Biology subjects

Pandey, M.

Publications and source records attributed to Pandey, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Histone modifications define distinct nucleosome positions in cell-free DNA

Circulating cell-free DNA (cfDNA) fragmentation patterns reflect nucleosome positioning. We asked whether variation in nucleosome positions in cfDNA can reveal chromatin states and associated histone modifications. Using cell-free chromatin immunoprecipitation sequencing (cfChIP-seq) in plasma from patients with prostate cancer, we identified 35,120 modification-associated positions (MAPs), loci where nucleosomes bearing active (H3K4me2) and repressive (H3K9me3) histone marks occupy reproducibly offset positions. These offsets recurred across histone marks, an independent cfChIP-seq cohort, and nuclease-digested chromatin from cell lines. MAPs were enriched in transcribed genes but depleted near transcription start sites and CTCF-binding sites where nucleosome positioning is constrained. Across 2,535 cfDNA sequencing datasets, nucleosome protection at a subset of MAPs correlated with tumor fraction (TF), reflecting differences in histone modification status between cancer-derived and non-malignant chromatin. In targeted sequencing panels, a 50-MAP model using fragments from < 0.001% of the genome distinguished samples with tumor fractions [≥]3% vs 0% (AUCs = 0.91-0.96 across prostate, breast, and lung cancers) and outperformed a state-of-the-art fragmentomics-based tumor fraction predictor. MAP-derived estimates correlated with reference TFs (r = 0.89) and longitudinal changes in TF (r = 0.91). MAP protection at ASCL1 binding sites identified neuroendocrine transformation of prostate cancer from cfDNA. These findings establish histone-modification-associated nucleosome positioning as a mutation-independent readout of tumor fraction and cancer state from routine cfDNA sequencing.

cancer biology↗

bioRxiv2026

microRNAs control temporal patterning of the vertebrate nervous system

Temporal patterning is essential for generation of neuronal diversity in the developing vertebrate nervous system. A shared sequence of temporal transcription factors (tTFs) partitions neurons by birth date across much of the central nervous system. The molecular mechanisms that control the timing of expression of these tTFs are incompletely understood. Here, we provide evidence that this process is under the control of microRNAs (miRNAs). Perturbing miRNA biogenesis by conditional deletion of Dgcr8 from the developing mouse nervous system extends the window during which neurons with early identities are generated, but abolishes late identities in the spinal cord, hindbrain and midbrain, and holds progenitors in an early transcriptional state. We further identify miRNAs of the let-7 and miR-9 families, which target transcriptional regulators of early progenitor and neuronal identities, as candidates for mediating this effect. Throughout the nervous system, levels of these miRNAs rise during the neurogenic period in progenitors, while levels in neurons correlate with their birth-date. Moreover, the sensitivity of tTF-encoding transcripts to miR-9 inversely correlates with their expression sequence, suggesting a model in which miR-9 controls the chronology of neuronal cell fate transitions by targeting specifiers of early progenitor and neuronal temporal identity in a level-dependent manner. Consistently, perturbations of miR-9 expression dynamics by gain and loss-of-function approaches perturb temporal patterning. Together, our results demonstrate a critical, evolutionary conserved role for miRNAs in temporal patterning and suggest that a temporal miR-9 expression gradient controls the timing of tTF expression in large parts of the developing vertebrate nervous system.

developmental biology↗

bioRxiv2026

Orthogonal perturbation of sulfur availability reveals antibiotic-induced synthetic lethality in Mycobacterium tuberculosis

Despite its essential role in growth, the impact of sulfur limitation on mycobacterial physiology and antibiotic responsiveness remains poorly understood. Here, we combined chemical-genetic perturbations and infection models to investigate the consequences of sulfur limitation in Mycobacterium tuberculosis (M. tuberculosis). We report that sulfur limitation restricted bacterial growth by rewiring metabolism, resembling nutrient starvation. CRISPR interference of the sulfate transporter (ST) revealed severe vulnerability and sensitised M. tuberculosis to anti-TB drugs. Inhibition of H2S production in macrophages further compromised the fitness of ST-deficient M. tuberculosis, indicating that the bacteria depend on host-derived sulfur during infection. Importantly, preventing sulfur acquisition attenuated both the drug-sensitive H37Rv and the drug-resistant clinical strain of M. tuberculosis, while enhancing the efficacy of Isoniazid (INH) in the murine model, resulting in sterilisation of infected lung tissues. Combined, our findings suggest that restricting sulfur uptake highlights a therapeutic vulnerability that enhances the efficacy of existing anti-TB drugs.

