Biology subjects

Kumar, A.

Publications and source records attributed to Kumar, A..

At least 73 records · Page 4Linked to original sources

bioRxiv2026

IRF7 deficiency increases disease severity independently of TLR7 recognition in Influenza A infection in mice

Influenza A virus (IAV) remains a major cause of respiratory morbidity and mortality, yet the role of Toll-like receptor 7 (TLR7), an RNA sensor, and its downstream signaling events, such as interferon regulatory factor 7 (IRF7), in IAV infection remain unclear. To address this question, we used single-cell RNA sequencing, genetic mouse models, and immunological analysis. Single -cell transcriptomic profiling of the infected lungs revealed robust upregulation of Tlr7 and genes associated with interferon pathways in dendritic cells and B cells, alongside widespread induction of Irf7 across immune and non-immune compartments. Tlr7-deficient mice exhibited normal viral control, lung pathology, and survival following IAV challenge. In contrast, Irf7 deficiency resulted in significantly increased disease severity, impaired early interferon responses, exacerbated bronchial epithelial hyperplasia, and defective early humoral priming. In assessing adaptive immunity, both Irf7-deficient andTlr7-deficient mice had reduced antihemagglutinin antibody production. Mechanistically, IRF7 protein expression and downstream signaling were largely preserved in TLR7-deficient mice, indicating that IRF7 activation during IAV infection occurs independently of TLR7. Collectively, these findings identify IRF7 as a non-redundant determinant of innate immunity and disease outcomes during IAV infection, while positioning TLR7 as a modulatory factor primarily influencing adaptive immune maturation. Our study refines current models of antiviral sensing by uncoupling receptor induction from functional necessity and highlights IRF7 as a critical downstream regulator dictating host defense against acute influenza A infection. ImportanceInfluenza A virus is a respiratory pathogen that remains a major threat to global health as a seasonal disease and a source of periodic pandemics. The outcomes of the infection can range from mild illness to severe pneumonia and death, particularly in vulnerable populations, yet the reasons why some individuals develop more severe disease are not fully understood. Early immune defenses in the lungs are critical for controlling the virus, but they can also contribute to harmful inflammation if not properly regulated. In particular, key sensors that detect viral genetic material and the signaling pathways that activate antiviral responses play an essential role in shaping these outcomes. The significance of our study lies in defining how these early immune mechanisms influence the course of influenza A infection, providing insight that may guide the development of improved therapies for influenza and related respiratory viruses.

immunology↗

bioRxiv2026

Morphology of petiole bending, senescence, epinasty, along with necrotic scarring in tomato leaves infiltrated with virulent Ralstonia pseudosolanacearum

Ralstonia pseudosolanacearum (Rps) belongs to the Ralstonia solanacearum species complex (RSSC). It is a vascular pathogen that causes lethal bacterial wilt disease in many plants, including tomato and eggplant. In this study, we infiltrated tomato leaves with the phytopathogenic bacterium at 109 CFU/mL and observed the development of necrotic scars in the infiltrated area at 48 hours post-infiltration. Interestingly, this response was followed by petiole bending toward the ground of the compound leaf. This was followed by the gradual senescence of the infiltrated leaflet only. In addition, the terminal leaflet infiltrated with the pathogen exhibited epinasty. None of the above symptoms were observed in leaves infiltrated with the known virulent deficient hrpB::{Omega} mutant. Surprisingly, all of the above symptoms were observed in leaves infiltrated with another well-known virulence-deficient mutant phcA::{Omega}. It indicated that the necrotic lesion caused in tomato leaves was hrp-dependent. Infiltration in eggplant leaves caused necrotic scarring and leaf senescence, which were relatively delayed. Necrotic scarring without petiole bending or senescence in tomato leaves was also observed due to infiltration of Pseudomonas aeruginosa SPT08, a tomato endophyte having plant growth promotion activity. The patho-phenotypes such as petiole bending, epinasty, and senescence observed in the case of tomato in this study were not reported earlier. We believe these phenotypes produced in tomato after leaf infiltration may be useful to study the virulence of this pathogen.

