Biology subjects

Natarajan, R.

Publications and source records attributed to Natarajan, R..

11 recordsLinked to original sources

bioRxiv2026

Epigenome Alterations and 3D Chromatin Architecture Remodeling in Inflammatory Macrophage Activation under Diabetic Conditions

Aberrant monocyte/macrophage activation in diabetes drives chronic inflammation and complications. While epigenetic mechanisms are implicated, the role of 3D-chromatin reorganization remains unclear. Using integrated multi-Omics, we profiled gene expression and 3D-chromatin architecture in human CD14+ monocyte-differentiated macrophages treated with high glucose + TNF- (HT) mimicking the diabetic milieu. HT induced inflammatory programs resembling those in diabetes, and dynamically altered chromatin accessibility, enhancer-promoter loops, transcriptionally active/inactive (A/B) compartments, and topologically associated domains. Inflammatory genes exhibited increased, whereas cell-cycle and metabolic genes showed reduced chromatin accessibility and enhancer-promoter interactions. These architectural changes facilitated the convergence of lineage-specific and signal-dependent transcription factors at enhancer-promoter loops, forming network hubs orchestrating pro-inflammatory responses. Similar enhancer-promoter interactions were observed in monocytes from individuals with diabetes. Perturbing chromatin interactions via CRISPR-interference targeting HT-induced enhancers suppressed inflammatory gene expression. Results from this first comprehensive enhancer connectome maps in macrophages under diabetic conditions reveal disease-associated rewiring of the 3D epigenome, highlighting epigenetic mechanisms as potential therapeutic targets. TeaserDiabetic conditions rewire 3D chromatin organization and enhancer-promoter interactions in human macrophages, promoting chronic inflammation.

genomics↗

bioRxiv2025

From Snapshots to Structure: A Novel Method for Reconstructing Directed Microbial Interaction Networks from Compositional Data

Microbial communities are shaped by complex ecological interactions, but inferring these from 16S rRNA gene sequencing remains challenging due to data compositionality and the limitations of correlation-based methods. We present a novel framework that reconstructs directed, signed, and weighted microbial interaction networks from cross-sectional compositional data, without requiring time-series or predefined dynamic models. Using asymmetric slopes and a perturbation-informed strategy, This method infers interaction polarity and strength while accounting for compositional constraints. Applied to a synthetic gut microbiome, the framework uncovered taxon-specific trajectories, directional dependencies, and persistent interaction plasticity. Persistent Directed Acyclic Graph motifs identified keystone initiators, while other taxa served as resilient hubs. A quadrant-based visualization clarified ecological influencers and responders. Inferred networks aligned interaction polarity with abundance trends, revealing a principle of polarity-driven succession. This approach enables predictive, mechanistic insights into microbial dynamics from static data, offering scalable tools for microbiome analysis, synthetic community design, and ecological theory development.

ecology↗

bioRxiv2025

Genetic differentiation in Anopheles stephensi from India and Ethiopia: insights from mitochondrial genome analysis

Anopheles stephensi is a primary malaria vector, particularly in urban areas of South Asia and the Middle East. Its recent spread into Africa has raised significant interest in understanding its genetic structure and evolutionary history. This study presents a comprehensive analysis of 98 mitochondrial genomes of An. stephensi from India, Pakistan, and Ethiopia, providing critical insights into the species genetic diversity patterns. High genetic diversity was observed among Indian samples, with two distinct genetic ancestries identified. While one ancestry was more prevalent in specific geographical regions, both lineages were found across all study sites, suggesting the co-existence of multiple lineages within these areas. Further analysis revealed significant genetic differentiation between Indian and Ethiopian populations, with limited overlap in shared mutations. Although some Ethiopian samples showed genetic relatedness to the SDA500 strain from Pakistan (used in genome sequencing by the Broad Institute), the majority of Ethiopian samples showed distinct genetic ancestry. The distinctiveness of Ethiopian populations, compared to other countries outside of Africa, was also reflected in the COI datasets analyzed in this study. However, further expanding the mitogenome dataset to include additional wild samples from regions such as Pakistan, Iran, Saudi Arabia, Sri Lanka and other African countries will provide a more comprehensive understanding of An. stephensis invasion history. Overall, the findings of this study highlight the significant genetic differentiation between Ethiopian and Indian An. stephensi populations, and existence of multiple lineages in Ethiopia indicating multiple independent introductions from different countries.

