Biology subjects

Kumar, S.

Publications and source records attributed to Kumar, S..

At least 181 records · Page 10Linked to original sources

bioRxiv2025

TRUHiC: A TRansformer-embedded U-2 Net to enhance Hi-C data for 3D chromatin structure characterization

High-throughput chromosome conformation capture sequencing (Hi-C) is a key technology for studying the three-dimensional (3D) structure of genomes and chromatin folding. Hi-C data reveals underlying patterns of genome organization, such as topologically associating domains (TADs) and chromatin loops, with critical roles in transcriptional regulation and disease etiology and progression. However, the sparsity of existing Hi-C data often hinders robust and reliable inference of 3D structures. Hence, we propose TRUHiC, a new computational method that leverages recent state-of-the-art deep generative modeling to augment low-resolution Hi-C data for the characterization of 3D chromatin structures. By applying TRUHiC to real low-resolution Hi-C data from the GM12329 cell line and across other publicly available Hi-C data for human and mice, we demonstrate that the augmented data significantly improve the characterization of TADs and loops across diverse cell lines and species. We further present a pre-trained TRUHiC on human lymphoblastoid cell lines that can be adaptable and transferable to improve chromatin characterization of various cell lines, tissues, and species.

bioinformatics↗

bioRxiv2025

Development of a thermostable and broadly neutralizing pan-sarbecovirus vaccine candidate

Zoonotic spillover of sarbecoviruses to humans resulted in theSARS-CoV-1 outbreak in 2003 and the current COVID-19 pandemic caused by SARS-CoV-2. In both cases, the viral spike protein (S) is the principal target of neutralising antibodies that prevent infection. Within spike, the immunodominant receptor-binding domain (RBD) is the primary target of neutralising antibodies in COVID-19 convalescent sera and vaccine recipients. We have constructed stabilized RBD derivatives of different sarbecoviruses: SARS-CoV-1 (Clade 1a), WIV-1 (Clade 1a), RaTG13 (Clade 1b), RmYN02 (Clade 2) and BtKY72 (Clade 3). Stabilization enhanced yield by an 3-23-fold. The RBD derivatives were conformationally intact as assayed by binding to multiple broadly neutralizing antibodies. The stabilized RBDs show significant enhancement in apparent Tm, exhibit resistance to a 2-hour incubation at temperatures up to 60 in PBS in contrast to corresponding WT RBDs, and show prolonged stability of over 15 days at 37 after lyophilization. In mice immunizations, both stabilization and trimerization significantly enhanced elicited neutralization titers by [~]100 fold. The stabilized RBD cocktail elicited high neutralizing titers against both homologous and heterologous pseudoviruses. The immunogenicity of the vaccine formulation was assessed in both naive and SARS-CoV-2 pre-immunized mice, revealing an absence of immune imprinting, thus indicating its suitability for use in future sarbecovirus-origin epidemics or pandemics. Author summaryThe COVID-19 pandemic was caused by the sarbecovirus SARS-CoV-2. Phylogenetically, sarbecoviruses are divided into four clades: Clade 1a, Clade 1b, Clade 2 and Clade 3 and within these clades, are many other sarbecovirus strains with pandemic or epidemic potential. It is therefore important to develop a broadly protective, pan-sarbecovirus vaccine formulation that can be cheaply and rapidly produced. While mRNA vaccine formulations are efficacious, they have stringent low temperature storage requirements and there is limited manufacturing expertise in low and middle income countries for this modality. Neutralizing antibodies are important for protection and in the case of SARS-CoV-2 are primarily directed against the Receptor Binding Domain (RBD) of the surface spike protein. In this study, we have designed and developed an adjuvanted, protein subunit, pan sarbecovirus vaccine formulation using stabilized RBD derivatives from diverse sarbecoviruses as immunogens. We demonstrate that the stabilized RBD derivatives have considerably enhanced yield and thermal stability relative to corresponding WT proteins and that the formulation remains stable for up to two weeks at 37{degrees}C. The formulation was found to be highly immunogenic in both naive and pre-immunized mice, eliciting neutralizing titers well above the known protective threshold, indicating its suitability for use in future sarbecovirus-origin epidemics or pandemics.

