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Khan, M. A.

Publications and source records attributed to Khan, M. A..

At least 19 recordsLinked to original sources

Copper-Mediated Antimicrobial Activity : Targeting Cytochrome c Complexes Across Bacterial Species

Copper (Cu) exerts potent antibacterial activity and contributes to mammalian immune defense. Although solvent exposed 4Fe-4S clusters in cytoplasmic dehydrogenases are major intracellular targets of Cu, its chemical reactivity and subcellular distribution suggest that additional cellular processes may be vulnerable to Cu toxicity. Here, we identify c-type cytochrome biogenesis as a conserved target of Cu excess across diverse pathogenic and environmental bacteria. Analysis of respiratory membrane complexes from pathogens, including Vibrio cholerae and Pseudomonas aeruginosa, revealed pronounced and selective sensitivity of c-type cytochrome-containing complexes to excess Cu. In P. aeruginosa, elevated Cu impaired the cbb3-type cytochrome c oxidase and NapBC-containing cytochrome c complexes while largely sparing complexes independent of c-type cytochromes, including the aa3-type cytochrome c oxidase and succinate dehydrogenase. In contrast, the caa3-type cytochrome c oxidase of Bacillus subtilis, which contains a covalently bound cytochrome c subunit, was also severely affected. Cu likewise depleted c-type cytochromes in plant-associated and photosynthetic bacteria, indicating that this vulnerability is broadly conserved. Complementary analyses in B. subtilis and Escherichia coli showed that Cu primarily disrupts c-type cytochrome assembly rather than promoting the degradation of preassembled complexes. These findings establish c-type cytochrome-containing respiratory complexes as conserved targets of Cu toxicity. Given their central role in electron transport and adaptation to oxygen-limited environments, disruption of cytochrome c biogenesis may contribute to Cu antimicrobial activity and expose a potential vulnerability in pathogens that rely on c-type cytochromes for microaerobic respiration and colonization of hypoxic host tissues.

microbiology↗

Version-aware question answering over living oncology guidelines

Living clinical guidelines revise recommendations as evidence emerges, so an AI answer can be faithful to a real guideline and still be out of date. Here we examine this failure using ASCOBench, 288 unique questions in 96 three-turn conversations grounded in versioned American Society of Clinical Oncology (ASCO) breast and prostate cancer guidelines, with oncologist-reviewed reference answers. Oncologists corrected one in four version-sensitive answers drafted by a frontier model, against fewer than one in ten factual ones. Across the guideline corpus, 19 recommendations changed between versions, seven of them reversals, yet only 1 of 14 superseded documents states that it has been replaced. With a strong model, retrieval over several guideline versions made stale answers four times more frequent than answering without retrieval. SentryLine, a verification-first system, lowered incorrect answers to 4.2-5.2% from 9.7-22.9% for baselines across three models. Recognizing change before a guideline declares it remains an open problem.

bioinformatics↗

MnSOD Diversifies, while FeSOD Dominates Superoxide Defense in Cyanobacteria

Cyanobacteria are unique among prokaryotes in possessing photosynthetic thylakoid membranes enclosing an internal lumen, where superoxide production is expected to be substantial. Thylakoid-associated superoxide dismutases (SODs) would seem the obvious first line of defense, yet many cyanobacteria rely instead on a single soluble cytoplasmic enzyme, raising the question of what role thylakoid-associated SOD isoforms actually play. Using Cyanothece sp. PCC 7425, which encodes both a cytoplasmic FeSOD and a thylakoid-associated MnSOD, we combined sequence analysis, structural, genetics, and biochemical approaches to characterise FeSOD and MnSOD cellular localisation and assess each enzyme's contribution to superoxide defense. Cyanobacterial MnSODs display diverse N-terminal architectures, consistent with soluble, transmembrane, or lipid-anchored forms, yet contribute only modestly to superoxide defense in Cyanothece PCC 7425 and, very likely, across cyanobacteria broadly. Soluble FeSOD instead provides the major line of defense, showing that thylakoid association does not guarantee physiological importance. This predominance of a cytoplasmic enzyme highlights the central role of cytoplasmic superoxide detoxification, consistent with superoxide being generated mainly at the PSI acceptor side, and extends to the chloroplast stroma of plants. Our findings support a model in which SOD distribution reflects metal availability, enzyme properties, and subcellular organisation : FeSOD protects the compartment harbouring the main targets of PSI-associated superoxide, whereas MnSOD is retained where thylakoid association offers additional local protection, but becomes dispensable when the local ROS burden is limited. Spatial matching between superoxide production, antioxidant localisation, and target vulnerability may thus shape the diversification and maintenance of antioxidant systems across cyanobacteria and chloroplasts.