zoology↗

bioRxiv2025

Single-Cell Multimodal Profiling Highlights Persistent Aortic Smooth Muscle Cell Changes in Diabetic Mice Despite Glycemic Control

BackgroundType 2 diabetes (T2D) is associated with accelerated vascular complications like hypertension and atherosclerosis. "Phenotypic switching" of vascular smooth muscle cells (SMC), a major driver of these complications, is enhanced in diabetes. Despite adequate glycemic control, SMC dysfunction can persist due to "metabolic memory" of prior hyperglycemia. However, the mechanisms of hyperglycemic memory associated with persistent SMC dysfunction are unclear. Here, leveraging single-cell (sc) multi-omics, we examined the effect of glucose normalization on transcriptomic and epigenomic changes associated with SMC phenotypic transition in T2D mice. MethodsWe treated T2D db/db mice with the antidiabetic drug dapagliflozin (DAPA) (db/dbDAPA) or vehicle (db/db), and non-diabetic control db/+ mice with vehicle for 6 weeks. Dissected aortas were subjected to scRNA-seq, scATAC-seq, and spatial transcriptomics (Xenium) to determine single-cell changes in gene expression and chromatin accessibility. ResultsDAPA treatment conferred effective glycemic control in db/db mice, with significant reductions in blood glucose/hemoglobin A1c. scRNA and scATAC-seq analysis of aortas identified major cell populations, including SMC, fibroblasts, endothelial and immune cells. SMC were further clustered into 9 subtypes, including contractile and fibromyocyte-like cells. Cell composition analysis revealed decreases in contractile SMC and increases in vascular remodeling associated fibromyocyte-like SMC in db/db versus db/+ mice. Interestingly, DAPA did not reverse diabetes-induced decreases in contractile markers but reversed changes in several fibromyocyte markers in db/db mice. Pseudotime trajectory analysis revealed increased activities of fibromyocyte enriched transcription factors (TFs) during contractile to fibromyocyte transition. Furthermore, increased expression of TFs regulating fibromyocyte phenotype (e.g. Atf4, Bach1, Hand2, Fosl2) in db/db were partially reversed by DAPA, whereas reduced contractile TF (Mef2c) expression was unchanged. Spatial transcriptomics analysis further mapped aortic cell types within intact aortas and confirmed that DAPA reversed alterations in key fibromyocyte but not contractile genes in db/db mouse aortas. ConclusionsPersistent epigenetic changes may contribute to sustained vascular remodeling and dysfunction in T2D. T2D reduced contractile SMC gene expression and related chromatin accessibility and promoted phenotypic transition to fibromyocytes. These changes are only partially reversed by a widely used antidiabetic drug like DAPA, underscoring the need for more effective therapies that target hyperglycemic memory.

biochemistry↗

bioRxiv2024

Mapping Endothelial-Macrophage Interactions in Diabetic Vasculature: Role of TREM2 in Vascular Inflammation and Ischemic Response

Diabetes mellitus (DM) significantly accelerates vascular diseases like peripheral arterial disease (PAD). Endothelial cells (ECs) and macrophages (M{Phi}s) singularly and synergistically are important contributors to DM-associated vascular dysfunction. Single-cell (sc) profiling technologies are revealing the true heterogeneity of ECs and M{Phi}s, but how this cellular diversity translates to cell-cell interactions, and consequentially vascular function, remains unknown. We leveraged scRNA sequencing and spatial transcriptome (ST) profiling to analyze human mesenteric arteries from non-diabetic (ND) and type 2 diabetic (T2D) donors. We generated a transcriptome and interactome map encompassing the major arterial cells and highlighted Triggering Receptor Expressed on Myeloid Cells 2 (TREM2) as a top T2D-induced gene in mononuclear phagocytes (MPs), with concomitant increases of TREM2 ligands in ECs. We verified DM-associated TREM2 induction in cell and mouse models, and found that TREM2 inhibition decreases pro-inflammatory responses in MPs and ECs, as well as increases EC migration in vitro. Furthermore, TREM2 inhibition using a neutralizing antibody enhanced ischemic recovery and flow reperfusion in DM mice subjected to hindlimb ischemia, suggesting that TREM2 promotes ischemic injury in DM. Finally, in human PAD, co-existing DM was associated with greater expression of TREM2 and its interaction with ECs, with a further increase in ischemic tissue compared to patient-matched non-ischemic tissue. Collectively, our study presents the first atlas of human diabetic vessels with single cell and spatial resolution, and identifies TREM2-EC interaction as a key driver of diabetic vasculopathies, the targeting of which may offer an opportunity to ameliorate vascular dysfunction associated with DM-PAD.

