Biology subjects

Singh, A.

Publications and source records attributed to Singh, A..

At least 217 records · Page 12Linked to original sources

bioRxiv2025

LuxS/AI-2 signaling in Salmonella Typhimurium regulates phoP/phoQ to protect against acidic pH for enhanced survival in macrophages

The intestinal milieu is largely characterized by the complex array of chemical compounds produced through the metabolic activity of resident microbiota. Enteric pathogens like Salmonella, which have evolved refined mechanisms to persist within this environment, utilize these microbial metabolites and self-produce quorum molecules as molecular cues to identify ecological niches and modulate their survival and virulence strategies. Salmonella quorum sensing involves producing and detecting Autoinducer-2 (AI-2) signaling molecules. Our research reveals that Salmonella Typhimurium enhances AI-2 biosynthesis and transport under acidic conditions, aiding environmental adaptation and facilitating pathogenesis in macrophages. AI-2 signaling regulates the pH-sensing two-component system genes, phoP/phoQ, ensuring cytosolic pH homeostasis, survival, and acid tolerance. It also involves regulating the lysine/cadaverine-mediated acid tolerance response and maintaining bacterial cytosolic pH. Furthermore, we show that the repressor LsrR protein, apart from the lsr promoter, binds to only one strand of the phoP promoter via its Y25 and R43 amino acids to negatively modulate phoP expression. Additionally this signaling ameliorates the intracellular survival by modulating Salmonella Pathogenicity Island-2 (SPI-2) regulators (ssrA/ssrB) and SPI-2 effector expression via PhoP. Mouse models demonstrate that AI-2 signaling is essential for colonizing the primary and secondary infection sites, showcasing its critical role in pathogenesis and low pH survival mechanisms in Salmonella.

microbiology↗

bioRxiv2025

The Cistrome Response to Hypoxia in Human Umbilical Vein Endothelial Cells

Hypoxic stress triggers transcriptional signaling mainly through hypoxia-inducible transcription factors (HIFs), which bind hypoxia response elements (HREs) in gene regulatory regions. However, only a small proportion ([~]1%) of known HREs are occupied by HIFs during hypoxia, suggesting the involvement of additional hypoxia-responsive factors. To address this gap, we utilized MNase-defined cistrome Occupancy Analysis sequencing (MOA-seq), with the term cistrome referring to all genomic regions where transcription factors and other trans-acting regulators are bound to cis-acting elements across the genome for a particular cell type or treatment. This MNase-based assay enables genome-wide, high-resolution (<30 bp) identification of transcription factor (TF) occupancy footprints embedded within larger regions, most of which were previously annotated as open or accessible chromatin. Applying this in situ cistrome mapping to fixed nuclei from endothelial cells under normoxia or hypoxia (1, 3, or 24 hours) revealed thousands of hypoxia-responsive genomic sites with dynamic TF footprints. The affected genes were enriched in canonical hypoxia-induced pathways, such as angiogenesis. Motif analysis identified over 100 candidate TFs potentially mediating these multifaceted genomic responses. By grouping hypoxia-modified occupancy signals across the hypoxia exposure times, we clustered differentially occupied MOA sites into defined 10 distinct TF kinetic clusters, half of which were associated with HIF1A. HIF1A-proximal binding sites suggested co-activators, while non-HIF1A clusters pointed to additional TFs that may have HIF1A-independent roles. This analysis provides insight into how multiple TF networks coordinate hypoxia responses and highlights the power of cistrome profiling to deepen our understanding of the complex genomic response to low oxygen conditions. KEY POINTSO_LIMOA-seq mapped TF occupancy at 21,765 sites in normoxia, including 7,444 beyond the known ENCODE cCREs. C_LIO_LIHypoxia for 1, 3, and 24h changes the cistrome occupancy at thousands of genes. C_LIO_LIClustering analysis of hypoxia-responsive footprints consolidated cistrome kinetics into HIF1A-associated and HIF1A-independent TFs. C_LI

genomics↗

bioRxiv2025

Decoupling Phase Separation and Fibrillization Preserves Activity of Biomolecular Condensates