microbiology↗

Reliable extraction of clinical-trial evidence with provenance, verification, and targeted review

Reliable extraction of trial characteristics and outcomes is essential for systematic reviews, yet incorrect values can alter evidence synthesis and are difficult to detect without clear source evidence. We evaluate EviSearch, a clinical evidence-curation system that links extracted values to source passages, independently verifies cited evidence, and prioritizes higher-risk cells for review. Using ten trial publications, a 133-column schema, reference annotations, and consistent scoring across model families, we assess answer quality, inter-reading agreement, evidence reproduction, targeted review, and evidence modality. In the Qwen evaluation, EviSearch achieved 91.70% accuracy, cited 100.0% of admitted values, and reproduced 98.9% independently. Reviewing 15.6% of cells increased accuracy to 95.22%.

bioinformatics↗

Answering clinicians' questions over trial evidence tables with verifiable, feedback-driven language models

Systematic reviews condense clinical trials into evidence tables, yet clinicians can interrogate these tables only through database queries, and many questions concern attributes that the table does not record, such as a drug's target class or a harmonised endpoint. Here we introduce FD-SCoPE, a language-model framework that answers both kinds of question, exposes the query, the selected trials and the derivation rule behind every answer, and learns from expert corrections. On an oncology evidence table of 159 immune checkpoint inhibitor trial records, FD-SCoPE completed all 140 clinician-style tasks (alternatives, 90.7--97.9%). For questions needing derived attributes it retrieved 99.3% of relevant trial records at a positive predictive value of 89.8% and outperformed four alternative approaches (derived-value F1 77.7% versus 64.8--73.4%). Corrections on 299 questions, simulated from reference answers, raised F1 on 1,201 unseen questions from 77.9% to 84.9%. Language models coupled with executable queries, verified programs and expert feedback can give clinicians auditable access to trial evidence.

bioengineering↗

Perfect 21-nucleotide matches to beneficial fungi are common in canonical antifungal dsRNA targets: an in-silico off-target hazard screen for spray-induced gene silencing

Double-stranded RNA (dsRNA) biopesticides that silence essential fungal genes by spray-induced gene silencing (SIGS) are advancing towards registration, underpinned by the claim that silencing is confined to sequence-matched target organisms, a claim that has never been tested systematically against beneficial fungi. We screened twelve dsRNA constructs (the whole transcripts of eleven canonical antifungal target genes of Fusarium graminearum: three CYP51 sterol 14-demethylases, six chitin synthases and two {beta}-tubulins, plus a concatenation of the three CYP51 transcripts modelling the flagship CYP3RNA design) for perfect 21-nucleotide (21-nt) identity, the primary match criterion of recent regulatory bioinformatics frameworks, against the transcriptomes of seven non-target fungi, including commercial biocontrol agents (Trichoderma harzianum, T. virens, Beauveria bassiana, Metarhizium anisopliae, M. brunneum), the arbuscular mycorrhizal fungus Rhizophagus irregularis and Saccharomyces cerevisiae. Eleven of the twelve constructs carried off-target hazard; only CYP51C was completely clean. TUB2b carried 580 perfect 21-nt matches and contained no hazard-free window of 250 consecutive 21-mer start positions, whereas 26.6-60.0% of screened windows were hazard-free in the designable genes. Hits landed overwhelmingly on orthologues of the targeted gene and concentrated in the Hypocreales; R. irregularis and S. cerevisiae were nearly clean. These are hazard findings, not risk findings: perfect siRNA-length matches to beneficial fungi are common in canonical antifungal dsRNA targets, and current regulatory screening panels contain no fungus that would detect them.

bioinformatics↗

Targeted genome editing of the non-model cyanobacterium Cyanothece PCC 7425 via CRISPR/Cas12a

