised an integrated in silico bioinformatics pipeline to identify and characterise novel PETase candidates from the Thermophilic actinobacteria Thermobifida cellulosilytica and Thermobifida halotolerans species. The PlasticDB database contains 228 plastic-degrading enzyme sequences. In which PETase (00188) is significantly homologous with two putative proteins, Hydrolase (ALF00495.1) and hypothetical protein (WOZ56011.1). The discrete optimized protein energy (DOPE) scores, stereochemical assessments, and homology modeling results closely mirrored our findings for both proteins, supporting their structural stability. The molecular dynamics simulations revealed that the putative ALF00495 variant exhibited more extensive and robust hydrogen-bonding networks, enhanced conformational stability, and increased structural compactness compared to the reference enzyme. The present in silico investigation underscores the potential of putative ALF00495 as a highly effective PETase biocatalyst for polyethylene terephthalate (PET) degradation. Collectively, these findings illustrate the utility of computational approaches of novel PET-degrading enzymes, thereby facilitating the development of sustainable biotechnological strategies to mitigate global plastic pollution.

bioinformatics↗

bioRxiv2025

Characterizing spatial functional microniches with SpaceTravLR

The advent of spatial omics has revolutionized our understanding of tissue biology; however, these technologies remain largely descriptive and do not capture how changes in gene regulation propagate across spatial neighborhoods. While in-silico perturbation methods and foundation models aim to model the impact of genetic perturbations, these methods are limited to single-cell approaches that lack spatial resolution. Other studies can delineate morphological domains based on transcriptional similarity, but not spatial functional microniches. We address this major unmet need by developing SpaceTravLR (Spatially perturbing Transcription factors, Ligands and Receptors), a novel interpretable machine learning approach that generalizes across tissues and species, uncovering spatial features linked to functional outcomes, thereby capturing functional microniches with spatial resolution. SpaceTravLR infers how single or combinatorial genetic perturbations rewire signals across the tissue neighborhood, by propagating effects through underlying spatially resolved molecular networks, thereby modeling how perturbations can reshape both the targeted cell and its surrounding neighborhood. SpaceTravLR defines novel spatial microniches across a range of tissues at different scales of organization (niches, neighborhoods and tissues), disease and developmental contexts. SpaceTravLRs perturbation predictions are made solely from spatial omics data and closely align with experimental validation or known outcomes based on mechanistic studies. Critically, our approach enables the generation of mechanistic hypotheses underlying identified niches. We show SpaceTravLR discovered a novel mechanism for Ccr4 that drives the spatial location of a pathogenic population of allergen-specific T helper 2 (Th2) cells as they develop in the lymph node, which was experimentally validated in a murine model. Overall, SpaceTravLR provides a novel interpretable and experimentally validated framework for uncovering how genes act individually and combinatorially through cell-intrinsic and cell-extrinsic circuits to shape spatial tissue organization and function.

systems biology↗

bioRxiv2025

Differentiation-Dependent Proximity Proteomics Identifies Novel Host Factors Linked to HPV16 E2 Function

Human papillomavirus 16 (HPV16) is a causative agent of oropharyngeal, cervical and anogenital cancers. The viral E2 protein is essential for viral genome replication, transcriptional regulation, episome maintenance, and activation of the host DNA damage response. Despite its central role, the full network of HPV16 E2 interactions with host proteins remains incompletely defined, particularly under differentiating conditions which support the complete viral life cycle. In this study, we used TurboID-based proximity labeling to characterize the interactome of HPV16 E2 and known host partner protein TOPBP1, in both undifferentiated monolayer and differentiating keratinocytes. We generated stable keratinocyte lines expressing doxycycline-inducible TurboID-tagged HPV16 E2 and confirmed that the tagged protein retained transcriptional, replicative, and DNA damage-inducing functions. Mass spectrometry analysis of streptavidin-enriched proteins identified both known and novel E2-associated host factors, including chromatin regulators, DNA repair proteins, and nucleolar components. Comparative analysis revealed a substantial overlap between E2 and TOPBP1 interactomes, and in situ validation by proximity ligation assay identified nucleolin (NCL) as a differentiation-dependent factor whose interaction with E2 is stabilized by TOPBP1. Functional studies demonstrated that NCL is required for episomal genome maintenance, highlighting a cooperative E2-TOPBP1- NCL axis critical for viral genome stability during differentiation. These findings provide a comprehensive view of the E2-associated protein landscape in stratified epithelial cells and reveal a mechanistic pathway through which HPV16 co-opts host factors to support genome maintenance, productive replication, and persistence. ImportanceHuman papillomaviruses (HPVs) establish persistent infections in stratified epithelia and rely on host DNA damage and repair factors to support their replication. The E2 protein is central to viral genome replication and maintenance, and depends heavily on its interaction with the host factor TOPBP1 for these functions. Here, we define the E2 and TOPBP1 interactomes in differentiating keratinocytes, and identify nucleolin (NCL) a critical differentiation- and TOPBP1-dependent E2 partner required for episomal genome stability. These findings expand the understanding of how HPV16 coordinates viral replication with host chromatin and DNA repair networks, uncovering a cooperative E2-TOPBP1-NCL axis that may represent a new target for antiviral intervention.

