Biology subjects

Mukund, K.

Publications and source records attributed to Mukund, K..

10 recordsLinked to original sources

bioRxiv2026

Spatially resolved tumor-microenvironment architecture defines therapeutic response in unresectable hepatoblastoma

Background: Hepatoblastoma exhibits variable therapeutic response that is not fully explained by current risk stratification. While prior studies have characterized tumor composition, the role of spatial organization in determining outcome, particularly in unresectable disease requiring transplantation under immunosuppression, remains unclear. Methods: We integrated spatial transcriptomics using the 10x Genomics Visium platform (n = 11 tumors) with single-cell spatial molecular imaging using NanoString CosMx (n = 3 tumors) on post-chemotherapy explant specimens across clinically defined groups (relapse-prone unresectable, non-relapse unresectable, and resectable hepatoblastoma). Spatial deconvolution, module scoring, spatial co-localization, and cell-cell interaction analyses were used to define region-level transcriptional programs and their underlying cellular organization. Results: We identified three spatial architectures associated with clinical outcome. Relapse-prone tumors exhibited a centralized, TME-dominated organization enriched for progenitor-like, cycling, and stress-responsive tumor cell states co-localized with SPP1+ TAMs and CAFs, with enrichment of hypoxia response, extracellular matrix remodeling, and Midkine (MDK-LRP1) signaling. Non-relapse tumors displayed a distributed architecture with compartmentalized tumor-immune interactions, increased immune engagement, and preserved epithelial differentiation, including inflammatory hepatocyte-like states. Resection samples showed reduced tumor cell state heterogeneity and more uniform TME-immune organization. Conclusions: Integration of regional and single-cell spatial transcriptomics across two platforms reveals that the chemo-remodeled tumor architecture of hepatoblastoma encodes spatially organized tumor cell-TME interactions as central determinants of therapeutic response.

cancer biology↗

bioRxiv2026

Spatial context of cellular heterogeneity in triple-negative breast cancer reveals actionable subtypes

Triple-negative breast cancer (TNBC) is an aggressive, heterogeneous disease with limited targeted treatment options. Leveraging bulk and spatial transcriptomics and cellular mapping of breast tissue from a large patient cohort, we identified three reproducible TNBC ecosystem subtypes that encode distinct spatial tumor-microenvironment architectures and clinically relevant treatment-response phenotype. Our analyses define: (1) an immune-exhausted subtype associated with immune checkpoint therapy (ICT); (2) a highly fibrotic/hypoxic subtype; and (3) a metabolically reprogrammed subtype characterized by nuclear-receptor and fatty-acid signaling. Spatial profiling further revealed subtype-specific organization of epithelial, immune, and stromal programs across tumor centers and invasive edges. Multiplexed imaging independently supported the contrasting immune-infiltrated and stromal-excluded architectures of the immune-engaged and fibrotic subtypes. The unique markers associated with the subtypes also provide the basis for subtyping and candidate therapeutic vulnerabilities. Our study provides a robust framework for personalized medicine, highlighting that targeting specific spatio-cellular architectures is critical to improving clinical outcomes.

cancer biology↗

bioRxiv2026

Single-cell transcriptional landscape of muscle-derived stem/progenitor cells reveals hallmarks of aging and rejuvenation

Muscle-derived stem/progenitor cells (MDSPCs) are an adult stem cell population with demonstrated regenerative and rejuvenative potential distinct from other muscle progenitor cells. However, their molecular identity and developmental status remain poorly defined. Using single-cell transcriptomics and proteomics, we comprehensively profiled murine MDSPCs across age groups. We show that MDSPCs exist along a transcriptional continuum of maturation--ranging from metabolically active, proliferative early-stage cells to late-stage, lineage-committed myogenic populations. While lacking canonical pluripotency markers, early-stage MDSPCs express gene programs associated with embryonic progenitor identity, suggesting a non-canonical, multipotent-like state. These features distinguish them from both satellite cells and committed myoblasts. Aging reshapes this continuum by reducing stemness-associated signatures while enhancing differentiation programs and oxidative stress. Our identification of distinct MDSPC states provide critical insights into mechanisms that underly tissue regeneration and aging. These findings offer a blueprint for development of future regenerative therapies to combat age-related functional decline.

cell biology↗

bioRxiv2026

Differential peripheral immune dynamics underlie therapeutic response to chemotherapy and chemo-immunotherapy in triple-negative breast cancer

Triple-negative breast cancer (TNBC) remains the most aggressive breast cancer subtype, with limited treatment options and variable response to immune checkpoint inhibitors. While tumor-infiltrating lymphocytes have been extensively studied, the integration of system-level peripheral immune dynamics with mechanistic immune regulation underlying therapeutic response and resistance remain poorly defined. Here, we integrate systems-level immune state modeling with pathway-level mechanistic inference to analyze single-cell RNA sequencing of peripheral blood mononuclear cells from advanced TNBC patients treated with paclitaxel alone (chemotherapy) or in combination with anti-PD-L1 antibody atezolizumab (combination). This framework leverages treatment arm, longitudinal sampling, and clinical response to resolve coordinated immune programs across lymphoid and myeloid compartments. Using this approach, we identified distinct treatment- and response-specific immune states in pre- and post-treatment. Chemotherapy responders displayed pre-treatment adaptive immune priming, whereas combination therapy responders exhibited pre-existing effector T cell activity coupled with tumor tissue PD-L1 expression. In contrast, chemotherapy non-responders developed persistent post-treatment immune dysregulation in regulatory and terminal effector programs, while combination therapy non-responders demonstrated maladaptive remodeling of adaptive and innate lymphoid compartments, including dysfunctional NK and metabolically reprogrammed myeloid populations. Across both regimens, pathways involving protein translation, metabolic adaptation, and stress signaling emerged as critical modulators of response. These findings suggest that coordinated adaptive-innate immune dynamics underlie therapeutic efficacy, whereas systemic immune exhaustion and myeloid immunoregulation lead to resistance. Projection of these peripheral immune programs onto independent I-SPY2 showed concordant associations with tumor immune phenotypes and pathological complete response, supporting generalizability of the identified systemic immune states. Our study demonstrates the utility of an integrative systems-level approach for linking peripheral immune state organization with mechanistic insights, informing immune response and resistance in TNBC.