Cyanobacteria are diverse photosynthetic microorganisms of great interest for fundamental science and sustainable biotechnological applications. However, their polyploidy makes genetic manipulation challenging and time-consuming. The development of CRISPR/Cas tools has greatly accelerated genome editing and metabolic engineering of few cyanobacterial model species. In this work, we extend the CRISPR/Cas12a system for targeted gene deletion in the non-model cyanobacterium Cyanothece PCC 7425, interesting for its ability to perform intracellular calcium carbonate (CaCO3) biomineralization, nitrogen fixation, etc. We demonstrate for the first time its tractability to gene knockout by generating deletion mutants of four genes (cax3-cax4, gor, and sodB) acting in metabolism and/or response to stresses, using Cas12a mediated homologous recombination. Importantly, full chromosome segregation was rapidly achieved after a single round of selection in all cases. All mutants were genotypically and phenotypically characterised. Moreover, biochemical analysis in the case of{Delta} sodB mutant further confirmed its targeted deletion. Overall, CRISRPR/Cas12a provides a rapid and efficient system for genome editing in Cyanothece PCC 7425, establishing this organism as a versatile model for studying oxidative stress pathways, metal toxicity and moreover, the still poorly known mechanism(s) of intracellular CaCO3 biomineralization. Key PointsO_LIRapid and efficient CRISPR/Cas12a editing established in Cyanothece PCC 7425. C_LIO_LIFully segregated knockout mutants obtained after single selection round. C_LIO_LIPlatform for nuclear waste bioremediation and other biotechnological applications. C_LI

microbiology↗

Simultaneous TCR and IL-2 agonism selectively enhances epitope-specific CD8 T cell responses during chronic viral infection

Interleukin-2 (IL-2) remains an attractive cytokine for enhancing antigen-specific CD8 T cell responses in cancer immunotherapy, but systemic toxicity hinders its broad clinical application. To address this, various IL-2-based therapeutics have been engineered with altered IL-2 receptor bias or targeted delivery to tumors, the tumor microenvironment, or immune cell populations. Ideally, IL-2 signals should be selectively delivered to antigen-specific CD8 T cells, boosting their responses and promoting effector differentiation while sparing non-targeted populations. Immuno-STATTM (Selective Targeting and Alteration of T cells) is a fusion protein platform comprising a bivalent peptide-MHC class I complex and an affinity-attenuated IL-2 mutein that co-stimulates TCR and IL-2 signaling in epitope-specific CD8 T cells. Here, we investigated whether a DbGP33-41-targeted Immuno-STAT enhances DbGP33-specific CD8 T cell responses in a mouse model of chronic lymphocytic choriomeningitis virus (LCMV) infection. Immuno-STAT treatment selectively expanded DbGP33-specific CD8 T cells with an effector-like phenotype. Non-targeted DbGP276-specific CD8 T cells showed little to no expansion in response to DbGP33-41-targeted Immuno-STAT therapy, underscoring the selectivity of this approach. However, minor changes in phenotypic markers, including increased expression of CD25 and CX3CR1, were observed in non-targeted CD8 T cells, likely reflecting bystander IL-2 signaling. Combining Immuno-STAT with PD-1 blockade augmented DbGP33-specific CD8 T cell responses more effectively than PD-1 blockade alone, with minor effects on the non-targeted DbGP276-specific population. These findings inform the clinical development of Immuno-STAT and other IL-2 therapeutics and highlight the value of coordinated TCR and IL-2 stimulation during chronic antigen exposure, alone or in combination with PD-1 blockade. IMPORTANCEInterleukin-2 (IL-2) is a key cytokine for promoting effector differentiation of antigen-specific CD8 T cells and remains an attractive agent in cancer immunotherapy, but systemic toxicity limits its clinical use. This study addresses a central challenge in IL-2-based immunotherapy: delivering IL-2 to cognate antigen-specific CD8 T cells while minimizing activation of non-targeted populations. Using a mouse model of chronic lymphocytic choriomeningitis virus (LCMV) infection, we show that the Immuno-STAT (Selective Targeting and Alteration of T cells) platform selectively expands targeted virus-specific CD8 T cells and enhances their function while limiting effects on non-targeted populations. We also show that combining Immuno-STAT with PD-1 blockade further enhances targeted virus-specific CD8 T cell responses during chronic LCMV infection. These findings provide mechanistic and preclinical support for integrating T cell receptor (TCR) specificity with IL-2 signaling to advance cancer immunotherapy and guide next-generation IL-2 therapeutics for cancer and chronic infection.

