Biology subjects

Agrawal, S.

Publications and source records attributed to Agrawal, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Sequential vaccination matures VRC01-class HIV-1 neutralizing antibodies in humans

Inducing a broadly neutralizing antibody (bnAb) response is a key goal of HIV-1 vaccine development. Despite significant progress, it is unknown whether vaccine-primed B cells can be reactivated and matured to secrete bona fide bnAbs. In the IAVI C107/C110 single-arm, open-label human trial, VRC01-class memory B cells previously primed by the GT1.1 germline-targeting envelope glycoprotein (Env) trimer were reactivated by a BG505 SOSIP.664 trimer boost. Somatic hypermutation in the activated B cells drove higher antibody affinity for the CD4-binding site on fully glycosylated, heterologous Env trimers. Three VRC01-class monoclonal antibodies derived from independent B cell lineages neutralized 18-31% of 119 viruses in a globally diverse panel. This work advances the HIV-1 germline-targeting vaccination concept from proof-of-priming towards proof-of-breadth and defines a benchmark for bnAb induction.

immunology↗

bioRxiv2026

The female larval fly CNS connectome: first draft

We release an enhanced FIB-SEM volume and associated neuron, mitochondria, synapse and glia automated segmentations for the complete, gap- and artifact-free central nervous system of the first instar female larval Drosophila melanogaster. Segmentation data is largely unproofread besides select neurons in the premotor and proprioceptive system and select subvolumes where synapses have been manually annotated, serving as training and evaluation data. The dataset represents the first complete central nervous system of the larval fly, and now awaits substantial improvement of machine vision approaches that effectively leverage domain knowledge for the automated yet data-guided proofreading, or substantial and costly human proofreading. All the data and methods are publicly available for further improvement and analysis.

neuroscience↗

bioRxiv2026

Sticking the landing: leg mechanosensory feedback coordinates the transition from flight to landing

Landing is an especially demanding stage of flight. Flying animals must rapidly transform multimodal sensory information into the coordinated movement of multiple limbs in order to transition from flight to a stable standing posture, often on surfaces that vary in stability, texture, and orientation. Failure to do so can be costly, leading to injury or death. Here, we examine the role of mechanosensory feedback in guiding landing in the fruit fly, Drosophila melanogaster. We describe a novel behavioral assay in which we deliver localized mechanical contact to individual legs of tethered, flying flies while simultaneously quantifying their three-dimensional behavioral kinematics. We find that mechanical contact of the distal legs reliably induces flight cessation, and initial leg contact triggers distinct patterns of inter-leg coordination. Recruitment of subsequent leg contacts predicts landing likelihood, suggesting that coordinated feedback from multiple legs reinforces the landing transition. Next, we combine synapse-resolution connectomes with optogenetic manipulations to identify the mechanosensory pathways underlying these behaviors. Finally, we describe a population of inhibitory ascending neurons that integrates mechanosensory input from the legs and facilitates the transition from visually-mediated landing initiation to touch-mediated flight cessation. Overall, our results reveal an important set of neural circuits that convert local tactile feedback into a coordinated, rapid behavioral state transition.

neuroscience↗

bioRxiv2026

Differential Associations of Microglial Inflammation on LATE-NC and Tangle-Related Hippocampal Atrophy