immunology↗

bioRxiv2025

Predictive Modeling of acute Graft-versus-Host-Disease using Machine Learning on Immune Cell and Cytokine Profiles at Engraftment

BackgroundAcute Graft-versus-Host-Disease (aGvHD) is a major immune complication following allogenic hematopoietic stem cell transplantation (Allo-HSCT), initiated by conditioning regimen-associated tissue damage. It involves the complex interplay of immune cells and cytokines. Our study aims to leverage machine learning (ML) algorithms on the immune and cytokine profile of Allo-HSCT recipients to develop biomarker-based classification models to predict the onset of aGvHD at the time of engraftment. Materials and MethodsSeventy patients diagnosed with hematological disorders who had undergone Ist Allo-HSCT were recruited from All India Institute of Medical Sciences, New Delhi, India. Peripheral blood (PB) was collected from the patients at the time of engraftment, and the immune cell subtypes and cytokine profiles were analyzed using flow cytometry and ELISA respectively. The individual cell counts were then processed using basic ML models, including support vector classifier with RBF kernel, Decision Tree, and Random Forest, chosen for their mathematical simplicity and feature importance advantage of Decision Trees and Random Forests. Various data settings were utilized in the study: combined immune and cytokine counts, immune cell counts only, cytokine counts only, T-cell counts only, NK cell counts only, dendritic cell counts only, and B-cell counts only. These configurations were selected to investigate how different data sets impact the prediction of aGvHD before its onset. ResultsAt the engraftment flow cytometric analysis of reconstituted lymphocytes in patients who developed aGvHD revealed that there was a remarkable decrease in the ratio of CD4+/CD8+ T-cell and Tregs, with an increase in the cytotoxic regulatory NK-cell, dendritic cells, and B-cell. The levels of pro-inflammatory cytokines (IFN-{gamma}, IL-1{beta}, IP-10, TNF-, IL-17, IL-12p70, MIP-1, MIP-1{beta}, RANTES), and Th17-and Th1-cells were elevated with consequent decline of the levels of anti-inflammatory cytokine IL-10, IL-2, IL-4 and Th2-, Th9-cells. Machine learning based on 48 parameters [all immune cell subsets n=34 and all cytokines (n=14)]. The correlation heat map shows a higher correlation of aGvHD with the cytokine profile with or without immune cells (accuracy: 1), T-cell alone (accuracy: 0.96); NK-cell alone (accuracy: 0.93); dendritic cells alone (accuracy: 0.90), B-cell alone (accuracy: 0.86). ConclusionThe current models classify perfectly, indicating the potential for a ML algorithm in predicting the onset of aGvHD. However, a study with a larger sample size is required to validate these classification models and mitigate the risk of overfitting observed due to the consistently high performance. The study also highlights the potential of cytokine profiles as a viable alternative to T-cell counts, as evidenced by the correlation heat map and classifier models. These findings provide valuable insights into dataset requirements and future directions for integrating ML models into aGvHD prediction.

