Biology subjects

Lal, M.

Publications and source records attributed to Lal, M..

6 recordsLinked to original sources

bioRxiv2026

Systemic Analysis of Patient Derived Esophageal Epithelial Organoid Model Reveals Cell State Heterogeneity and Conservation of Differentiation Hierarchy

Background and Aims: Eosinophilic esophagitis (EoE) features prominent epithelial dysregulation that persists despite resolution of eosinophilia. Interleukin-13 (IL-13) is known to be a key upstream driver of epithelial abnormalities in EoE. We sought to benchmark an IL-13 esophageal organoid model against the in vivo epithelial state in EoE at a single cell resolution, to define in the role of IL-13 in aberrant epithelial development and inflammation in EoE, and to validate the IL-13 organoid as a model system to study the epithelial changes seen in EoE. Methods: We performed scRNA-Seq on esophageal biopsies from control and EoE patients, and esophageal biopsy-derived organoids with or without IL-13. We compared cellular composition, differentiation trajectories, pathway enrichment, and differential gene expression within both systems, and assessed findings at a protein level. Results: Seven distinct epithelial cell clusters were identified and preserved in both biopsies and organoids. EoE biopsies demonstrated expansion of cycling cells, whereas IL-13-treated organoids showed shift in the composition of the suprabasal compartments. Pseudotime topology was preserved across tissues, with a shift away from terminal differentiation in both EoE biopsies and IL-13-treated organoids. IL-13 reproduced changes in the transcription of central EoE genes and the dysregulation of epithelial proliferation and differentiation pathways seen in EoE. There was broad activation of immune related pathways within both EoE biopsies and IL-13-treated organoids, however, biopsies additionally showed activation in several immune and extracellular matrix remodeling programs that IL-13 alone did not reproduce. Conclusion: IL-13-treated esophageal organoids replicate key epithelial features of EoE including dysregulated epithelial development, impaired cornification, and inflammatory signals, while preserving lineage architecture, providing a tractable platform for epithelial-targeted mechanistic and therapeutic studies.

cell biology↗

bioRxiv2025

Restructured genomes may have shaped the evolution of clade-specific traits in mammals

Genomic rearrangements (GRs) are pervasive in mammalian evolution, yet their contribution to adaptive trait divergence remains poorly defined. By examining 71 mammalian genomes across eight major clades, we uncovered 206 clade-specific disruptions of ancestral synteny. These rearrangements consistently localize near genes underpinning clade-specific physiological, metabolic and behavioural traits and coincided with the accelerated expression rates in the affected lineage. The disruption of otherwise syntenic chromatin contacts and the fusion of domains with contrasting epigenetic states implied that the alteration in regulatory adjacency may underlie the expression divergence. Primate-specific rearrangements exhibited signatures of selective constraint, including fixation across species, reduced recombination, elevated linkage disequilibrium, and enhanced co-expression of genes flanking rearranged loci, indicating that these genomic architectures are selectively maintained. Our observations imply that the clade-specific genomic rearrangements repeatedly reconfigured the mammalian regulatory landscape and likely served as an evolutionary substrate for lineage-specific adaptation.

evolutionary biology↗

bioRxiv2025

A unique two-excipient heat stable tablet formulation of oral insulin: preliminary results

We report a novel formulation approach for development of a thermostable oral insulin tablet. Using freeze drying to form a heat stable tablet in a single-step process, we demonstrate hydroxypropyl beta cyclodextrin (HP-{beta}-CD) encapsulated lipophilic ion-pair complex of insulin using bile salt achieves intestinal absorption and sustained glucose levels. The tablets produced using this simple approach with only two excipients offer protection from enzymatic and stomach acid degradation and facilitate insulin uptake, without any need for specialized drug manufacturing or enteric coating. Insulin in this innovative formulation is thermotolerant, capable of maintaining stability even under heat stress at 30-40{degrees}C/65-75% RH. The convenient presentation of insulin as a thermostable oral tablet presents a low-cost scalable manufacturing method that simplifies the logistics of storage, transport, and distribution in any setting, including areas where cold storage maybe limited or unavailable. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=141 SRC="FIGDIR/small/635377v1_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@16b4b64org.highwire.dtl.DTLVardef@122c11forg.highwire.dtl.DTLVardef@b50c0borg.highwire.dtl.DTLVardef@29bf28_HPS_FORMAT_FIGEXP M_FIG Our unique formulation approach protects insulin from stomach and temperature induced degradation, improves intestinal permeability providing a sustained release of insulin for glycemic control. The freeze dried tablet product format is easily scalable and flexible, increasing accessibility across all populations. C_FIG

biochemistry↗

bioRxiv2024

Proton pump inhibitors modulate esophageal epithelial barrier function and crosstalk with eosinophils

BackgroundEosinophilic esophagitis (EoE) is a chronic allergic disease characterized by esophageal dysfunction, type-2 inflammation, and esophageal eosinophilic infiltrate. While proton pump inhibitor (PPI) therapy is commonly used for EoE management, the underlying mechanism of action remains unclear. MethodsAir-liquid interface culture of esophageal epithelial cells was employed to investigate the impact of the PPI omeprazole on barrier integrity in IL-13-treated cultures. Epithelial chemokine secretion was assessed following stimulation with IL-13 and omeprazole, and the migration of eosinophils from healthy human donors was evaluated using 3 {micro}m pore-sized transwells. A co-culture system of epithelial cells and eosinophils was employed to study chemokine secretion and eosinophil adhesion and activation markers. ResultsOmeprazole treatment in the IL-13-treated air-liquid interface (ALI) model resulted in 186 differentially expressed genes and restored barrier integrity compared to ALI treated with IL-13 alone. Omeprazole treatment reduced STAT6 phosphorylation, downregulated calpain 14, and upregulated desmoglein-1 in the IL-13-treated air-liquid interface samples. IL-13-induced upregulation of Eotaxin-3, CXCL10, and periostin, but this was downregulated by omeprazole. Further, the expression of CD11b, CD18, and CD69 was lower on eosinophils from omeprazole-treated epithelial-eosinophil co-cultures, which also had lower levels of eotaxin-3, CXCL10, CCL2, and CCL4. ConclusionOmeprazole reduced the effects of IL-13 in both the epithelial air-liquid interface model and eosinophil-epithelial co-cultures, reducing barrier dysfunction, chemokine expression, and upregulation of eosinophil adhesion markers.