Age-dependent transition of metastable, liquid-like protein condensates to amyloid fibrils is an emergent phenomenon of numerous neurodegeneration-linked protein systems. A key question is whether the thermodynamic driving forces underlying reversible phase separation and maturation to irreversible amyloids are distinct and separable. Here, we address this question using an engineered version of the microtubule-associated protein Tau, which forms biochemically active condensates. Liquid-like Tau condensates exhibit rapid aging to amyloid fibrils under quiescent, cofactor-free conditions. In particular, the Tau condensate interface promotes fibril nucleation, thereby impairing condensate activity in recruiting tubulin and catalyzing microtubule assembly. Remarkably, a small molecule metabolite, L-arginine, selectively impedes condensate-to-fibril transition without perturbing phase separation in a valence and chemistry-specific manner. By enhancing condensate viscoelasticity, L-arginine counteracts age-dependent decline in the biochemical activity of Tau condensates. These results provide a proof-of-principle demonstration that small molecule metabolites can reinforce the metastability of protein condensates against a liquid-to-amyloid transition, thereby preserving condensate function.

biophysics↗

bioRxiv2025

The experimentally evolved fluconazole-resistant Clade II isolates of Candidozyma auris exhibit a distinct lipid compositional landscape, highlighting intra-clade sphingolipid heterogeneity

The intrinsic resistance of Candidozyma auris to antifungal drugs poses a major therapeutic challenge, with conventional resistance mechanisms providing only partial explanations. Sphingolipids (SLs), known for their interclade heterogeneity, play a crucial role in antifungal resistance. This study examined the SL landscape in two drug-susceptible clade II isolates, C-line and P-line, from distinct geographical origins, which were experimentally evolved to develop stable fluconazole (FLC) resistance. The progenitors displayed distinct SL profiles, P1 had higher PhytoCer and OHPhytoCer, indicating a more active acidic SL biosynthesis branch, whereas C1 exhibited elevated OHGlcCer, OHCer, and LCBs, reflecting a greater role of the neutral biosynthesis branch. The principal component analysis (PCA) also confirmed distinct segregation of the two progenitors. Upon evolution, P1.1 and C1.1 adaptors showed significant SL alterations. P1.1 exhibited PhytoCer enrichment, while C1.1 showed reduced OHGlcCer alongside increased PhytoCer, dhCer and OHPhytoCer levels. Notably, OHGlcCer remained unchanged in P1.1, whereas LCBs and OHPhytoCer decreased compared to P1. Despite these lineage-specific differences between the progenitors, both evolved replicates exhibited increased PhytoCer as a common denominator like what is also observed in clinical FLC-resistant isolates. These findings highlight intra-clade SL variability and suggest that specific SLs contribute to FLC resistance in C. auris.

microbiology↗

bioRxiv2025

A new corrector rescues F508del-CFTR folding through stabilization of the TMD1-NBD1 linker

While Trikafta has turned many CF patients into people that lead relatively healthy lives, additional modulators are still needed. We developed an acylsulfonamide-type C2 corrector X307810 that is potent and shows a distinctive mode of action in rescuing F508del-CFTR from degradation at the endoplasmic reticulum. We tracked the de-novo folding and assembly of each CFTR domain with a radio-active pulse chase - limited proteolysis folding assay and determined when and where X307810 works on the newly synthesized protein. X307810 rescued the Golgi form of F508del-CFTR to 80% of wild-type values. To our knowledge, such a dramatic increase has never been attained with a single corrector. Zooming in on X307810 mode of action revealed that the corrector changed protease resistance of the linker between TMD1 and NBD1 during late stages of CFTR folding. X307810 is the first corrector that added a unique new fragment to the typical limited-proteolysis pattern. Other C2 correctors do not change fragments, but portray an increase in fragment quantity characteristic of domain assembly in wild-type and corrected F508del-CFTR. X307810 instead extended protection of TMD1 from intracellular loop 2 to the unstructured regulatory insertion of NBD1. These results provide new and important insights into the impact of acylsulfonamide correctors on CFTR structure and function. SIGNIFICANCE STATEMENTCFTR is an anion channel, mutations in which cause cystic fibrosis (CF). Corrector compounds allow misfolded missense CFTR mutants to escape from degradation in the endoplasmic reticulum, which is the basis for CF therapy, in combination with a potentiator. How correctors improve folding is incompletely understood. We here report on X307810 having a novel mode of action on post-translational domain assembly of newly synthesized CFTR. Our in-cell folding assay shows that X307810 stabilizes the linker between the first transmembrane domain (TMD1) and the first nucleotide binding domain (NBD1) into the Regulatory Insertion; it strengthens the TMD1-NBD1-ICL4 interface. The action of X307810 boosts egress of F508del-CFTR from the ER to an unprecedented 80% for a single modulator.

