Biology subjects

Wickramasinghe, N.

Publications and source records attributed to Wickramasinghe, N..

5 recordsLinked to original sources

bioRxiv2026

TOLERANCE REGIONS FOR COMPOSITIONAL DATA WITH APPLICATION TO REFERENCE REGIONS FOR HEALTHY MICROBIOME PROFILES

AO_SCPLOWBSTRACTC_SCPLOWImbalances in the human microbiome are associated with numerous diseases, highlighting the need for benchmarks that define healthy microbiome composition and identify abnormal deviations. Although the microbiome is increasingly studied as a potential clinical marker, statistical approaches for constructing reference regions of healthy microbiome composition remain relatively underexplored. This work develops statistical methods to construct reference regions for healthy microbiome data, addressing three main challenges. First, since microbiome data contain relative rather than absolute information, standard statistical methods are not directly appropriate. Therefore, microbiome profiles are treated as compositional data satisfying a sum constraint, and log-ratio transformations are used to analyze them in real space while preserving their relative structure. Second, reference regions are constructed as tolerance regions rather than confidence regions, so that they cover a pre-specified proportion of the healthy population with a given confidence level. The proposed framework incorporates both parametric and nonparametric approaches for constructing these tolerance regions. Parametric methods are considered when the ilr-transformed data approximately follow an elliptical distribution, where they can yield smaller regions while maintaining the desired coverage. Nonparametric approaches provide a flexible alternative by avoiding distributional assumptions. Third, because microbiome data are multidimensional and difficult to interpret, quantitative and graphical tools are introduced to assess atypicality and identify which microbial taxa contribute most to deviations from healthy profiles. Simulation studies are conducted to evaluate the performance of the proposed methods. The methodology is then demonstrated by constructing reference regions for healthy microbiome profiles using real-world data. Finally, the approach is applied to microbiome datasets comparing healthy and patient profiles to assess whether patient samples are identified as atypical and to examine which taxa contribute to these deviations. Overall, the proposed framework provides a clear and statistically robust approach for defining healthy microbiome reference regions and detecting atypical microbiome profiles.

microbiology↗

bioRxiv2026

Single-cell RNA editing defines clinically relevant cellular states in chronic myelomonocytic leukemia

BackgroundChronic myelomonocytic leukemia (CMML) is a clinically heterogeneous myeloid malignancy with limited therapeutic options and suboptimal risk stratification. Although single-cell RNA sequencing has refined disease classification through gene expression profiling, post-transcriptional mechanisms--particularly adenosine-to-inosine (A-to-I) RNA editing--remain unexplored at single-cell resolution. We hypothesized that cell-specific RNA editing programs contribute to CMML heterogeneity and define distinct, clinically actionable cellular states in CMML. MethodsWe developed a single-cell-aware computational framework for high-confidence identification and quantification of RNA editing events. Candidate sites were detected at pseudo-bulk depth using stringent filters and subsequently quantified at single-cell resolution. The pipeline incorporated dual alignment, barcode correction, artifact removal, and exclusion of genomic variants to ensure specificity. We applied this framework to discovery and independent validation CMML cohorts. Editing-defined cellular states were identified by unsupervised clustering of single-cell editing profiles and evaluated for associations with clinical stage, TET2 status, survival, and response to hypomethylating agent (HMA) therapy. Regulatory mechanisms were assessed by analyzing ADAR1/ADAR2 expression and relationships between editing levels and target gene expression. ResultsWe identified 3,326 high-confidence A-to-I RNA editing sites and delineated reproducible editing-defined cellular states. A granulocyte-monocyte progenitor-like editing state (edClu1_sub0) aligned with an inflammatory, monocytic-biased transcriptional program and was significantly associated with adverse survival, advanced-stage disease and TET2-mutant CMML, supporting it as a high-risk biomarker-defined subpopulation. In contrast, states such as edClu3 and edClu6 were enriched in earlier-stage, TET2-wild-type CMML and correlated with improved outcomes. Editing-defined states demonstrated systematic remodeling following HMA therapy, indicating treatment-responsive post-transcriptional programs. The high-risk state exhibited elevated ADAR1 and reduced ADAR2 expression, suggesting enzyme-specific regulatory imbalance as a potential therapeutic vulnerability. Integrative analyses further nominated immune-related genes--including LAPTM5, CTSS, and CD83--as CMML-specific oncogenic RNA editing targets, with coordinated increases in editing and expression within the aggressive state. ConclusionsRNA editing represents a clinically informative and mechanistically relevant layer that refines CMML stratification at single-cell resolution, independent of gene expression. These findings provide a framework for integrating post-transcriptional regulation into precision oncology and highlight RNA editing signatures as biomarkers for risk assessment, treatment monitoring, and therapeutic targeting in hematologic malignancies.

cancer biology↗

bioRxiv2024

Benzene metabolites increase vascular permeability by activating heat shock proteins and Rho GTPases