cancer biology↗

bioRxiv2025

Co-targeting MERTK and EGFR with a Bispecific Antibody Overcomes Drug Resistance Across Mutations in Exons 19, 20, and 21

Resistance of lung cancer to EGFR-specific tyrosine kinase inhibitors (TKIs), such as osimertinib, often arises from secondary mutations or the activation of bypass signaling pathways. We noted elevated levels of GAS6 and its receptor, MERTK, in patients acquiring resistance to osimertinib, hence hypothesized that the GAS6-MERTK axis can serve as a therapeutic target. GAS6 promoted cell survival and an anti-GAS6 antibody we generated delayed tumor relapses in a xenograft model. Likewise, MERTK ablation sensitized lung cancer cells to osimertinib due to a newly described EGFR-to-MERTK crosstalk. Hence, we developed Bis3, a bispecific antibody targeting both MERTK and EGFR and promoting their degradation. Bis3 plus TKIs cooperatively inhibited the growth of TKI-resistant lung cancer spheroids and markedly delayed relapses of patient-derived xenografts harboring the clinically challenging exon-20 mutations. These findings establish the GAS6-MERTK axis as a driver of drug resistance and provide a rationale for clinical development of Bis3.

cancer biology↗

bioRxiv2025

Aging-Driven Immunosuppression: The Role of Tregs in the Ovarian Tumor Microenvironment

Epithelial ovarian cancer (EOC) incidence and mortality increase with age, driven in part by chronic inflammation, diminished T cell output, and heightened regulatory T cell (Treg)-mediated immunosuppression. In aged EOC-bearing mice, we observed reduced survival, accompanied by impaired CD4 and CD8T cell responses and a marked expansion of FOXP3 Tregs exhibiting elevated IL-10 and TGF{beta} expression. Metabolic profiling revealed enhanced oxidative phosphorylation in Tregs from aged mice, along with a fivefold increase in intracellular succinate levels. This accumulation of succinate within the aged tumor microenvironment was found to potentiate Treg suppressive function. Notably, pharmacologic inhibition of -ketoglutarate dehydrogenase reversed this effect, restoring effector T cell activity. These findings highlight succinate driven metabolic reprogramming as a central mechanism of age related Treg dysfunction in EOC and suggest that targeting succinate metabolism may offer a promising strategy to rejuvenate antitumor immunity in elderly patients.

immunology↗

bioRxiv2025

Sensitizing Immune-Refractory Ovarian Tumors via p53 Mutation-Tailored Immunotherapy

High-grade serous ovarian cancer demonstrates limited responsiveness to immune checkpoint inhibitors, owing in part to immunosuppressive environments shaped by nearly universal p53 aberrations. Utilizing an immunocompetent mouse model and individual p53 mutations, we identified a dependence of the p53-R270H mutation (equivalent of human R273H) on regulatory T cells (Tregs) and the PD-1/PD-L1 axis. Analysis of patient datasets associated R273H with elevated levels of two p53 targets, PD-L1 and amphiregulin (AREG), a Tregs growth factor. In contrast to p53-R172H tumors, where there was limited activity, dual antibody therapy targeting AREG and PD-L1 selectively and effectively inhibited R270H tumors. This involved polarization toward M1 macrophages, infiltration of CD8+ T cells, diminished Ly6G+ neutrophils and downregulation of interleukin-4. In patient-derived R273C organoids, the combination treatment reduced the CD4/CD8 ratio. This study is the first to establish a mutation-tailored therapeutic approach that leverages the capacity of p53 to modulate immunosuppressive mechanisms.