biochemistry↗

bioRxiv2025

CABaNe, an automated, high content ImageJ macro for cell and neurite analysis

Measuring neurite length is crucial in neurobiology because it provides valuable insights into the growth, development, and function of neurons. In particular, neurite length is fundamental to study neuronal development and differentiation, neurons responses to drugs, neurodegenerative diseases and neuronal plasticity. Surprisingly, there is currently a lack of tools for high content neurite analysis. In this article, we present CABaNe, as an open source, high content, rule based Image J macro for cell analysis, including their neurite length. This macro possesses a graphical interface, metadata production, as well as verification means before and after analysis. Rule based and machine learning based programming have been tested for cell identification. After testing, we had better precision and adaptability using rule based cell identification. We challenged CABaNe with currently used techniques, which are manual or assisted. When tested on a small sample, CABaNe demonstrated a massive speed increase in capacity to treat dataset while maintaining or increasing precision when compared to manual measurement. When tested on a large data set, comparing different conditions, we successfully highlighted differences between conditions, in a fully automated manner. Therefore, CABaNe is viable as a high content option for cell analysis, for neurite length and other parameters. It is a base of code that can be used for other analysis or to train deep learning models. In the future, we expect this tool to be widely used in both basic and applied neurobiology research. Significance statementWhen studying neuronal cell differentiation, an important morphological parameter is neurite length. This parameter requires measuring the protrusions length of analysed cells. However, this analysis done manually can be long, as each individual cell must be measured independently. Currently, efficient single cell tools exist to assist the measurement, such as NeuronJ. However, there is currently no available automated tool for this analysis, and manual techniques suffer operator bias. In this paper, we present a macro to fully automatize neurite length and other parameters measurement, for each cell, in each image, in each condition.

neuroscience↗

bioRxiv2025

Asymmetric Histone Inheritance Regulates Differential Transcription Re-initiation and Cell Fate Decisions in Mouse Olfactory Horizontal Basal Cells

The olfactory epithelium (OE) possesses an adult stem cell population, the horizontal basal cells (HBCs), to permit lifelong tissue regeneration. Here we show that HBCs exhibit asymmetric inheritance of histone H4 but not H2A-H2B during OE regeneration in mice. Primary HBC cultures further revealed asymmetric histone inheritance for H3 and H3.3. Upon mitotic exit, asymmetric histone inheritance correlates with asynchronous transcription re-initiation and differential enrichment of p63, a key transcription factor for HBC cell fate. Disruption of asymmetric histone inheritance abolished these asymmetric cellular features and attenuated OE regeneration and smell behavior recovery. Single-cell RNA sequencing of paired HBC daughters in culture further supported asymmetric multilineage cell fate priming. Together, these findings reveal asymmetric histone inheritance in a mammalian adult stem cell lineage and highlight its biological significance in neural tissue regeneration and animal behavior.

developmental biology↗

bioRxiv2025

Simultaneous immunomodulation and epithelial-to-mesenchymal transition drives lung adenocarcinoma progression

