Biology subjects

Tran, S.

Publications and source records attributed to Tran, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Deep learning-based identification and quantification of rare circulating hybrid cells in orthotopic pancreatic cancer models

SignificanceRare-cell identification in fluorescence microscopy remains challenging because targets are sparse and background varies between specimens. Combining specimen-specific fluorescence enrichment with image classification may enable efficient and more specific automated detection of rare cells. AimWe developed a two-stage framework to identify and quantify candidate rare circulating hybrid neoplastic cells (CHCs, ECAD+/CD45+) in peripheral blood mononuclear cell (PBMC) preparations from tumor-bearing and tumor-naive mice. ApproachPBMCs from 28 mice were imaged by multichannel fluorescence microscopy. Matched unstained samples established animal-specific ECAD and CD45 background distributions for candidate cell enrichment. Blinded multi-annotator consensus labels were used to train a convolutional neural network (CNN) from DAPI, ECAD, and CD45 image crops. Generalization was evaluated by leave-one-animal-out validation across 10 random initializations. Final classification used a 10-model ensemble, and rare-cell burden was compared between groups using negative-binomial regression with total segmented-cell count as an exposure. ResultsOf the 1,065,512 segmented cells, enrichment retained 10,176 candidates (0.96%), reducing the search space by >99%. Four of five evaluable tumor-bearing animals showed reproducible held-out discrimination, with median quantified area under the receiver operator characteristic curve (AUROCs) of 0.918-0.951; one animal was a reproducible outlier (median AUROC, 0.338). Ensemble deployment identified 157.94 positive-consensus cells per 50,000 segmented cells in tumor-bearing animals versus 49.55 in controls. The estimated rare-cell rate was 3.15-fold higher in tumor-bearing animals (95% CI, 0.91-10.99; two-sided p=0.071; prespecified one-sided p=0.036). ConclusionsSpecimen-specific fluorescence enrichment combined with supervised image classification reduced the cellular search space and enabled automated quantification of a rare CHC (ECAD+/CD45+) phenotypes. Cross-animal validation also identified specimen-specific generalization failure, highlighting the importance of biological-specimen-level validation.

cancer biology↗

bioRxiv2026

Promfusion: a synthetic fusion promoter enabling enhanced and balanced photoreceptor transgene expression

Achieving efficient and balanced transgene expression in both rods and cones remains a major challenge in retinal gene therapy. Current promoters either lack specificity or fail to provide sufficient cellular coverage and expression level. To address this limitation, we developed and evaluated two fusion promoters, Pikali and Nocchu, by combining PR1.7, a cone-specific promoter and GRK1, a promoter most active in rods. Here, we show that Pikali and Nocchu outperform their parental promoters, driving broader and more balanced GFP expression in rods and cones of human iPSC-derived retinal organoids. These constructs achieved transduction in 30% to 45% of photoreceptors, with higher expression levels than GRK1 and broader cellular coverage than PR1.7. Our findings establish Pikali and Nocchu as excellent candidates for retinal gene therapy, overcoming the limitations of existing promoters. By combining specificity, efficiency, and extensive photoreceptor targeting, these fusion constructs represent a novel and promising strategy for next-generation gene therapy vectors, addressing inherited retinal dystrophies and advancing clinical translation.

genetics↗

bioRxiv2026

Decoding the BRCA2 reversion principles underlying PARP inhibitor resistance

Reversion mutations that restore BRCA2 function represent a major mechanism of resistance to poly(ADP-ribose) polymerase inhibitors (PARPi) in BRCA2-mutant cancers. Predicting these events could inform treatment strategies, identify patients at increased risk of acquiring PARPi resistance, and improve interpretation of secondary variants. Here, we use an isogenic cell system and CRISPR editing to define the principles governing BRCA2 reversion. We show that local sequence context dictates the spectrum of reversions, whereas domain architecture determines which events confer PARPi resistance. We characterize two routes of reversion that operate both within and across exons: DNA-level reading-frame restoration and transcript-level rescue via alternative splicing. Lastly, we identify distinct exon 11 reversion mechanisms, including large genomic deletions and recurrent splice isoforms predicted to remove all eight BRC repeats. These findings define a predictive code for BRCA2 reversion and PARPi resistance.