BACKGROUND: Accumulations of AD and LATE-NC both contribute to changes in hippocampal volume, possibly via distinct and/or overlapping mechanisms. Microglia-driven inflammation is a shared pathway associated with both AD and LATE-NC. However, the extent to which microglia inflammation is associated with hippocampal volume is less understood. OBJECTIVE: Examine the relationship between AD and LATE-NC with hippocampal volume in persons with differing levels of microglia inflammation. METHODS: Cerebral hemispheres from 441 older adults who came to autopsy were studied. All hemispheres underwent ex-vivo MRI and detailed neuropathologic examination for neurodegenerative and cerebrovascular pathologies. Microglia were quantified in the hippocampal CA1/subiculum region using machine learning-based classifiers trained on digitized CR3-43-stained images via the HALO digital pathology platform. First, linear regression models examined the association of microglia with hippocampal volume, adjusting for demographics, postmortem interval (PMI), and common age-related pathologies. Second, linear regression models were employed to examine whether microglia density modified associations of {beta}-amyloid, tangle, or LATE-NC on hippocampal volume. RESULTS: Participants had a mean age of 90 years at death with 75% being women. Intermediate or high likelihood ADNC was present in 64% and LATE-NC (stage 2/3) was present in 52%. In linear regression models, adjusting for demographics and PMI, higher microglia density was associated with a lower hippocampal volume to hemisphere ratio (estimate = -0.021 SE=0.01, p=0.002); however, after adjusting for common age-related pathologies the association was attenuated (p=0.70). {beta}-amyloid, tangles, and LATE-NC remained independently associated with a lower hippocampal volume. The association of LATE-NC with hippocampal volume was stronger in brains with greater microglia burden (estimate for the interaction term = -0.016; SE=0.01, p=0.002). No interactions were seen between {beta}-amyloid or tangles with microglia on hippocampal volume. In stratified analyses, microglial density modified the association between LATE-NC and hippocampal volume, independent of AD neuropathologic status. CONCLUSION: Microglia-driven inflammation strengthens the association of LATE-NC, but not AD pathology, on hippocampal volume loss. These findings emphasize the importance of inflammatory pathways [when interpreting MRI-based neurodegeneration markers] in aging and mixed pathology.

pathology↗

bioRxiv2026

Fission yeast RPA-TERT-Tpz1TPP1 complex promotes telomere extension and suppresses telomere recombination

Telomerase maintains chromosome ends by extending telomeric DNA, yet how recruited telomerase becomes productively engaged remains poorly understood. Recent studies found that Replication Protein A (RPA) contributes to telomerase stimulation through interaction with TERT in humans and with the TPP1 ortholog Est3 in budding yeast, suggesting a direct role in telomerase activation. Here, we provide genetic and structural modeling evidence for a RPA-Trt1TERT-Tpz1TPP1 ternary complex that promotes telomere extension while suppressing recombination in fission yeast. Guided by results from genetic screen, followed by AlphaFold3 modeling and systematic mutagenesis of RPA, Trt1, and Tpz1, we identify four key interfaces supporting telomerase function: Ssb1RPA1-Trt1, Ssb2RPA2-Trt1, Ssb2RPA2-Tpz1, and the TEL-patch-mediated Trt1-Tpz1 interaction. Notably, Tpz1-R81, previously assigned as the TEL patch, instead contacts Ssb2 in the complex. Epistasis and suppressor analyses indicate that the newly identified RPA-Trt1 and RPA-Tpz1 interfaces collaborate with the Trt1-Tpz1 interface to allow telomerase activation after recruitment. Furthermore, comparative analyses using AlphaFold3 suggest that these interactions are likely conserved in budding yeast and humans. Collectively, these findings support a model in which RPA serves as an essential component of the active telomerase complex, coordinating TERT and TPP1-like factors to enable productive telomerase engagement. Author SummaryTelomeres are specialized dynamic protective structures at the ends of eukaryotic chromosomes that must be properly maintained to preserve genome stability. Telomerase extends telomeric DNA, but how recruited telomerase becomes fully activated to promote telomere extension remains poorly understood. In this study, we use fission yeast to investigate the role of the conserved single-stranded DNA-binding protein complex Replication Protein A (RPA) in this process. We find that RPA forms a functional complex with the telomerase catalytic subunit TERT and Tpz1, a component of the telomere protection complex shelterin and the fission yeast ortholog of human TPP1. Genetic and structural analyses identify multiple interactions within the RPA-TERT-Tpz1 complex that are required for efficient telomere extension. Disrupting these interactions allows telomerase recruitment but prevents productive telomerase action at chromosome ends. Our results further suggest that similar mechanisms may operate in other organisms, including budding yeast and humans. These findings provide insight into how telomerase activity is regulated at chromosome ends.