immunology↗

bioRxiv2025

Topoisomerase IIIb protects from tumorigenesis and immune dysregulation

Topoisomerase III-beta (Top3b) reduces nucleic acid torsional stress and intertwining generated during RNA and DNA metabolism while protecting the genome from pathological R-loops, which otherwise result in DNA breakage and genome instability. By studying Top3b knockout mice (Top3b-KO), we find that the loss of Top3b accelerates the development of spontaneous lymphoid tumors arising in spleens and lymph nodes, the organs with prominent Top3b expression. Aging Top3b-KO mice also display splenomegaly and systemic immune alterations including neutrophilia and lymphopenia suggestive of chronic inflammation. At the molecular level, Top3b deficiency causes genome-wide R-loop accumulation in splenocytes as measured by CUT&Tag sequencing. Increased R-loops is associated with genomic DNA breaks and activation of immune signaling pathways including the IL-6 signaling, interleukin-7 signaling and cGAS-STING. Moreover, knocking-out Top3b promotes the rapid development of syngeneic EL4 T-cell lymphomas. In conclusion, our work implies that, in addition to its role in preserving the nervous system, Top3b protects from tumorigenesis and immune dysregulations. SignificanceTopoisomerase III-beta (TOP3B) is the only dual RNA-DNA topoisomerase. Its inactivation has previously been shown to be critical for neurodevelopmental disorders in humans and R-loop suppression in cell line models. Here, we demonstrate that loss of Top3b accelerates spontaneous lymphomagenesis and promotes syngeneic lymphoma growth in association with innate immune defects and R-loop accumulation in Top3b-KO mice. These findings provide evidence for a previously unappreciated role of Top3b as a tumor suppressor gene and immune regulator.

cancer biology↗

bioRxiv2025

AAV-mediated MUC5AC siRNA delivery to prevent mucociliary dysfunction in asthma

The main structural components of mucus produced in the lung are mucin 5B (MUC5B) and mucin 5AC (MUC5AC) where a relatively higher expression of MUC5B is typical in health. In the lungs of individuals with asthma, there is a shift from MUC5B to MUC5AC as the predominantly secreted mucin which has been shown to impair mucociliary clearance (MCC) and increase mucus plug formation in the airways. Given its role in asthmatic lung disease, MUC5AC represents a potential therapeutic target where a gene delivery approach could be leveraged to modulate its expression. For these purposes, we explored adeno-associated virus serotype 6 (AAV6), as a lung-tropic viral gene vector to target airway epithelial cells and reduce MUC5AC expression via siRNA delivery. We confirmed that AAV6 was able to transduce epithelial cells in the airways of healthy mice with high transgene expression in mucus-secreting goblet cells. Using multiple particle tracking analysis, we observed that AAV6 was capable of penetrating both normal and MUC5AC-enriched mucus barriers. Successful transduction with AAV6 was also achieved in IL-13 stimulated human airway epithelial (HAE) cells differentiated at air-liquid interface (ALI). AAV6 expressing MUC5AC-targeting siRNA was evaluated as a prophylactic treatment in HAE cell cultures before IL-13 challenge. IL-13 stimulated HAE cultures treated with AAV6-MUC5AC siRNA had significantly reduced MUC5AC mRNA and protein expression compared to untreated controls. Mucociliary transport in IL-13 stimulated HAE cultures was also maintained and comparable to healthy controls following AAV6-MUC5AC siRNA treatment. Together, these findings support that AAV6 may be used as an inhaled gene therapy to suppress MUC5AC overexpression and restore normal airway clearance function in asthma.

cell biology↗

bioRxiv2025

Assessing PARP trapping dynamics in ovarian cancer using a CRISPR-engineered FRET biosensor

Poly(ADP-ribose) polymerase inhibitors (PARPi) have revolutionised the treatment of ovarian high grade serous carcinoma (HGSC), especially those with defective homologous recombination. However, the emergence of resistance poses a critical challenge, as over 50% of patients relapse within three years. The mechanisms underlying changes in PARP trapping, a central aspect of PARPi efficacy, are not well understood due to limitations in current experimental methodologies. Existing techniques lack resolution and throughput, impeding efforts to study PARP trapping dynamics over time with single-cell resolution. Effective tools to study PARP trapping in live cells are urgently needed to elucidate resistance mechanisms and inform therapeutic strategies. To address this, we used CRISPR-Cas9 gene editing to dual-label endogenous PARP1 with EGFP and mCherryFP in OVCAR4 cells to develop a novel intramolecular FRET-based biosensor that enables real-time, single-cell visualization of PARP trapping dynamics in live cells. High-content fluorescence lifetime imaging microscopy (FLIM) revealed dose dependent PARP trapping upon exposure to PARP inhibitor and distinguished between the trapping efficiencies of four different PARPi (veliparib, olaparib, rucaparib, talazoparib). Moreover, we found reduced PARP trapping in PARPi-resistant models, both in vitro and in vivo, providing critical evidence for altered PARP trapping as a resistance mechanism and illustrating the potential of this FRET biosensor to interrogate resistance mechanisms quantitatively. This PARP trapping biosensor represents a transformative advance, enabling dynamic, high-resolution analysis of mechanisms underlying cancer drug resistance. It provides critical insights into the heterogeneity of PARPi resistance, with implications for developing more effective therapies and improving personalised treatment strategies for ovarian cancer patients. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=58 SRC="FIGDIR/small/642798v1_ufig1.gif" ALT="Figure 1"> View larger version (11K): org.highwire.dtl.DTLVardef@1c5ee67org.highwire.dtl.DTLVardef@1a6d101org.highwire.dtl.DTLVardef@e3a2bborg.highwire.dtl.DTLVardef@d0ba03_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2025