cancer biology↗

bioRxiv2025

Homeostatic Activation of 26S Proteasomes by Protein Kinase A Protects against Cardiac and Neurobehavior Malfunction in Alzheimer's Disease Mice

Alzheimers Disease (AD) patients often show brain and cardiac malfunction. AD represents a leading cause of morbidity and mortality worldwide, but the demand for effective treatment for AD is far from being met. This is primarily because AD pathogenesis, including brain-heart interaction, is poorly understood. Proteasome functional insufficiency is implicated in AD; as such, proteasome enhancement promises a potentially new strategy to treat AD. The proteasome can be activated by protein kinase A (PKA) via selectively phosphorylating Ser14-RPN6/PSMD11 (p-S14-RPN6); however, whether p-S14-RPN6 is altered and what role p-S14-RPN6 plays in AD remain unclear. Hence, this study was conducted to address these critical gaps. We found that genetic blockade of the homeostatic p-S14-Rpn6 via germline knock-in of Rpn6S14A (referred to as S14A) significantly reduced proteasome activities in the cerebral cortex but did not discernibly impair learning and memory function in 4-month-old mice or cause cardiac dysfunction before 12 months of age. Increases in Ser14-phosphorylated Rpn6 in the cerebral cortex and markedly elevated A{beta} proteins in the myocardium were observed in young 5XFAD mice, a commonly used AD model. When introduced into the 5XFAD mice, S14A significantly aggravated the learning and memory deficits as revealed by the radial arm water maze tests and accelerated cardiac malfunction as measured by serial echocardiography in the same cohort of 5XFAD mice. Thus, the present study establishes for the first time that homeostatic activation of 26S proteasomes by basal p-S14-RPN6 or PKA activity protects against both the brain and heart malfunction in the 5XFAD mice.

physiology↗

bioRxiv2025

Ser14-phosphorylated Rpn6 Limits Proteostasis Impairment and Pathology in Both Brain and Heart of Tauopathy Mice

Alzheimers disease (AD) patients often display neurobehavioral and cardiac impairments, but the underlying factors remain unclear. Ser14 phosphorylation in RPN6 (p-S14-RPN6) mediates the activation of 26S proteasomes by protein kinase A (PKA). Proteasome priming is implicated in protection by cAMP-PKA against AD, but this remains to be established. Hence, this study was conducted to interrogate homeostatic p-S14-RPN6 in AD. The recently validated Rpn6S14A knock-in (S14A) mice were crossbred with the PS19 tauopathy mice (RRID: IMSR_JAX:008169). The resultant wild type (WT), PS19, and PS19::S14A littermates were compared. Expedited declines in cognitive and motor functions as indicated respectively by significant decreases in object recognition and discrimination indexes and rotarod time were observed in PS19::S14A mice vs. PS19 mice, which is associated with more pronounced synaptic losses, microglial activation, and gliosis in the hippocampus. Compared with WT and PS19 mice, PS19::S14A mice showed exacerbated cardiac malfunction, cardiac hypertrophic responses and fibrosis, and greater increases of total and hyperphosphorylated tau proteins and ubiquitin conjugates in both hippocampi and hearts. These findings demonstrate that genetic blockade of p-S14-RPN6 exacerbates tauopathy in both the brain and heart, which for the first time establishes that homeostatic p-S14-RPN6 promotes proteostasis and protects against pathogenesis in AD.

cell biology↗

bioRxiv2025

Bactericidal activity of ZnO nanoparticles-anti TB drugs combination towards H37Rv strain and multidrug-resistant isolates of Mycobacterium tuberculosis via SufB splicing inhibition