cancer biology↗

bioRxiv2026

STRADA Deficiency Impairs Cortical Interneuron Development in Humans and Mice

Polyhydramnios, Megalencephaly, and Symptomatic Epilepsy syndrome (PMSE/STRADA-related disorder) is a rare neurodevelopmental disorder characterized by megalencephaly (ME), early-onset drug-resistant epilepsy, neurocognitive impairment, and high early mortality, often due to status epilepticus. PMSE is caused by a multi-exon deletion in STRADA, encoding STRADA, which regulates the mechanistic target of rapamycin (mTOR) pathway. GABAergic inhibitory interneurons (INs) critically modulate the excitatory:inhibitory balance in cortical and hippocampal networks, and IN deficits contribute to epileptogenesis in several epileptic encephalopathies. However, no studies have investigated INs in PMSE. We used a multimodal approach to study INs in a Strada-/- mouse model engineered with the same causative 5-exon deletion identified in human PMSE. We demonstrate that Strada/STRADA loss causes a reduction of INs in the somatosensory cortex and a corresponding increase in the striatum, representative of remnant ganglionic eminence progenitor origin, in Strada-/- mice and a single PMSE brain tissue specimen. RNA sequencing comparing wildtype to Strada-/- cortex and striatum corroborated these findings, revealing increased IN-related gene expression (e.g., Dlx2) in the striatum and decreased IN-related gene expression (e.g., Pvalb) in the developing cortex. Cytoskeletal (e.g., Tpp3, Kank4, Map1a) and mTOR-associated genes (e.g., Rictor, Cryab) are differentially expressed in the developing cortex, mature striatum, and mature cortex of Strada-/- mice. Functional validation confirmed enlarged INs in mouse and human Strada/STRADA-deficient brain and enhanced S6 phosphorylation in Strada-/- striatum. Together, these findings suggest STRADA/Strada loss contributes to failed IN migration -- the first such report in a developmental, mTOR-associated megalencephaly syndrome -- highlighting INs as a therapeutic target for seizure prevention in PMSE. Key PointsO_LI- Reduced numbers of cortical inhibitory interneurons were observed in the cerebral cortex of Strada-/- mice, with striatal interneuron aggregation C_LIO_LI- Reduced numbers of cortical inhibitory interneurons, with an aggregation in striatum, were observed in human PMSE brain, supporting the observations in Strada-/- mouse C_LIO_LI- Transcriptomic analysis in Strada-/- mice reveals evidence of early developmental interneuron and cytoskeletal dysfunction C_LIO_LI- We introduce a loss of cortical interneurons as a salient feature of PMSE developmental pathogenesis, potentially contributing to a loss of inhibitory modulation C_LIO_LI- This is the first study proposing interneuron migration impairment in the developmental pathogenesis of an mTOR-associated megalencephaly syndrome C_LI

neuroscience↗

bioRxiv2026

Large-scale Visuomotor Reaction Time Self-Testing Reveals Subtle Motor Changes in Older Adults with Subjective Cognitive Impairment

IntroductionAffordable tools for early Alzheimers disease (AD) detection could support drug development and early intervention. Subtle motor changes may indicate preclinical AD, but hand response selection and initiation speeds are understudied. This study assessed whether unsupervised, online visuomotor reaction time (RT) tests relate to subjective cognitive impairment (SCI), a validated high risk state for future conversion to AD MethodsA total of 910 participants (age 66.3{+/-}7.5, 70.8% female) completed assessments of simple and choice visuomotor RT tests at home as part of the online TAS Test protocol; they also completed the Cambridge Neuropsychological Test Automated Battery (CANTAB) episodic memory and executive function tests. Among them, 142 participants reported SCI. ResultsOn the TAS Test visuomotor tests, SCI was associated with 8.4% [1.4%, 15.4%] longer RT ( (p = .008; adjusted for task complexity), greater odds of time-out failure (OR = 1.35 [1.01, 1.81]; p = .037), and greater variance in RT (log-variance (SCI - comparison) = .094 [.028, .159]; p < .001). There were no significant differences between the SCI and comparison groups on any of the CANTAB tests. After adjusting for SCI status, none of the CANTAB tests were significantly associated with RT. DiscussionSCI was associated with longer and more variable visuomotor RT, and greater odds of time-out failure, while not being associated with tests of memory and executive function. Cognitive test scores did not explain a significant amount of variance in visuomotor RT. Taken together, these results support a hypothesis that people with SCI may be experiencing earlier visuomotor deficits that are distinct from (or precede) decline in episodic memory and executive function. Visuomotor tasks that record RT may be more sensitive to preclinical manifestations of cognitive decline than more traditional tests of cognitive function.