Human insula neurons respond to simple sounds during passive listening

The insula is critical for integrating sensory information from the body with that arising from the environment. Although previous studies suggest that posterior insula is sensitive to sounds, auditory response properties of insula neurons have not previously been reported. Here, we provide the first report of a population of human single neuron data from the insula and provide comparative data from the primary auditory cortex, recorded intracranially from human participants during passive listening. In each condition, more than 330 single neurons were recorded in 11 participants. Almost a third of neurons in posterior insula and a smaller subset in anterior insula responded to simple tones and clicks. Responsive neurons were distributed throughout posterior and anterior insula and showed preferred frequency tuning. Onset latencies in the insula were similar to those in the primary auditory cortex but response durations were significantly shorter. Overall, these data highlight that insula neurons respond to auditory stimuli even in non-behaviorally relevant contexts and suggest an important contribution of audition to the postulated integrative functions of insular cortex.

neuroscience↗

bioRxiv2025

Investigating the demographic history of Sindhi population inhabited in West coast India

BackgroundSouth Asian populations are genetically well stratified due to multiple waves of migration, admixture events, and endogamy. India remains a rich resource for population genomics studies with many small and socioculturally homogeneous communities whose origins and demographic histories are largely unknown. In this study, we analysed such a small Sindhi settlement in the Thane district in Maharashtra of West coast India using genome-wide autosomal SNP data using both frequency- and haplotype-based approaches. ResultsOur analyses suggest that the West coast Indian Sindhi community is very unique and has significant population affinity with a group more closely related to the Pakistani Burusho than to the Pakistani Sindhi, as it has an additional East/Southeast Asian component. Furthermore, the sharing of haplotype and IBD suggests recent gene flow from the local Konkani population on the west coast of India into Indian Sindhi. Admixture modelling suggested that Indian Sindhi admixture with the East/Southeast Asian source group could be 40-50 GBP, explaining their current unique demographics. However, apart from this additional admixture, they share the basic genetic composition of the Pakistan/NWI groups, as reflected in PCA, outgroup F3 and IBD sharing. ConclusionThese new findings suggest that Indian Sindhi settlement from the Thane in Maharashtra in West coast of India derive their genetic ancestry not directly from Pakistani Sindhis but from other groups related to Burusho in Pakistan. The study therefore encourages further research to identify the heterogeneous nature of migrations to the Indian subcontinent and thus further decipher its unique demographics.

genetics↗

bioRxiv2025

Exploring vulnerable building blocks in protein-protein interaction networks of breast tumor and adjacent normal tissues

