Biology subjects

Singh, S.

Publications and source records attributed to Singh, S..

At least 109 records · Page 6Linked to original sources

bioRxiv2025

Design and Synthesis of Peptide-Polyester Conjugates for Cell-Mediated Scaffold Degradation

Biodegradable thermoplastic polyesters are promising biomaterials for tissue engineering due to their processability and mechanical properties. Polycaprolactone (PCL) is particularly attractive for load-bearing applications but does not degrade at the same rate as new tissue formation, which may compromise functional regeneration. This study presents a strategy for cell-mediated scaffold remodeling by incorporating a protease-cleavable peptide directly into the PCL backbone. Linear peptide-PCL conjugates were synthesized with poly(ethylene glycol) (PEG) spacers flanking the peptide to enhance protease access. A functional proteomics approach was used to identify a fast-degrading peptide sequence (Fast) selectively cleaved by multiple cell types. Conjugates containing Fast or its scrambled control (ScrFast) were combined with an RGDS-PCL conjugate and fabricated into scaffolds. Including Fast and ScrFast peptides did not impair cell adhesion to the scaffolds. Cy3 labeling enabled real-time quantification of scaffold degradation in the presence of collagenase or human mesenchymal stromal cells (hMSCs). Fast-PCL scaffolds degraded significantly faster than ScrFast-PCL in both conditions, demonstrating sequence-dependent and cell-directed resorption. Integrating protease-sensitive peptides into the polymer backbone is therefore an effective approach to fabricate solid scaffolds that degrade in response to cells. This platform can be adapted to couple cellular processes to scaffold remodeling to enhance tissue regeneration.

bioengineering↗

bioRxiv2025

How many crystal structures do you need to trust your docking results?

Structure-based drug discovery relies on the prediction of protein-bound poses of new molecule designs, the accuracy of which can impact downstream prioritization. While it is expected that crystal structures of similar molecules would provide the best template for predicting the poses of new designs, the time and cost required motivates identifying a point of diminishing returns for collecting new structures. Using 403 crystal structures of SARS-CoV-2 main protease from the open science COVID Moonshot project, we explore the tradeoff between the cost and utility of obtaining crystal structures for accurately predicting poses of designed molecules. We observe that similar reference ligands enable superior pose prediction and show that success plateaus after approximately five crystal structures per generic Bemis-Murcko scaffold, exceeding 95% for the campaign's lead series. This work provides practical recommendations for resource allocation in structure-enabled drug discovery campaigns.

biophysics↗

bioRxiv2025

NEST-Scoring, a Novel miRNA Target Gene Profile Network Analysis of Placenta-Derived Extracellular Vesicles in a Transgenic Rat Model of Preeclampsia

Preeclampsia is a multisystem hypertensive disorder of pregnancy and a leading cause of maternal morbidity and mortality. Despite its increasing incidence and the debilitating nature of its cerebrovascular complications, the underlying mechanisms remain incompletely understood. The goals of this study were to 1) determine whether middle cerebral artery (MCA) hemodynamics are altered in late gestation (LG) or two months postpartum in transgenic rats with preeclampsia compared to normal pregnant Sprague-Dawley (SD) rats, and 2) evaluate the microRNA (miRNA) profiles of circulating placental-derived extracellular vesicles (EVPD) using the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway framework using NEST-Scoring [Node, Edge, System, Topology], a novel target gene profile network analysis. Our data showed elevated blood pressure in transgenic preeclampsia rats at both LG and two months post-partum (PP-2M) compared to normal pregnant SD rats in the setting of hypertension. The heart rate was also significantly higher in preeclampsia rats at LG. No differences were observed in left MCA (LMCA) velocities between strains or time points. However, LMCA resistance and pulsatility indexes were lower at PP-2M in transgenic preeclampsia rats compared to SD rats. Exposure to preeclampsia differentially altered the miRNA profiles of circulating EVPD in transgenic preeclampsia rats at both LG and PP-2M. The identified miRNA targets were associated with key vascular and cellular regulatory pathways, suggesting a mechanistic link between placental dysfunction and postpartum vascular alterations in this preeclampsia model. Overall, this study suggests that the TGA-PE rat model could be a valuable platform to study the mechanistic link between preeclampsia and cerebrovascular disease.