pathology↗

bioRxiv2026

The Vagus Nerve conducts viable translocation of gut flora to the lungs that impacts interstitial lung disease severity in mice

Communication between gut microbiota and extraintestinal organs is increasingly recognized, yet elucidation of relevant translocation mechanism(s) remains enigmatic. Vagus neuroanatomy and reports of vagal protein transfer to extraintestinal organs suggest that this "superhighway" could translocate bacteria. Here we explore whether the vagus superhighway can translocate bacteria to extraintestinal organs. Gavage of green fluorescent protein-expressing Escherichia coli (GFP-E. coli) into germ-free (GF) or specific-pathogen free (SPF) C57BL/6 mice yielded high bacillary loads in the stomach and lungs, followed by the heart, stool and peripheral muscles, despite negative blood cultures. Notably, confocal microscopy and culture revealed GFP-E. coli within the vagus nerve within five minutes of gavage suggesting rapid translocation. Metagenomic analysis of stool, lung, heart, vagus nerve, and muscle from non-gavaged SPF mice demonstrated significant microbial overlap, supporting that bacterial translocation occurs despite the presence of endogenous microflora. Remarkably, subdiaphragmatic vagotomy performed prior to GFP-E. coli gavage resulted in marked reductions of bacterial transduction in the lungs and other extraintestinal organs, except muscle. Furthermore, vagotomy significantly reduced lung fibrosis in SPF mice following intranasal bleomycin administration. In lung cancer patients undergoing lobectomy, vagotomy inhibited postsurgical reductions in forced vital capacity. These findings identify the vagus nerve as a literal gut-lung axis, facilitating viable bacterial translocation and influencing lung severity.

microbiology↗

bioRxiv2026

Species diversity increases information flow about predation in bird communities

The Biodiversity-Ecosystem Functioning (BEF) literature has shown species diversity to be essential for ecosystem functioning and services. Yet although acquiring information through interspecific networks can impact ecosystem functioning, it is unclear how it is modulated by species diversity. Eliciting vocal responses using predator models across a latitudinal gradient, we first show that the species diversity of birds increases public information about predation both in the low-cost system of mobbing and in the higher-cost system of alarm calls. A similar result was also found across a fragment area gradient for mobbing; this system was then used to test how species diversity affects interspecific information flow in mobbing communities. We set up two BEF playback experiments, manipulating the species richness level of the playback sound files by varying the number of species producing mobbing calls (one, two, four, eight species). In an experiment in which the call rate across treatments was held constant, and only heterospecific responses were counted, increasing species richness of the sound files increased the number of species and individuals responding, the number of calls produced and their frequency range, and decreased latency to call. An experiment in which call rate increased with the addition of species in each treatment showed a similar, but stronger pattern. There was little evidence that the signals of one particular species changed responses. This supports the hypothesis that the species diversity of a community is a key component influencing the quantity and quality of information flow inside it.

ecology↗

bioRxiv2026

HES3-dependent regulatory functions in development and fusion-positive rhabdomyosarcoma