Tumor-adjacent normal tissues (TANTs) histologically and morphologically look normal and are commonly used as a control in patient-based cancer studies. Previous studies have revealed that TANTs present a unique transitional state between healthy normal and tumor tissues. However, there is little or no knowledge about the landscape of protein-protein interactions (PPIs) in TANTs and how they differ from the tumor tissues. Here, we integrate the PPI data mapped onto the differentially expressed genes in TANTs and tumor tissues compared to healthy normal tissues to comprehensively construct and analyze the PPI networks of TANTs and breast tumor tissues (viz., Luminal A, Luminal B, Her2, Basal, and Normal-Like). First, these PPI networks were analyzed using network influence and vulnerability analyses from the NetVA R package. Consequently, our study revealed 134 vulnerable proteins (VPs), 21 vulnerable protein pairs (VPPs), and 94 influential proteins (IPs) commonly shared across all six tissue networks. Further, we identified a set of 34 proteins as common hubs and another set of seven proteins as common bottlenecks across all six tissue networks. Next, these VPs, IPs, hubs, and bottlenecks were investigated for their associations with various diseases, including cancers, and found to share a significant number of well-known cancer-associated proteins, viz., AR, BRCA1, ERBB2, FN1, FOXA1, JUN, MKI67, and NRAS. Thus, by applying network vulnerability, influence, and gene-disease association-based analyses, we suggest lists of known and novel candidates along with their associated protein complexes potentially involved in breast cancer tumorigenesis and present across TANTs and different breast cancer subtypes.

bioinformatics↗

bioRxiv2025

ZEB2 signaling is essential for ureteral smooth muscle cell differentiation and maintenance

Mowat-Wilson Syndrome (MWS) is a multiple congenital anomaly syndrome caused by mutations in the ZEB2, which plays a critical role in cell fate determination and differentiation during development. Congenital anomalies of the kidney and urinary tract (CAKUT) have been reported in MWS patients. However, the role of ZEB2 in urinary tract development and the cellular and molecular mechanism underlining the CAKUT phenotypes in MWS remains unknown. We performed ZEB2 protein expression analysis in the developing mouse ureter. We generated Zeb2 ureteral mesenchyme-specific conditional knockout mice by crossing Zeb2 floxed mice with Tbx18Cre mice (Zeb2 cKO) and analyzed the urinary tract phenotypes in Zeb2 cKO mice and wild-type littermate controls by gross and histological examination. Ureteral cellular and molecular phenotypes were studied using TAGLN, ACTA2, FOXD1, POSTN, CDH1, TBX18, and SOX9 ureteral cell-specific markers. We found that ZEB2 is expressed in TBX18+ ureteral mesenchymal cells during mouse ureter development. Deletion of Zeb2 in developing ureteral mesenchymal cells causes hydroureter and hydronephrosis phenotypes, leading to obstructive uropathy, kidney failure, and early mortality. Cellular and molecular marker analyses showed that the TAGLN+ACTA2+ ureteral smooth muscle cells (SMCs) layer is not formed in Zeb2 cKO mice at E15.5, but the FOXD1+ and POSTN+ tunica adventitia cells layer is significantly expanded compared to wild-type controls. CDH1+ urothelium cells are reduced considerably in the Zeb2 cKO ureters at E15.5. Mechanistically, we found that Zeb2 cKO mice have significantly decreased TBX18 expression but an increased SOX9 expression in the developing ureter at E14.5 and E15.5 compared to wild-type littermate controls. Our results show that ZEB2 is essential for ureter development by maintaining ureteral mesenchymal cell differentiation into normal ureteral SMCs. Our study also shed new light on the pathological mechanism underlying the developmental abnormalities of the urinary tract phenotypes in MWS patients. Author SummaryHydroureter and hydronephrosis are common congenital anomalies with high incidence (1:100 to 1:500) that can lead to obstructive uropathy and renal failure in the pediatric population. Mowat-Wilson Syndrome (MWS), caused by heterozygous mutations in the ZEB2 gene, is a genetic disease with multiple congenital developmental defects, including hydroureter and hydronephrosis. However, the molecular function of ZEB2 in ureter development and pathogenesis of hydroureter and hydronephrosis remains unknown. Here, we show that ZEB2 is expressed in the developing ureteral mesenchymal cells, and deletion of ZEB2 in ureteral mesenchymal cells leads to ureteral smooth muscle cell loss, which is replaced by tunica adventitia cells causing hydroureter and hydronephrosis phenotype. Hence, our work not only demonstrates the critical role of ZEB2 in ureter development but also provides molecular mechanisms of urinary tract anomalies in MWS patients.