bioinformatics↗

bioRxiv2025

Targeted αGalCer/CD1d Therapy Engages Invariant Natural Killer T Cells to Facilitate Cardiac Healing in Chronic Doxorubicin-Induced Cardiomyopathy

Invariant natural killer T (iNKT) cells are a unique subset of innate immune cells activated by T cell receptor (TCR) signaling through CD1d molecules presenting lipid antigens. By localizing to specific tissues, iNKT cells play critical roles in maintaining homeostasis and regulating pathophysiology, making them attractive therapeutic targets for inflammatory diseases. However, their frequency in the heart and potential roles in mitigating inflammation-induced cardiac damage remain poorly understood. In this study, we examined the distribution of cardiac iNKT subsets and their response to TCR-directed alpha Galactosyl ceramide/cluster of differentiation 1d (GalCer/CD1d) complexes in a mouse model of Doxorubicin (Dox)-induced cardiotoxicity. In healthy mice, the heart harbored distinct iNKT subsets, dominated by pro-inflammatory iNKT1 cells, followed by iNKT2 subsets. Treatment with GalCer/CD1d complexes preferentially expanded the iNKT1 subset. In Dox-induced cardiotoxicity, this treatment unexpectedly increased both IFN-{gamma}, a hallmark cytokine of iNKT1 cells, and IL-10, a key anti-inflammatory mediator typically associated with regulatory iNKT subsets. Despite the expansion of iNKT1 cells and elevated IFN-{gamma} levels, GalCer/CD1d treatment did not exacerbate cardiac damage and showed modest clinical improvements compared to controls. These findings highlight the complexity of iNKT-mediated immune regulation in the heart and emphasize the need for modified TCR-directed immunotherapeutics to skew immune responses toward a regulatory phenotype. Such approaches could hold promise for treating inflammatory cardiac diseases, including Dox-induced myocarditis, myocardial infarction, and autoimmune myocarditis.

immunology↗

bioRxiv2025

Lower Airway Dysbiosis in NTM+ Bronchiectasis is Associated with NET-Predominant Severe Phenotypes

RationaleThe discoveries of neutrophilic inflammation and Pseudomonas-dominant pulmonary dysbiosis have helped pave the way for host-directed therapy in bronchiectasis. Substantial knowledge gaps remain about the interplay between neutrophilic signatures and microbes in non-tuberculous mycobacterial lung disease (NTM-LD), a phenotypically diverse lung infection that is increasingly prevalent in the United States and other parts of the world. ObjectivesEvaluate the lower airway microbiota and neutrophilic traits in NTM- and NTM+ bronchiectasis. Methods16S rRNA gene sequencing, cell counts and neutrophil extracellular trap (NET) immunoassays were performed on bronchoscopic lower airway samples in 200 bronchiectasis subjects (108 NTM-, 92 NTM+). A preclinical model of oral commensal micro-aspiration and NTM infection was used to profile the murine lower airways with flow cytometry and a NET assay. Measurements and Main ResultsLower airways of NTM+ bronchiectasis patients were enriched with Mycobacterium and oral commensals (e.g., Veillonella, Prevotella). NET levels were higher in NTM+ BAL. Mycobacterium and oral commensals co-occurred with NET and neutrophils in network studies. Distinct oral commensal taxa associated with severe disease phenotypes such as cavitary disease and exacerbators. In a murine micro-aspiration model, the combination of oral commensals and Mycobacterium led to a sustained pro-inflammatory immune response marked by an increase in Th17, {gamma}8T cells, PD-1+ T lymphocytes as well as higher NET levels. ConclusionsOur analyses showed that distinct microbiome features beyond the primary pathogen can contribute to neutrophilic inflammation and severe disease phenotypes in bronchiectasis/ NTM-LD.

immunology↗

bioRxiv2025

Fetal and maternal immune cells exhibit tandem maturation across gestation and dysregulation in preterm birth