bioinformatics↗

bioRxiv2025

Phage N4 uses a SAR endolysin-holin system for host cell lysis

Abstract Bacteriophages (phages) cause active host cell lysis to terminate their infection and release progeny into the environment. However, some phages have systems to delay their lysis, and thereby increase progeny yield, in specific conditions: a phenomenon called lysis inhibition (LIN). Two dissimilar phages of Escherichia coli are known to exhibit LIN: T4 and N4. In T4, a multi-protein mechanism stalls lysis and maintains the LIN state in response to superinfection in a high phage population density. However, the lysis proteins responsible for T4 lysis and LIN are not conserved with phage N4. In this study, we characterize the phage N4 proteins involved in lysis by molecular and genetic means. We define the functions of the minimal gene set required for lysis through heterologous expression and complementation. Furthermore, by sequence comparison with a selected mutant library that does not induce LIN, we have identified genomic regions both within and outside the lysis cassette involved in N4 LIN. We propose a model where N4 lysis proteins that execute rapid N4 lysis can be regulated to induce LIN. Despite the lack of conservation with T4 components, our study suggests that direct modulation of lysis initiation may be common and provides a springboard for identifying similar mechanisms in other phages. Importance Phages are viruses that kill only bacteria. To do so, they use lysis proteins to disrupt the structural components of the bacterial envelope. There are commonalities between the phages that infect bacteria with similar structures, but there are also interesting differences we can exploit to learn more about specific phages or their bacterial hosts. In this study, we characterize the lysis proteins of the E. coli phage N4. Our results suggest that lysis regulation controls phage yield in N4 differently than in well-studied phage T4. Future studies on the relationship between lysis proteins and phage yield could provide handles to use this information for optimal large-scale phage production for clinical or industrial applications.

microbiology↗

bioRxiv2025

stk32a links sleep homeostasis to suppression of sensory and motor systems

Sleep is regulated by a homeostatic process and associated with an increased arousal threshold, but the genetic and neuronal mechanisms that implement these essential features of sleep remain poorly understood. To address these fundamental questions, we performed a zebrafish genetic screen informed by human genome-wide association studies. We found that mutation of serine/threonine kinase 32a (stk32a) results in increased sleep and impaired sleep homeostasis in both zebrafish and mice, and that stk32a acts downstream of neurotensin signaling and the serotonergic raphe in zebrafish. stk32a mutation reduces phosphorylation of neurofilament proteins, which are co-expressed with stk32a in neurons that regulate motor activity and in lateral line hair cells that detect environmental stimuli, and ablating these cells phenocopies stk32a mutation. Neurotensin signaling inhibits specific sensory and motor populations, and blocks stimulus-evoked responses of neurons that relay sensory information from hair cells to the brain. Our work thus shows that stk32a is an evolutionarily conserved sleep regulator that links neuropeptidergic and neuromodulatory systems to homeostatic sleep drive and changes in arousal threshold, which are implemented through suppression of specific sensory and motor systems.

neuroscience↗

bioRxiv2025

Pth4 neurons define a novel hypothalamic circuit that promotes sleep via brainstem monoaminergic neurons