microbiology↗

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

Ribosome profiling reveals extensive translational alterations in steatohepatitis-associated hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is one the most lethal cancer types. While infections with hepatitis B or hepatitis C viruses remain the primary risk factors for HCC development worldwide, metabolic disease-associated steatohepatitis has become the fastest growing etiology of HCC, particularly in the West. Our study characterizes, for the first time, the remodeling of the translation landscape in steatohepatitis-associated HCC using ribosome profiling and mass spectrometry techniques. In striking contrast with the transcriptional alterations, which do not show strong dependence on associated co-morbidity, translational alterations are broader in the steatohepatitis compared to the viral background. These alterations affect hundreds of genes, whose products are often involved in subcellular protein localization. By quantifying the relationship between the ribosome occupancy of upstream or downstream open reading frames (uORFs or dORFs) and coding regions (CDSs), we provide evidence of uORFs attenuating the translation efficiency of CDSs in HCC. We also identify numerous novel translated regions, including from RNAs currently annotated as non-coding, some yielding peptides that can be reproducibly identified in mass spectrometry datasets. Our study thus provides novel molecular data on HCC with a focus on the steatohepatitis etiology, reveals unexpectedly extensive translational control in this co-morbidity, and gives multiple hints and candidate targets for follow-up experiments.

systems biology↗

bioRxiv2026

Automated Ventricle Assessment via Three-dimensional Anatomical Reconstruction (AVA-TAR): a computational toolkit for autonomous lateral ventricle assessment in preclinical hydrocephalus models

IntroductionCurrent workflows for studying hydrocephalus in rodent models rely on manual segmentation or qualitative assessment of ventricular size on small animal magnetic resonance imaging, which are both inefficient and prone to variability. Atlas-based methods enable more streamlined segmentation, but their analysis is limited to morphologically normal samples. ObjectiveThis study aimed to develop and internally validate a deep learning model that performs automated segmentation of lateral ventricles in rodent brain MRIs, allowing for 3D ventricle reconstruction, morphological analysis, and ventriculomegaly detection. MethodsFour U-Net++ neural networks, each with different encoder backbones, were trained using 307 rodent brain MRIs (262 rats, 45 mice), each with manually segmented lateral ventricles serving as the ground truth. Model performance was evaluated using the Dice coefficient, intersection over union (IoU), and Hausdorff index. The most optimal model was evaluated further for its ability to quantify ventricle volume, convexity, surface area, and symmetry. ResultsThe U-Net++ model with an EfficientNet-B1 encoder achieved high accuracy (Dice: 0.823 {+/-} 0.136; IoU: 0.721 {+/-} 0.85). Further assessment of its morphological predictions found strong correlations with manual measurements of ventricular morphology, with Pearson and interclass correlation coefficients exceeding 0.96 across all metrics. The full validated pipeline was packaged into a publicly available application, hosted at https://ava-tar.org. ConclusionThis study introduces a deep learning tool for automated segmentation and morphological analysis of lateral ventricles in rodent MRIs. The tools efficiency and accuracy in quantifying ventricle morphology offers significant utility in preclinical hydrocephalus research with potential future application in the clinical setting.

neuroscience↗

bioRxiv2025

A microfluidic rheometer for tumor mechanics and invasion studies

Clinically, the feel, touch, and shape of a solid tumor are important diagnostic methods for determining the malignant state of the disease. However, there are limited tools for quantifying the mechanics and the malignancy of the tumor in a physiologically realistic setting. Here, we developed a microfluidic rheometer - termed the microrheometer - that enables simultaneous measurements of tumor spheroid mechanics and their invasiveness into a 3D extracellular matrix (ECM). The microrheometer consists of a pneumatic pressure control unit for applying controlled static or cyclic compression to tumor spheroids, and a sample chamber for containing spheroid embedded ECM. The innovation here lies in the integration of a polyacrylamide membrane force sensor within the sample chamber, enabling a direct force measurement in a physiologically relevant setting. We found that both tumor stiffness and the viscoelastic properties of the tumor are closely correlated with tumor invasiveness. The microrheometer allowed us to measure tumor mechanics in a short time (less than a minute) and has the potential to be used clinically in the future. We note that the microrheometer here can be easily extended to studies of mechanics of single cell, nucleus, as well as other cell/tissue types.

bioengineering↗

bioRxiv2025

Dissecting genomic regions and candidate genes for pod borer resistance and component traits in pigeonpea minicore collection