developmental biology↗

bioRxiv2025

NEDD4 promotes Sertoli cell proliferation and adult Leydig cell differentiation in the murine testis

Successful testis development relies on the coordinated differentiation and assembly of various cell types to establish both endocrine and reproductive functions. The ubiquitin ligase NEDD4 has emerged as a key player in murine testis development, with this enzyme being implicated in gonadal sex determination and spermatogonial stem cell differentiation. Here, we report hitherto uncharacterized roles of NEDD4 in postnatal testis development. Utilizing Nr5a1- and Amh-Cre drivers to conditionally ablate Nedd4 in testicular somatic cells, we show that NEDD4 promotes Sertoli cell proliferation through the modulation of the PI3K-AKT signaling pathway. This ubiquitin ligase also ensures proper differentiation of adult Leydig cells and may contribute to murine steroidogenesis. Furthermore, NEDD4 is essential for adrenal gland differentiation, as its loss results in adrenal dysgenesis. These findings highlight NEDD4 as a crucial factor in testis development, emphasizing the importance of ubiquitination and post-translational modifications in reproductive biology.

developmental biology↗

bioRxiv2025

Decoding DNA methylation and non-coding RNAs mediated regulatory landscape of breast tumor and adjacent normal tissues

Tumorigenesis not only involves perturbations of mRNAs but also microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and DNA methylation (DNAm). Additionally, the tumor-adjacent normal tissues (TANTs) that are used as controls in cancer studies are not completely normal and, if explored systematically, can help to understand tumorigenesis better. In this regard, expression and DNAm profiles of breast tumor tissues (viz., Luminal-A, Luminal-B, Her2+, Basal-like, and Normal-like) and TANTs were used to construct and analyze their integrative networks. These networks included regulations among genes, transcription factors, lncRNAs, and miRNAs, along with gene/lncRNA methylations. This followed the identification of candidate gene PCLAF having transitivity value one across all six tissue networks. Further, 503 common hubs (388 protein-coding, 100 miRNAs, and 15 lncRNAs), including seven methylated genes (SPI1, STAT5A, RORC, SPDEF, ELF5, HOXB2, and RUNX3), and 149 common bottlenecks (145 protein-coding, three miRNAs, and one lncRNA), including three methylated genes (SPI1, SPDEF, and RUNX3) and one methylated lncRNA (PART1), were identified. Moreover, 145 nodes, including three methylated genes (SPI1, SPDEF, and RUNX3) and three miRNAs (hsa-miR-34a, hsa-miR-149, and hsa-miR-141), were identified as both hubs and bottlenecks (HBs) across all six tissues. However, none of the lncRNAs were found HBs therein. Genes and lncRNAs with higher degrees, betweenness, eigenvector centrality, and pagerank were found more preferably methylated than others. Further, pathway analysis of hubs and bottlenecks across all six tissues revealed their significant involvement in the pathway of Transcriptional misregulation in cancer. Overall, these findings uncover new insights into the epigenetic mechanisms of tumorigenesis.