immunology↗

Selective identification of the herb Picrorhiza kurroa and probiotic Lactobacillus fermentum as a synbiotic with fermentation-enhanced physicochemical, biological, and metabolomic properties

PurposeAlthough secondary metabolites of medicinal plants can modulate the gut microbiota, their prebiotic and synbiotic potential is not fully explored. This study aimed to identify novel medicinal plant-probiotic combination(s) that show prebiotic and synbiotic effects through mutual synergism and reciprocal interactions. MethodsTen Himalayan region medicinal plants were screened for their selective prebiotic efficacy by studying in vitro proliferation of three species of lactic acid bacteria (LAB) and concurrent suppression of E. coli. The top-performing plants were evaluated for synergism with LAB through fermentation of pure extracts, followed by physicochemical, biological, and metabolomic profiling. ResultsAmong the ten plant species, Picrorhiza kurroa (PK) and Adhatoda vasica (AV) exhibited promising prebiotic attributes with PAS scores of 0.50 and 0.44, respectively, while Lactobacillus fermentum (LF) emerged as the most compatible probiotic strain. Unlike AV, fermentation of PK with LF demonstrated superior probiotic growth (2.2-fold increase), elevated total flavonoids (21.6% increase), and improved antioxidant capacity (24.02% increase) compared to unfermented PK. Fermented PK significantly enhanced cytoprotective effects and mitigated oxidative (ROS levels/lipid peroxidation) and inflammatory damage (NO/IL-6 levels) in macrophages and muscle cells exposed to separate exogenous stressors (LPS and H2O2). Elemental (ICP-OES) and metabolomic analysis (LC-MS/UHPLC) revealed that LF metabolised major elements of PK (Ca/Fe/K/Na/Cu) and induced biotransformation of large secondary metabolites, including the characteristic iridoid glycosides of PK, into smaller, more abundant metabolites. ConclusionsPK-LF combination is identified as a synbiotic, and its fermented product is a superior bioactive product that can be developed into innovative nutraceuticals or herbal formulations.

biochemistry↗

PRECISION EVOLUTIONARY MEDICINE: A COMPUTATIONAL GRAPH-THEORETICAL FRAMEWORK FOR PATHOGEN-SPECIFIC ANTIBIOTIC CYCLING IN MULTI-DRUG-RESISTANT GRAM-NEGATIVE INFECTIONS

BackgroundThe Proliferation of Multi-drug resistant (MDP) ESKAPE pathogens threatens to compromise the efficacy of standard antibiotic pharmacopoeia. Current antimicrobial stewardship strategies predominantly rely on reactive antibiograms selecting therapeutic agents based on immediate phenotypic susceptibility. This approach, while clinically expedient, often inadvertently selects for cross-resistance, driving the evolutionary trajectory toward pan-drug resistance. A paradigm shift is required toward predictive strategies that exploit evolutionary trade-offs, specifically Collateral Sensitivity (CS), where the acquisition of resistance to one agent induces hypersensitivity to another. MethodsWe developed a computational graph-theory framework to map the evolutionary trajectories of three critical Gram-negative pathogens: Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa. Drawing upon validated CS interaction matrices from experimental evolution literature, we constructed directed weighted graphs where nodes represent antibiotics and edges represent evolutionary sensitivity trade-offs. A closed-loop cycle optimization algorithm was deployed to identify pathogen-specific "Trap Loops" sequences of three or more antibiotics that force the pathogen into a state of high sensitivity. These loops were validated via stochastic in-silico clinical trials simulating 18 months of treatment, explicitly modeling clinical error and biological noise. ResultsThe model identified distinct, optimal cycling protocols for each pathogen. For E. coli, an Aminoglycoside-Beta Lactam loop (Gentamicin to Cefuroxime to Fosfomycin) demonstrated sustained suppression of resistance accumulation in silico. For K. pneumoniae, a novel Rifampicin to Doxycycline to Colistin loop was identified. For P. aeruginosa, a Tobramycin to Ciprofloxacin to Piperacillin sequence proved optimal. Stochastic simulations demonstrated that while standard reactive care resulted in progressive resistance accumulation (Normalized Resistance > 2.5), the graph-optimized protocols suppressed resistance within the therapeutic window (Normalized Resistance < 0.2) for the duration of the simulation. ConclusionWe demonstrate, through computational modeling, that antibiotic resistance trajectories can be strategically constrained by optimizing the temporal sequence of existing agents. This study provides a computational framework to inform the transition from reactive prescribing toward precision evolutionary steering. These protocols are intended to complement, not replace, clinical judgment and local antibiograms, particularly regarding pharmacokinetic constraints.