BackgroundPigeonpea is an important leguminous food crop primarily grown in tropical and subtropical regions of the world and is a rich source of high-quality protein. The biotic (weed, disease, and insect-pests) and abiotic stresses have significantly reduced the production and productivity of pigeonpea. Helicoverpa armigera, also known as pod borer, is a major pest in pigeonpea. A substantial investigations needed for comprehending the genetic and genomic underpinnings of resistance to H. armigera. Genetic improvement by genomics-assisted breeding (GAB) is an effective approach for developing high yielding H. armigera resistance cultivars. Still yet, no genetic markers and genes linked to this key trait have been detected in pigeonpea. In this context, a set of 146 pigeonpea minicore accessions were evaluated for four H. armigera resistance component traits namely pod borer resistance (PBR), days to 50% flowering (DF), days to maturity (DM), and grain yield (GY) for three consecutive seasons under field conditions. ResultsPhenotypic data of pod borer resistance and component traits, along with the whole-genome resequencing (WGRS) data for 4,99,980 SNPs, were utilized to perform multi-locus genome-wide association study (GWAS) analysis. Two models (SUPER, and FarmCPU) detected 14 significant marker-trait associations (MTAs) for PBR and three component traits. The MTAs with significant effect were mainly identified on chromosomes CcLG02, CcLG04, CcLG05, CcLG07 and CcLG11. These MTAs subsequently delineated with key candidate genes associated with pod borer resistance (Probable carboxylesterase 15, microtubule-associated protein 5, FAR1-RELATED SEQUENCE, and Omega-hydroxypalmitate O-feruloyl transferase 4), days to maturity (RING-H2 finger protein ATL7 and Leucine-rich repeat receptor-like protein kinase), and grain yield (Secretory carrier-associated membrane protein, and Glutaredoxin-C5 chloroplastic). ConclusionThese research findings reported significant MTAs and candidate genes associated with pod borer resistance and component traits. Further lab-based pod bioassay screening identified four minicore accessions, namely ICP 10503, ICP 655, ICP 9691 and ICP 9655 (moderately resistance genotypes), showing least damage rating and larval weight gain %, compared to the susceptible checks. After validating the significant MTAs, the associated SNP markers can be effectively utilised in indirect selection, which offers potential gains for such quantitative traits with low heritability and can improve insect management more sustainably. The significant MTAs, candidate genes and resistant accessions, reported in this study may be utilized for the development of pod borer-resistant pigeonpea varieties.

plant biology↗

bioRxiv2025

Convolvulus pluricaulis mediates its pharmacological effects via sod1, rdl, glut1, GABA-B-R1 and CG6293 orthologs in Drosophila melanogaster

Convolvulus pluricaulis, commonly known as Shankhpushpi, has been extensively used in the management of disorders of the nervous system, including depression and anxiety. The plant extract has also been demonstrated to function as an antioxidant. However, the molecular effectors underlying the beneficial effects of Shankpushpi are yet to be identified. In this study, we have utilized the fruit fly Drosophila melanogaster to identify the metabolic and molecular targets that mediate the beneficial effects of dietary Shankpushpi intake. Metabolomic analysis revealed changes in Ascorbic acid, glucose, and Adenosine monophosphate in the head tissue of fruit flies that were fed Shankpushpi for 20 days. Subsequent gene expression analysis revealed significant changes in expression of glut 1 (Glucose transporter 1), CG6293 (Ascorbate transporter), rdl (Resistant to dieldrin), GABA-B-R1 (GABA-B receptor subtype 1) and sod 1 (Superoxide dismutase 1) in the head tissue of adult flies that were exposed to different doses of Shankpushpi. Consistent with the expression data, knockdown of sod 1, glut1, GABA-B-R1, and CG6293 but not sod 2 abolished the Shankpushpi-mediated resistance to paraquat-induced oxidative stress. To uncover downstream effectors that are responsible for the antidepressant and anxiolytic effects of Shankpushpi, we examined the effects of dietary intake of Shankpushpi in a stress-induced model of depression. Administration of Shankpushpi during development alleviated depression-like behavior in Drosophila. Wild-type adult flies that were fed Shankpushpi accumulated high levels of Ascorbate in the head tissue, and knockdown of Ascorbate transporter abolished the antidepressant activity of Shankpushpi in the stress-induced model. Thus, indicating that Shankpushpi-induced antidepressant effects are associated with increased Ascorbate transport. Taken together, our analysis using Drosophila melanogaster as a model has uncovered five conserved downstream effectors responsible for the antioxidant activity and one conserved effector responsible for the antidepressant activity of Convolvulus pluricaulis.