Lung cancer remains the deadliest cancer in the United States, with lung adenocarcinoma (LUAD) as its most prevalent subtype. While computed tomography (CT)-based screening has improved early detection and enabled curative surgeries, the molecular and cellular dynamics driving early-stage LUAD progression remain poorly understood, limiting non-surgical treatment options. To address this gap, we profiled 2.24 million cells from 122 early-stage LUAD patients using multiplexed imaging mass cytometry (IMC). This analysis revealed the molecular, spatial, and temporal dynamics of LUAD development. Our findings uncover a binary progression model. LUAD advances through either inflammation, driven by a balance of cytotoxic and regulatory immune activity, or fibrosis, characterized by stromal activation. Surprisingly, tumor cell populations did not increase significantly. Instead, they displayed a mixed phenotypic profile consistent with epithelial-to-mesenchymal transition (EMT), effectively masking the expansion of malignant cells. Furthermore, we addressed discrepancies between CT-based and histology-based subtyping. CT scans, while non-invasive, often mischaracterize invasive fibrotic tumors--which account for 20.5% of LUAD cases--as mild, non-solid ground glass opacities (GGOs). Using high-content IMC imaging, we demonstrate that these tumors harbor significant risks and advocate for improved diagnostic strategies. These strategies should integrate molecular profiling to refine patient stratification and therapeutic decision-making. Altogether, our study provides a high-resolution, systems-level view of the tumor microenvironment in early-stage LUAD. We characterize key transitions in oncogenesis and propose a precision-driven framework to enhance the detection and management of aggressive disease subtypes.

cancer biology↗

bioRxiv2025

Syngap+/- CA1 pyramidal neurons exhibit upregulated translation of long mRNAs associated with LTP

In the Syngap+/- model of SYNGAP1-related intellectual disability (SRID), excessive neuronal protein synthesis is linked to deficits in synaptic plasticity. Here, we use Translating Ribosome Affinity Purification and RNA-seq (TRAP-seq) to identify mistranslating mRNAs in Syngap+/- CA1 pyramidal neurons that exhibit enhanced synaptic stability and impaired long-term potentiation (LTP). We find the translation environment is significantly altered in a manner that is distinct from the Fmr1-/y model of Fragile X Syndrome (FXS), another monogenic model of autism and intellectual disability (ID). The Syngap+/- translatome is enriched for regulators of DNA repair, and mimics changes induced with chemical LTP (cLTP) in WT. This includes a striking upregulation in the translation of mRNAs with a longer length (>2kb) coding sequence (CDS). In contrast, long CDS transcripts are downregulated with induction of Gp1 metabotropic glutamate receptor induced long-term depression (mGluR-LTD) in WT, and this profile is mimicked in the Fmr1-/y model. Together, our results show the Syngap+/- and Fmr1-/y models mimic the translation environments of LTP and LTD, respectively, consistent with the dysregulation of these plasticity states in each model. Moreover, we show that translation of >2kb mRNAs is a defining feature of LTP that is oppositely regulated during LTD, revealing a novel mRNA signature of plasticity.

neuroscience↗

bioRxiv2025

Cholesterol efflux protein, ABCA1, supports anti-cancer functions of myeloid immune cells

Although immune therapy has seen significant advances, the majority of breast and other solid tumors do not respond or quickly develop de novo resistance. One factor driving resistance is highly immune suppressive myeloid cells (MCs) such as macrophages. Previous work has established clinical links between cholesterol and cancer outcome, and that MC function can be regulated through disruption in cholesterol metabolism. Thus, we screened for proteins that were expressed in MCs, involved in cholesterol homeostasis and whose expression was associated with survival; we identify the cholesterol efflux protein ABCA1. Preclinical studies revealed that ABCA1 activity resulted in increased anti-cancer functions of macrophages: enhanced tumor infiltration, decreased angiogenic potential, reduced efferocytosis, and improved support of CD8+ T cell activity. Mechanistically, different AKT isoforms are involved, through both PI3K dependent and independent mechanisms. Assessment of human blood and breast tumors revealed correlations between ABCA1 in macrophages and angiogenic potential, VEGFA, and CD8 T cell abundance and activity, highlighting the clinical relevance of our findings. The culmination of the effects of ABCA1 on MC function were demonstrated through increased tumor growth and metastasis in mice with MC specific knockout of ABCA1. Therefore, modulating ABCA1 activity within MCs may represent a novel approach to immune therapy.

cancer biology↗

bioRxiv2025

Prevalence and mechanisms of high-level carbapenem antibiotic tolerance in clinical isolates of Klebsiella pneumoniae