Benzene is a ubiquitous environmental and occupational pollutant abundant in household products, petrochemicals, and cigarette smoke. It is also a well-known carcinogen and hematopoietic toxin. Population-based studies indicate an increased risk of heart failure in subjects exposed to inhaled benzene, which coincides with the infiltration of immune cells into the myocardium. However, the mechanisms of benzene-induced cardiovascular disease remain unknown. Our data suggests that benzene metabolites trans,trans-muconaldehyde (MA), and hydroquinone (HQ) propagate endothelial activation and apoptosis analyzed by endothelial-specific microparticles in C57BL/6J mice plasma. Subcutaneous injections of MA and HQ increased vascular permeability by 1.54 fold and 1.27 fold correspondingly. In addition, the exposure of primary cardiac microvascular endothelial cells to MA increased vascular permeability detected by transendothelial monolayer resistance and by fluorescently labeled dextrans diffusion. The bulk RNA sequencing of endothelial cells exposed to MA for 2, 6, and 24 hours showed MA-dependent upregulation of heat shock-related pathways at 2 and 6 hours, dysregulation of GTPases at 6 hours, and altered cytoskeleton organization at 24 hours of exposure. We found that the HSP70 protein induced by MA in endothelial cells is colocalized with F-actin foci. HSP70 inhibitor 17AAG and HSP90 inhibitor JG98 attenuated MA-induced endothelial permeability, while HSP activator TRC enhanced endothelial leakage. Moreover, MA induced Rac1 GTPase activity, while Rho GTPase inhibitor Y-27632 attenuated MA-induced endothelial permeability. We showed that benzene metabolites compromised the endothelial barrier by altering HSP- and GTPase-related signaling pathways.

pharmacology and toxicology↗

bioRxiv2021

Identification and characterization of hPSC-derived FOXA2+ progenitor cells with ventricular cardiac differentiation potential

While much progress has been made in understanding early cardiac development, the precise mechanisms that specify the different cardiomyocyte subtypes remain poorly understood. Recent data from our lab have shown that transient Foxa2 expression identifies a progenitor population with exclusive ventricular differentiation potential in the mouse heart. Here we have translated this concept to the human pluripotent stem cell (hPSC) system. Using a FOXA2-GFP reporter cell line we characterized expression of FOXA2 during hPSC cardiac differentiation and found that a subset of cardiac mesoderm precursors transiently expresses FOXA2. Gene expression analysis of FOXA2+ and FOXA2- cardiac mesoderm revealed that both populations similarly express early cardiac specification markers such as PDGFRA, TBX5, and ISL1, while other key candidates including TBX20 and GATA4 are significantly upregulated in the FOXA2+ population. Isolation and subsequent differentiation of FOXA2+ and FOXA2- populations demonstrates their comparable differentiation potential to both cardiomyocytes and epicardial cells. However, cardiomyocytes derived from FOXA2+ precursors showed enhanced differentiation efficiency toward ventricular cardiomyocytes compared to cardiomyocytes derived from FOXA2- precursors. To identify new mechanisms that regulate ventricular specification, we performed small molecule screening and found that inhibition of the EGFR pathway strongly increased the cardiac mesoderm population in general, and the FOXA2+ precursors in particular. Finally, we have identified a combination of cell surface markers to specifically isolate FOXA2+ cardiac precursors. In summary, our results suggest that FOXA2+ cardiac mesoderm harbors ventricular-specific differentiation potential and isolation of these cells permits the generation of cultures enriched for ventricular cardiomyocytes. Generating such enriched cardiac populations will be relevant for regenerative medicine approaches, as well as for disease modeling from induced pluripotent stem cells.

developmental biology↗

bioRxiv2020

Notch Signaling Commits Mesoderm to the Cardiac Lineage

During development multiple progenitor populations contribute to the formation of the four-chambered heart and its diverse lineages. However, the underlying mechanisms that result in the specification of these progenitor populations are not yet fully understood. We have previously identified a population of cells that gives rise selectively to the heart ventricles but not the atria. Here, we have used this knowledge to transcriptionally profile subsets of cardiac mesoderm from the mouse embryo and have identified an enrichment for Notch signaling components in ventricular progenitors. Using directed differentiation of human pluripotent stem cells, we next investigated the role of Notch in cardiac mesoderm specification in a temporally controlled manner. We show that transient Notch induction in mesoderm increases cardiomyocyte differentiation efficiency, while maintaining cardiomyocytes in an immature state. Finally, our data suggest that Notch interacts with WNT to enhance commitment to the cardiac lineage. Overall, our findings support the notion that key signaling events during early heart development are critical for proper lineage specification and provide evidence for early roles of Notch and WNT during mouse and human heart development. Summary statementEarly fate decisions are dictated by the embryonic signaling environment. We show that Notch signaling is active during early mouse development and that activating Notch in human cardiac mesoderm enhances cardiomyocyte differentiation efficiency.

developmental biology↗