molecular biology↗

bioRxiv2025

Sub-clinical exposure to Streptococcus pyogenes drives the development of immunity

Age-related decline in Streptococcus pyogenes infection rates suggests that immunity develops progressively through repeated exposure during early life. However, the intensity or duration of exposure required is unknown, as to why some individuals appear to develop immunity, despite having few or no previously detected infections. Here, drawing on samples from a human challenge model of pharyngeal S. pyogenes infection, we investigate whether symptomatic disease is required for induction of humoral and cellular immunity. Challenge with M75 S. pyogenes induced M75-specific serum IgG and IgA antibodies and memory B cell in both symptomatic and asymptomatic participants, with responses persisting for at least 6 months. Purified IgG from asymptomatic participants exhibited significantly enhanced binding to M75 S. pyogenes and were bactericidal when transferred into a murine model of pharyngeal infection. M75-specific IgG from these participants had an altered Fc glycosylation signature, indicative of enhanced effector function and ability to limit inflammation. However, S. pyogenes challenge had no impact on cellular or humoral immune responses to a conserved cryptic epitope, p*17. These findings show that asymptomatic (or sub-clinical) exposure to M75 S. pyogenes generates functional immune responses and contributes to the streptococcal immunity that emerges by adulthood.

microbiology↗

bioRxiv2025

Telomerase reverse transcriptase is required for resistance to mycobacterial infection

Age is an important risk factor for infections such as tuberculosis (TB). Telomerase is expressed in immune cells yet leukocyte telomere length declines during ageing suggesting an age-dependent loss of telomerase activity in the immune system. Leukocyte telomere length has been correlated with worse outcomes in TB patients, however the mechanisms linking telomere biology to TB susceptibility and response to therapy are unexplored. Here we use the zebrafish-Mycobacterium marinum model to investigate the role of telomerase in TB resistance. We find depletion and inhibition of Tert, the catalytic subunit of telomerase, increases bacterial burden in zebrafish embryos. The Tert depletion infection susceptibility phenotype could not be rescued by p53 or STING depletion suggesting a non-canonical role for Tert in controlling mycobacterial infection. Consistent with a previously described role for Tert in developmental hematopoiesis, we find Tert is necessary for demand-driven emergency myelopoiesis to support containment of extended mycobacterial infection. Our findings establish a previously undescribed role for host telomerase in supporting infection demand-driven hematopoiesis to control infection.

immunology↗

bioRxiv2025

HIF1α and HIF2α mRNA Expression in Oral Squamous Cell Carcinoma does not correlate with protein expression

BackgroundOral cancer is one of the common cancers among men, its presentation is usually late. Tumor growth leads to hypoxia, and HIF1 and HIF2 are important regulators of hypoxia induced pathways, inducing angiogenesis and tumor growth. This study compares the expression levels of HIF1 and HIF2 mRNA in OSCC tissues to adjacent normal mucosa. MethodsRNA was isolated from 85 OSCC tissues and adjacent normal mucosa followed by real-time (RT) PCR to quantify HIF1 and HIF2 expression using GAPDH and {beta}-actin respectively as reference genes. ResultsHIF1 overexpression was detected in 76.47% of case and 71.76% of controls (p=0.4906), whereas HIF2 overexpression occurred in 91.76% of cases 94.11% of controls (p=0.35). HIF1 and HIF2 expression level were not significantly different in OSCC tissues compared to adjacent normal mucosa. ConclusionHIF1 and HIF2 play important role in hypoxia induced pathways and tumor progression, yet this study found no significant variation in expression between OSCC tissues and surrounding normal tissues. This suggest that their expression may be due to physiological adaptability to hypoxia or stress, or may be due to use of adjacent tissue as control and loss of protein expression could be due to post translational modifications.

cancer biology↗

bioRxiv2025

GplR1, an unusual TetR-like transcription factor in Mycobacterium abscessus, controls the production of cell wall glycopeptidolipids, colony morphology, and virulence