Antibiotic tolerance is the ability of bacteria to survive normally lethal doses of antibiotics for extended time periods. Clinically significant Enterobacterales, for example, can exhibit high tolerance to the last-resort antibiotic meropenem. Meropenem tolerance is associated with formation of cell wall-deficient spheroplasts that readily recover to rod shape and normal growth upon removal of the antibiotic. Both the true prevalence of tolerance, and genetic mechanisms underlying it, remain poorly understood. Here, we find that meropenem tolerance is widespread among clinical Enterobacterales. Using forward genetics, we uncover novel tolerance factors in a hypertolerant isolate of the ESKAPE pathogen Klebsiella pneumoniae. We find that multiple mechanisms contribute to tolerance, and that cell envelope stress responses (PhoPQ, Cpx, Rcs and OmpR/EnvZ) collectively promote spheroplast stability and recovery, while the lytic transglycosylase MltB counteracts it. Our data indicate that tolerance is widespread among clinical isolates, and that outer membrane maintenance is a key factor promoting survival of tolerant K. pneumoniae.

microbiology↗

bioRxiv2025

State or personality trait: Determinants of boldness and shoal size preference in adult zebrafish

Animals adjust their behavior in response to physiological states to optimize the trade-off between energy acquisition and survival. A key question in animal personality research is whether behavioral variation is driven by consistent physiological state differences or stable personality traits. This study evaluates boldness and shoal size discrimination in adult male zebrafish (Danio rerio) across three hunger states: same-day feeding (H0), 24-hour food deprivation (H1), and 48-hour food deprivation (H2). Behavioral assessments were conducted over two testing cycles, with each individual undergoing every test twice for each hunger state within each cycle. The assays comprised the Open Field Test (OFT), Emergence Test (ET), and Social Preference Test (SPT), with the SPT conducted under binary (4 vs. 2 fish) and ternary (4 vs. 2 vs. 1 fish) choice conditions. Hunger significantly reduced emergence latency, but did not affect exploratory behavior in the OFT. Hunger also enhanced preference for larger shoals above chance in the binary SPT during the second testing cycle, though this effect was absent in ternary choices. Testing cycle effects revealed habituation-driven increases in boldness in both the tests and a progressive shift toward larger shoal preferences in the binary SPT. Among all assays, only the OFT showed significant repeatability, making it a reliable measure of boldness. However, it did not show consistent individual differences in plasticity due to hunger. These results highlight the crucial role of labile physiological states, such as hunger and habituation, in driving behavioral variation and underscore the importance of designing studies that disentangle state-dependent behaviors from stable personality traits in animal personality research.

animal behavior and cognition↗

bioRxiv2025

Spatial gene expression of human coronary arteries revealed the molecular features of diffuse intimal thickening in explanted hearts

BackgroundDiffuse intimal thickening (DIT) is a pre-clinical stage of atherosclerosis characterized by thickened intima. The molecular basis of its susceptibility to atherogenesis is unknown, and mechanistic investigations cannot be performed in commonly used mouse models, in which DIT does not exist. Vascular smooth muscle cells (SMCs) are the predominant cell type that occupies the intima and media of DIT. The molecular differences between these two layers may reveal the earliest phenotypic changes in SMCs to promote atherosclerosis. MethodsWe benchmarked the RNA quality of human coronary arteries from autopsies (n=7) and freshly explanted hearts (n=7) and performed Visium spatial gene expression on tissue sections with DIT. SMC-enriched intima and media were compared to find differentially expressed genes. The gene ontology features of SMC-enriched intima in this study were also compared to those in the atherosclerotic lesions, as previously revealed by single-cell RNA-sequencing studies. ResultsAlthough autopsy samples met the RNA quality standard for Visium (DV200 [≥] 30%), only arteries from freshly explanted hearts exhibited reliable performance. Genes enriched in TGF-{beta}-mediated remodeling of the extracellular matrix were overrepresented in the intima, including versican and biglycan. SMCs enriched in the intima are dedifferentiated, but unlike those in the lesions, they are not proinflammatory. ConclusionsOur findings indicate that autopsy samples are not ideal to distinguish subtle differences among cell phenotypes. Dedifferentiated SMCs in the DIT are distinct from the proinflammatory SMCs in atherosclerotic lesions. SMCs in thickened intima may lead to lipid retention but not necessarily the onset of atherosclerosis. Research Perspective1) What is New? O_LIPostmortem coronary arteries, which are frequently collected by biobanks, have degraded RNA, which are not suitable for identifying subtle differences in the transcriptome profiles. C_LIO_LICoronary arteries from explanted hearts allow for more faithful representation of spatial gene expression across the vessel wall as compared to ones from autopsy hearts. C_LIO_LIThickened intima in diffuse intimal thickening, which exists in everyone, is unlikely to undergo atherogenesis without additional stimuli such as inflammation. C_LI 2) What Question Should be Addressed Next? O_LIThe current RNA quality standard of spatial transcriptomics needs to be carefully benchmarked in biobank samples to control sequencing performance and meaningful data interpretation. C_LIO_LIHow inflammation changes smooth muscle cell phenotypes may explain why everyone has diffuse intimal thickening, but those with chronic inflammatory disease have a high risk of coronary artery disease. C_LIO_LIFuture research should focus on the interplay between smooth muscle cell phenotypes and the extracellular matrix to understand the etiology of coronary artery disease. C_LI