Appropriate regulation of maternal immune cells in the pregnant uterus is essential for successful pregnancy, yet the impact of immune cells in placental villi (PV) on placental health remain understudied. We enriched immune cells from term and preterm PV for transcriptomic and functional analyses. Maternal and fetal immune cells were abundant, with maternal chimerism increasing at term. Fetal lymphocytes displayed enhanced prostaglandin-D signatures, while maternal lymphocytes were enriched for antigen presentation pathways. Inflammatory cytokines and expanded maternal and fetal T cell clones peaked at term but did not induce cytotoxicity in placental organoids, whereas expanded T cells from idiopathic preterm cases impaired trophoblast growth and endocrine function ex vivo. These findings reveal significant immune chimerism within PV in both health and disease yet implicate PV T cells in idiopathic preterm birth. One Sentence SummaryFetal-maternal immune chimerism is characteristic of all placental villi, yet unchecked T cells and cytokines can hinder trophoblast growth and potentially precipitate preterm birth.

immunology↗

bioRxiv2025

Circular RNA Pde4dip regulates myogenesis by interacting with Zfp143 mRNA: A novel regulatory axis

Many transcriptional and post-transcriptional regulators tightly regulate skeletal muscle myogenesis, including recently discovered circular RNAs (circRNAs). In this study, we used a crosslinking-based sequencing method called CliPP-Seq, wherein we performed AMT-mediated Cross-Linking of RNA-RNA duplexes followed by Poly-A RNA Pulldown and sequencing to identify mRNA-interacting circRNAs in the mRNA samples of mouse C2C12 myoblasts and myotubes. BLAST analysis of the circRNAs with mRNAs identified their potential interacting partners. Interestingly, silencing of the circular RNA Pde4dip (circPde4dip) altered the target mRNA Zfp143 (zinc finger protein 143) expression and suppressed the differentiation of C2C12 myoblasts into myotubes. In summary, we identified unexplored mRNA-interacting circRNAs and their possible role in muscle cell differentiation, specifically the circPde4dip-Zfp143 mRNA interaction as one of the key regulators of myogenesis. HighlightsO_LIIdentified mRNA-associated circRNAs in differentiating C2C12 myoblasts C_LIO_LIThe first report identifying the regulation of myogenesis by circRNA-mRNA interaction C_LIO_LIcircPde4dip regulates C2C12 differentiation by interacting with Zfp143 mRNA C_LI

molecular biology↗

bioRxiv2025

Non-Invasive Diagnostic Evaluation of Urinary Exosomal Let-7c Cluster Expression in Bladder Cancer Using Machine Learning Approaches

BackgroundBladder cancer (BCa) diagnosis typically relies on invasive cystoscopy, which is effective but costly and uncomfortable. Urinary microRNAs (miRNAs), especially exosomal ones, are promising non-invasive biomarkers due to their stability in biological fluids and disease specificity. However, challenges such as population variability, methodological inconsistencies and normalization issues hinder their clinical translation, emphasizing the need for innovative approaches to enhance diagnostic performance. ObjectiveTo evaluate the diagnostic potential of urinary exosomal let-7c cluster (let-7c-5p, miR-99a-5p and miR-125b-5p) in BCa patients by integrating miRNA expression data with Machine Learning (ML) models. MethodsUrine samples were collected from 66 participants, including 50 BCa patients and 16 healthy controls (HC). Exosomal miRNAs were isolated and quantified using Quantitative Real-Time-Polymerase-Chain-Reaction (qRT-PCR). Statistical analysis and hypothesis tests were conducted to explore the nature and diagnostic relevance of individual biomarkers. A logistic regression classifier was applied to evaluate both the combined and differential diagnostic capabilities of the selected biomarkers. Accuracy, precision, recall and AU-ROC scores were used to assess model performance. Bioinformatics analysis was performed to identify pathways associated with the features prioritized by the ML models, ensuring their relevance to BCa. ResultsThe result revealed significant differentiation between BCa patients and HC, with miR-99a-5p (p=0.013, AU-ROC=0.71) and miR-125b-5p (p=0.047, AU-ROC=0.64) demonstrating reliable diagnostic performance (let-7c-5p showed weaker discrimination, AU-ROC=0.65, p>0.1). The logistic regression ML model achieved an accuracy of 80.0% (AU-ROC=0.86, recall=100%) in distinguishing cancer from HC and 53.3% (AU-ROC=0.63) when applied to miRNA-only grade classification. When clinical variables were integrated with miRNA expression, performance improved to 73.3% accuracy (AU-ROC=0.61) for high-versus low-grade differentiation. Across Ta-T2, miR-99a-5p displayed relatively better separation, whereas let-7c-5p and miR-125b-5p showed weak stage-related differences. The integration of bioinformatics analysis confirmed the biological relevance of these miRNAs in BCa-related pathways, including PI3K-Akt, p53, NF-{kappa}B and RAS/MAPK signaling, with hub genes such as TP53, MYC, EGFR, and CCND1 identified, further validating the diagnostic utility of the selected biomarkers. ConclusionUrinary let-7c cluster miRNAs demonstrate promising diagnostic potential when analyzed with ML models, offering a non-invasive alternative to conventional methods. These findings highlight the promise of ML-based approaches alongside molecular markers for advancing clinical diagnostics in BCa.