HES3/Her3 is a transcription factor that functions in non-canonical STAT3 signaling to promote the renewal of neural stem cells and has roles in multiple cancer contexts. To study its role in development and disease, we previously generated a CRISPR/Cas9 zebrafish knockout of her3, the ortholog to human HES3. HES3 is also a cooperating gene in fusion-positive rhabdomyosarcoma, an aggressive pediatric cancer, where HES3 prevents terminal myogenic differentiation, and high expression correlates with worse patient outcomes. Here, we utilize our her3/HES3 knockout model with chromatin and transcriptional profiling techniques to assess its role during early zebrafish gastrulation with the goal of understanding the function of this transcription factor and how these activities are co-opted in cancer. We found that the Her3/HES3 preferential binding motif is distinct from other HES-family members, including a CG-rich E-box motif, that it leverages to modulate the expression of genes involved in neurogenesis and WNT signaling. We also determined that motif preferences of Her3/HES3 altered its interactions with DNA, allowing it to function canonically as a transcriptional repressor with additional duality as an activator. In the context of PAX3::FOXO1, a monogenic driver of fusion-positive rhabdomyosarcoma, we find that Her3/HES3 plays an influential role in modulating the initial activities of this core oncogenic transcription factor. Upon expressing PAX3::FOXO1 in early developing zebrafish embryos, her3 knockout allowed for enhanced activation of neural programs, which are observed in the human disease, along with alterations to cell adhesion programs. Patient tumor samples could be clustered and stratified based on HES3 expression alone. We saw that patient PAX3::FOXO1-positive tumors with high levels of HES3 contained a more neural identity than those with low levels of HES3, altogether suggesting HES3 plays a critical role in regulating this neural signature during both the initial functions of PAX3::FOXO1 and in established tumors.

cancer biology↗

bioRxiv2026

Integrated Multi-Omics Identifies Lineage-Dependent Myeloid Cells Recruitment and the APP-CD74 Axis as an Immunoregulatory Target in Pediatric High-Grade Glioma

Diffuse intrinsic pontine glioma (DIPG) is a devastating pediatric brain tumor with limited treatment options. Emerging evidence indicates infiltration of tumor-associated macrophages (TAMs) within tumor sites, accompanied by an immunosuppressive tumor microenvironment (TME). However, the mechanisms underlying macrophage recruitment and communication between TAMs and other cellular compartments within brain tumors remain poorly understood. Bulk RNA sequencing of 26 DIPG autopsy specimens with matched normal brain tissue, single-cell RNA sequencing data from eight DIPG patients integrated with public pediatric high-grade glioma (pHGG) datasets, and in vitro transwell and flow cytometry assays collectively indicated that DIPG tumors actively recruit monocytes through chemokine-mediated mechanisms. The chemokine expression of tumor cells is driven by a mesenchymal-like (MES-like) lineage state rather than histone mutations, as evidenced by significant correlation between MES-like lineage scores and chemokine expression scores across 46 pHGG cell lines. CellChat analysis identified APP-CD74 signaling as a prominent tumor cell-TAM interaction pathway, supported by immunofluorescence validation. Notably, APP expression was significantly reduced in DIPG tumor tissues compared with normal brain tissue at both the RNA and protein levels. Recombinant APP stimulation of THP-1-derived macrophages induced a robust proinflammatory response, including upregulation of M1-like markers, enrichment of interferon-related pathways, and elevated secretion of inflammatory cytokines. Collectively, these findings indicate that APP suppression in tumors attenuates the antitumor activity of TAMs and promotes an immunosuppressive microenvironment. Furthermore, protein modeling and docking analyses identified the APP-CD74 binding interface, providing a structural basis for therapeutic targeting.