pathology↗

bioRxiv2025

Bioenergetic reprogramming of macrophages reduces drug tolerance in Mycobacterium tuberculosis

Eradication of Mycobacterium tuberculosis (Mtb) requires strategies targeting bacteria inside the host. Mtb exhibits heterogeneity in redox metabolism inside macrophages to evade killing by anti-TB drugs. If and how macrophage physiology correlates with bacterial redox heterogeneity and drug tolerance remains unclear. Using a fluorescent reporter of mycobacterial redox potential, flow sorting, and RNA sequencing of infected macrophages, we characterized transcriptional and metabolic responses of macrophages harboring redox-diverse Mtb populations. We found that macrophages with suppressed glycolysis and elevated oxidative phosphorylation (OXPHOS) correlated with Mtb populations exhibiting reductive stress and drug tolerance. Conversely, macrophages with elevated glycolysis and suppressed OXPHOS displayed higher mitochondrial reactive oxygen species through reverse electron transport, resulting in oxidative stress in Mtb and enhancing drug efficacy. Computational and genetic approaches identified Nrf2 as a key regulator of macrophage bioenergetics driving redox heterogeneity and drug tolerance in Mtb. Redirecting macrophage metabolism from OXPHOS to glycolysis using an FDA- approved antiemetic drug, meclizine, subverted redox heterogeneity and diminished drug tolerance in macrophages and mice. The pharmacological profile of meclizine (Cmax and AUClast) indicated no adverse interactions with first-line anti-TB drugs in mice. Our data demonstrate the feasibility of reprogramming macrophage metabolism to reduce drug tolerance in Mtb infection.

microbiology↗

bioRxiv2025

Macrophage depletion restores the DRG microenvironment and prevents axon degeneration in bortezomib-induced neuropathy

Peripheral neuropathy is a common and debilitating side effect of the chemotherapeutic bortezomib (BTZ). To explore the mechanisms underlying BTZ-induced neuropathy (BIPN), we developed a mouse model that replicates the route of administration and approximates the prolonged BTZ exposure experienced by patients. We find that male mice treated with BTZ experience more severe sensorimotor dysfunction and axon loss compared to females and observed similar results when analyzing human data. Using single cell RNA-sequencing, we reveal that BTZ significantly alters the dorsal root ganglia (DRG) microenvironment in mice, producing pronounced sex-specific changes in satellite glial cells (SGCs) in males and females and dysregulation of the extracellular matrix (ECM), particularly in males. These changes are accompanied by expansion of macrophages, which is more pronounced in males. We identify four macrophage subtypes in the DRG, including a pro-fibrotic population that is exclusively associated with BIPN. Depletion of macrophages via anti-CSF1R treatment in male mice prevents BTZ-induced SGC activation and aberrant collagen deposition in DRGs, potently preserves peripheral axons, and improves functional outcomes. These findings highlight SGCs, neuroinflammation and dysregulation of the ECM as drivers of sex-specific differences in BIPN and suggest that targeting neuroinflammation is a promising therapeutic strategy to treat this disease. One Sentence SummaryInflammation and neurofibrosis in DRGs underlie sex-specific differences in bortezomib-induced neuropathy and are promising treatment targets.