molecular biology↗

bioRxiv2025

Multidrug resistant E. coli isolate along with ESBL production and Antimicrobial Susceptibility pattern from patients of Urinary Tract Infection from tertiary care hospital, Delhi

BackgroundThird generation Cephalosporins resistances among Escherichia coli due to production of ESBL, mainly the bla-CTX-M, bla-TEM and bla-SHV genes, poses serious challenges in the clinical utility of these drugs in healthcare settings. This study was undertaken to detect prevalence of ESBL producing MDR E. coli isolates by various phenotypic and molecular method from in or out patients with urinary tract infection (UTI). MethodsA total of 56 non-repetitive isolates of E. coli from in or out patients of UTI were subjected to antimicrobial susceptibility testing. Screening for the production of extended-spectrum {beta}-lactamases (ESBL) was determined in third generation Cephalosporins resistant isolates by minimum inhibitory concentration (MIC) E-strip, followed by phenotypic confirmation by DDST, CDST and ESBL E-strip method. Further confirmation was done by molecular method, PCR was carried out for detection of bla-CTX-M, bla-TEM and bla-SHV. ResultsAll strains (56/56) were observed as ESBL producers by MIC E-strip method, 94.64% (53/56) isolates were observed as ESBL producer by DDST and 67.86% (38/56) were observed by CDST. The overall ESBL production among all MDR E. coli isolates was 89.29% (50/56) which includes any one of the three genes. The prevalence of bla-CTX-M (80.36%, 45/56) was highest, followed by bla-TEM (50%, 28/56) and bla-SHV (10.71%, 6/56). ConclusionIn our study we found bla-CTX-M gene is predominantly circulating among all three ESBL genes in the clinical isolates of MDR E. coli that were producers of ESBL.

microbiology↗

bioRxiv2025

The gerotherapeutic drugs rapamycin, acarbose, and phenylbutyrate extend lifespan and enhance healthy aging in house crickets.

The house cricket (Acheta domesticus) is a promising preclinical geroscience model due to its short lifespan, low maintenance, age-associated functional decline, and responsiveness to geroprotective drugs. Continuous dosing with rapamycin, acarbose, and phenylbutyrate extends lifespan; whether intermittent dosing offers similar benefits remains unknown. We tested 274 sex-matched crickets given 2-week intermittent dosing of each drug starting at mid-age (8-weeks), followed by behavioral testing at 10-weeks (geriatric stage). Assays included Y-maze olfactory discrimination, open-field exploration, and treadmill performance. Locomotor gaits were identified by velocity-based K-means clustering (silhouette > 0.5). A subset was monitored for post-treatment survival using Kaplan-Meier analysis. Olfactory preference was preserved by all drugs (ds = -1.82 to -1.28, Ps < 0.01), with strongest effects in rapamycin-treated individuals. Rapamycin-treated males matched or exceeded juvenile locomotor activity; phenylbutyrate reduced male activity (d = 1.49, P < 0.05) and acarbose increased walking-to-running ratios (d = -0.75, P < 0.05). Rapamycin increased central exploration and freezing (d = -1.55, P < 0.0001), while acarbose and phenylbutyrate increased peripheral freezing (d = -0.76, P < 0.05). Rapamycin and phenylbutyrate extended maximum running time (ds = -2.30 to -1.32, Ps < 0.0001), with sex-specific jumping gains in rapamycin-treated females and acarbose-treated males. Post-treatment lifespan was prolonged by rapamycin (HR = 0.42, P < 0.001) and reduced by acarbose in females (HRs = 2.92 to 3.03, Ps < 0.05). Intermittent rapamycin preserved survival, cognition, and locomotion, while acarbose and phenylbutyrate produced selective benefits, supporting A. domesticus as a scalable model for geroprotective drug discovery.

