Biology subjects

Singh, A. K.

Publications and source records attributed to Singh, A. K..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

ATRX Loss Predicts Poor Outcomes and Reveals a Therapeutic Vulnerability to TEAD Inhibition in Soft Tissue Sarcomas

ATRX is one of the most frequently altered genes in sarcoma and encodes an ATP-dependent chromatin remodeler implicated in maintaining heterochromatin. However, ATRX alterations have not been leveraged for sarcoma treatment. We observed loss of ATRX protein in 14% of soft tissue leiomyosarcoma (STLMS, n =127), 53% of uterine leiomyosarcoma (ULMS, n = 95), 37% of undifferentiated pleomorphic sarcoma (UPS, n = 82), and 8% of dedifferentiated liposarcoma (DDLPS, n = 84). ATRX loss was associated with significantly worse outcomes in ULMS, UPS, and DDLPS. ATRX knockout in sarcoma cells increased proliferation in cooperation with TP53 deletion. ATRX knockout led to chromatin de-repression and enrichment of PRDM4 and NFIX transcription factor (TF) motifs. PRDM4 and NFIX knockdown in ATRX-mutant sarcoma lines resulted in reduced proliferation and invasion suggesting epistatic relationship. Consistent with the known functional relationship between PRMD4 and YAP1, we observed that ATRX/TP53 KO cells were more sensitive to the TEAD inhibitor VT103 compared to TP53 KO and ATRX WT controls. Overall, our results identify ATRX loss as a prognostic factor of worse outcomes, implicate the ATRX-PRDM4-YAP1 axis as a novel underlying mechanism, and suggest use of TEAD inhibition as a potential therapeutic strategy for ATRX-deficient sarcomas. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=45 SRC="FIGDIR/small/689992v1_ufig1.gif" ALT="Figure 1"> View larger version (13K): org.highwire.dtl.DTLVardef@a759ecorg.highwire.dtl.DTLVardef@100c580org.highwire.dtl.DTLVardef@1a675c9org.highwire.dtl.DTLVardef@17f1f91_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2025

The Ies6 subunit is essential for INO80-mediated nucleosome organization

ATP-dependent nucleosome remodelers of the INO80 family regulate chromatin by sliding, spacing and positioning nucleosomes. The INO80 remodeler is organized into structural modules that regulate its remodeling activity. Here, we investigate the role of the Ies6 subunit within the Arp5-Ies6 module towards nucleosome positioning and spacing in Saccharomyces cerevisiae. We show that Ies6 is critical for establishing genome-wide nucleosome organization. Deletion of IESC reduces nucleosome spacing by 3 bp and disrupts regular nucleosome arrays across most genes. Surprisingly, deletion of IESC is synthetically lethal with the deletion of ISW2, a remodeler from the ISWI family, indicating functional redundancy in nucleosome organization. Notably, INO80 binding directly predicts the role of Ies6 in INO80-mediated nucleosome organization, whereas changes in gene expression do not correlate with altered nucleosome spacing or array regularity. Together, our results highlight the essential role of the Ies6 subunit in INO80-mediated chromatin organization.

molecular biology↗

bioRxiv2025

E3 ubiquitin ligase SKP2 limits autophagy during S. aureus infection

Ubiquitination is a posttranslational modification that affects protein function, stability, and localization and is thereby balancing protein homeostasis. During infection, ubiquitination is crucial in regulating host cell signaling pathways in pathogen recognition, clearance and mounting an efficient immune response. S. aureus is an opportunistic pathogen that is able to invade and multiply within both phagocytic and non-phagocytic mammalian cells depending on virulence factor expression of the respective S. aureus strain. Selective autophagy serves as a host defense mechanism to combat intracellular bacterial persistence by targeting and degrading intracellular pathogens. However, S. aureus can subvert autophagosomal degradation and exploit these organelles for intracellular replication. We examined the role of the E3 ligase S-phase kinase-associated protein 2 (SKP2), a component of the SKP1-Cullin1-F-box (SCF) - complex, during S. aureus infection in alveolar epithelial and in macrophage-like cells. Upon S. aureus infection, we demonstrate increased SKP2 abundance through acetylation-induced stabilization and translocation into the cytoplasm. Cytoplasmic SKP2 modulated autophagy induction. By downregulation of SKP2, the level of the autophagy marker LC3-II was elevated which was accompanied by increased survival of intracellular S. aureus. Conversely, SKP2 overexpression in host cells reduced LC3-II levels followed by reduced intracellular bacteria. These findings underscore that SKP2 is an important regulator of autophagy, preventing excessive autophagy from being exploited by S. aureus. In conclusion, our findings reveal novel molecular mechanisms involved in the interaction between host cells and S. aureus providing potential approaches for targeted therapeutic intervention. ImportanceStaphylococcus aureus is a major pathogen responsible for a wide range of human and animal infections and toxin-mediated syndromes. For many years, S. aureus was mainly recognized as an extracellular pathogen. However, it has been shown that S. aureus can survive in epithelial cells and phagocytes. Intracellular persistence complicates the treatment by protecting the bacteria from antibiotics and immune detection. Elimination of pathogens from intracellular compartments relies on cellular mechanisms such as recognition and ubiquitination by host E3 ligases followed by selective autophagy. S. aureus has developed strategies to manipulate this process by evading degradation by interfering with autophagosome formation or even exploiting the formation of autophagosomes as replication niches. The present study reveals an intricate cellular response pathway that is involved in the intracellular recognition and elimination of the pathogen. This knowledge opens new avenues towards targeted treatment.