immunology↗

bioRxiv2026

A Long-lived Avatar for Modeling Age-Related Vascular Disease

BackgroundCurrent microphysiological models do not support long-term investigations into the chronic effects of vascular risk factors and the development of vascular diseases. Prolonged culture frequently leads to cellular senescence and loss of functional integrity, resulting in variability and inconsistency in modeling chronic vascular responses. Here we aimed to develop and sustain a long-term multicellular human vascular avatar, addressing the critical need for long-term disease modeling and drug testing. MethodsTo identify the optimal media for longevity, cell identity and function were assessed by morphology, qPCR, beta-gal staining, ELISA, bulk RNA-seq and single cell RNA-seq analysis. After optimizing the culture media, iPSCs-derived ECs and VSMCs from unaffected and Hutchinson-Gilford Progeria Syndrome (HGPS) donors were grown in Gravitational Lumen Patterning (GLP) Vessel- Chips for 1-6 months to generate a long-lived vascular avatar for the study of vascular aging. ResultsGuided by quantitative morphological analyses and bulk RNAseq profiling, we generated a novel optimized culture media VSL (VEGF, SB431542 as a TGF-{beta} inhibitor, low fetal bovine serum) that enhances the long-term health of vascular endothelial cells (ECs). Furthermore, we modified the VSL formulation (mVSL) by modulating 8Br-cAMP, FGF, PDGF, and a cell viability enhancer HMH1015 levels to enhance EC-VSMC (vascular smooth muscle cell) crosstalk and support long-term cellular viability. Subsequently, we maintained and characterized a human vascular avatar with a three-dimensional extracellular matrix environment and 3D vascular architecture for over 180 days. Finally, we demonstrated that this long-lived human vascular avatar enabled modeling vascular aging using iPSC-derived vascular cells from patients with Hutchinson-Gilford Progeria Syndrome (HGPS). ConclusionsWe have successfully engineered and maintained a human vascular avatar for over 180 days. The vascular avatar provides a robust platform for modeling disease-associated vascular aging and for evaluating therapeutic strategies targeting chronic vascular disorders.

bioengineering↗

bioRxiv2026

Transcription initiation profiling defines the regulatory logic of astrocyte gene regulation

Astrocytes are central regulators of neuroinflammation, yet the mechanisms by which they convert common inflammatory signals into cell type-specific transcriptional responses remain poorly understood. Here we mapped transcription initiation genome-wide in primary mouse astrocytes stimulated with interleukin-1B (IL-1B) and defined the active regulatory elements that drive astrocyte reactivity. We find that inducible enhancer transcription in astrocytes is encoded by a transcription-initiation grammar in which lineage-restricted transcription factors, particularly NFIA and TEAD4, cooperate with inflammatory transcription factors such as NF-{kappa}B, AP-1 and IRF to drive stimulus-dependent transcription activation. The motifs of these inflammatory transcription factors show a strong positional bias upstream of induced transcription start sites, supporting their direct role in controlling initiation upon stimulation. Moreover, NF-{kappa}B and TEAD4 motifs are preferentially associated with sites showing altered patterns of transcription initiation in response to inflammatory stimulus. Comparison with stimulated macrophages revealed that, despite substantial overlap in induced genes, astrocytes exhibit a largely distinct enhancer repertoire, indicating that shared inflammatory signals are interpreted through cell type-specific regulatory landscapes. Finally, transcribed astrocyte regulatory elements are functionally conserved in human astrocytes and are enriched for genetic risk variants associated with neurological disorders. Together, these findings define a cell type-specific regulatory logic for astrocyte inflammatory responses and link astrocyte enhancer regulation to human disease susceptibility.

genomics↗

bioRxiv2026

Modeling healthy proteomic profiles for anomaly detection using subspace learning based one-class classification

High-throughput plasma proteomics provides sensitive and scalable measurements of thousands of systemic protein profiles from minimally invasive blood samples, creating new opportunities for disease detection and population-scale health monitoring. However, robust statistical modeling remains challenging due to high dimensionality, limited availability and high diversity of diseased samples, resulting in class imbalance in clinical cohorts. Here, we present a subspace One-Class Classification (OCC) framework for proteomics-driven anomaly detection that models healthy proteomic profiles as a reference distribution. To address the limitations of conventional hyperparameter tuning in severely imbalanced data settings, we introduce a fully data-driven parameter estimation strategy that infers all model parameters directly from intrinsic properties of the healthy training data, without using any disease labels. Using plasma proteomics data generated with Olink, we evaluate a family of subspace and graph-embedded subspace extensions of Support Vector Data Description, in which all models operate on learned low-dimensional representations rather than the original feature space. Models are trained exclusively on a healthy reference cohort and evaluated on heterogeneous disease conditions, including multiple cancer types and an independent COVID-19 cohort, with all disease samples withheld from training to enable unbiased assessment of cross-disease generalization. Across disease contexts, the evaluated one-class models yield stable and balanced detection performance, demonstrating that learning structured low-dimensional representations of healthy proteomic variation captures intrinsic biological organization that generalizes across disease-specific perturbations. These results establish healthy-profile-based, subspace one-class learning as a robust and disease-agnostic framework for screening in high-dimensional plasma proteomics.

