Biology subjects

Nanchahal, J.

Publications and source records attributed to Nanchahal, J..

5 recordsLinked to original sources

bioRxiv2026

Rank-based integration identifies convergent disease mechanisms across omics

The rapid growth of omics studies offers new opportunities to uncover disease mechanisms, yet findings from individual studies or single omics may be influenced by cohort-, platform- and layer-specific variation. Integrating evidence across studies and omics layers can reveal robust biological signals that are reproducible across molecular layers, but differences in assay platforms, sample sizes and feature coverage complicate direct combination of summary statistics. Here we present the Omics Rank-Based Integration Tool (ORBIT), a direction-aware framework for prioritizing concordant signals across omics layers using only within-dataset feature ranks and effect directions. ORBIT tests directional rank consistency across omics layers against a closed-form variance-gamma null distribution while accounting for inter-dataset correlation and incomplete feature overlap. Simulations show that ORBIT maintains well-calibrated false-positive rates under inter-omics correlation, increasing numbers of omics layers and missingness, while detecting concordant signals with increasing power as the number of layers grows. We applied ORBIT to tubulointerstitial transcriptomic data from patients with chronic kidney disease in the C-PROBE cohort and proteomic data from the Kidney Precision Medicine Project, identifying a concordant injury programme marked by inflammatory and fibrotic remodeling together with impaired energy metabolism. We also used ORBIT to integrate ten transcriptomic, four proteomic and one translatomic datasets in dilated cardiomyopathy heart tissue, identifying extracellular matrix remodeling and mitochondrial energy failure as the dominant concordant biological programmes. In both diseases, ORBIT prioritized concordant genes and identified pathways that were not significant in any single omics layer alone. These results show that directional rank integration can be used for integrating heterogeneous omics summary data and prioritizing robust molecular mechanisms.

bioinformatics↗

bioRxiv2025

Thrombospondin Encapsulated Dense Particles accelerate wound healing and downregulate fibrotic phenotypes

Extracellular particles (EP) released by cells are heterogenous, with extracellular vesicles (EV) believed to be the major component. To investigate different EV subpopulations, we conducted a panel screen of 15 fluorescent EV markers in 4 adherent cell lines. Nanoflow cytometry identifies TSPAN14 as the best EV marker in 3 of 4 cell lines. Surprisingly, less than 50% of EPs are labelled by the top 2 EV markers in half the cell lines. The EV marker negative EPs are detergent resistant, non-lipophilic, dense and have Thrombospondin shells by dSTORM; and were thus named Thrombospondin Encapsulated Dense particles (ThrEDs). ThrEDs are ubiquitous, contain extracellular matrix regulators and are released following cell stress. ThrEDs accelerate scratch-wound closure and downregulate the fibrotic phenotype in Dupuytrens disease patient myofibroblasts. The TSP-1 C-terminus is exposed on the surface of ThrEDs, opening engineering applications.

cell biology↗

bioRxiv2024

A single cell and spatial genomics atlas of human skin fibroblasts in health and disease

Fibroblasts are critical cells that shape the architecture and cellular ecosystems in multiple tissues. Understanding fibroblast heterogeneity and their spatial context in health and disease has enormous clinical relevance. In this study, we constructed a spatially-resolved atlas of human skin fibroblasts from healthy skin and 23 skin disorders. We define 6 major skin fibroblast populations in health and a further three skin disease-specific fibroblast subtypes, and demonstrate the fibroblast composition in different types of skin disease. We characterise a human-specific fibroblastic reticular cell (FRC)-like subtype in the skin perivascular niche and postulate their origin from prenatal skin lymphoid tissue organiser (LTo)-like cells. We also show that inflammatory myofibroblasts (IL11+MMP1+CXCL5+IL7R+) are a conserved fibroblast subtype in inflammatory disorders and cancers across multiple human tissues. We provide a harmonised nomenclature for skin fibroblasts that integrates previous findings from human skin and other tissues.

cell biology↗

bioRxiv2024

Engineered HMGB1 Construct with Tandem HMG B Domains that Promotes Tissue Regeneration without Potential for Deleterious Inflammation or Thrombosis

Fully reduced High Mobility Group Box 1 (HMGB1) binds CXCL12 and signals via CXCR4 when released into the extracellular space. It acts as a chemokine and transitions stem cells from quiescent G to a primed GAlert state. Cells in GAlert rapidly enter G1 in response to activating factors released by tissue injury to promote tissue repair. However, oxidative conversion of FR-HMGB1 into the disulfide form activates proinflammatory pathways via TLR-2, TLR-4 and RAGE. Peptide mapping and NMR spectroscopy identified a conserved CXCL12-binding motif within each Box and adjacent flanking regions. We decoupled the regenerative and inflammatory functions using an engineered construct (dBB12L), comprising tandem Box B domains with a flexible linker. dBB12L exhibited CXCL12 binding and accelerated repair equivalent to FR-HMGB1. Importantly, dBB12L lacked detectable RAGE binding and did not signal via TLR-2 and TLR-4, establishing it as a potential therapeutic to promote tissue repair without deleterious inflammation.

biochemistry↗

bioRxiv2021

A Simple Ultrafast Multicolor Immunolabelling and Clearing Approach for Whole-Organ and Large Tissue 3D Imaging

High-resolution whole-organ imaging of cleared tissues captures cellular and molecular insights within the intact tissue and tumour microenvironments. However, current immunolabelling and clearing methods are complicated and time-consuming; extending to several weeks. Here, we developed Simple Ultrafast Multicolor Immunolabelling and Clearing or SUMIC, a method that enables multicolor immunolabelling and clearing of whole murine organs and human tissues within 2 to 2.5 days. Moreover, SUMIC is simple, robust, non-hazardous and versatile comprising antigen retrieval, permeabilization, collagenase-based digestion, immunolabelling, dehydration, and clearing. SUMIC permits quantitative and singlecell resolution analysis and detection of rare cells in whole organs, for example, round SMA positive cells in the thymus. Upon volumetric imaging, SUMIC-processed samples retain normal tissue architecture and can be used for paraffin-embedding and histology. We employed the SUMIC method for whole-organ mapping of lymphatic vessels across different ages and organs. This analysis revealed the expansion of lymphatic vessels in endocrine tissues but not in any other organs with aging. Hence, SUMIC will accelerate discoveries compared to other whole organ imaging pipelines.

physiology↗