microbiology↗

bioRxiv2025

A Python framework for magnetic tweezers real-time image processing and microscope control

Magnetic tweezers are a popular biophysical instrument for manipulating and measuring single molecules. Most groups rely on custom-built setups tailored to specific experiments, making it challenging to implement and share software. Typically, image acquisition and hardware control are automated via LabVIEW, while real-time video processing is implemented in C++/CUDA libraries. Live processing can eliminate the need to store raw video, enabling high throughput, fast acquisition rates, and simplified experimental workflows. However, no open-source general-purpose software framework currently unifies these capabilities for magnetic tweezers experiments. Here, we introduce MagTrack and MagScope open-source Python-based tools designed to fill this gap. MagTrack is an image-processing library that efficiently determines bead positions from magnetic-tweezers videos using CPU or GPU computation. MagScope is a comprehensive software framework offering a graphical user interface, real-time hardware control, data acquisition, and video processing. It is built on a multiprocessing architecture for responsive, high-throughput computation. Together, MagTrack and MagScope offer a fully customizable, end-to-end, open-source Python alternative to proprietary or fragmented systems, enabling laboratories to adapt and extend the framework according to their experimental needs.

biophysics↗

bioRxiv2025

{triangleup}FOSB in the nucleus accumbens core is required for increased anxiety, but not decreased social motivation, following estrogen withdrawal in female mice

During pregnancy, estrogen levels rise dramatically, but quickly drop to prepartum levels following birth, and remain suppressed until ovulation resumes. This "postpartum estrogen withdrawal" state has been linked to changes in the brain and behavior in humans and rodents. Previous research has demonstrated that following a hormone-simulated pseudopregnancy (HSP), an experimental model of postpartum estrogen withdrawal, female mice show increased anxiety-like behaviors and decreased social motivation. Further, these behavioral changes occur concurrently with an increase in {Delta}FOSB, a transcription factor associated with stable long-term plasticity, in the nucleus accumbens core. To test whether this increase in {Delta}FOSB is required for these behavioral changes, we used a viral-mediated gene transfer approach to prevent {Delta}FOSB-mediated transcription in the NAcC during HSP and found that it reduced the high-anxiety behavioral phenotype in estrogen-withdrawn females. However, preventing {Delta}FOSB-mediated transcription had little effect on social motivation. Together, these results suggest that postpartum estrogen withdrawal increases {Delta}FOSB in the NAc core to impact anxiety-like behaviors, but not social motivation, following estrogen withdrawal.

neuroscience↗

bioRxiv2025

Targeting tumor antioxidant pathways with novel GSTP1/M2 inhibitors for cancer treatment

Glutathione transferase (GSTP1 and GSTM2) are tractable targets for anticancer drug development. In this work, a series of 6-(7-nitro-2,1,3-benzoxadiazol-4-ylthio)hexanol (NBDHEX) based analogues were designed, synthesized, and evaluated both theoretically and experimentally as GSTP1 and GSTM2 inhibitors. Among the synthesized compounds, 3h showed selective inhibition toward GSTP1 while 5b showed selective inhibition of GSTM2. Compounds 5b and 5c exhibited stronger potency while compound 3h showed slightly lower potency against the tested cancer cells than its parent molecule NBDHEX. Comprehensive biological studies were conducted on the effect of 3h, 5b and 5c towards breast cancer MDA-MB-231 and pancreatic MiaPaCa-2 cell lines revealed that 3h, 5b and 5c could activate JNK pathway and induce cell apoptosis. Furthermore in vivo experiments using NSG mice demonstrated that 5b significantly reduced tumor growth when administered in combination with gemcitabine, effectively overcoming gemcitabine resistance in the MiaPaCa-2 cell model through targeted inhibition of GSTM2. These findings suggests that, 5b could become a promising candidate for further development as a potential antitumor agent in cancer therapy.