molecular biology↗

bioRxiv2026

EML4-ALK Fusion Rewires Transcriptomic, miRNA, and CAF-Associated Programs in Non-Small Cell Lung Cancer

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=186 SRC="FIGDIR/small/717853v1_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@a696f3org.highwire.dtl.DTLVardef@1005c11org.highwire.dtl.DTLVardef@9c65bborg.highwire.dtl.DTLVardef@1dafb2d_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstractC_FLOATNO C_FIG This study establishes an integrative framework that combines paired mRNA/miRNA profiling with immune microenvironmental features to clarify how EML4-ALK fusions shape transcriptomic and post-transcriptional networks in Non-small cell lung cancer (NSCLC). Using paired mRNA-seq and miRNA-seq data generated from the same patients, we compared fusion-positive and fusion-negative NSCLC across three interconnected layers: (i) transcriptome architecture, including differential expression, pathway, and network analyses; (ii) the miRNA-mRNA regulatory axis, encompassing dysregulated miRNAs, target repression and sponging, and fusion-specific regulatory pairs; and (iii) the tumor microenvironment, with emphasis on immune and stromal infiltration, particularly cancer-associated fibroblast (CAF)-linked extracellular matrix (ECM) and adhesion programs. Our analyses revealed a distinct reprogramming pattern in fusion-positive NSCLC, marked by activation of metabolic and proteostasis pathways, including N-glycan metabolism coupled to ER export, together with attenuation of immune-stromal communication, adhesion, ECM, calcium signaling, and PI3K/VEGF-axis transcription relative to fusion-negative NSCLC. We also identified fusion-associated microRNA perturbations, including an exclusively upregulated miR-3065-centered regulatory hub predicted to repress ECM- and adhesion-related genes (PDGFRB, CTSK, COL4A2, SPARC, FBN1, and LUM) in fusion-positive tumors, in contrast to broader miRNA network rewiring in fusion-negative tumors targeting ciliary and mitotic hubs. Tumor microenvironment analysis further distinguished the subtypes, with fusion-positive tumors showing reduced CAF infiltration relative to fusion-negative tumors and concordant gene-CAF associations. By linking mechanistic insight with candidate biomarkers and targetable pathway nodes, this work provides a basis for precision strategies in both fusion-positive and fusion-negative cohorts and broadens the therapeutic perspective beyond kinase inhibition alone.

systems biology↗

bioRxiv2026

Proviral dynamics and HIV-1C viral diversity in the context of HIV-TB co-infection