bioinformatics↗

bioRxiv2026

Greater hypoxic burden predicts weaker gray matter-CSF coordination independent of non-hypoxic arousals: Implications for glymphatic activity

Study ObjectivesObstructive sleep apnea (OSA) is a risk factor for neurodegeneration, and glymphatic impairment may be one mechanistic pathway. Anti-phase coordination between brain pulsations and CSF flow, reflecting compensatory CSF displacement during each vascular pulsation cycle, supports glymphatic activity. This study examined whether hypoxic burden and sleep fragmentation, two distinct OSA pathologies, are differentially associated with brain pulsation-CSF flow dynamics. MethodsThis cross-sectional study included 28 individuals with newly identified OSA and 8 without OSA. Participants completed in-lab polysomnography or WatchPAT testing, providing measures of hypoxic burden, quantified as time below 90% oxygen saturation (T90), and non-hypoxic sleep fragmentation, quantified as respiratory effort-related arousals (RERAs). Participants also completed 7T resting-state functional MRI to estimate global BOLD-CSF, defined as anti-phase cross-correlation between blood-oxygen-level-dependent (BOLD) signal and CSF inflow. Associations were examined using correlation and hierarchical regression. Exploratory analyses examined region-specific BOLD-CSF and brain pulsation strength, quantified as BOLD amplitude. ResultsGreater T90 was associated with weaker global BOLD-CSF, independent of RERAs and covariates ({beta}=0.08,p=0.03). Greater T90 was also associated with higher BOLD amplitude across temporal, frontal, and parietal regions, but this elevation in amplitude was not accompanied by stronger region-specific BOLD-CSF coupling ({beta}=0.001,p>0.05). In contrast, among regions where BOLD amplitude was not associated with T90, greater BOLD amplitude predicted stronger region-specific BOLD-CSF ({beta}=-0.004,p<0.001). RERAs were not associated with global BOLD-CSF or BOLD amplitude. ConclusionsIn OSA, hypoxic burden may be the primary feature associated with impaired brain pulsation and CSF dynamics that support glymphatic activity. These alterations may be pronounced in the temporal lobe, where elevated pulsations were uncoupled from compensatory CSF displacement.

neuroscience↗

bioRxiv2026

High cRel-expressing germinal center B cells favor precursor plasma cell generation

Germinal centers (GCs) are the site of antibody affinity maturation by the process of somatic hypermutation (SHM) and produce long-lived plasma cells (PCs). GC B cells circulate between two distinct zones: the light zone (LZ) and the dark zone (DZ). It has been demonstrated that the transcription factor NF{kappa}B cRel is required for B cell proliferation and GC B cell maintenance. cRel-deleted GC B cells show reduced SHM and affinity maturation. In contrast, transgenic overexpression of cRel does not affect SHM and results in little or no increase in affinity maturation. Therefore, the function of cRel in regulating SHM and GC B cell-derived PC generation remains unknown. To understand the function of cRel in GC B cell selection, we have used cRel fluorescence reporter mice, which provide insight into cRel function in GC B cells at the level of natural expression variation. We found that about 6-9% of LZ cells increased cRel expression compared to DZ cells, and high cRel-expressing LZ cells showed increased SHM and increased expression of IRF4 and cyclin D2, though cMyc expression remained similar. Combining single-cell RNA-Seq and flow cytometry, we revealed that high cRel-expressing LZ cells are enriched for precursor PCs (pre-PCs), not precursor memory B cells (pre-MBCs). Our findings provide insight into the physiologic function of cRel in regulating GC B cell output.