cancer biology↗

bioRxiv2025

Breaking Barriers: Transitioning from X-ray Crystallography to Cryo-EM for Structural Studies of ATAD2B

Cryo-electron microscopy (cryo-EM) has transformed structural biology by enabling near-atomic resolution of large macromolecular complexes without the need for crystallization. Here, we describe our laboratorys transition from X-ray crystallography to single-particle cryo-EM to investigate the ATPase family AAA+ domain-containing protein 2B (ATAD2B), a chromatin regulator implicated in epigenetic signaling. We outline the challenges encountered during protein expression, purification, and sample preparation, including co-purification of the chaperonin GroEL, and strategies employed to overcome these obstacles. Our workflow highlights critical steps in sample optimization, grid vitrification, and data processing using CryoSPARC, cisTEM, and Topaz, as well as computational requirements for high-resolution reconstructions. We also discuss model building, refinement, and validation approaches, emphasizing best practices for new cryo-EM users. This work provides practical insights for structural biologists adopting cryo-EM, particularly for large, flexible protein complexes, and underscores the importance of integrated approaches combining biochemical, computational, and imaging strategies.

biochemistry↗

bioRxiv2025

Identification of donor landraces for early vegetative stage salinity tolerance in wheat by employing multivariate selection indices

Soil salinity (EC of [≥]4 dS m-1) is a major abiotic stress leading to decreased crop production due to osmotic, ionic, and cellular ionic imbalance balance. The current study aims to identify salinity-tolerant wheat landraces by investigating morpho-physiological traits. Three hundred fifty wheat landraces and check lines were evaluated for salt stress (15 dS m-1) tolerance in a hydroponic set-up. The clustering analysis categorized 350 genotypes into four control and 15 dS m-1 conditions clusters. Across the multi-trait genotype-ideotype distance index (MGIDI), Smith Hazel Index (SHI), and Stress Susceptibility Index (SSI), seven genotypes were consistently identified as tolerant among the top 150. In comparison, 12 genotypes were consistently classified as least tolerant. These identified tolerant landraces serves as important resources and novel salt tolerance donors for wheat. The tolerant*sensitive, tolerant* tolerant check, crosses can be used for generating RIL populations to delineate genetic basis of salt tolerance of newly identified lines.

physiology↗

bioRxiv2025

Genetic and environmental factors regulating soybean reproductive stages and their transitions

The reproductive stage of soybean is influenced by the effect of genotype, environment, and their interactions. While days to flowering and days to full maturity have been studied, a systematic and comprehensive study that investigates the variation in days to each stage and the role of maturity-related genes and environmental variables is lacking. Therefore, we studied 508 unique accessions from the USDA germplasm collection from maturity group 0-IV, and a set of 67 near-isogenic lines differing for maturity-related genes. Field experiments and evaluations were conducted in central Iowa, USA. The days to each of the reproductive stages, R1-R8, were recorded. We report considerable variation in the duration of reproductive growth stages between flowering and maturity, which is largely explainable by known flowering and maturity genes as well as environmental variables, day length, and growing degree days. Besides the known maturity-related genes E1, E2, and Dt1, we identified two novel SNPs, such as Glyma.01G180600 and Glyma.10G221300, as potential targets for genetic regulation of reproductive stages. We also captured two other loci, Glyma.08G216800 and Glyma.04G088100 for day length and growing degree days, respectively, that revealed dynamic regulation of environmental gradients on the reproductive stages. Furthermore, we developed a random forest-based genetic maturity model that can predict genetic and environmental effects across a wide range of genotypes. This study broadens the understanding of the factors that contribute to reproductive development, which will help to develop cultivars that combine the optimal combinations of stage durations for a higher seed yield and enhanced resilience.

genetics↗

bioRxiv2025

Synthesis and biological evaluation of glutathione-responsive 2-alkoxycarbonyl allyl niclosamide prodrugs as anticancer agents