immunology↗

bioRxiv2024

Loss of conserved noncoding elements likely shaped the evolution of regressed phenotypes in cavefish

The Mexican cavefish, Astyanax mexicanus, is a captivating model for probing cave adaptations, showcasing pronounced divergence in traits like vision, brain morphology, behaviour, pigmentation, and hypoxia tolerance compared to its surface-dwelling counterpart. Very few protein-coding variants are identified in cave-morphs, and the vast phenotypic gap between the two morphs remains inadequately explained. We investigated the noncoding genomes of teleosts and found that 3,343 conserved non-coding elements (CNEs) were independently lost in cave-morphs. These CNEs, confirmed in Zebrafish, displayed enhancer-associated histone modifications, possessed binding sites of neuronal transcription factors and interacted with cognate genes through chromatin loops. Genes crucial for eye and nervous system development were located adjacent to CNEs lost in cave morphs. Notably, these flanking genes were gradually downregulated during embryonic development of cave-morphs, contrasting with surface morphs. These insights underscore how compromised developmental pathways, stemming from the loss of distal regulatory elements, contribute to the regression of phenotypes in cave morphs. Article SummaryDespite availability of genome sequences and allied datasets, the genetic underpinning of regressed traits of cavefish remains enigmatic. By aligning the genome sequences of teleosts, we identified thousands of noncoding elements specifically lost in cavefish, exhibited enhancer-associated hallmarks, and were enriched with the binding sites of neuronal transcription factors. Their cognate genes were associated with eye and nervous system development, and exhibited developmental downregulation in cavefish. This study highlights how the loss of regulatory elements impacted the cavefish evolution and adaptation.

genomics↗

bioRxiv2024

Interferon-γ signaling in eosinophilic esophagitis has implications for epithelial barrier function and programmed cell death.

ObjectiveEosinophilic esophagitis (EoE) is a chronic esophageal inflammatory disorder characterized by eosinophil-rich mucosal inflammation and tissue remodeling. Transcriptional profiling of esophageal biopsies has previously revealed upregulation of type I and II interferon (IFN) response genes. We aim to unravel interactions between immune and epithelial cells and examine functional significance in esophageal epithelial cells. Design We investigated epithelial gene expression from EoE patients using single-cell RNA sequencing and a confirmatory bulk RNA-sequencing experiment of isolated epithelial cells. The functional impact of interferon signaling on epithelial cells was investigated using in vitro organoid models. ResultsWe observe upregulation of interferon response signature genes (ISGs) in the esophageal epithelium during active EoE compared to other cell types, single-cell data, and pathway analyses, identified upregulation in ISGs in epithelial cells isolated from EoE patients. Using an esophageal organoid and air-liquid interface models, we demonstrate that IFN-{gamma} stimulation triggered disruption of esophageal epithelial differentiation, barrier integrity, and induced apoptosis via caspase upregulation. We show that an increase in cleaved caspase-3 is seen in EoE tissue and identify interferon gamma (IFNG) expression predominantly in a cluster of majority-CD8+ T cells with high expression of CD69 and FOS. ConclusionThese findings offer insight into the interplay between immune and epithelial cells in EoE. Our data illustrate the relevance of several IFN-{gamma}-mediated mechanisms on epithelial function in the esophagus, which have the potential to impact epithelial function during inflammatory conditions. Key MessagesWhat is already known about this topic: O_LIThe transcriptome of esophageal biopsy tissue reproducibly distinguishes eosinophilic esophagitis from histologically normal tissue, with evidence of mixed inflammatory signals. C_LIO_LIInterferon response signature genes are elevated in EoE biopsy tissue compared to controls, suggesting T1 in addition to T2 cytokine signaling within EoE mucosa. C_LI What this study adds: O_LIWe observe reproducible, robust upregulation of interferon signature genes in esophageal epithelium, and we confirm that esophageal epithelium expresses functional IFN-a and IFN-{gamma} receptors. C_LIO_LIIFN-{gamma} treatment of epithelial organoids has several detrimental effects, including decreased proliferation, organoid formation, and increased caspase activation. C_LIO_LIAnalysis of single-cell RNA-sequencing data from of EoE biopsy tissue during active disease and remission identified that a CD8+ population expressing high levels of FOS, ITGAE, and ITGA1 expresses high levels of IFNG C_LI How this study might affect research, practice, or policy: O_LIWe identify esophageal epithelium as the cellular source for interferon response gene signature in EoE and a CD8+ tissue-resident memory T-cell population was the main source of IFNG. C_LIO_LIFurther mechanistic studies are required to identify how non-T2 signaling mechanisms like IFN-{gamma} signaling contribute to EoE pathogenesis, and if this pathway can be targeted as an adjunctive therapy for EoE. C_LI

immunology↗