pharmacology and toxicology↗

bioRxiv2025

Nuclear Fetuin-A Drives Adipocyte Senescence via HIF-1 α During Obesity

Fetuin-A (FetA), a liver derived glycoprotein, has emerged from genome-wide association studies and epidemiological surveillance as a serum biomarker linked to obesity-driven type 2 diabetes mellitus (T2D), primarily due to its contribution to adipose tissue dysfunction. Here, we uncovered an eccentric role of nuclear FetA in visceral white adipocytes of obese T2D conditions. Hypoxia-inducible factor-1 (HIF-1) facilitates the nuclear translocation of FetA via direct interaction, a process that promotes the emergence of a senescence-associated secretory phenotype (SASP). While nuclear co-localization of FetA and HIF-1 strongly promotes adipocyte senescence, silencing FetA alone is sufficient to prevent senescence, even in conditions of HIF-1 overexpression or lipid-rich hypoxic stress. Although nuclear FetA does not directly bind to DNA, it enhances HIF-1 transcriptional activity, potentiating the activation of senescence markers such as {beta}-galactosidase and p53. Selective knockdown of FetA in obese mice notably reduced adipocyte senescence in visceral white adipose tissue (vWAT) and improved fasting glycemic control. Collectively, our findings reveal a previously unrecognized nuclear function for FetA in orchestrating adipocyte senescence in obesity, establishing nuclear FetA as a potential therapeutic target for obesity related metabolic diseases.

cell biology↗

bioRxiv2025

CRISPR/Cas9-mediated identification of human macrophage SphK1 as druggable target for development of anti-leishmanial chemotherapeutics

Sphingosine-1-phosphate (S1P) is a bioactive lipid that regulates apoptosis, autophagy, inflammation, and intracellular pathogen survival. While S1P signaling has been implicated in Leishmania donovani infection, the specific roles of its biosynthetic enzymes Sphingosine kinases SphK1 and SphK2 in host macrophage remains poorly defined. Here, we delineate the role of SphK1 in modulating host-pathogen interactions using CRISPR/Cas9-mediated knockout and pharmacological inhibition in THP-1 macrophages. We generated and validated CRISPR constructs targeting SphK1 (promoter, SBS, exon 6) and SphK2 (exon 3). SphK1 Knockout was confirmed at transcript and protein levels, accompanied by a marked reduction in SphK1 enzymatic activity and S1P levels. Functionally, SphK1 knockout macrophages exhibited decreased intracellular L. donovani burden, elevated TNF-, and reduced IL-10, and increased autophagic and apoptotic markers, suggesting a pro-inflammatory, cell-death-prone state. Pharmacological inhibition using the selective SphK1 inhibitor, PF-543 recapitulated these findings, showing reduced phosphorylated SphK1, enhanced p38MAPK activation, and augmented autophagy and apoptosis. Conversely, the SphK2 inhibitor ABC294640 had minimal effect, reinforcing the predominant role of SphK1. Together, our study identifies SphK1 as a critical host factor that facilitates L. donovani survival by modulating lysosomal stress, immune evasion, and cell fate pathways. Targeting SphK1-S1P signalling may offer a novel therapeutic approach for visceral leishmaniasis.

molecular biology↗

bioRxiv2025

Sulbactam-Durlobactam Plus Ceftriaxone Dosing and Novel Treatment Regimens for Mycobacterium abscessus Lung Disease