cell biology↗

bioRxiv2022

Regulation of Nuclear Transcription by Mitochondrial RNA

Chromatin-associated RNAs (caRNAs) form a relatively poorly recognized layer of the epigenome. The caRNAs reported to date are transcribed from the nuclear genome. Here, leveraging a recently developed assay for detection of caRNAs and their genomic association, we report that mitochondrial RNAs (mtRNAs) are attached to the nuclear genome and constitute a subset of caRNA, which we termed mt-caRNA. In four human cell types analyzed, mt-caRNAs preferentially attach to promoter regions. In human endothelial cells (ECs), the level of mt-caRNA-promoter attachment changes in response to environmental stress that mimics diabetes. Suppression of a non-coding mt-caRNA in ECs attenuates stress-induced nascent RNA transcription from the nuclear genome, including that of critical genes regulating cell adhesion, and abolishes stress-induced monocyte adhesion, a hallmark of dysfunctional ECs. Finally, we report increased nuclear localization of multiple mtRNAs in the ECs of human diabetic donors, suggesting many mtRNA translocate to the nucleus in a cell stress and disease-dependent manner. These data nominate mt-caRNAs as messenger molecules responsible for mitochondrial-nuclear communication and connect the immediate product of mitochondrial transcription with the transcriptional regulation of the nuclear genome.

genomics↗

bioRxiv2021

Dual adhesive unipolar polysaccharides synthesized by overlapping biosynthetic pathways in Agrobacterium tumefaciens

Agrobacterium tumefaciens, is a member of the Alphaproteobacteria that pathogenizes plants, and associates with biotic and abiotic surfaces via a single cellular pole. A. tumefaciens produces the unipolar polysaccharide (UPP) at the site of surface contact. UPP production is normally surface-contact inducible, but elevated levels of the second messenger cyclic diguanylate monophosphate (cdGMP) bypass this requirement. Multiple lines of evidence suggest that the UPP has a central polysaccharide component. Using an A. tumefaciens derivative with elevated cdGMP and mutationally disabled for other dispensable polysaccharides, a series of related genetic screens have identified a large number of genes involved in UPP biosynthesis, most of which are Wzx-Wzy-type polysaccharide biosynthetic components. Extensive analyses of UPP production in these mutants have revealed that the UPP is comprised of two genetically, chemically and spatially discrete forms of polysaccharide, and that each requires a specific Wzy-type polymerase. Other important biosynthetic, processing and regulatory functions for UPP production are also revealed, some of which are common to both polysaccharides, and a subset of which are specific to each species. Many of the UPP genes identified are conserved among diverse rhizobia, whereas others are more lineage specific. Plain language summaryBacteria attach to a wide variety of surfaces including host tissues, via externalized structures described as adhesins. We define a large set of genes involved in synthesis of a complex unipolar adhesin comprised of two distinct polysaccharides, that is required for surface attachment by the plant-associated pathogen Agrobacterium tumefaciens.

microbiology↗

bioRxiv2019

Dynamic changes in RNA-chromatin interactome promote endothelial dysfunction

Chromatins are pervasively attached by RNAs. Here, we asked whether global RNA-chromatin contacts are altered in a given cell type in a disease context, and whether these alterations impact gene expression and cell function. In endothelial cells (ECs) treated by high-glucose and TNF, we employed single-cell RNA-sequencing and in situ mapping of RNA-genome interaction (iMARGI) assay to delineate temporal changes in transcriptome and RNA-chromatin interactome. ECs displayed dramatic and heterogeneous changes in single cell transcriptome, accompanied by a dynamic and strong increase in inter-chromosomal RNA-DNA interactions, particularly among super enhancers (SEs). These SEs overlap with genes contributing to inflammatory response and endothelial mesenchymal transition (EndoMT), two key aspects of endothelial dysfunction. Perturbation of a high-glucose and TNF-activated interaction involving SEs overlapping LINC00607 and SERPINE1 attenuated the pro-inflammatory and pro-EndoMT gene induction and EC dysfunction. Our findings highlight RNA-chromatin contacts as a crucial regulatory feature in biological and disease processes, exemplified by endothelial dysfunction, a major mediator of numerous diseases.

genomics↗

bioRxiv2019

Reduced Plasma Ascorbic Acid Levels in Recipients of Myeloablative Conditioning & Hematopoietic Cell Transplantation