BackgroundART effectively suppresses HIV replication and restores CD4+ T cells; however, long-lived HIV latent reservoirs enable viral persistence. Tuberculosis (TB) co-infection further impacts HIV latency and enhances viral replication. Given the high prevalence of latent TB infection (LTBI) in TB-endemic settings, understanding its impact on HIV biology is critical. Our study aims to investigate the influence of TB co-infection on HIV reservoir dynamics, viral diversity, and drug resistance mutations in ART-naive individuals. MethodologySamples from 90 ART-naive HIV-1C individuals, stratified based on IGRA and TB diagnosis, were used in this study. Plasma and PBMCs were isolated for viral RNA and DNA extraction respectively. Total proviral DNA was quantified using gag PCR. Full-length env and pol genes were amplified, purified and sequenced using ONT and Illumina platforms. Pol sequences were subjected to Drug Resistance Mutation (DRM) analysis via Stanford HIVdb with a minimum threshold mutation frequency of [≥]10%. Full length env sequences were used for phylogenetic analysis by aligning with Indian Subtype C reference sequence and phylogenetic tree was generated using ggplot2. ResultProviral load analysis showed no significant differences across HIV+LTBI-, HIV+LTBI+, and HIV+TB+ groups, although a trend toward higher levels was observed in HIV+TB+ individuals. Correlation analysis revealed distinct immune associations, with HIV+LTBI+ individuals showing positive correlations with activation and PD-1 expression. Longitudinal analysis of proviral loads demonstrated a modest decline in proviral load post-ART but remained persistent for up to 18-20 months following initiation of ART accompanied by low level ongoing viral replication. DRM analysis revealed a 33% prevalence in ART-naive individuals, with higher occurrence in HIV+LTBI+ group. Of the identified DRMs, 38% (5/13) and 71% (5/7) in sequences obtained from PBMC and plasma respectively were attributed to polymorphic mutations associated with Integrase strand transfer inhibitors (INSTIs). DRMs within plasma and PBMC derived viruses showed high concordance. Phylogenetic analysis of env sequences indicated overlapping viral populations between the 3 groups, with greater diversity in PBMCs compared to plasma. ConclusionThe study highlights that HIV reservoir dynamics, drug resistance, and viral diversity are significantly influenced by TB co-infection. While proviral loads were comparable, LTBI-associated immune activation and granuloma niches may have driven viral diversification and DRM emergence. High concordance between compartments and presence of transmitted resistance underscore the need for baseline screening, multi-compartment analysis, and sustained surveillance.

microbiology↗

bioRxiv2026

Fusion-driven post-transcriptional network orchestrates ferroptosis resistance, dormancy, and immune remodeling in PRCC-TFE3 renal cell carcinoma

TFE3-rearranged papillary renal cell carcinoma (pRCC) remains poorly understood due to its rarity and complex biology. By integrating matched mRNA and miRNA sequencing from the TCGA-KIRP cohort, this study reveals a fusion-specific post-transcriptional program orchestrating ferroptosis resistance, metabolic adaptation, adhesion loss, immune remodeling, and dormancy-associated signaling. Fusion-positive tumors exhibited coordinated upregulation of antioxidant and mTORC1 components (SOD2, GPX4, G6PD, NQO1, FNIP2, RRAGC), reinforced by loss of miRNA-mediated repression. In parallel, elevated miRNAs (miR-185, miR-148a, miR-130b, miR-342) suppressed MAPK, Wnt, and tight-junction genes, generating a low-proliferative, adhesion-deficient state. AGO2-compatible miRNA-mRNA structural modeling validated key duplexes, linking miRNA regulatory specificity to fusion-driven transcriptional outputs. Immune profiling revealed reduced CD3 T cells but enrichment of CD8 and NK cells, supporting a remodeled yet persistence-permissive microenvironment. Finally, connectivity mapping analysis identified candidate leads targeting the MAPK-Wnt axis. These findings define a multilayered RNA regulatory architecture unique to PRCC-TFE3 tumors.

systems biology↗

bioRxiv2026

In Vitro Prebiotic Potential of Purified Black Rice Oligosaccharides: Simulated Digestion Stability, Short-Chain Fatty Acid Production, and Probiotic Biofilm Formation