Classical studies identified a critical role for the hypothalamus in regulating sleep and wake states, but few such hypothalamic neuronal populations have been identified. Here we describe a sleep-promoting population of hypothalamic neurons that expresses the neuropeptides QRFP and parathyroid hormone 4 (Pth4) in zebrafish. Optogenetic stimulation of these neurons results in a large increase in sleep that requires pth4 but not qrfp. Noradrenergic locus coeruleus (LC) neurons and serotonergic raphe neurons (RN) in the hindbrain express distinct pth receptors, and genetic epistasis and cell ablation experiments revealed that Pth4 neuron-induced sleep is suppressed in mutants that lack noradrenaline in the LC or lack the serotonergic RN. Pth4 neuron-induced sleep is also suppressed in serine/threonine kinase 32a (stk32a) mutants, possibly via stk32a-expressing neurons in the prethalamus that express pth receptors. These results identify QRFP/Pth4 neurons as a novel hypothalamic sleep-promoting population and support a model in which distinct sleep- and wake-promoting hypothalamic populations act via monoaminergic neurons in the hindbrain to control vigilance state.

neuroscience↗

bioRxiv2025

Evaporative cooling signals for wound healing in plants

Repairing damaged tissues is essential for the survival of all organisms. In plants, tissue injury rapidly triggers defense and repair programs. However, the molecular mechanisms linking early injury cue to the later stages of wound repair remain unclear. Here, we show that wounding of Arabidopsis leaves induces localized low temperature at the injury site, likely caused by evaporative cooling, which is accompanied by an activation of cold-responsive genes. Using thermal imaging combined with computer vision and deep learning, we developed a workflow to monitor the dynamics of wound healing in a quantitative, non-invasive and real-time manner. Mechanistically, we show that C-repeat Binding Factor (CBF) transcription factors are required for the activation of injury-associated cold response and downstream salicylic acid (SA) signaling. The CBF-SA module promotes lignin deposition and wound repair. Together, these findings reveal a link between a wound-induced biophysical cue and the tissue repair program.

plant biology↗

bioRxiv2025

Sufficient levels of BECLIN1 are required for intestinal epithelial cell homeostasis and protection against unwanted intestinal inflammation

The prototypical autophagy regulator BECLIN1, orchestrates both autophagic and endocytic trafficking, and its homozygous deletion in the intestinal epithelium leads to intestinal disruption bearing similarities to inflammatory bowel disease (IBD). However, complete loss of BECLIN1 is rare in human disease. To model the effects of a partial reduction in BECLIN1, we examined mice with a monoallelic deletion of Becn1 in the intestinal epithelium, which decreased BECLIN1 protein levels by approximately 50%. Unlike the fatal phenotype following homozygous Becn1 deletion, the heterozygous mice were grossly normal, though they presented with significantly shorter small intestines. Gastrointestinal organoids derived from the mice also displayed disrupted endocytic trafficking and altered cytoskeletal dynamics resulting in mislocalisation of junctional proteins such as E-CADHERIN. In the mice, these changes were associated with impaired goblet cell function and maturation accompanied by abnormal mucin production, composition and secretion, resulting in compromised mucus barrier integrity. The mice also exhibited heightened susceptibility to dextran sulfate sodium (DSS)-induced colitis, emphasising the critical role of BECLIN1 in mediating protection against unregulated inflammation. Investigation of BECLIN1 levels in biopsies from patients with inflammatory bowel disease (IBD) revealed changes in its expression across distinct states of inflammation with reduced levels observed in highly inflamed regions in some patients, consistent with the gastrointestinal defects seen in mice with reduced BECLIN1. Hence, this study provides crucial insights into the multifaceted importance of BECLIN1 sufficiency in the intestinal epithelium to prevent pathophysiology. This highlights the potential of BECLIN1 as a biomarker and therapeutic target for IBD management.