neuroscience↗

bioRxiv2025

Distinct causes of three phenotypic hallmarks of hematopoietic aging

Hematopoietic aging is characterized by chronic inflammation associated with myeloid bias, HSC accumulation, and functional HSC impairment. Yet it remains unclear how inflammation promotes these aging phenotypes. NF{kappa}B both responds to and directs inflammation, and we present an experimental model of elevated NF{kappa}B activity ("I{kappa}B-") to dissect its role in hematopoietic aging phenotypes. We found that while elevated NF{kappa}B activity is not sufficient for HSC accumulation, HSC-autonomous NF{kappa}B activity impairs their functionality, leading to reduced bone marrow reconstitution. In contrast, myeloid bias is driven by the I{kappa}B- proinflammatory bone marrow milieu as observed functionally, epigenomically, and transcriptomically. A new scRNA-seq HSPC labeling framework enabled comparisons with aged murine and human HSC datasets, documenting an association between HSC-intrinsic NF{kappa}B activity and quiescence, but not myeloid bias. These findings delineate separate regulatory mechanisms that underlie the three hallmarks of hematopoietic aging, suggesting that they are specifically and independently therapeutically targetable. SummaryAging is associated with inflammation and three hallmark hematopoietic dysfunctions. Using mouse models and single-cell analyses we report that each has a different cause: HSC accumulation is NF{kappa}B-independent, HSC functional impairment is driven by NF{kappa}B within HSCs, and myeloid bias is driven by the NF{kappa}B-altered milieu.

immunology↗

bioRxiv2025

Rescue of hippocampal synaptic plasticity and memory performance by Fingolimod (FTY720) in APP/PS1 model of Alzheimer's disease is accompanied by correction in metabolism of sphingolipids, polyamines, and phospholipid saturation composition

Previously, our metabolomic, transcriptomic, and genomic studies characterized the ceramide/sphingomyelin pathway as a therapeutic target in Alzheimers disease, and we demonstrated that FTY720, a sphingosine-1-phospahate receptor modulator approved for treatment of multiple sclerosis, recovers synaptic plasticity and memory in APP/PS1 mice. To further investigate how FTY720 rescues the pathology, we performed metabolomic analysis in brain, plasma, and liver of trained APP/PS1 and wild-type mice. APP/PS1 mice showed area-specific brain disturbances in polyamines, phospholipids, and sphingolipids. Most changes were completely or partially normalized in FTY720-treated subjects, indicating rebalancing the "sphingolipid rheostat", reactivating phosphatidylethanolamine synthesis via mitochondrial phosphatidylserine decarboxylase pathway, and normalizing polyamine levels that support mitochondrial activity. Synaptic plasticity and memory were rescued, with spermidine synthesis in temporal cortex best corresponding to hippocampal CA3-CA1 plasticity normalization. FTY720 effects, also reflected in other pathways, are consistent with promotion of mitochondrial function, synaptic plasticity, and anti-inflammatory environment, while reducing pro-apoptotic and pro-inflammatory signals.

neuroscience↗

bioRxiv2025

Cell-death induced immune response and coagulopathy promote cachexia in Drosophila

Tumors can exert a far-reaching influence on the body, triggering systemic responses that contribute to debilitating conditions like cancer cachexia. To characterize the mechanisms underlying tumor-host interactions, we utilized a BioID-based proximity labeling method to identify proteins secreted by Ykiact adult Drosophila gut tumors into the bloodstream/hemolymph. Among the major proteins identified are coagulation and immune-responsive factors that contribute to the systemic wasting phenotypes associated with Ykiact tumors. The effect of innate immunity factors is mediated by NF{kappa}B transcription factors Relish, dorsal, and Dif, which in turn upregulate the expression of the cachectic factors Pvf1, Impl2, and Upd3. In addition, Ykiact tumors secrete Eiger, a TNF-alpha homolog, which activates the JNK signaling pathway in neighboring non-tumor cells, leading to cell death. The release of damage-associated molecular patterns (DAMPs) from these dying cells presumably amplifies the inflammatory response, exacerbating systemic wasting. Targeting the inflammatory response, the JNK pathway, or the production of cachectic factors could potentially alleviate the debilitating effects of cancer cachexia.

genetics↗