bioinformatics↗

bioRxiv2025

Brain bases for navigating acoustic features

Whether physical navigation shares neural substrates with mental travel in other behaviourally relevant domains is debated. With respect to sound, pure-tone working memory in humans elicits hippocampal as well as auditory cortical and inferior frontal activity, and rodent work suggests that hippocampal cells that usually track an animals physical location can also map to tone frequency when task-relevant. We generated a sound dimension based on the density of random-frequency tones in a stack, resulting in a percept ranging from low- ("beepy") to high-density ("noisy"). We established that unlike tone frequency, which listeners automatically associate with vertical position, this density dimension elicited no consistent spatial mapping. During functional magnetic resonance imaging, human participants held in mind the density of a series of tone stacks and, after a short maintenance period, adjusted further stacks to match the target ("navigation"). Density of the currently heard sound was represented most strongly in bilateral non-primary auditory cortex, specifically bilateral planum polare, while density of the maintained target was represented in right anterior hippocampus and left inferior temporal gyrus. Encoding and maintenance activity in bilateral hippocampus, inferior frontal gyrus, planum polare and posterior cingulate was positively associated with subsequent navigation success. Bilateral inferior frontal gyrus and hippocampus were among regions with elevated activity during adjustment, compared to a parity-judgment condition with closely matched acoustics and motor demands. Bilateral orbitofrontal cortex was more active when navigation was toward a target density than when participants adjusted density in a control condition with no particular target. We find that self-initiated travel along a non-spatial auditory dimension engages a brain system overlapping with that supporting physical navigation. Key PointsO_LIWork in rodents suggests that navigation in physical space and the active analysis of sounds share a neural substrate in the hippocampus, supporting the use of common computational mechanisms. C_LIO_LIWe examined the human brain system for navigation through an acoustic environment to a remembered target. C_LIO_LIIn addition to high-level auditory cortex we demonstrate involvement of the hippocampus in acoustic navigation along with other sites in frontal and cingulate cortex that also support physical navigation. C_LI

neuroscience↗

bioRxiv2025

siRNA-based Therapeutic Candidate Targeting PRDM2 for Inhibition of Lung Cancer Progression

Lung cancer is the leading cause of tumor-related fatalities worldwide. The current precision therapies are effective but target only those molecules that are impacted in a minority of lung cancer patients. Positive Regulatory Domain 2 (PRDM2), a member of the PRDM gene family, also known as Retinoblastoma Interacting Zinc finger (RIZ) protein. RIZ is found to be misregulated in more than 60% of lung cancer patients, representing a significantly affected population when compared to other mutation-prone oncogenic factors. RIZ expresses two contrasting variants, a tumor suppressor RIZ1, and an oncogenic RIZ2 protein. In lung cancer, the RIZ1/RIZ2 ratio alters, and the epigenetic silencing of RIZ1 promotes RIZ2 overexpression. In this study, we used siRNA (ARIZ-047) to knockdown and inhibit the effect of the oncogenic protein RIZ2. Inhibiting RIZ2 with ARIZ-047 treatment increased RIZ1 expression and decreased the viability of a lung cancer cell line (A549). The ARIZ-047 treatment also upregulated the negative regulators of the Wnt signaling pathway and restrained the tumor progression in the xenograft mice model. In conclusion, this study identifies ARIZ-047 as a targeted therapy in lung cancer, which specifically inhibits RIZ2 and suggests the role of the Wnt signaling pathway in RIZ2 overexpression. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=127 SRC="FIGDIR/small/636957v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@1a5eb34org.highwire.dtl.DTLVardef@1f4dc2forg.highwire.dtl.DTLVardef@a3ce29org.highwire.dtl.DTLVardef@33f576_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2025

Functional Interrogation of Neuronal Subtypes via Intersectional Expression of Optogenetic Actuator Reveals Non-linear Components in a Linear Circuit

Investigating signal integration in a neural circuit is oftentimes challenging when the circuit contains neuronal subtypes that are transcriptomically similar, due to the lack of tools to express optogenetic actuators with high cellular specificity and to deliver light with high spatiotemporal accuracy. Here, we demonstrate the use of a split GAL4-based genetic "AND" gate to express Chrimson in specific touch receptor neuron (TRN) subtypes in the C. elegans touch response circuit. Combining this intersectional strategy for transgene expression with high-throughput optical targeting and behavioral quantification, we optogenetically interrogated the role of each TRN subtype in mediating the mechanosensor-induced escape response and in integrating signals that trigger the opposite motor output. Surprisingly, we found that although the response of the overall circuit linearly combines the competing anterior and posterior stimuli, this linearity is comprised of antagonistic non-linear contributions from the anterior and posterior sensors, which conspire to generate a linear response.

neuroscience↗

bioRxiv2025

Th1 and Th2 cytokines profile of serum samples from dengue positive cases from Northeast India