cell biology↗

bioRxiv2025

Hydrogenase-driven ATP synthesis from air

All cells require a continuous supply of the universal energy currency, adenosine triphosphate (ATP), to drive countless cellular reactions. The universally conserved F1Fo-ATP synthase regenerates ATP from ADP and Pi by harnessing a transmembrane electrochemical proton gradient (pmf). Bacteria have evolved a wide diversity of pmf-forming proteins to make ATP using light, organic, and inorganic energy sources. Recently, we proposed that many bacteria survive using atmospheric trace gases to produce ATP when limited for other energy sources. However, there is no direct proof that atmospheric energy sources are sufficient to generate pmf or drive ATP synthesis. Here, we show that the membrane-associated hydrogen:quinone oxidoreductase Huc from Mycobacterium smegmatis enables ATP synthesis from air. Purified Huc couples H2 oxidation to the reduction of various ubiquinone and menaquinone analogues. We designed and optimised a minimal respiratory chain in which Huc is reconstituted into liposomes with a pmf-generating terminal oxidase and the ATP-generating F1Fo-ATP synthase. Our experiments show that passive hydrogen exchange from air to solution is sufficient for the electron transfer and pmf generation required to accumulate ATP. Finally, by combining continuous culture bioenergetics measurements with theoretical calculations, we show this process is sufficient for mycobacteria to sustain pmf and ATP synthesis (two ATP molecules per H2 oxidised) for maintenance energy requirements during nutrient starvation. These findings prove that atmospheric energy sources are dependable lifeline substrates that enable continuous energy conservation during nutrient starvation. In addition, this work provides a new tool for ATP production in synthetic applications, which unlike other approaches is traceless without by-product accumulation.

microbiology↗

bioRxiv2025

Biaxial testing and sensory texture evaluation of plant-based and animal deli meat

Animal agriculture is one of the largest contributors to global carbon emissions. Plant-based meats offer a sustainable alternative to animal meat; yet, people are reluctant to switch their diets and spending habits, in large due to the taste and texture of plant-based meats. Deli meat is a convenient form of protein commonly used in sandwiches, yet little is known about its material or sensory properties. Here we performed biaxial testing with multiple different stretch ratios of four plant-based and four animal deli meats and fit accurate material models to the resulting stress-stretch data. Strikingly, the plant-based products, turkey, ham, deli, and prosciutto, with stiffnesses of 378 {+/-} 15 kPa, 343 {+/-} 62 kPa, 213 {+/-} 25 kPa, and 113 {+/-} 56 kPa, were more than twice as stiff as their animal counterparts, turkey, chicken, ham, and prosciutto, with 134 {+/-} 46 kPa, 117 {+/-} 17 kPa, 117 {+/-} 21 kPa, and 49 {+/-} 21 kPa. In a complementary sensory texture survey, n = 18 participants were able to correlate the physical stiffness with the sensory brittleness, with Spearmans correlation coefficient of{rho} = 0.857 and p = 0.011, but not with the sensory softness or hardness. Notably, the participants perceived all four plant-based products as less fibrous, less moist, and less meaty than the four animal products. Our study confirms the common belief that plant-based products struggle to meet the physical and sensory signature of animal deli meats. We anticipate that integrating rigorous mechanical testing, physics-based modeling, and sensory texture surveys could shape the path towards designing delicious, nutritious, and environmentally friendly meats that mimic the texture and mouthfeel of animal products and are healthy for people and for the planet. Data and code are freely available at https://github.com/LivingMatterLab/CANN.

bioengineering↗

bioRxiv2024

Retinal organoids mirror CRISPR/Cas9 gene editing efficiency observed in vivo

Human retinal organoids are in vitro 3D structures that recapitulate key molecular and structural characteristics of the in vivo retina. They include the presence of all essential retinal cell types including photoreceptors, making them relevant models for preclinical development of gene therapies. A critical knowledge gap exists in understanding their utility for gene editing optimization, particularly for specific genetic disorders. We assessed the potential of retinal organoids for optimizing CRISPR/Cas9-mediated gene editing, focusing on the therapeutically relevant RHO gene implicated in autosomal dominant Retinitis Pigmentosa (adRP). Using retinal organoids, in vitro HEK293T cells, and two humanized mouse models carrying different RHO mutations, we compared editing efficiencies. We observed that retinal organoids have lower transfection efficiency compared to HEK293T cells. Notably, they exhibited editing efficiencies more closely aligned with those found in vivo. We also observed similar delivery patterns of CRISPR/Cas9 tools in both retinal organoids and mouse retinas. These delivery patterns and editing efficiencies remained consistent across dual AAV systems and transiently delivered ribonucleoprotein complexes. Our findings demonstrate that retinal organoids achieve editing outcomes comparable to those observed in vivo underscoring their utility as part of a preclinical testing platform for genome editing, with implications for advancing gene therapy research in inherited retinal diseases. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=156 HEIGHT=200 SRC="FIGDIR/small/630388v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@94478borg.highwire.dtl.DTLVardef@e50970org.highwire.dtl.DTLVardef@ce998corg.highwire.dtl.DTLVardef@1c2bbdf_HPS_FORMAT_FIGEXP M_FIG C_FIG eTOCRetinal organoids can be used to mirror in vivo mouse retina to develop CRISPR therapeutics. Here, Pulman and colleagues show similar ranges of gene editing and delivery dynamics between the organoids and in vivo mouse retina, highlighting the organoids underexplored potential for evaluating gene editing therapies in retinal diseases.