Hematopoietic cell transplantation (HCT) conditioned using myeloablative conditioning (MAC) is complicated by end organ injury due to endothelial dysfunction and graft versus host disease. Mucositis and oxidant injury results in micronutrient deficiency. Ascorbic acid (AA) levels were measured in 15 patients undergoing HCT conditioned with MAC (11 allogeneic and 4 autologous HCT). Ascorbate levels declined post conditioning to 27.3 ({+/-}14.1) by day 0 (p <0.05 compared with baseline), reaching a nadir level of 21.5 ({+/-}13.8) on day 14 (p <0.05) post-transplant. Patients undergoing allogeneic HCT continued to have low AA levels to day 60 post transplant, whereas recipients of autologous HCT recovered plasma AA levels to normal. The role of AA in maintaining endothelial function and hematopoietic as well as T cell recovery is provided, developing the rationale for repletion of vitamin C following HCT.

physiology↗

bioRxiv2018

Risk stratification of allogeneic stem cell recipients with respect to the potential for development of GVHD via their pre-transplant plasma lipid and metabolic signature

The clinical outcome of allogeneic hematopoietic stem cell transplantation (SCT) is strongly influenced from the complications arising during the post-transplant immune restoration and has been well studied and described. However, the metabolic status of the recipient pre-transplant also has the potential to influence this outcome and has never been studied before and has the potential to enable risk stratification with respect to the development of transplant associated complications such as graft vs. host disease (GVHD). In order to better understand this aspect of transplant related complications we investigated the pre-transplantation metabolic signature to assess the possibility of pre-transplant risk stratification. This pilot study was composed of 14 patients undergoing myeloablative conditioning followed by either HLA matched related, unrelated donor, or autologous stem cell transplantation. Blood samples were taken prior to transplant and the plasma was comprehensively characterized with respect to its lipidome and metabolome via LCMS and GCMS. The results indicated a significantly pro-inflammatory metabolic profile in patients who eventually developed Graft vs. Host Disease (GVHD). The data revealed 5 potential pre-transplant biomarkers (1-monopalmitin, diacylglycerol (DG) 38:5, DG 38:6, 2-aminobutyric acid, and fatty acid (FA) 20:1) that demonstrated high sensitivity and specificity towards predicting post-transplant GVHD development. The predictive model developed demonstrated an estimated predictive accuracy of risk stratification of 100%, with an Area under the Curve of the ROC of 0.995 with 100%. The likelihood ratio of 1-monopalmitin (infinity), DG 38:5 (6.0) and DG 38:6 (6.0) also demonstrated that a patient with a positive test result for these biomarkers pre-transplant will likely have very high odds of developing GVHD post-transplant. Collectively the data demonstrates the possibility of using pre-transplant metabolic signature for risk stratification of SCT recipients with respect to development of GVHD.

biochemistry↗

bioRxiv2017

LTRs activated by Epstein-Barr virus-induced transformation of B cells alter the transcriptome

Endogenous retroviruses (ERVs) are ancient viral elements that have accumulated in the genome through retrotransposition events. Although they have lost their ability to transpose, many of the long terminal repeats (LTRs) that originally flanked full-length ERVs maintain the ability to regulate transcription. While these elements are typically repressed in somatic cells, when this repression is lost, they can function as transcriptional enhancers and promoters. The mechanisms driving LTR activation, however, are not well understood. Epstein-Barr virus (EBV), which transforms primary B cells into continuously proliferating cells, is a tumor virus associated with lymphomas. We report here that transformation of primary B cells by EBV leads to genome-wide activation of LTR enhancers and promoters. The activation of LTRs coincides with local DNA hypomethylation and binding by transcription factors such as RUNX3, EBF1, and EBNA2. The set of EBV-activated LTRs is unique to transformed B cells when compared to other cell lines known to have activated LTRs. Furthermore, we found that EBV-induced LTR activation impacts the B cell transcriptome by upregulating transcripts driven by cryptic LTR promoters. These transcripts include genes important to oncogenesis of Hodgkin lymphoma, as well as those found in other cancers such as HUWE1/HECTH9. These data suggest that the activation of LTRs by EBV may be important to the pathology of EBV-associated cancers. Altogether, our results indicate that EBV-induced transformation of B cells alters endogenous retroviral element activity, thereby impacting host gene regulatory networks and oncogenic potential.

genomics↗