BackgroundDengue fever is a fast-spreading acute arboviral infection transmitted by a human-Aedes mosquito cycle. Northeastern India is an endemic zone for dengue; regular outbreaks have been reported. However, molecular details of the virus infection in the host have not been established. Studies on dengue immunopathogenesis have primarily utilized data from American and Southeast Asian regions, with insufficient representation from India. ObjectiveThe present study aimed to characterize the Th1/Th2 cytokine expression profiles from dengue cases in different parts of northeastern India. Statistical analysis cum ResultsAmong the panel of Th1/Th2 cytokines, IFN-{gamma}, IL-2, IL-4, IL-5, IL-10, IL-13, and TNF- cytokines are found to be higher in dengue-infected patients. Anti-inflammatory cytokines are somehow regulated differently in male-female patients. ConclusionThis clinical study on dengue patient samples for cytokine profiling revealed distinct cytokine patterns and their regulation, but further investigation is needed to correlate with disease severity to identify potential biomarkers for disease progression.

microbiology↗

bioRxiv2025

Polyamine biosynthesis dysregulation in Alzheimer's disease and Down syndrome cellular models

BACKGROUNDIndividuals with Down Syndrome (DS) frequently develop early onset Alzheimers disease (AD) with pathological hallmarks closely resembling AD due to several triplicated genes on chromosome 21. Polyamines are small, organic molecules that play a pivotal role for growth and differentiation, and a dysregulation of polyamine pathways is implicated in AD pathology. However, their role in DS-associated AD is unclear. METHODSWe analyzed polyamines and their metabolite levels in mouse hippocampal cells and human DS-AD and AD hippocampal tissue and assessed the effects of the ODC inhibitor difluoromethylornithine (DFMO) on A{beta}42 aggregation and protein expression in DS fibroblasts. RESULTSAmyloid-{beta}42 increased polyamine levels via ornithine decarboxylase (ODC) activation in a dose-dependent manner. DFMO reduced A{beta}42 aggregation, decreased amyloid precursor protein (APP) levels, and normalized proteins linked to AD pathology in DS fibroblasts. Polyamine levels were elevated in DS-AD hippocampal tissue, with colocalization of ODC and A{beta}42 aggregates. CONCLUSIONThese findings suggest that polyamine biosynthesis may exacerbate A{beta}42 toxicity and APP expression, contributing to AD progression in DS. The ability of DFMO to reduce A{beta}42 aggregation and restore protein homeostasis presents the polyamine pathway as a therapeutic target for DS-AD management.

biochemistry↗

bioRxiv2025

Assembly, Annotation, and Comparative Analysis of the Mitochondrial Genome of Winged Bean (Psophocarpus tetragonolobus): Insights into Evolutionary Adaptation and Codon Usage Bias

The winged bean (Psophocarpus tetragonolobus) is an underutilized, nutritionally dense legume with significant agricultural potential due to its adaptability to tropical environments and nitrogen-fixing capabilities. This study presents the assembly, annotation, and comparative analysis of its complete mitochondrial genome, spanning 366,925 bp. The genome comprises 64 genes, including 38 protein-coding genes, 12 tRNA genes, and 6 rRNA genes. Codon usage analysis revealed moderate bias in mitochondrial genes, primarily shaped by mutational pressures, while tRNA gene content aligns with codon preferences, optimizing translational efficiency. Phylogenetic analysis placed P. tetragonolobus within the Phaseoleae tribe, clustering closely with Glycine max and Vigna radiata, while synteny analysis highlighted high genomic conservation with related legumes. Ka/Ks ratio analysis underscored strong purifying selection in core mitochondrial genes, reflecting functional constraints essential for energy metabolism. Comparative analyses of mitochondrial and chloroplast genomes revealed distinct evolutionary pressures, with chloroplast genes exhibiting more significant variability influenced by functional roles in photosynthesis. These findings provide valuable insights into the evolution and adaptation of P. tetragonolobus, establishing a foundation for its potential application in sustainable agriculture and crop improvement programs.

genomics↗