immunology↗

bioRxiv2026

Interference Between Motor Memories Arises From Implicit Recalibration

Interference between consecutively acquired motor memories is a defining feature of sensorimotor adaptation, yet its mechanistic origin remains unresolved. Because adaptation is supported by separable explicit strategies and implicit recalibration, it offers a means to identify the learning process that gives rise to interference. Across four visuomotor adaptation experiments, we examined the conditions under which the acquisition of a new, competing motor memory influences the expression of a previously acquired memory. We selectively biased new learning towards either explicit or implicit processes, and quantified its impact on the recall of the original memory 24-hours later. Under standard adaptation conditions, participants exhibited classic interference, such that re-learning was indistinguishable from naive performance. However, when new learning was driven primarily by explicit strategies induced through delayed endpoint feedback, interference was markedly attenuated and the original memory was preserved. In contrast, when the competing memory was implicitly forged under error-clamp conditions, robust interference emerged. Furthermore, disrupting posterior parietal cortex (PPC) with cathodal hd-tDCS prior to implicit learning attenuated interference, indicating that intact PPC processing is required for incorporating new learning into an existing sensorimotor representation. Taken together, these findings suggest that interference reflects the integration of new learning into a shared representational substrate via implicit recalibration, a process that limits the coexistence of competing motor memories.

neuroscience↗

bioRxiv2026

Recurrent LINE 1 exonization drives transcriptome remodelling in NSCLC

The only autonomously active transposable elements in the human genome are Long interspersed nuclear element-1 (LINE-1) elements. These elements are known to play an important role in changing the transcriptome. LINE-1 sequences affect gene regulation during post-transcription processing, along with their established role in retrotransposition. Exonization is one mechanism where the LINE-1 integrated genome undergoes alternative splicing to produce new isoforms of transcripts. Our work mainly highlights the effect of LINE-1 associated exonization, focusing on the formation of isoforms of transcripts. Using Non-small cell lung cancer (NSCLC) as a model, we conducted a detailed transcriptome study that combines splice junction profiling with gene expression data. Our results show that LINE-1 sequences are often included as exons in host transcripts, leading to the formation of new exons and their various isoforms. The events are validated by solid splice junction evidence that proves the reliability and reproducibility. In particular, it was observed that repetitive analyses revealed certain LINE-1 exonization events that were consistent. The finding indicates that LINE-1 act as recurrent sources of splice ready sequences. Though exonizations do not necessarily affect the total expression levels of genes, our study reveals that they certainly contribute to transcript diversity. The diversity of isoforms generated potentially contributes to the effects of gene function. This study is limited to NSCLC, but it is likely that the exonizations events play a crucial role in the altering RNA diversity in cancers. Therefore the study elucidates new insights into how transposable elements modify gene structure and function during cancer development.

genomics↗

bioRxiv2026

LINE-1 ORF2p endonuclease activity links DNA damage signalling to enhancer associated chromatin remodeling

Aberrant expression of Long Interspersed Element-1 (LINE-1/L1) retrotransposons is increasingly linked to genomic instability in cancer, particularly in the context of compromised p53 function. The endonuclease (EN) domain of the LINE-1 ORF2 protein (ORF2p) generates DNA strand breaks, yet its role in shaping downstream chromatin and transcriptional responses remains poorly defined. Here, we investigate the impact of ORF2p-EN activity on DNA damage response signalling and epigenomic remodelling in A375 melanoma cells using a L1 expression system. ORF2p-EN led to activation of ATM dependent DNA damage signalling, evidenced by increased {gamma}H2AX accumulation. The EN induced DNA damage showed enrichment of yH2AX at fragile hotspot regions, consistent with localized DNA damage. We also observed increase in levels of the DNA repair factor XRCC5, suggesting a possible engagement of non-homologous end joining pathway. EN-induced DNA damage correlated with increased P300 activity and enhanced H3K27ac enrichment at regulatory regions, linking DNA damage signalling with chromatin acetylation. Pharmacological inhibition of ATM attenuated both {gamma}H2AX accumulation and H3K27ac levels, supporting a model in which chromatin remodelling occurring downstream of DNA damage signalling. Collectively, our findings position ORF2p endonuclease activity as an initiating source of DNA damage that is followed by chromatin remodelling and transcriptional reprogramming, with p53 acting as a critical modulator of this axis. These results provide mechanistic insight into how LINE-1 activation may contribute to oncogenic gene expression programs in cancer.