microbiology↗

Post-translational modifications within fibrinaloid microclot complexes distinguish Pre-COVID-19 Postural Orthostatic Tachycardia Syndrome, Long COVID, and Long COVID-POTS and reveal disease-specific molecular pathways

BackgroundPre-COVID-19 Postural orthostatic tachycardia syndrome (PC-POTS), Long COVID, and their overlap (LC-POTS) are chronic post-viral conditions marked by debilitating symptoms despite frequently normal routine laboratory results. We previously identified insoluble fibrinaloid microclot complexes (FMCs) in Long COVID. It is not known whether FMCs are also present in PC-POTS, or whether post-translational modifications (PTMs) within FMC-entrapped proteins contribute to disease mechanisms. MethodsPlatelet-poor plasma from healthy controls, PC-POTS patients (collected prior to the COVID-19 pandemic), Long COVID (without POTS) and LC-POTS patients underwent fluorescence imaging flow cytometry to quantify FMCs. Proteomic analyses were performed on insoluble protein fractions using a double trypsin digestion strategy and data-independent liquid chromatography-tandem mass spectrometry (LC-MS/MS). Differential protein abundance, PTMs, and amyloidogenicity were compared across groups. ResultsMeasured with imaging flowcytometry in objects/mL, higher levels of FMCs were present in disease groups compared to controls, although not statistically significant. Statistically significant differences potentially lay within FMC sizes and composition. Furthermore, despite only a few dysregulated proteins, FMC proteomics revealed extensive and disease-specific peptides with PTM dysregulation across coagulation, immune, and metabolic pathways. Long COVID displayed FMCs with PTMs of coagulation proteins including prominent advanced glycation end-products (AGE)- and oxidation-based modifications of fibrinogen subunits, particularly fibrinogen subunit A (FIBA), resembling diabetic glycation profiles. FMCs in PC-POTS showed fewer fibrinogen PTMs but markedly increased modifications in metabolic proteins, including oxidised apoA1 and apoB, and immune patterns with complement-related proteins (C3, C4A/B, IC1), immunoglobulin G1 (IGG1) and alpha 2 macroglobulin (A2MG). LC-POTS shared coagulation pathology with Long COVID and immune pathology with PC-POTS. Many dysregulated peptides were determined by in silco methods to be highly amyloidogenic, consistent with FMCs as {beta}-sheet-rich aggregates. Protein-level differences were minimal compared with PTM changes. ConclusionsThis study provides the first evidence that post-translational modifications (PTMs) within fibrinaloid microclots complexes (FMCs) uniquely distinguish pre-COVID-19 POTS, Long COVID, and Long COVID-POTS. Because PC-POTS samples were collected before SARS-CoV-2, their PTM patterns reflect intrinsic disease biology, allowing a clear separation from Long COVID-related changes. PTM profiling revealed pro-coagulant fibrinogen modifications in Long COVID and LC-POTS, metabolic-oxidative disruptions in Long COVID and PC-POTS, and immune dysregulation in PC-POTS and LC-POTS. None of these is detectable with routine assays, and all are independent of protein abundance. The consistent presence of amyloidogenic peptides suggests a contribution to microvascular dysfunction. These findings define disease-specific PTM landscapes and support new diagnostic and therapeutic avenues across autonomic and post-viral disorders.

physiology↗

Identifying tissue states by spatial protein patterns related to chemotherapy response in triple-negative breast cancer