Black rice oligosaccharides (BO) were extracted with 80% aqueous ethanol (v/v) and purified by charcoal-celite chromatography followed by dialysis using a 500 Da molecular weight cut-off (MWCO) membrane, yielding an oligosaccharide fraction with a degree of polymerisation (DP) between three and eight (DP3-DP8; 2.87 {+/-} 0.29% w/w). MALDI-TOF MS showed sodium adduct ions from m/z 527 to 1330, and GC-MS analysis of hydrolysed samples identified glucose and galactose as the major monomers, while ketosyl residues were detected in the intact fraction by selective staining and are most plausibly attributed to fructosyl units based on cereal origin and DP distribution. BO showed high resistance to simulated salivary, gastric, and pancreatic digestion (only 2.08 {+/-} 0.51%, 0.34 {+/-} 0.03%, and 4.29 {+/-} 0.73% hydrolysis, respectively) with approximately 93% remaining carbohydrate available for fermentation. All Lactobacillus strains showed positive prebiotic activity scores, with the highest response observed for Lactobacillus rhamnosus (1.165 {+/-} 0.255) and Lactobacillus plantarum (0.980 {+/-} 0.163). Fermentation produced metabolically relevant short-chain fatty acids (SCFA), mainly acetate (34.82 {+/-} 2.08 mM), as well as strain-dependent propionate and butyrate levels. BO greatly promoted probiotic biofilm formation, with biomass reaching 391.33 {+/-} 26.08% and viable cell counts of 9.01 {+/-} 0.70 log CFU/mL relative to the control. Collectively, the results indicate that BO represents a digestion-resistant, hexose-based oligosaccharide series that is selectively utilised by probiotic lactobacilli, promotes SCFA production and enhances biofilm development. To our knowledge, this work is the first to combine structural profiling with in vitro functional evaluation of a purified, low-DP oligosaccharide fraction obtained from black rice. HighlightsO_LIPurified oligosaccharides (DP3-DP8) were obtained from black rice using charcoal-celite chromatography followed by dialysis. C_LIO_LIStructural analysis confirmed that the oligosaccharides were hexose-based and composed mainly of glucose and galactose. C_LIO_LIBlack rice oligosaccharides exhibited higher resistance to simulated gastric and intestinal digestion compared with starch. C_LIO_LIPositive prebiotic activity scores were observed due to selective utilisation by probiotic Lactobacillus strains. C_LIO_LIFermentation of black rice oligosaccharides significantly increased short-chain fatty acid production. C_LIO_LIPurified oligosaccharides enhanced probiotic biofilm formation, indicating improved colonisation potential. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=179 SRC="FIGDIR/small/705216v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@9a5915org.highwire.dtl.DTLVardef@14eac7aorg.highwire.dtl.DTLVardef@1db8baorg.highwire.dtl.DTLVardef@14ad50a_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2026

Structural basis for conserved and distinct antigen recognition by a lineage of malaria-protective antibodies

Monoclonal antibodies (mAbs) targeting the Plasmodium falciparum circumsporozoite protein (PfCSP) have demonstrated substantial promise in preventing malaria infection and disease. PfCSP is characterized by a central region composed of repetitive NANP motifs, which serve as major targets for protective antibodies. Several potent mAbs targeting this region exhibit homotypic Fab-Fab interactions, which enhance antigen binding and contribute to their neutralization potency. Among these, mAb 399, encoded by the IGHV3-49/IGKV2D-29 (VH3-49/VK2D-29) germline lineages, forms head-to-head inter-Fab contacts mediated primarily by germline-encoded residues. In this study, we determined high-resolution X-ray crystal and cryo-EM structures of two additional Fabs, derived from the same germline lineages, 7160 and 7118, in complex with PfCSP-derived peptides. Both Fabs bound the NANP6 repeats with high affinity (KD 5-10 nM). Fab 7160 formed similar inter-Fab homotypic interactions to Fab 399 upon binding to an extended repeat peptide (NANP), indicating a conserved mode of recognition. In contrast, Fab 7118, which features a longer CDRH3, does not form homotypic contacts. Instead, Fab 7118 induced a bend in the peptide and adopted a distinct binding mode, which prevents inter-Fab interactions. A cryo-EM structure of Fab 7118 in complex with a recombinant shortened PfCSP construct (rsCSP) further revealed potential disruptions at inter-Fab contact sites. These findings highlight the structural versatility of VH3-49/VK2D-29-derived antibodies and demonstrate that CDR loop variations within a shared antibody lineage can modulate antibody conformation, homotypic Fab-Fab interactions, and epitope engagement. Our study provides mechanistic insights into the diverse strategies by which CSP-specific antibodies can achieve high-avidity binding and protective immunity.