Mycobacterium abscessus is a major human pathogen, mostly infecting people with pre-existing lung conditions such as cystic fibrosis. The production of glycopeptidolipids (GPL) is a major determinant of virulence of this bacterium, with clinical isolates that lack GPL generally exhibiting more aggressive clinical behavior. The current paradigm is that GPL production is abolished in vivo via irreversible, spontaneous mutations taking place as part of in-host evolution. Little is known about the mechanisms or extent to which GPL production may be regulated. Here we describe an unusual TetR-like transcription factor of M. abscessus, MAB_1638, that appears to be a strong positive regulator of the entire GPL biosynthesis and export gene cluster through a combination of direct and indirect mechanisms. The inactivation of mab_1638 abolished GPL production and thus led to stable rough colony morphology, as well as increased virulence in infection models, characteristic of rough, non-GPL-producers. Transcriptome analysis found the mab_1638 mutant had 118 differentially expressed genes, including the GPL locus and a second, recently described GPL-like locus that produces a related glycosylated lipopeptide called GP8L. Chromatin Immunoprecipitation and sequencing revealed a consensus inverted-repeat DNA sequence motif characteristic of genes regulated by mab_1638. Together, mab_1638 appears to encode a transcription factor required for production of GPL and therefore having a profound effect on virulence traits. We propose naming this gene GPL regulator 1 (gplR1). This finding raises the important possibility that M. abscessus strains appearing smooth in laboratory growth conditions may nonetheless downregulate GPL-cluster genes in other conditions, including in-patient conditions, and thus acquire the phenotypic characteristics of rough strains. ImportanceMycobacterium abscessus is an important human pathogen, causing disease that is difficult to treat. M. abscessus strains have been observed to have two distinct colony morphologies, smooth and rough, which substantially impact clinical presentation. Rough strains are associated with later-stage, more severe disease and are more virulent in animal models. Smooth morphology is conferred by a molecule called glycopeptidolipid in the outer cell envelope, and rough morphology is known to occur when mutations inactivate genes required for glycopeptidolipid biosynthesis. Little is known about the possibility that glycopeptidolipid production could be regulated. Here we have identified a transcription factor that is required for glycopeptidolipid biosynthesis, indicating that glycopeptidolipid production is indeed a regulated process, and raising the important possibility that strains exhibiting smooth morphology in the lab may down-regulated GPL production in the human host and thereby acquire the virulence properties of rough strains.

microbiology↗

bioRxiv2025

Primary tuberculous mycobacterial granulomas provide a niche for superinfecting Mycobacterium abscessus

Prior and concurrent tuberculosis infection are among the most important susceptibility factors for nontuberculous mycobacterial infection in Asia. Here we model this process in zebrafish with a primary Mycobacterium marinum infection followed by a secondary M. abscessus infection. We demonstrate preferential growth of secondary M. abscessus infection inside primary M. marinum granulomas. Granuloma-resident secondary M. abscessus is protected from macrophage-mediated immune control and antibiotic therapy. Successful colonization is driven by expansion of M. abscessus feeding on caseum produced by the primary M. marinum ESX-1 virulence program in a nutritionally separate niche from M. marinum. Our data suggest tuberculous granulomas may provide a long-lasting niche for the growth of the opportunistic pathogen Mycobacterium abscessus.

microbiology↗

bioRxiv2025

Comparison of embolic effects between permanent and novel resorbable microspheres in a porcine renal artery embolization model for TAE

PurposeThis study evaluated porcine renal artery embolization using resorbable alginate microspheres versus permanent microspheres (Embozene), assessing vessel recanalization, local/systemic foreign body reactions, and potential complications. Materials and MethodsTwelve Yorkshire swine (3 female, 9 male) underwent unilateral kidney arterial embolization with either Embozene or resorbable microspheres. Angiography was performed to confirm embolization. Vessel recanalization for was determined through angiography. The effect of embolization was evaluated by assessment of serum chemistry markers and by renal histopathology at 1, 3, 7 and 28 days post-procedure. ResultsEmbolization procedures with both embolic agents were performed with 100% technical success. Hematology, coagulation factors and serum chemistry were largely unremarkable throughout the study period of 28 days. Alginate resorbable alginate microspheres facilitated compete recanalization and revascularisation within the initial 24hr observation window, while the permanent microsphere remained present at all evaluated time points. No inflammation was observed with resorbable microsphere whereas Embozene-induced inflammation was minimal to mild. Vascular histopathologic alteration with resorbable microspheres was limited and resolved by 24 hours, whereas Embozene caused sustained injury extending alteration to the internal elastic lamina, tunica media or adventitia. ConclusionAlginate resorbable microsphere demonstrated effective temporary embolization with a recanalization time of around 24 hours together with complete renal tissue recovery, no systemic impact, and minimal local reaction compared to Embozene. The findings suggest that embolization using resorbable microspheres is safe and may be suitable for use where temporary embolization of vessels is required.

