Biology subjects

Mantri, M.

Publications and source records attributed to Mantri, M..

14 recordsLinked to original sources

bioRxiv2026

Single-cell splice isoform usage reveals distinct axes of cellular identity and senescence

Alternative splicing greatly expands the diversity of gene products encoded by the human genome. Single-cell transcriptomic atlases have characterized human cell types through gene-level expression, but short-read sequencing has limited the ability to resolve full-length isoforms and their functional consequences. Here, we present a cross-tissue single-cell long-read isoform atlas spanning 26 human tissues. We identify hundreds of thousands of novel isoforms along with their cell-type-specific usage, and discover that over one-third of expressed isoforms are absent from existing reference databases. We further demonstrate that isoform usage is a structured, measurable axis of cellular identity that is distinct from gene expression. Applying this framework to cellular senescence, we resolve p16INK4a and p14ARF transcripts from the CDKN2A locus in individual cells and uncover cell-type-dependent isoform remodeling associated with the p16INK4a senescence program. This isoform-resolved single-cell atlas offers a versatile framework to dissect the cellular logic of isoform regulation in senescence and beyond.

genomics↗

bioRxiv2026

High-resolution spatial transcriptomics maps viral tropism and reveals spatially organized immune modules in viral encephalitis

Viral encephalitis is a debilitating disease that most commonly affects vulnerable populations, including the very young and elderly. Despite its severity, few countermeasures exist due to the structural and immunological complexities of the central nervous system (CNS). To better understand the spatial dynamics of viral spread and the concurrent host immune responses, we used high-resolution spatial transcriptomics to profile reovirus infection in the neonatal mouse brain at 3, 5, and 7 days post-infection. We constructed a comprehensive spatiotemporal atlas of infection, which revealed viral dissemination from sites of cerebrospinal fluid circulation to neighboring brain parenchyma, with enriched infection in the thalamus and midbrain coincident with Slc17a6 (VGLUT2) excitatory neurons. Unbiased spatial gene co-expression network analysis uncovered rich gene lists linked to temporal waves of host immune responses, originating with interferon-stimulated gene modules, followed by myeloid cell infiltration and adaptive cytotoxic T-cell responses at times of peak disease. Furthermore, we identified spatial correlation between viral transcripts and several upregulated host snoRNA-related genes (e.g., Nop58 and Snhg1) with high-confidence, suggesting viral use of host ribosomal modification machinery. We also observed a strong anti-correlation of astrocyte markers with reovirus transcripts, suggesting glial cell disruption. This work provides a high-definition spatial framework to understand interactions between viral infection and host immunity in the brain.

microbiology↗

bioRxiv2026

A NON-CANONICAL ROLE FOR NOTCH3 IN BUILDING THE INTESTINAL LYMPHATIC NICHE

Lymphatic dysfunction drives severe and often intractable human diseases, yet the cellular mechanisms that establish functional lymphatic vasculature remain poorly understood. In the intestine, lacteals are specialized lymphatic vessels that absorb dietary lipids and rely on surrounding villus smooth muscle to propel lymph, forming the muscular-lacteal complex (MLC). How distinct mesenchymal populations coordinate assembly of this functional lymphatic unit remains unknown. By integrating developmental single-cell profiling, genetic lineage tracing, conditional mouse genetics, and functional assays of lipid absorption, we identify Notch3 as a central organizer of MLC development that coordinates communication between distinct mesenchymal lineages. While Notch3 promotes smooth muscle differentiation within the PDGFR lineage, PDGFR{beta} lineage cells do not directly contribute to villus smooth muscle. Instead, they function as Notch3-dependent signaling hubs that instruct expansion and differentiation of neighboring PDGFR smooth muscle progenitors via paracrine TGF{beta} signaling. Loss of Notch3 in PDGFR{beta} cells disrupts MLC development, impairs intestinal lipid absorption, and causes postnatal growth failure and lethality. Restoration of TGF{beta} signaling rescues the structural, functional, and survival defects caused by Notch3 loss, identifying TGF{beta} as a critical downstream effector of the Notch3 pathway. Furthermore, selective inhibition of canonical Notch signaling in the PDGFR{beta} lineage fails to phenocopy Notch3 deletion, revealing a non-canonical mechanism of Notch3 function in intestinal mesenchymal development. Together, these findings establish PDGFR{beta} cells as essential mesenchymal signaling organizers and define a new paradigm in which lineage-specific, non-canonical Notch3 signaling coordinates villus stromal communication to build a functional intestinal lymphatic niche.

developmental biology↗

bioRxiv2026

Tabula Sapiens reveals the non-coding RNA landscape across 22 human organs and tissues