bioengineering↗

bioRxiv2024

BECLIN-1 is Essential for the Maintenance of Gastrointestinal Epithelial Integrity by Regulating Endocytic Trafficking, F-actin Organization and Lysosomal Function

Disrupted intestinal homeostasis and barrier function are key contributors to the development of various diseases, including inflammatory bowel disease (IBD). BECLIN-1, a core component of two class III phosphatidylinositol 3-kinase (PtdIns3K) complexes, has a dual role in autophagy and endocytic trafficking. Emerging evidence suggests it is involved in maintaining intestinal integrity which involves its endocytic trafficking function. To gain insights into the fatal gastrointestinal (GI) phenotype observed in BECLIN-1 knockout adult mice, organoids derived from these animals were used to investigate the role of BECLIN-1 in GI epithelial function. BECLIN-1 deletion led to disrupted localization of CADHERIN-1/E-CADHERIN to adherens junctions (AJs) and OCCLUDIN to tight junctions (TJs), resulting in the mislocalization of these critical barrier proteins. Lysosomal dysfunction was also observed, characterized by impaired cargo degradation. In addition, the filamentous actin (F-actin) cytoskeleton became disorganized though this was not associated with changes in the interaction between F-actin and CATENIN BETA-1/BETA-CATENIN nor in alterations in BETA-CATENIN localization, though BETA-CATENIN levels were reduced. These effects were all less pronounced or absent in organoids lacking the autophagy-only regulator ATG7 (autophagy related 7), further emphasizing the involvement of BECLIN-1s protein trafficking role in the maintenance of gut homeostasis and barrier function. These findings provide new insights into processes involved in epithelial dysfunction, deepening our understanding of mechanisms underlying intestinal disease.

cell biology↗

bioRxiv2024

Mutagenesis Sensitivity Mapping of HumanEnhancers In Vivo

Distant-acting enhancers are central to human development. However, our limited understanding of their functional sequence features prevents the interpretation of enhancer mutations in disease. Here, we determined the functional sensitivity to mutagenesis of human developmental enhancers in vivo. Focusing on seven enhancers active in the developing brain, heart, limb and face, we created over 1700 transgenic mice for over 260 mutagenized enhancer alleles. Systematic mutation of 12-basepair blocks collectively altered each sequence feature in each enhancer at least once. We show that 69% of all blocks are required for normal in vivo activity, with mutations more commonly resulting in loss (60%) than in gain (9%) of function. Using predictive modeling, we annotated critical nucleotides at base-pair resolution. The vast majority of motifs predicted by these machine learning models (88%) coincided with changes to in vivo function, and the models showed considerable sensitivity, identifying 59% of all functional blocks. Taken together, our results reveal that human enhancers contain a high density of sequence features required for their normal in vivo function and provide a rich resource for further exploration of human enhancer logic.

genomics↗

bioRxiv2024

The oncometabolite D-2-hydroxyglutarate promotes DNA hypermethylation at lineage-specific enhancers controlling microglial activation in IDHmut gliomas