bioengineering↗

bioRxiv2025

Resorbable alginate embolic microsphere for Musculoskeletal embolization applications

Resorbable embolic agents can be used for musculoskeletal (MSK) pain relief applications using a Transarterial Embolisation (TAE) technique. However, inconsistent particle size and shape, degradation rates, and unpredictable resorption and excretion of the breakdown products, limit their widespread clinical adoption. The present study reports self-degradable, rehydratable, freeze-dried, resorbable Ca2+-crosslinked alginate microspheres as a novel vascular embolic agent. The alginate lyase enzyme was incorporated into the alginate microspheres to achieve a controlled degradation rate under physiological conditions. Whilst the feasibility of alginate microspheres as embolic agents has been demonstrated, this is the first study where the controlled release is achieved in physiological conditions. To incorporate the alginate lyase enzyme in the alginate matrix, its activity was reversibly inhibited by preparing an alginate lyase-alginate-excipient mixture in a pH 3.6-3.9 buffered solution. An electrostatic encapsulator enabled the scalable preparation of microspheres of size 210 {+/-} 8 {micro}m at room temperature. The results showed that freeze-dried microspheres regained their shape and size within two minutes after reconstitution with saline, along with active alginate lyase. The reperfusion time of alginate microspheres was evaluated using digital subtraction angiography (DSA) and compared with imipenem and celestine (IMP-CS)in a porcine renal arterial embolisation model. It was observed that most of the blood vessels reperfused within 130-210 minutes, and complete vascular blush was recovered within 24 hours. Embolization with resorbable alginate microspheres induced recoverable ischemic necrosis in the targeted renal arteries. This unique feature of resorbable alginate microspheres in inducing ischemic necrosis, potentially in pain-propagating neovessels, makes it an ideal candidate embolic agent for treating MSK-associated pain using the TAE technique.

bioengineering↗

bioRxiv2024

Immunotherapeutic strategy to prevent progression and complications of acute rheumatic fever

Acute rheumatic fever (ARF) is an autoimmune disease triggered by antibodies and T-cells targeting the Group A streptococcal (GAS, Strep A) bacterium, often leading to rheumatic heart disease (RHD). Long-term antibiotic therapy is recognized as a cornerstone of public health programs to prevent reinfection and progression of ARF. However, better tools to slow disease progression, and mitigate its lifelong consequences are required. Evidence obtained in a preclinical model suggests that this can be achieved. Using the rat autoimmune valvulitis model, we explored the potential of low-dose interleukin 2 (LD-IL-2) as an immunotherapeutic intervention. In this model injection of recombinant Strep A M5 protein (rM5) to Lewis rats induce autoimmune complications, cardiac tissue inflammation and conduction abnormalities. In animals injected with rM5 and treated with LD-IL-2, no cardiac functional or histological changes were observed. LD-IL-2 therapy effectively reduced the production of cross-reactive antibodies against cardiac tissue and induced a significant increase in classical regulatory T-cells (Treg) and CD8+ Tregs in the mediastinal (heart-draining) lymph nodes. These novel findings suggest LD-IL-2 will be an effective immunotherapeutic agent for treating ARF/RHD.

immunology↗

bioRxiv2024

pH dependent direct sulfhydrylation pathway is required for pathogenesis of Mycobacterium tuberculosis

Methionine is essential for the survival of Mycobacterium tuberculosis (M. tuberculosis) inside the host. However, the transsulfuration pathway, a major contributor of methionine, is dispensable for the growth of M. tuberculosis suggesting redundancy in the methionine biosynthesis pathway. Orthologues of MetZTB in other bacterial species are known to operate a redundant single-step methionine biosynthesis pathway called direct sulfhydrylation. In this study, we demonstrate that genetic disruption of the metZ-mediated direct sulfhydrylation pathway in M. tuberculosis hinders growth at low pH, an effect mitigated by methionine supplementation. Computational analyses, including in-silico molecular docking and molecular dynamics (MD) simulations, reveal enhanced binding of the MetZ substrate, O-succinyl homoserine (OSH), to the active site of MetZ at acidic pH. Intriguingly, despite increased intracellular ATP levels, a relative decrease in the frequency of Bedaquiline (BDQ)-induced persisters is observed in metZ-deficient strain, suggesting a role of direct sulfhydrylation pathway in modulating BDQ sensitivity. Finally, we demonstrated that the absence of metZ impedes the ability of M. tuberculosis to grow inside the host.

microbiology↗