The biological significance of non-coding RNAs has been increasingly appreciated as their roles in various cellular processes are uncovered. However, single-cell transcriptomic profiling of human samples has focused primarily on protein-coding genes by targeting polyadenylated RNA transcripts, leaving the expression patterns of non-coding RNA underexplored. Here, we expand Tabula Sapiens to the non-coding transcriptome with single-cell and single-nucleus total RNA sequencing across 22 human organs and tissues. By simultaneously profiling both polyadenylated and non-polyadenylated transcripts, the resulting dataset enables joint analysis of the protein-coding and non-coding transcriptomes at single-cell and subcellular resolution. Using these data, we assessed the cell type specificity of non-coding genes and found that a greater proportion of non-coding genes are differentially expressed by single cell types compared to protein-coding genes. We then compared single-cell and single-nucleus data from the same samples to infer subcellular localization patterns, revealing cell type-dependent nuclear and cytoplasmic enrichment of specific non-coding RNAs. Next, we showed that tRNA repertoires are cell type-specific and that this specificity is not simply explained by differences in codon usage across cell types. Finally, we characterized dynamic expression patterns of non-coding RNAs across the cell cycle and senescence-associated cell states, identifying non-coding genes with putative roles in cell division and growth arrest. Our work establishes a resource for investigating the landscape of non-coding RNAs across a diverse set of human tissues and cell types.

cell biology↗

bioRxiv2025

Single-cell transcriptomics reveals targeted modulation of inflammatory repertoire by SOCE blockers

Store-operated calcium entry (SOCE) plays a critical role in regulating intracellular calcium signaling and is essential for immune cell functions. SOCE blockade with pyrazole derivative BTP2 has been explored as an anti-inflammatory strategy in preclinical models and Zegocractin (CM4620) is being investigated in Phase 2 clinical trials as an immunoregulatory agent. However, the mode of action and differential effects of SOCE blockade on diverse immune cell types remain largely unknown, limiting the precision of current therapeutic applications. Here, we used multiplexed single-cell RNA sequencing to investigate the effects of two prototypic SOCE blockers, BTP2 and CM4620, on polyclonally-stimulated, normal human peripheral blood mononuclear cells (PBMCs). The data revealed that SOCE blockade suppresses the expression of cytotoxicity-associated genes in CD8{square} effector T cells and natural killer (NK) cells, restoring them to levels comparable to those in unstimulated cells. Strikingly, SOCE blockade preserved activation-induced expression of anti-inflammatory genes in CD4{square} regulatory T cells, maintaining their tolerance phenotype even after SOCE blockade. These findings suggest that SOCE blockers modulate immune responses with greater selectivity than conventional immunosuppressants by reducing cytotoxicity while preserving tolerance-associated pathways, highlighting their potential for managing immune-mediated conditions, including organ transplantation. KEY POINTSO_LISOCE blockers BTP2 and CM4620 reduce cytotoxic gene expression in CD8{square} T cells and NK cells. C_LIO_LISOCE blockade preserves anti-inflammatory programs in CD4{square} Tregs, supporting selective immune modulation. C_LI

immunology↗

bioRxiv2025

A Temporal and Spatial Atlas of Adaptive Immune Responses in the Lymph Node Following Viral Infection

The spatial organization of adaptive immune cells within lymph nodes is critical for understanding immune responses during infection and disease. Here, we introduce AIR-SPACE, an integrative approach that combines high-resolution spatial transcriptomics with paired, high-fidelity long-read sequencing of T and B cell receptors. This method enables the simultaneous analysis of cellular transcriptomes and adaptive immune receptor (AIR) repertoires within their native spatial context. We applied AIR-SPACE to mouse popliteal lymph nodes at five distinct time points after Vaccinia virus footpad infection and constructed a comprehensive map of the developing adaptive immune response. Our analysis revealed heterogeneous activation niches, characterized by Interferon-gamma (IFN-{gamma}) production, during the early stages of infection. At later stages, we delineated sub-anatomical structures within the germinal center (GC) and observed evidence that antibody-producing plasma cells differentiate and exit the GC through the dark zone. Furthermore, by combining clonotype data with spatial lineage tracing, we demonstrate that B cell clones are shared among multiple GCs within the same lymph node, reinforcing the concept of a dynamic, interconnected network of GCs. Overall, our study demonstrates how AIR-SPACE can be used to gain insight into the spatial dynamics of infection responses within lymphoid organs.

immunology↗

bioRxiv2024

Bone mineral density affects tumor growth by shaping microenvironmental heterogeneity