microbiology↗

bioRxiv2026

Ancient human genomes from Ladakh reveal Tibetan, South Asian, and Central Asian admixture over the last three millennia

The trans-Himalayan region of Ladakh occupies a strategic position at the crossroads of South Asia, the Tibetan Plateau, and Central Asia, with archaeological evidence pointing to long-term cultural exchanges across these regions. However, the human genetic history of Ladakh remains largely unexplored. We generated paleogenomic data from seven individuals recovered from two sites in Western Ladakh - the Old Lady Spider Cave and Hanu - of which six are dated to 531-585 CE and one to the 19th century CE. The older individuals share substantial genetic ancestry with Tibetan groups but also harbor major contributions from two additional sources: one corresponding to the currently-oldest observation of the Ancestral North Indian genetic component that characterizes several present-day populations in North India and Pakistan, and another related to ancient Central Asian groups, with admixture events occurring between [~]2,100-2,500 years ago. In contrast, the later individual falls within a previously described ancient northern Himalayan genetic cline based on [~]1,100-1,300-year-old individuals from Himachal Pradesh, with ancestries related to ancient Tibetan and Steppe-related sources. Stable isotope analysis suggests that these individuals were local to Ladakh in late life and practiced an agro-pastoralist subsistence. Our study establishes that Ladakhs central role in Eurasian economic and socio-cultural networks was shaped by dynamic and sustained gene flow linking high-altitude Himalayan groups with both lowland South Asia and Inner Asia.

genetics↗

bioRxiv2026

Identification of a Novel miRNA Expression Signature for Lung Adenocarcinoma Using Systematic Machine Learning Optimization

Lung adenocarcinoma (LUAD), the most common lung cancer subtype, urgently requires reliable microRNA (miRNA) biomarkers for early detection and therapy. This study introduces a machine learning framework integrating feature stability analysis, precision-recall curves, and resampling strategies (e.g., SMOTE) to robustly identify miRNA signatures from imbalanced TCGA-LUAD data (564 samples: 519 tumor, 45 normal). We selected 8 stable features (hsa-mir-143, hsamir-210, hsa-mir-21, hsa-mir-183, hsa-mir-96, hsa-mir-182, hsa-mir-130b, hsa-mir-141) with 100% cross-fold stability via 10-fold cross-validation. A Random Forest classifier yielded excellent training performance (AUC: 1.0000; accuracy: 98%) and good generalization on an independent test set (AUC: 0.8438; accuracy: 75%). Consistent feature importance across folds supports biological relevance over overfitting. The framework mitigates class imbalance, high dimensionality, and distribution shifts--key hurdles in biomarker discovery. These reproducible miRNAs hold promise as non-invasive diagnostic tools, though external validation underscores generalization challenges across cohorts.

cancer biology↗

bioRxiv2026

Can AI Conduct Autonomous Scientific Research? Case Studies on Two Real-World Tasks

Recent advances in artificial intelligence (AI) have prompted claims about autonomous "AI scientists," yet systematic evaluations of these capabilities remain scarce. This exploratory study investigates whether current AI frameworks can execute scientific research tasks beyond isolated demonstrations. We tested eight open-source AI frameworks (Agent Laboratory, AutoGen, BabyAGI, GPT Researcher, MOOSE-Chem2, SciAgents, SciMON, and Virtual Lab) on two tasks that aimed to reproduce research on algorithm development from recent papers in uncertainty quantification and protein interaction discovery. In our evaluation, no framework completed a full research cycle from literature understanding through computational execution to validated results and scientific paper writing. While all systems showed competence in conceptual tasks such as planning and summarization, they consistently failed at robust implementation. Every framework produced sophisticated hallucinations. Deployment proved demanding, requiring substantial debugging and technical expertise, which undermines common claims about the democratization of science with AI. Despite these limitations, the frameworks showed promise as research assistants for methodological planning and ideation under careful human supervision. Our findings suggest that the explored AI systems cannot yet autonomously conduct scientific research, but may provide real value for specific subtasks within the research workflow. We offer preliminary observations to help researchers and developers better understand the gap between advertised and actual capabilities of AI in science.