Tuberculosis (TB) remains a significant global health threat, claiming millions of lives annually. Despite advancements in treatment, the emergence of drug-resistant strains has hindered effective TB control. The current management for TB is prolonged with severe side effects, leading to poor patient compliance. Metal-based nanoparticles are shown to manage drug-sensitive TB when combined with anti-TB drugs. However, mycobactericidal potential of nanoparticles towards drug-resistant TB is not confirmed yet. This work explores the bactericidal potential of Zinc Oxide Nanoparticles (ZnONPs, 40 nm) in managing both drug-sensitive and drug-resistant TB in combination with anti-TB drugs. It was found that ZnONPs inhibit generation of active SufB protein via splicing inhibition, an essential event for Mycobacterium tuberculosis (Mtb) survival. While TEM and UV-visible spectroscopy identified NPs[~]protein interaction, SEM visualised extensive membrane damage in H37Rv and multidrug-resistant (MDR) Mtb cells. Alamar blue assay and spread plate method detected minimum inhibitory concentration and minimum bactericidal concentration of ZnONPs towards H37Rv strain and MDR Mtb isolates. In vitro studies identified a combination with ZnONPs that reduced effective doses for anti-TB drugs towards H37Rv and MDR Mtb isolates. A correlation to splicing inhibition was made by performing Alamar blue assay in SufB intein-less microbe, Mycobacterium smegmatis. A similar drug combination, attenuated the mycobacterial load, inflammation in the spleen & lungs, and protected against Mtb induced splenomegaly in infected mice. Thus, ZnONPs can be used as potent additive in anti-TB regimen to manage drug-susceptible and drug-resistant TB, addressing challenges such as prolonged therapy, drug toxicity and poor patient compliance.

microbiology↗

bioRxiv2025

Inducible re-epithelialization of cancer cells increases autophagy and DNA damage: implications for breast cancer dormancy

Epithelial lineage differentiation is pivotal to mammary gland development and it can pause metastasis of breast cancer (BC) by inducing tumor dormancy. To simulate this, we expressed epithelial genes in mesenchymal BC cells. Inducible expression of the epithelial OVOL genes in metastatic BC cells suppressed proliferation and migration. We found that C1ORF116, an OVOLs target, is susceptible to genetic and epigenetic aberrations in BC. It is regulated by steroids and functions as a putative autophagy receptor that inhibits antioxidants like thioredoxin. Accordingly, boosting epithelialization lowered glutathione, elevated reactive oxygen species and increased both DNA oxidation and double strand breaks. Epithelialization also associated with redistribution of NRF2 and an altered interplay among p38, ATM, and the other kinases regulating the DNA damage response. Hence, hormonal regulation of OVOLs and chronic stress might permit epithelial differentiation and retard exit from dormancy, while altering redox homeostasis and permitting DNA damage accumulation, which may awaken dormant tumors.

cancer biology↗

bioRxiv2025

Obligate cross-feeding of metabolites is common in soil microbial communities

Many microorganisms are refractory to laboratory cultivation. One possible explanation, known as the great plate count anomaly, is metabolic dependencies among community members. However, systematic studies of these interactions in communities like soil are missing, hindering advances in understanding these ecologically important ecosystems. Here, we address this issue by systematically analysing 6,931 bacterial isolates of 27 soil microbial communities. We find that the growth of up to 50% of all community members depended essentially on supplementation with amino acids, vitamins, or nucleotides. In 73% of cases, supplementation with multiple amino acids was necessary. Genomic analysis of 62 strains revealed that accumulation of insertion sequences and specific gene loss was associated with the observed auxotrophies. Finally, genome-scale metabolic models, computational analyses, and cocultivation experiments demonstrated that other co-occurring genotypes complemented the metabolic needs of auxotrophs, thus facilitating their growth. Our results demonstrate that soil bacteria exist within integrated metabolic networks, which hampers their cultivation.

microbiology↗

bioRxiv2025

TMPRSS2-ERG confers resistance to antiandrogens: mechanism and therapeutic implications

Approximately 50% of prostate cancer (PCa) patients harbor fusions involving the TMPRSS2 and ERG genes. Despite this, tailored therapies targeting the fused gene, tERG, remain undeveloped. Our study analyzed biopsy samples from two clinical trials assessing the efficacies of androgen receptor (AR) signaling inhibitors (ARSIs). The results revealed that tERG promotes resistance to ARSIs and is associated with elevated levels of the glucocorticoid receptor (GR). Subsequent assays showed that GR directly interacts with tERG, alleviates allosteric autoinhibition and prevents chemotherapy-induced tERG degradation. In PCa models, either inhibiting GR or lowering cortisol levels suppressed tumor growth in tERG-positive models, but not in fusion-negative models. In addition, patient-derived fusion-positive xenografts displayed enhanced sensitivity to combined GR and AR inhibitors. Collectively, these findings highlight TMPRSS2-ERG as a new biomarker and propose that simultaneous inhibition of GR and AR may specifically benefit tERG-positine patients. However, GR stimulatory corticosteroid therapies may not be advisable for this patient subgroup.

cancer biology↗