Tumor-associated microglia and macrophages (TAMs), the most abundant myeloid populations in gliomas, shape immune responses through transcriptional programs influenced by the tumor microenvironment. Although these programs differ according to tumor IDH status, the underlying epigenetic mechanisms remain poorly understood. Here, we uncover widespread DNA hypermethylation in the myeloid compartment of IDH-mutant gliomas, predominantly at distal enhancers enriched for motifs of core microglial transcription factors (TFs). This remodeled enhancer landscape strongly correlated with reduced activity of TF regulons and coordinated repression of immunomodulatory programs that normally support microglial activation. Using primary human microglia, we show that prolonged exposure to the oncometabolite D-2-hydroxyglutarate (D-2HG) reduces TET activity and increases 5mC/5hmC ratios near TF-binding motifs within enhancers affected ex vivo. Consistent with these epigenetic alterations, D-2HG-treated microglia exhibited transcriptional signatures compatible with blunted proinflammatory responses, whereas pharmacological inhibition of mutant IDH in patients partially restored microglial immune reactivity. Altogether, our findings reveal a chronic D-2HG-driven epigenetic priming mechanism that promotes a hyporesponsive microglial state, providing a rationale for the immunologically cold phenotype of IDH-mutant gliomas and offering insight into how IDH-targeted therapies may reshape microglial immune responses.

cancer biology↗

bioRxiv2024

Dissecting the oncogenic mechanisms of POT1 cancer mutations through deep scanning mutagenesis

Mutations in the shelterin protein POT1 are associated with diverse cancers, but their role in cancer progression remains unclear. To resolve this, we performed deep scanning mutagenesis in POT1 locally haploid human stem cells to assess the impact of POT1 variants on cellular viability and cancer-associated telomeric phenotypes. Though POT1 is essential, frame-shift mutants are rescued by chemical ATR inhibition, indicating that POT1 is not required for telomere replication or lagging strand synthesis. In contrast, a substantial fraction of clinically-validated pathogenic mutations support normal cellular proliferation, but still drive ATR-dependent telomeric DNA damage signaling and ATR-independent telomere elongation. Moreover, this class of cancer-associated POT1 variants elongates telomeres more rapidly than POT1 frame-shifts, indicating they actively drive oncogenesis and are not simple loss-of-function mutations.

cancer biology↗

bioRxiv2024

Metabolic rewiring in fat-depleted Drosophila reveals triglyceride:glycogen crosstalk and identifies cDIP as a new regulator of energy metabolism

Tissues store nutrients as triglyceride (TG) or glycogen at specific ratios, but how these reserves are sensed and balanced remains poorly understood. Here we show that blockage of de novo lipogenesis (DNL) in the Drosophila fat body (FB) triggers a cell autonomous metabolic switch characterized by severe fat depletion and profound glycogen accumulation that supports animal development. Despite lipid loss, Drosophila develop normally but exhibit shortened lifespans and impaired female fecundity. Mechanistically, we identify SREBP-dependent metabolic rewiring that facilitates a switch from TG to glycogen storage, triggered by fatty acid deficiency when DNL is inhibited, and which is rescued by dietary fatty acids. Fat depleted FBs require glycolysis but exhibit blunted mitochondrial metabolism, and no dependence on lactate utilization. Finally, we identify histone acetyltransferases (HATs) Nej and Tip60, which support SREBP activity, as essential for this metabolic switch. Collectively, we propose that in response to DNL deficiency, the fat-depleted FB undergoes a SREBP-mediated TG-to-glycogen metabolic switch preserving organismal development at the cost of reproductive success. Key findingsO_LIFat body-specific FASN1 loss leads to fat-depleted but viable Drosophila that complete their developmental lifecycle by rewiring energy metabolism to store glycogen instead of fat C_LIO_LIFASN1-deficient larvae functionally rely on glycogen synthesis and glycolysis, but not lactate metabolism, and display blunted TCA metabolism C_LIO_LIMetabolic screening reveals a SREBP-dependent TG:glycogen metabolic switch in response to blockage of DNL fatty acid biosynthesis C_LIO_LIHistone acetyltransferases (HATs) Nej and Tip60, and acetyl-CoA synthase, are required for the TG:glycogen metabolic switch C_LI

cell biology↗