BackgroundIDSA guideline-based therapy achieves sputum culture conversion rates in 20-34% of patients with Mycobacterium abscessus (MAB) lung disease (LD). Double-{beta}-lactam combinations have been proposed to improve cure, based on time-kill curves. MethodsWe performed minimum inhibitory concentrations (MICs) experiments followed by hollow fiber system model of MAB-LD (HFS-MAB) exposure-effect studies with sulbactam-durlobactam administered every 8h (q8h), q12h, and q24h, to identify target exposures. Next, the sulbactam-durlobactam target exposure plus ceftriaxone was administered in the HFS-MAB inoculated with three different MAB isolates, as was the sulbactam-durlobactam-ceftriaxone combination with epetraborole and omadacycline (SDCEO).{gamma} -slopes (kill-speed) were calculated for all regimens. The minimal sulbactam-durlobactam clinical doses that achieved target exposure were identified using Monte Carlo experiments. ResultsCeftriaxone reduced sulbactam-durlobactam MICs by 8-tube dilutions. In the HFS-MAB, sulbactam-durlobactam microbial kill and antimicrobial resistance were linked to % time concentration persists above MIC (%TMIC), with target exposure of 50%. Sulbactam-durlobactam killed 3.85 log10 CFU/mL below day 0 burden (B0) with regrowth. Sulbactam-durlobactam plus ceftriaxone killed without regrowth and demonstrated Bliss additivity.{gamma} of bacterial population in >95% of virtual subjects were 2.28 (0.97-4.80) log10 CFU/mL/day for sulbactam-durlobactam-ceftriaxone and 2.91 (1.65-4.93) log10 CFU/mL/day for SDCEO. The optimal sulbactam-durlobactam dose co-administered with ceftriaxone was 2G q8h for creatinine clearance >90 mL/min, 2G q12h for 60-90 mL/min, 1G q12h for [≥]30 to <60 mL/min, and 1G q24h for <30 mL/min. ConclusionSulbactam-durlobactam-ceftriaxone achieved the highest microbial kill encountered so far in the HFS-MAB. Sulbactam-durlobactam-ceftriaxone should be tested as the backbone for novel treatment shortening regimens.

pharmacology and toxicology↗

bioRxiv2025

Promoter evolution in HIV-1C establishes latent reservoirs highly resistant to reversal

Latent viral reservoirs remain a major barrier to curing HIV-1, with the long-terminal repeat (LTR) and Tat playing crucial roles in regulating viral transcription. Subtype-specific transcription factor binding site (TFBS) variations within the LTR significantly influence latency and reservoir stability. In earlier work, we identified HIV-1C LTR variants with duplicated TFBS motifs, including NF-{kappa}B, AP1, RBEIII, and TCF-1/LEF-1. Using five cell models, including Jurkat and primary CD4 T cells, we compared canonical R-LTR and variant R2-LTR strains. Across sub-genomic reporters, single-round infections, and full-length viral vectors, we found that the balance between RBEIII and NF-{kappa}B motifs governs stability of latency. The two-viruses-one-cell system that normalized confounding environmental factors further revealed that latency is primarily controlled by intrinsic transcriptional circuits rather than external stimuli. In longitudinal studies of HIV-1 individuals from acute and chronic infection phases, we observed dominant R strains during early infection and the spontaneous emergence of R2 strains in nearly half of chronic-phase subjects, a process accelerated by ART. Upon CD4 T cell activation, R strains preferentially rebounded, while R2 strains showed strong resistance to reversal, even in subjects harbouring a co-infection. Together, these findings establish the clinical significance of LTR variation in latency regulation and identify the R2 phenotype as a critical determinant of reservoir persistence. These results underscore the importance of addressing reservoir heterogeneity in cure strategies, particularly in HIV-1C-prevalent regions.

microbiology↗

bioRxiv2025

Responders vs. non-responders to mesenchymal stromal cells in knee osteoarthritis patients: mechanistic correlates of donor cell attributes and patient features

Mesenchymal stromal cell (MSC) injection has afforded heterogenous outcomes in knee osteoarthritis (KOA). Herein, a framework that dually correlates KOA patient responsiveness to baseline autologous bone marrow-derived MSC(M) donor batch attributes and baseline clinical and biomarker features is provided. Using clinical trial data, we demonstrated that MSC(M) with increased immunomodulatory potency are more efficacious. Multivariable MSC(M) genes correlated strongly with responder status and to 12- and 24-month improvements in Knee Injury and Osteoarthritis Outcome Scores. Responder MSC(M) donor batches had unique microRNA expression and ability to polarize CD14+ monocytes in vitro. KOA Responders had lower baseline physical activity and trended toward more severe baseline KOA. Baseline local but not systemic biomarkers showed trending correlations to patient responsiveness. 42% of KOA patients were Responders at 24 months, emphasizing durability of single MSC(M) injections. Together, our analytical methodology defines critical quality attributes of potent MSC(M) donor batches and identifies putative KOA patient theratypes to MSC treatments. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=159 HEIGHT=200 SRC="FIGDIR/small/665028v4_ufig1.gif" ALT="Figure 1"> View larger version (49K): org.highwire.dtl.DTLVardef@18bbb07org.highwire.dtl.DTLVardef@a406e8org.highwire.dtl.DTLVardef@c18c8corg.highwire.dtl.DTLVardef@f2731c_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2025