cancer biology↗

bioRxiv2026

HIPK2-and IKKβ-dependent phosphorylation stabilizes TAp63α during the oocyte DNA damage response

TAp63, a member of the p53 family, serves as a central quality control factor in oocytes, safeguarding genomic integrity during the prolonged dictyate arrest of meiosis. In healthy oocytes, TAp63 is maintained in an inactive dimeric state; upon DNA damage, it undergoes phosphorylation-dependent tetramerization, enabling transcriptional activation of pathways that determine oocyte fate. While the upstream activation cascade of TAp63 has been well characterized, the mechanisms that regulate its stability during the DNA damage response remain incompletely understood. Here, we identify the kinases HIPK2 and IKK{beta} as key regulators of TAp63 stability. We show that TAp63 interacts with both kinases and is phosphorylated at distinct residues, T452 by HIPK2 and S4/S12 by IKK{beta} in vitro and in vivo, in addition to previously described CHK2 and CK1-mediated phosphorylation. Functionally, these phosphorylation events do not primarily contribute to activation, but instead stabilize TAp63 by limiting MDM4-dependent ubiquitination and subsequent proteasomal degradation. Mechanistically, our data support a model in which CHK2 and CK1 initiate TAp63 phosphorylation, while HIPK2 and IKK{beta} act in a complementary manner to maintain protein stability during genotoxic stress. Disruption of HIPK2 or IKK{beta} activity reduces TAp63 stability, whereas their inhibition in vivo attenuates oocyte loss following DNA damage, resulting in increased preservation of the follicle pool. Importantly, these effects are observed across multiple systems, including mouse models and ex vivo goat ovary cultures, supporting an evolutionarily conserved role for this regulatory axis. Together, our findings uncover a previously unidentified layer of TAp63 regulation, in which phosphorylation not only contributes to its activation but also enhances protein stability, thereby fine-tuning oocyte responses to DNA damage. Our results further indicate that HIPK2 and IKK{beta}-mediated phosphorylation modulates oocyte survival under genotoxic stress, highlighting this pathway as a potential target for strategies aimed at limiting oocyte loss.

cell biology↗

bioRxiv2026

Elucidation of putative key genes involved in the regulation of triple negative breast cancer development and progression

The molecular basis of triple-negative breast cancer (TNBC), a highly aggressive and therapy-resistant subtype of breast cancer, is poorly understood. This study aims to identify key genes and pathways involved in TNBC development and progression using a systems biology approach followed by experimental validation. Here, two transcriptome microarray datasets from the GEO database were analysed using the R package LIMMA to detect differentially expressed genes (DEGs) in TNBC tumors. Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) enrichment analyses using the DAVID database were performed to identify DEGs regulated biological functions and pathways. Further, a protein-protein interaction (PPI) network was constructed using the STRING online database, and the topological properties were determined using MCODE and Cytohubba plug-ins. The expression and the prognostic value of the hub genes were validated using the Cancer Genome Atlas (TCGA) survival analysis. We found 727 DEGs, of which 473 were downregulated and 254 were upregulated in TNBC vs. non-TNBC samples. The GO and KEGG analyses indicated that the DEGs were mainly related to cell adhesion, tumorigenesis, and cellular immunity. The PPI network had shown six hub genes, namely CCND1, CDH1, ESR1, FN1, IL6, and PPARG, as the top key regulators. All these genes were validated by quantitative real-time PCR in the TNBC cell line using non-TNBC cell line as a calibrator, and the obtained results were in accordance with the bioinformatics data. This information may contribute to understanding the various molecular mechanisms that drive the development and progression of TNBC tumors.