bioinformatics↗

bioRxiv2025

A metabolic hierarchy directs cell cycle transition and morphogenesis

To optimize survival, cells must align differentiation and proliferation with metabolic status. Yet, how metabolic cues fine-tune cell cycle programs and morphogenesis remain unclear. Here, we show that cytosolic redox dynamics critically govern cell cycle transitions in Caulobacter crescentus. By integrating evolutionary genetics with fluxomics, we uncover temporally orchestrated shifts in core metabolic pathways that remodel cytosolic redox across the cell cycle. Early stages channel carbon flux toward unsaturated fatty-acid synthesis and a reverse-TCA to drive cytosolic oxidation-coupled G1-S transition. The later stages depend on an enhanced forward-TCA cycle that promote cytosolic reduction-driven proliferation. Strikingly, perturbing fatty-acid synthesis or reverse/forward-TCA uncouples growth from proliferation. Intriguingly, a biphasic glucose uptake program dictates the cell cycle-stage-specific metabolism. These findings reveal an unprecedented metabolic-redox circuitry coordinating morphogenesis with cell cycle progression in a carefully choreographed menage a trois.

microbiology↗

bioRxiv2025

Global Hypomethylation in Cell-free DNA Enables Non-invasive Colorectal Cancer Screening: Results from a Retrospective Validation Study

Global DNA hypomethylation is a defining hallmark of colorectal cancer (CRC) but is poorly captured by existing cell-free DNA (cfDNA) technologies, which typically interrogate only a fraction of CpG sites and are biased toward CpG islands. We developed Asima Rev, an electrical-impedance cfDNA assay that can differentiate healthy individuals from those with cancer by measuring cfDNA aggregation patterns associated with methylation state, enabling functional detection of genome-wide hypomethylation. In a cohort of 46 treatment-naive CRC patients and 33 controls, Asima Rev achieved 96% sensitivity and 94% specificity, with longitudinal monitoring in six patients fully concordant with clinical outcomes. Interrogation of 11 public methylation array datasets showed that whole array analyses underestimate global changes. However, restricting analyses to OpenSea regions, where cfDNA is enriched, revealed patterns consistent with Asima Rev and a significant 5.8% global hypomethylation in CRC tissue compared to adjacent normal tissue. Hypomethylation was not observed in immune cell genomic DNA (gDNA), a major contributor to cfDNA, supporting a predominantly tumor-derived contribution to the observed cfDNA signal. Together, these results demonstrate that Asima Rev captures a cfDNA signal consistent with true global methylation loss and outperforms locus-specific assays by measuring structural consequences of pan-genomic epigenetic alterations.

bioinformatics↗

bioRxiv2025

The 9p21.3 Coronary Artery Disease Risk Locus Modulates Vascular Cell-State Transitions via Enhancer-Driven Regulation of MTAP