Breast cancer bone metastasis is the leading cause of mortality in patients with advanced breast cancer. Although decreased mineral density is a known risk factor for bone metastasis, the underlying mechanisms remain poorly understood because studying the isolated effect of bone mineral density on tumor heterogeneity is challenging with conventional approaches. Here, we investigate how bone mineral content affects tumor growth and microenvironmental complexity in vivo by combining single-cell RNA-sequencing with mineral-containing or mineral-free decellularized bone matrices. We discover that the absence of bone mineral significantly influences fibroblast and immune cell heterogeneity, promoting phenotypes that increase tumor growth and alter the response to injury or disease. Importantly, we observe that the stromal response to matrix mineral content depends on host immunocompetence and the murine tumor model used. Collectively, our findings suggest that bone mineral density affects tumor growth by altering microenvironmental complexity in an organism-dependent manner.

bioengineering↗

bioRxiv2023

A Spatiotemporal Molecular Atlas of the Ovulating Mouse Ovary

Ovulation is essential for reproductive success, yet the underlying cellular and molecular mechanisms are far from clear. Here, we applied high-resolution spatiotemporal transcriptomics to map out cell-type- and ovulation-stage-specific molecular programs as function of time during follicle maturation and ovulation in mice. Our analysis revealed dynamic molecular transitions within granulosa cell types that occur in tight coordination with mesenchymal cell proliferation. We identified new molecular markers for the emerging cumulus cell fate during the preantral-to-antral transition. We describe transcriptional programs that respond rapidly to ovulation stimulation and those associated with follicle rupture, highlighting the prominent roles of apoptotic and metabolic pathways during the final stages of follicle maturation. We further report stage-specific oocyte-cumulus cell interactions and diverging molecular differentiation in follicles approaching ovulation. Collectively, this study provides insights into the cellular and molecular processes that regulate mouse ovarian follicle maturation and ovulation with important implications for advancing therapeutic strategies in reproductive medicine.

genomics↗

bioRxiv2023

Spatiotemporal reconstruction of the origin and assembly of smooth muscles in the intestinal villus

Intestinal smooth muscles are the workhorse of the digestive system. Inside the millions of finger-like intestinal projections called villi, strands of smooth muscle cells contract to propel absorbed dietary fats through the adjacent lymphatic vessel, called the lacteal, sending fats into the blood circulation for energy production. Despite this vital function, how villus smooth muscles form, how they assemble alongside lacteals, and how they repair throughout life remain unknown. Here we combine single-cell RNA sequencing of the mouse intestine with quantitative lineage tracing to reveal the mechanisms of formation and differentiation of villus smooth muscle cells. Within the highly regenerative villus, we uncover a local hierarchy of subepithelial fibroblast progenitors that progress to become mature smooth muscle fibers, via an intermediate contractile myofibroblast-like phenotype. This continuum persists in the adult intestine as the major source of renewal of villus smooth muscle cells during adult life. We further found that the NOTCH3-DLL4 signaling axis governs the assembly of villus smooth muscles alongside their adjacent lacteal, and we show that this is necessary for gut absorptive function. Overall, our data shed light on the genesis of a poorly defined class of intestinal smooth muscle and pave the way for new opportunities to accelerate recovery of digestive function by stimulating muscle repair.

developmental biology↗

bioRxiv2022

In situ polyadenylation enables spatial mapping of the total transcriptome

Spatial transcriptomics reveals the spatial context of gene expression, but current methods are limited to assaying polyadenylated (A-tailed) RNA transcripts. Here we demonstrate that enzymatic in situ polyadenylation of RNA enables detection of the full spectrum of RNAs, expanding the scope of sequencing-based spatial transcriptomics to the total transcriptome. We apply this Spatial Total RNA-Sequencing (STRS) approach to study skeletal muscle regeneration and viral-induced myocarditis. Our analyses reveal the spatial patterns of noncoding RNA expression with near-cellular resolution, identify spatially defined expression of noncoding transcripts in skeletal muscle regeneration, and highlight host transcriptional responses associated with local viral RNA abundance. In situ polyadenylation requires the addition of only a single step to a widely used protocol for spatial RNA-sequencing, and thus could be broadly and quickly adopted. Spatial RNA-sequencing of the total transcriptome will enable new insights into spatial gene regulation and biology.

genomics↗

bioRxiv2021

Spatiotemporal transcriptomics reveals pathogenesis of viral myocarditis

A significant fraction of sudden death in children and young adults is due to myocarditis, an inflammatory disease of the heart, most often caused by viral infection. Here we used integrated single-cell and spatial transcriptomics to create a high-resolution, spatially resolved map of reovirus-induced myocarditis in neonatal murine hearts. We assayed hearts collected at three timepoints after reovirus infection and studied the temporal, spatial, and cellular heterogeneity of host-virus interactions. We further assayed the intestine, the primary site of reovirus infection to establish a full chronology of molecular events that ultimately lead to myocarditis. We implemented targeted enrichment of viral transcripts to establish the cellular targets of the virus in the intestine and the heart. Our data give insight into the cell-type specificity of innate immune responses, and into the transcriptional states of inflamed cardiac cells in reovirus-infected heart. We find that inflamed endothelial cells recruit cytotoxic T cells and undergo pyroptosis in the myocarditic tissue. Analyses of spatially restricted gene expression in myocarditic regions and the border zone around those regions identified immune-mediated cell-type specific injury and stress responses. Overall, we observe a dynamic and complex network of cellular phenotypes and cell-cell interactions associated with viral myocarditis.