Reprogrammed mitochondrial metabolism is recognized as an important target for anticancer therapy. Niclosamide, an FDA approved anthelmintic agent with mitochondrial uncoupling activity, has shown promise as an anticancer agent. However, off target mitochondrial toxicity has rendered the utility of this agent at clinically effective doses. Here, we synthesize a variety of prodrugs on the niclosamide template based on the Baylis-Hillman (BH) reaction, with the hypothesis that niclosamide will be released upon the reaction with cellular nucleophiles, including thiols. Consistent with this hypothesis, the BH-prodrugs release the parent niclosamide in the presence of cysteine and glutathione, and the cancer cell proliferation inhibition properties of the lead candidates are retained when compared to the parent niclosamide. Mitochondrial respiration assays illustrate that niclosamide acutely uncouples the mitochondria, and the lead BH-prodrug 6b does not, providing evidence of this prodrug strategy in mitigating off target toxicities. In a dose escalation study, the lead candidate 6b is generally well tolerated in healthy mice as evidenced by zero mortality, normal grooming pattern, and normal weight gains. Finally, 6b exhibits 54% volume tumor growth inhibition properties in a syngraft model of breast cancer in mice. The studies herein provide a novel methodology for the application of BH prodrugs on the niclosamide template and the anticancer applications.

pharmacology and toxicology↗

bioRxiv2025

BRD4 regulates Aurora B kinase activity

BRD4, a pleiotropic regulator of chromatin structure and transcription, plays critical roles in cancer and immune responses. Unlike other transcriptional regulators, BRD4 largely remains bound to chromosomes during early mitosis. Here we report that BRD4 also regulates mitosis through its direct interaction with and phosphorylation of Aurora B kinase, an essential regulator of mitosis. BRD4 binding to Aurora B inhibits its kinase activity, preventing autophosphorylation and phosphorylation of the key mitotic targets histone H3 and MCAK, the mitotic centromere associated kinesin. This inhibition is relieved during metaphase when JNK is activated and phosphorylates BRD4, triggering its transient release from chromatin. Importantly, Aurora B activity during mitosis inversely correlates with BRD4 binding and directly correlates with JNK activation and BRD4 release. Our findings thus reveal a regulatory mechanism whereby Aurora B activity is directly controlled by BRD4, which in turn is regulated by JNK. Significance StatementBRD4 has been extensively characterized for its role in regulating chromatin structure and transcription. But its function during mitosis has remained unclear. This study reveals a novel mechanism by which BRD4 directly regulates mitotic progression through its interaction with and inhibition of Aurora B kinase, a central player in chromosome segregation. The timely release of BRD4 from chromatin via JNK-mediated phosphorylation enables Aurora B activation at a critical stage of mitosis. These findings uncover a previously unrecognized BRD4-Aurora B-JNK signaling axis that integrates chromatin dynamics with mitotic control, offering new insights into cell cycle regulation and potential therapeutic targets in cancer.

cell biology↗

bioRxiv2025

Low Angle Ring Illumination Stereomicroscopy (LARIS): A high-resolution imaging method of compound eyes in Drosophila and other insects.

The compound eyes of Drosophila are widely used to gain valuable insights into genetics, developmental biology, cell biology, disease biology, and gene regulation. Various parameters, such as eye size, pigmentation loss, formation of necrotic patches, and disorientation, fusion or disruption of ommatidial arrays are commonly assessed to evaluate eye development and degeneration. In this study, we developed an improved optical alignment imaging technique named "Low Angle Ring Illumination Stereomicroscopy" (LARIS), which provides high-contrast images of the Drosophila compound eye. By capturing images of the same eye using different optical alignments of the stereomicroscope, we achieved the highest resolution with minimal reflection through the LARIS method. The images captured using LARIS clearly show ommatidial fusion, disorientation, and pigmentation loss in the Drosophila eye compared to those obtained with conventional imaging method. We believe that LARIS will open new avenues for improved imaging of the compound eyes of Drosophila and other insects.

cell biology↗

bioRxiv2025

Heat Stress and Soil Microbial Disturbance Influence Soybean Root Metabolite, Microbiome Profiles, and Nodulation