Triple-negative breast cancer (TNBC) is an aggressive malignancy with limited targeted therapies and variable responses to conventional chemotherapy, influenced by intratumoral heterogeneity and complex tumor microenvironment (TME) interactions. Understanding spatiotemporal cellular interplay and tissue organization is crucial for advancing tumor biology and improving patient stratification. Spatially resolved proteomics, such as Imaging Mass Cytometry (IMC), offers a powerful approach to dissect the TME. We present an end-to-end computational pipeline for robust quantitative analysis of large-scale IMC datasets, addressing the challenge of batch effects through image-level contrast adjustment. Applying this framework to 813 tissue regions encompassing over 4 million cells from 63 TNBC patients, we revealed distinct spatial arrangements of cell types between chemotherapy responders and non-responders. Non-responders showed reduced cytotoxic T-cell infiltration into tumor regions and increased spatial co-localization between fibroblasts and macrophages, a pattern that persisted and intensified after chemotherapy treatment. To integrate these complex spatial-molecular relationships, we used graph neural networks (GNNs) to predict treatment response from pre-treatment samples with AUROC=0.71. Interpretability analysis identified B7H4, CD11b, CD366, and FOXP3 as the most predictive protein markers, with fibroblasts, cancer cells, and CD8+ T cells being the most informative cell types. This study introduces a scalable analytical framework for spatial proteomics with interpretable predictions, suggesting features of tissue state that could guide treatment decisions in TNBC and further our understanding of the spatial determinants of therapeutic response.

cancer biology↗

Tumor nutrient stress gives rise to a drug tolerant cell state in pancreatic cancer

Systemic therapies are the standard of care for most pancreatic ductal adenocarcinoma (PDAC) patients but provide limited benefit due to pervasive resistance. The fibrotic tumor microenvironment (TME) is thought to drive resistance by restricting perfusion and drug delivery. Here, we show that therapeutically relevant drug concentrations are achieved even in poorly perfused, therapy-resistant murine PDAC tumors, indicating that impaired delivery alone does not explain drug resistance. Instead, we find TME exposure imprints a therapy-resistant state upon PDAC cells. These observations raised the question of how the TME imposes this state. Poor perfusion alters nutrient availability in the TME. To model this, we developed Tumor Interstitial Fluid Medium (TIFM), which recapitulates TME nutrient conditions. TIFM cultured PDAC cells acquire a therapy-resistant phenotype that mirrors resistance observed in the TME. In this state, cytotoxic and targeted therapies retain on-target activity but fail to trigger cell death, resulting in therapeutic tolerance. Mechanistically, drug tolerance is driven by suppression of apoptotic priming and can be reversed by inhibition of the anti-apoptotic regulator BCL-XL. These results identify TME-driven reprogramming of cell death as a key mechanism of therapy resistance in PDAC and establish TIFM as a physiologically relevant model for studying microenvironment-induced drug resistance.

cancer biology↗

Mitochondrial organization in the developing proximal tubule is controlled by LRRK2

The proximal tubule of the nephron resorbs water, amino acids and glucose, and its energy demands are high. Formation of the cellular machinery for energy production is an essential step in proximal tubule epithelial cell (PTC) differentiation, and this report focuses on how mitochondria in nascent PTCs are redistributed from their initial apical position to their ultimate basolateral location. We found that mitochondria move from the apical to basolateral side of the PTC coincident with the initiation of lumen flow and that proximal tubules deficient in filtration (aglomerular mice and kidney organoids) maintain their mitochondria in the apical position, indicating that flow is necessary and sufficient for localization. Further, we show that mitochondrial localization depends on the activity of LRRK2 in vitro and in vivo. Modeling the effect of fluid flow on PTCs demonstrates that LRRK2 activity is regulated by fluid shear stress, providing an explanation for how onset of flow in the newly differentiated proximal tubule may trigger the apical-to-basolateral dissemination of mitochondria that forms the template for subsequent PTC maturation. Our findings indicate that mitochondrial redistribution is one component of a cellular program in the nascent PTC that drives function and that this process is regulated by flow.

developmental biology↗

bHLH35 mediates specificity in plant responses to multiple stress conditions

How biological systems respond to stress is a fundamental question in biology, primarily addressed using the reductionist approach of applying one stress condition at a time. In nature, however, organisms experience a multitude of stresses, simultaneously or sequentially, questioning the validity of the reductionist approach for predicting plant responses to stress under natural conditions. Here, we reveal that in the flowering plant Arabidopsis thaliana, the transcriptional regulator bHLH35 is required for plant survival under a specific set of stress conditions that includes a combination of salinity, excess light, and heat, occurring simultaneously (but not for each of these stresses applied individually or in any other combination). Under these conditions, bHLH35 interacts with NAC069 and binds the promoter of LBD31, also specifically required for survival under the 3-stress combination. Our findings uncover a high degree of specificity in the response of organisms to stress, a specificity that would not have been revealed using the reductionist approach, and one that should be taken into consideration when developing agronomically important crops with heightened resilience to climate change.