cancer biology↗

bioRxiv2026

Recombinant measles virus equipped with BNiP3, a pro-apoptotic gene, targets β-catenin pathway in triple negative breast cancer cells

Oncolytic virotherapy is an emerging cancer therapy using genetically modified viruses. We previously reported engineering of measles virus with BNiP3, a proapoptotic gene for oncolytic purposes. The recombinant virus had shown promising results in breast cancer cells with a bias towards TNBC, an invasive and an aggressive subtype. Here, we investigated the mechanistic insights of anti-tumor effects induced by the recombinant virus. Initially, TNBC and non-TNBC tumor cell lines were compared bioinformatically using the available gene expression data through protein-protein interaction network using different topological properties. Four hub genes involved in tumor development and progression were identified to be the top genes in both the data sets. Of which, CTNNB1 gene encoding {beta}-catenin was found to be the significant one; as {beta}-catenin pathway is known to be a driver of tumor cell invasion and migration, the impact of the virus on this pathway was investigated in breast tumor cells. The results had demonstrated a notable decrease in {beta}-catenin expression and its downstream targets, cyclin D1, MMP7 reducing the migration potential of TNBC cells following virus infection. These findings suggest that the recombinant measles virus could be one of the effective treatment modalities to target invasive TNBC tumors. In vivo validation of engineered virus is ongoing to explore the therapeutic application of this virus. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=126 SRC="FIGDIR/small/718830v1_ufig1.gif" ALT="Figure 1"> View larger version (57K): org.highwire.dtl.DTLVardef@19d321dorg.highwire.dtl.DTLVardef@1450ebeorg.highwire.dtl.DTLVardef@cb191eorg.highwire.dtl.DTLVardef@1de2d16_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIUse of recombinant measles virus with a pro-apoptotic gene, BNiP3 to target breast cancer cells C_LIO_LIIdentification of top regulatory genes in breast cancer development and progression C_LIO_LIReduction of {beta}-catenin expression encoded by CTNNB1 gene in TNBC cells following virus infection C_LIO_LIDownregulation of {beta}-catenin downstream targets in TNBC cells with virus infection C_LIO_LIInhibition of migratory potential of TNBC cells following infection C_LI

cancer biology↗

bioRxiv2026

GANGE: Achieving Sequencing Without Sequencing With Diffusion Guided Generative Genomic Transformer

The genome of a species is its book of life, but opening that book remains a costly affair due to the limitations the existing sequencing technologies pose. Short reads sequencers struggle to capture long and complex genomes, though have high fidelity rate. To counter that long reads from IIIrd generation sequencers are used, which are full of indel errors. Thus, reads from both approaches are collectively used with very high coverage, making the sequencing projects unreasonably high of cost and unapproachable to majority. Here we present a first of its kind generative deep-learning system, GANGE, which not just recovers the correct sequence with high accuracy from indel prone ONT reads at manifold lesser coverage but also extends it by 4kb, achieving sequencing without sequencing, horizontally as well as vertically while maintaining >92% accuracy consistently. This all makes it possible to drastically pull down sequencing project cost. GANGE was tested across A. thaliana, O. sativa genomes and Human chromosome 1 where it delivered outstanding assembly performance. Besides this, it was also used to accurately generate 2kb upstream promoters of all the genes from 12 different species, demonstrating that one can now also take up regulomics research just using RNA data alone when genome sequence is not available. With this all, GANGE brings a democratic turning point in the area of genomics and sequencing research.

bioinformatics↗