genomics↗

bioRxiv2020

Strength in numbers: Large-scale integration of single-cell transcriptomic data revealsrare, transient muscle progenitor cell states in muscle regeneration

Skeletal muscle repair is driven by the coordinated self-renewal and fusion of myogenic stem and progenitor cells. Single-cell gene expression analyses of myogenesis have been hampered by the poor sampling of rare and transient cell states that are critical for muscle repair, and do not provide spatial information that is needed to understand the context in which myogenic differentiation occurs. Here, we demonstrate how large-scale integration of new and public single-cell and spatial transcriptomic data can overcome these limitations. We created a large-scale single-cell transcriptomic dataset of mouse skeletal muscle by integration, consensus annotation, and analysis of 23 newly collected scRNAseq datasets and 79 public single-cell (scRNAseq) and single-nucleus (snRNAseq) RNA-sequencing datasets. The resulting compendium includes nearly 350,000 cells and spans a wide range of ages, injury, and repair conditions. Combined, these data enabled identification of the predominant cell types in skeletal muscle with robust, consensus gene expression profiles, and resolved cell subtypes, including endothelial subtypes distinguished by vessel-type of origin, fibro/adipogenic progenitors marked by stem potential, and many distinct immune populations. The representation of different experimental conditions and the depth of transcriptome coverage enabled robust profiling of sparsely expressed genes. We built a densely sampled transcriptomic model of myogenesis, from stem-cell quiescence to myofiber maturation and identified rare, short-lived transitional states of progenitor commitment and fusion that are poorly represented in individual datasets. We performed spatial RNA sequencing of mouse muscle at three time points after injury and used the integrated dataset as a reference to achieve a high-resolution, local deconvolution of cell subtypes. This analysis identified the temporal variation in the colocalization of immune cell subtype interactions with myogenic progenitors during injury recovery. We provide a public web tool to enable interactive exploration and visualization of this rich single-cell transcriptomic resource. Our work supports the utility of large-scale integration of single-cell transcriptomic data as a tool for biological discovery.

genomics↗

bioRxiv2020

Uncovering Transcriptional Dark Matter via Gene Annotation Independent Single-Cell RNA Sequencing Analysis

Single-cell RNA sequencing (scRNA-seq) enables the study of cell biology with high resolution. scRNA-seq expression analyses rely on the availability of a high quality annotation of genes in the genome. Yet, as we show here with scRNA-seq experiments and analyses spanning human, mouse, chicken, mole rat, lemur and sea urchin, gene annotations often fail to cover the full transcriptome of every cell type at every stage of development, in particular for organisms that are not routinely studied. To overcome this hurdle, we created a scRNA-seq analysis routine that recovers biologically relevant information beyond the scope of the best available gene annotation. This is achieved by performing single-cell expression analysis on any region in the genome for which transcriptional products are detected. Our routine identifies transcriptionally active regions (TARs) using a hidden Markov model, generates a matrix of expression levels for all TARs across all cells in a dataset, performs single-cell TAR expression analysis to identify TARs that are biologically significant, and then annotates biologically significant TARs using gene homology analysis. This procedure leverages single-cell expression analyses as a filter to direct annotation efforts to biologically significant transcripts in complex tissues and thereby uncovers biology to which scRNA-seq would otherwise be in the dark.

bioinformatics↗

bioRxiv2020

Spatiotemporal single-cell RNA sequencing of developing hearts reveals interplay between cellular differentiation and morphogenesis

Single-cell RNA sequencing is a powerful tool to study developmental biology but does not preserve spatial information about cellular interactions and tissue morphology. Here, we combined single-cell and spatial transcriptomics with new algorithms for data integration to study the early development of the chicken heart. We collected data from four key ventricular development stages, ranging from the early chamber formation stage to the late four-chambered stage. We created an atlas of the diverse cellular lineages in developing hearts, their spatial organization, and their interactions during development. Spatial mapping of differentiation transitions revealed the intricate interplay between cellular differentiation and morphogenesis in cardiac cellular lineages. Using spatially resolved expression analysis, we identified anatomically restricted gene expression programs. Last, we discovered a stage-dependent role for the small secreted peptide, thymosin beta-4, in the coordination of multi-lineage cellular populations. Overall, our study identifies key stage-specific regulatory programs that govern cardiac development.

genomics↗