plant biology↗

Synthetic torpor in the rat recapitulates key deatures of torpor and protects the heart from ischaemia-reperfusion injury

During times of environmental stress, many animals enter torpor: a reversible protective physiological state typically characterised by reductions in core temperature, heart rate and oxygen consumption. Species that naturally enter this hypothermic and hypometabolic state are tolerant of ischaemia-reperfusion injury. Consequently, there is a growing interest in utilizing aspects of torpor for clinical applications, such as protection from stroke or myocardial infarction. It is currently unknown, however, whether a torpor-like state is protective in animals that do not naturally enter torpor. Using viral vector-mediated chemogenetic activation of the medial preoptic area of the hypothalamus, we induced synthetic torpor in the rat, a species that does not naturally enter torpor. We demonstrate this state is cardioprotective in an ex vivo ischaemia-reperfusion injury model with an ~40% reduction in infarct size. Synthetic torpor-induced cardioprotection of the normothermic, isolated heart is not dependent on prior hypothermia in vivo. Phosphoproteomic analysis of cardiac tissue indicates the protective effects of synthetic torpor may be mediated by parallel activation of cell survival and stress tolerance pathways and inhibition of cell death pathways. These findings provide important insights into the mechanisms of organ protective effects of synthetic torpor states with implications for future clinical translation in humans.

neuroscience↗

ACSL4 activity drives TNBC metastasis by positively regulating Histone H3 Acetylation mediated SNAIL expression

Triple-Negative Breast Cancer (TNBC) has profound unmet medical need globally for its devastating clinical outcome associated with rapid metastasis and lack of targeted therapies. Recently, lipid metabolic reprogramming has emerged as a major driver of breast cancer metastasis. Here, we unveil a strong association between the heightened expression of fatty acid metabolic enzyme, acyl-CoA synthetase 4 (ACSL4) and TNBC, which is primarily attributed by the selective absence of progesterone receptor (PR). Loss of ACSL4 function, either through genetic ablation or pharmacological inhibition significantly reduces metastatic potential of TNBC. Global transcriptome analysis reveals that ACSL4 activity markedly influences the gene expression pattern associated with TNBC migration. Mechanistically, ACSL4 alters fatty acid oxidation (FAO) and cellular acetyl-CoA levels, leading to the hyper-acetylation of particularly H3K27Ac and H3K9Ac marks resulting in overexpression of SNAIL during the course of TNBC metastatic spread to lymph node and lungs. Further, human TNBC metastasis exhibits positive correlation between ACSL4 and SNAIL expression. Altogether, our findings provide new molecular insights regarding the intricate interplay between metabolic alterations and epigenetic modifications, intertwined to orchestrate TNBC metastasis and posit a rational understanding for the development of ACSL4 inhibitors as a targeted therapy against TNBC.

cancer biology↗

Adaptive therapy achieves long-term control of chemotherapy resistance in high grade ovarian cancer

Drug resistance results in poor outcomes for most patients with metastatic cancer. Adaptive Therapy (AT) proposes to address this by exploiting presumed fitness costs incurred by drug-resistant cells when drug is absent, and prescribing dose reductions to allow fitter, sensitive cells to re-grow and re- sensitise the tumour. However, empirical evidence for treatment-induced fitness change is lacking. We show that fitness costs in chemotherapy-resistant ovarian cancer cause selective decline and apoptosis of resistant populations in low-resource conditions. Moreover, carboplatin AT caused fluctuations in sensitive/resistant tumour population size in vitro and significantly extended survival of tumour-bearing mice. In sequential blood-derived cell-free DNA and tumour samples obtained longitudinally from ovarian cancer patients during treatment, we inferred resistant cancer cell population size through therapy and observed it correlated strongly with disease burden. These data have enabled us to launch a multicentre, phase 2 randomised controlled trial (ACTOv) to evaluate AT in ovarian cancer.

cancer biology↗