The 9p21.3 locus is the strongest genetic association with coronary artery disease (CAD), yet its causal mechanisms remain unresolved. We map the regulatory architecture of 9p21.3 in disease-relevant vascular cells, identifying 12 enhancers within the CAD risk haplotype that respond dynamically to inflammatory and metabolic stress in fibroblasts and smooth muscle cells. These activated states are enriched for CAD heritability, implicating stress-responsive vascular wall cells in disease pathophysiology. Dense CRISPRi tiling integrated with fine-mapping and genomic constraint across >500,000 individuals nominates MTAP as the effector gene, with rs1537371 as a likely causal variant. Perturbation and multi-modal analyses show that MTAP loss induces pro-fibrotic and angiogenic programs and sensitizes vascular cells to TGF-{beta}-driven pathological transitions. Our findings reveal a vascular-specific enhancer network through which noncoding variation at 9p21.3 modulates CAD risk via MTAP--a previously unrecognized regulator of vascular remodeling located 269 kb from the risk haplotype. HighlightsO_LI9p21.3 CAD risk locus harbors 12 functional enhancers active in vascular wall cell types C_LIO_LICAD heritability is enriched in stressed vascular fibroblasts and smooth muscle cells C_LIO_LIHigh-resolution CRISPRi-MAC-seq maps 9p21.3 enhancer-gene and SNP-gene interactions C_LIO_LIMTAP identified as a causal effector gene regulated by 9p21.3 fine-mapped and constrained variants C_LIO_LIMTAP modulates TGF-{beta}-driven pathological vascular cell transitions C_LI

genomics↗

bioRxiv2025

A Pan-Cancer Blueprint of Early Tumor Microenvironment Reprogramming

Metabolic disruption is a defining early event in tumorigenesis, yet its coordination with transcriptional and inflammatory remodeling remains unclear. Across fourteen first-stage solid tumors, we integrate transcriptomic, metabolic, immune, microRNA, and network-topological analyses to construct a blueprint of early tumor microenvironment reprogramming. Gene-network evolution revealed preferential attachment of proliferative hubs (FOXM1, CDK1, CCNB1, CDC20, TOP2A) accompanied by loss of neighborhood connectivity in key metabolic regulators (PPARA, PPARG, PRKACA/B, CREB1, SRC), indicating early erosion of lipid sensing, oxidative restraint, and metabolic-neuronal signaling. Pathway analysis demonstrated consistent suppression of fatty acid degradation and PPAR signaling, establishing a shift toward anabolic growth. ADH1B was uniformly downregulated across all cancers, linking impaired aldehyde metabolism to redox stress and inflammatory activation. Integration of inflammatory and apoptotic modules highlighted recurrent IRG-AG pairs, including IL11-MMP9-FGF10, forming a conserved inflammation-apoptosis-metabolism axis. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=166 SRC="FIGDIR/small/688523v1_ufig1.gif" ALT="Figure 1"> View larger version (52K): org.highwire.dtl.DTLVardef@4648a0org.highwire.dtl.DTLVardef@4a2885org.highwire.dtl.DTLVardef@aa6940org.highwire.dtl.DTLVardef@1e41847_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LINetwork evolution reveals "trigger genes" shaping early oncogenic transformation C_LIO_LIFOXM1 attachment and PPAR/CREB1 detachment coordinate metabolic reprogramming C_LIO_LIUniform ADH1B downregulation in 14 cancers links metabolic imbalance with inflammation C_LIO_LIIntegrated multi-omics uncovers a blueprint of early tumor-microenvironment shifts C_LI

cancer biology↗

bioRxiv2025

HIV Env trimers elicit NHP apex cross-neutralizing antibodies mimicking human bNAbs

As a chronically replicating virus, HIV has evolved extreme sequence variability and effective shielding of functionally constrained spike protein determinants by host-derived glycans. Broadly neutralizing antibodies (bNAbs), though rare, can be isolated from people living with HIV, revealing conserved Env sites as key targets for vaccine development. One such target is the apex of the envelope glycoprotein (Env) spike. Here, we identified a vaccination strategy using heterologous HIV Env trimers covalently coupled to liposomes for multivalent display that resulted in the elicitation of cross-neutralizing HIV serum antibody responses in all immunized non-human primates (NHPs). Critically, we isolated a set of monoclonal antibodies (mAbs) that cross-neutralized multiple divergent HIV clinical isolates. High-resolution cryoEM structural analysis of mAbs from three different NHPs demonstrated that they targeted the Env trimer apex in a manner remarkably similar to that of the human infection-elicited, apex-directed bNAb PG9, representing a substantial advance in HIV vaccine development.

immunology↗