Humanized mice enable in vivo evaluation of engineered plasma cell biology and therapeutic function

Engineered plasma cells (ePCs) offer a durable strategy for in vivo delivery of therapeutic antibodies, but standard immunodeficient mouse models lack human immune factors critical for plasma cell survival and function. We utilized a humanized mouse model in which NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG) mice were engrafted with human CD34+ stem cells as recipients for infusions with autologous ePCs. In this setting, ePCs localized to plasma cell niches and stably secreted antibodies for over three months. To improve the selection of antibodies for secretion, we developed a B cell receptor surface display screen that identified candidate antibody sequences with high secretion potential. An anti-SARS-CoV-2 antibody (clone 297) selected by this method showed robust secretion both in vitro and vivo, and serum from ePC-engrafted mice potently neutralized SARS-CoV-2 pseudovirus. Together, these findings establish a physiologically relevant model for testing human ePCs, and offer a generalizable strategy for optimizing antibody selection to support long-term therapeutic delivery.

molecular biology↗

bioRxiv2025

Age-dependent tumor-immune interactions underlie immunotherapy response in pediatric cancer

Pediatric cancers originate in rapidly growing tissues within the context of a developing host. However, the interactions between cancer cells and the developing immune system are incompletely understood. Here, we established a suite of pediatric syngeneic mouse cancer models across diverse anatomical sites and compared their tumor immune microenvironment with that in adult mice. Tumors in pediatric mice exhibited significantly accelerated growth and diminished leukocyte infiltration, dominated by naive-like PD-1low/CD8+ T cells, and proliferative MHCIIlow/PD-L1hi/CD86low macrophages. Tumor-infiltrating leukocytes in pediatric mice were enriched for MYC targets, which was also observed in pediatric patient samples. Furthermore, pediatric mice displayed poor responses to anti-PD-1/PD-L1 or bispecific T cell engager antibodies, which could be reversed by inducing a proinflammatory microenvironment via MYC inhibition or inducing macrophage polarization to an MHCIIhi phenotype. These findings underscore the significant influence of young age on cancer immune responses and reveal potential new therapeutic opportunities for pediatric cancers. HIGHLIGHTSO_LIAllograft tumors exhibit markedly accelerated growth in pediatric hosts compared to adults. C_LIO_LITumors growing in pediatric mice have reduced leukocyte infiltration, dominated by naive-like PD-1low/CD8+ T cells, and MHCIIlow/M2-like macrophages. C_LIO_LIEnrichment of MYC target genes is observed in pediatric mouse tumors and confirmed in primary patient tumor samples. C_LIO_LIPediatric mice display reduced response to anti-PD-1/PD-L1 and BiTE immunotherapy, which can be reversed by remodeling the TIME, using either MYC inhibition or macrophage polarization. C_LI

cancer biology↗

bioRxiv2025

Blood-brain-barrier permeable fluorescent astrocyte probes.

The brains astrocytes play pivotal roles in brain homeostasis, but their contributions to neural circuit function are only beginning to be explored. In order to study astrocytes in their native environment, the field needs imaging probes that are cell-specific, non-toxic, and complementary to existing genetic techniques. We recently described a panel of cationic fluorophores that selectively label rodent and zebrafish astrocytes at low concentrations and short incubation times. Here, we expand on those first-generation astrocyte probes with a new class of brighter and more photostable dyes that allow for imaging across various wavelengths. We demonstrate these probes subcellular localization to the mitochondria and ability to cross the blood-brain barrier in zebrafish. This new class of astrocyte markers will aid researchers in visualizing and identifying subpopulations of astrocytes in both rodent and zebrafish model systems.

neuroscience↗