Heat stress is a major limiting factor for soybean productivity worldwide. Recent studies have highlighted the critical role of the plant microbiome in enhancing plant resilience to heat stress. However, our understanding of the molecular and physiological mechanisms underlying root-microbiome interactions under heat stress remains limited. To elucidate the role of native soil microbes in the heat tolerance of soybean genotypes, we analyzed rhizosphere bacterial and fungal communities via 16S rRNA and ITS sequencing, and characterized root metabolites and anatomical traits in response to microbiome composition and heat stress. Soybean plants were grown under controlled conditions in either natural soil containing native microbiota or in microbiome-disturbed soil (via 3-hour autoclaving), under both optimal and elevated temperature regimes. Alpha and beta diversity analyses revealed significant microbial shifts between treatments. Distinct clustering of bacterial, fungal, and metabolite profiles was observed under high temperature and microbial disturbance. Nodule-forming bacteria such as Rhizobium and Janthinobacterium were markedly suppressed, and belowground traits exhibited sensitivity, with significantly reduced nodule numbers and nodulation efficiency under high temperature and soil microbial perturbation. Non-targeted root metabolomics identified 372 differentially accumulated metabolites. Integrative multi-omics analysis revealed associations between metagenomic profiles, metabolite levels, and nitrogen-fixation traits, implying a coordinated modulation of root physiological processes. These findings contribute to a growing understanding of how heat stress interacts with rhizosphere microbial communities and may support future efforts in breeding climate-resilient soybean cultivars.

plant biology↗

bioRxiv2025

Reprogramming of Cellular Plasticity via ETS and MYC Core-regulatory Circuits During Response to MAPK Inhibition in BRAF-mutant Colorectal Cancer

BackgroundAberrant enhancer dynamics play a critical role in the initiation and progression of colorectal cancer (CRC). BRAFV600E-mutated metastatic CRC may be a unique subtype, exhibiting a strong epigenetic phenotype. Interestingly, bromodomain 2, a reader protein for H3K27ac-marked enhancers, was found to be synthetically lethal in CRC with BRAF + EGFR inhibition. DesignWe evaluated the effectiveness of targeting aberrant enhancers with bromodomain and extraterminal (BET) + MAPK pathway inhibitors in patient-derived xenograft models of metastatic CRC, followed by comprehensive profiling of transcriptomic and chromatin dynamics upon BET inhibitor combination treatment. ResultsThe combination of BET and standard MAPK inhibitors has demonstrated improved efficacy against BRAFV600E CRC and selective improvements against RAS-mutant CRC in vivo. We showed that BET + MAPK inhibition induced a profound downregulation of the MAPK signaling pathway compared to MAPK inhibition alone. The loss of activation signal on enhancers, as determined by H3K27ac, led to dysregulation of core-regulatory circuitries of CRC, especially loss of the auto-regulatory mechanism of the MAPK downstream E26 transformation-specific transcription factor family. Single nucleus multiome (RNA + ATAC) sequencing further distinguished differential transcriptomic and chromatin dynamics at cell type levels. Profound downregulation of well-differentiated cell types confirmed deep inhibition of MAPK signaling and downstream transcription factors. On the other hand, dedifferentiated cell populations were abundant after MAPK or combination inhibition, suggesting therapy-induced cell state switching and adaptation. ConclusionWe are evaluating BET + BRAF + EGFR inhibition in patients with treatment-refractory BRAFV600E metastatic CRC. ClinicalTrial.gov identifier: NCT06102902. What is already known on this topicEnhancer aberrations emerge as critical epigenetic features in the progression of colorectal cancer (CRC). However, the dynamics of active enhancer and the therapeutic potential of enhancer blockade, particularly in CRC tumors with BRAFV600E mutation, is not well understood. What this study addsThis study demonstrates improved efficacy of BET inhibitor combination therapies in diverse patient-derived models and reveals epigenetic reprogramming driven cellular plasticity in BRAFV600E-mutated CRC. How this study might affect research, practice or policyOur findings support treatment with BET + BRAF + EGFR inhibitors for patients with BRAFV600E-mutant mCRC [NCT06102902]. This study also highlights the potential of combining epigenetic agents to standard targeted therapy, offering a novel treatment option for this subset of patients.

cancer biology↗

bioRxiv2025

Time Series GWAS for Iron Deficiency Chlorosis Tolerance in Soybean using Aerial Imagery

AbstractThe use of drones has become a commonly used tool by plant scientists to aid in plant phenotyping endeavors. Iron deficiency chlorosis (IDC) is a commonly observed abiotic stress in soybean fields with high soil pH levels. IDC severity is visually classified, and recent work has shown that digital imaging techniques using both ground and UAS-acquired imagery can be utilized for automated severity ratings. In our study, we compared the classification accuracy of two flight altitudes to determine the optimal flight parameters for IDC phenotyping. In addition to this, we investigated the ability to use image-predicted scores for genome wide association study (GWAS), as well as the effect of IDC on traits such as canopy area and canopy growth and development. We also report a tool for semi-automated plot extraction from orthomosaic images that can be easily integrated with UAS. We noted that 43 days after planting was an ideal time for IDC severity ratings as the highest number of significant SNPs were reported at this timepoint.

genetics↗

bioRxiv2025

The WAC-downWAC domain in the yeast ISW2 nucleosome remodeling complex forms a structural module essential for ISW2 function but not cell viability

BackgroundATP-dependent nucleosome remodeling complexes of the imitation switch (ISWI) family slide and space nucleosomes. The ISWI ATPase subunit forms obligate complexes with accessory subunits whose mechanistic roles remain poorly understood. In bakers yeast, the Isw2 ATPase subunit associates with Itc1, the orthologue of human ACF1/BAZ1A. Prior data suggested that the genomic deletion of the 374 N-terminal amino acids from Itc1 (hereafter called itc1{Delta}N) leads to a gain-of-toxic-function phenotype with severe growth defects in the BY4741 genetic background, possibly due to defective nucleosome spacing activity of the mutant complex. ResultsHere we show that the deletion encompasses a novel motif termed downWAC that forms a conserved structural module with the N-terminal WAC domain. The module is predicted to interact with DNA. However, it does not form a stable interaction interface with the remainder of the complex. Instead, it is connected through a long disordered polypeptide linker to the remainder of the complex. Curiously, the itc1{Delta}N allele does not lead to measurable growth defects in haploid BY4741 and diploid BY4743 strains. It also does not alter genome-wide nucleosome organization in wild-type cells. To rule out that potentially redundant remodeling factors obscure itc1{Delta}N-associated phenotypes, we repeated experiments in cells devoid of ISW1 and CHD1 remodelers with the same results. Only at known target genes of the ISW2 complex was the nucleosome organization perturbed in itc1{Delta}N cells. ConclusionsWe conclude that the deletion of Itc1 N-terminus is indistinguishable from the full deletion of either ITC1 or ISW2. As such, itc1{Delta}N should be considered a null allele of ISW2. We propose a model, in which the WAC-downWAC module, along with a flexible protein linker, helps ISW2 in searching for its target genes and positioning +1-nucleosomes.

molecular biology↗

bioRxiv2025

Amino acid repeat signatures underlying human-pathogen interactions

Emerging evidence suggests that amino acid homorepeats (HRs) in proteins (HRPs) contribute to protein interactability. What is the role of HRs in human-pathogen protein interactions? We find that pathogens engage physiologically important human HRPs, thereby affecting diverse host physiological processes. From the pathogen standpoint, (i) eukaryotic pathogens engage more HRPs but with host-sparse HRs, leading to disparate and discriminate interactions, (ii) prokaryotic pathogens engage less HRPs but with host-abundant non-polar HRs via host protein proxies bringing about discriminate or promiscuous interactions and (iii) viral pathogens engage more HRPs with host-abundant polar uncharged HRs affecting promiscuous interactions using host-partner HR tract mimicry. To propel further research, we introduce a resource Hi-PHI (http://hiphi.iisertirupati.ac.in/) cataloging critical information about human and pathogen HRPs and HRs. We propose mechanisms to (i) repurpose drugs targeting human HRPs engaged by pathogens for treating different infections and (ii) exploit HRs and their flanks as targets for pathogen-targeted anti-infectives.

systems biology↗

bioRxiv2025

Microfluidic Nano-Plasmonic Imaging Platform for Purification- and Label-Free Single Small Extracellular Vesicle Counting

Tumor-derived circulating small extracellular vesicles (sEVs) is a promising non-invasive biomarker for disease diagnosis. However, their quantitative detection remains challenging due to their small size and the complexity of blood plasma. Typically, sample preparation like purification is required. This study presents a purification-free approach using a microfluidic chip integrated with PANORAMA (Plasmonic nano-aperture label-free imaging) for label-free single sEV counting in plasma. CD63, CD9, and CD81 antibodies, specific biomarkers for most sEVs, are functionalized on AGNIS (arrayed gold nanodisks on invisible substrate) for selective capture. The automated microfluidic platform minimizes manual errors and allows precise programming of flow rates, directions, and media for optimization. Only 20 {micro}L of plasma is required, and the analysis is completed within 60 minutes. This platform shows great potential as a sensitive and efficient tool for detecting circulating sEVs without purification or labeling.

bioengineering↗