bioinformatics↗

bioRxiv2026

Spatial Landscape of Pregnancy-Associated Triple Negative Breast Cancer and Mammary Gland Involution

Pregnancy-associated triple negative breast cancer (PA-TNBC) is one of the highest-risk breast cancers, marked by an aggressive phenotype that lacks targeted treatment options. Studies have shown that post-lactational mammary gland involution plays a role in this increased risk. To delineate the underlying mechanisms, our study characterized the transcriptional state of the epithelia and surrounding microenvironment in women with PA-TNBC, comparing those diagnosed pre-involution (PRE) and post-involution (POST, <3 years after delivery). Spatial transcriptomics using the GeoMx Digital Spatial Profiler was performed on treatment-naive PA-TNBC tissues from 33 women (10 PRE, 23 POST). Regions of interest were segmented with pan-cytokeratin staining. We found that the most prominent transcriptional differences between PRE and POST epithelia occurred in the adjacent non-invasive regions and during the transition into invasive TNBC. POST non-invasive epithelia uniquely showed inflammatory and developmental pathway activation, while the transition into TNBC involved increased chromatin remodeling and cell migration pathways. Further, the tumor microenvironment (TME) in POST showed the highest proportion of immune cells and the highest prevalence of tumor- and immune exhaustion-associated cell states. Finally, a pseudotime analysis of POST transcriptional dynamics found that women diagnosed 1-2 years after delivery exhibited the strongest evidence for inflammatory signaling across the tissue. Our results highlight biological mechanisms distinguishing PRE and POST PA-TNBC across tissue regions and cell types. We emphasize the importance of early detection of malignant molecular signatures in morphologically normal epithelium in post-involution women and suggest that targeting the TME may improve treatment efficacy in post-involution PA-TNBC.

cancer biology↗

bioRxiv2025

A novel subtyping method for TNBC with implications for prognosis and therapy

The biological heterogeneity of triple-negative breast cancer (TNBC) poses significant challenges for diagnosis, prognosis, and treatment. While prior TNBC subtype classifications exist, they are not widely used clinically. Here, we aimed to subtype TNBC based on transcriptomic profiles using cell type and state heterogeneity in tumor tissue from 250 pre-treatment women (127 African-American and 123 European-American). We identified three major subtypes and three distinct groups exhibiting unique cell-type composition and mechanisms: Subtype-1 immune signaling/T-cell response; Subtype-2 pro-fibrotic and immune desert; Subtype-3 fatty acid and nuclear receptor signaling. Subtype-1 showed potential responsiveness to immunotherapy, while Subtypes-2 and 3 suggested alternative therapeutic targets. In Subtype-3, which contained a patient group with high ESR1, (but not high ER protein expression) we identified putative mutations in the gene that are unique to these patients. This framework provides a path toward personalized TNBC treatment and is accessible through a user-friendly RShiny application for clinical use.

bioinformatics↗

bioRxiv2025

Spatially distinct cellular and molecular landscapes define prognosis in triple negative breast cancer

BackgroundTriple-negative breast cancer is a prevalent breast cancer subtype with the lowest 5-year survival. Several factors contribute to its treatment response, but the inherent molecular and cellular tumor heterogeneity are increasingly acknowledged as crucial determinants. MethodsSpatial transcriptomic profiling was performed on FFPE tissues from a retrospective, treatment-naive group of women with differential prognoses (17 with >15 years survival-good prognosis (GPx) and 15 with <3 years survival-poor prognosis (PPx)) using GeoMX(R) Digital Spatial Profiler. Regions of interest were segmented on pan-cytokeratin and analyzed for tumor and stromal components, probed using GeoMx human whole transcriptome atlas (WTA) panel. Data quality control, normalization, and differential analysis was performed in R using GeomxTools and linear mixed models. Additional analyses including cell-type deconvolution, spatial entropy, functional enrichment, TF-target / ligand-receptor analysis and convolution neural networks were employed to identify significant gene signatures contributing to differential prognosis. ResultsHere we report on the spatial and molecular heterogeneity underlying differential prognosis. We observe that the state of the epithelia and its microenvironment (TME) are transcriptionally distinct between the two groups. Invasive epithelia in GPx show a significant increase in immune transcripts with the TME exhibiting increased immune cell presence (via IF), while in PPx they are more metabolically and translationally active, with the TME being more mesenchymal/fibrotic. Specifically, pre-cancerous epithelia in PPx display a prescience of aggressiveness as evidenced by increased EMT-signaling. We identify distinct epithelial gene signatures for PPx and GPx, that can, with high accuracy, classify samples at the time of diagnosis and likely inform therapy. ConclusionsTo the best of our knowledge, this is the first study to leverage spatial transcriptomics for an in-depth delineation of the cellular and molecular underpinnings of differential prognosis in TNBC. Our study highlights the potential of spatial transcriptomics to not only uncover the molecular drivers of differential prognosis in TNBC but also to pave the way for precision diagnostics and tailored therapeutic strategies, transforming the clinical landscape for this aggressive breast cancer subtype.

cancer biology↗

bioRxiv2024

The molecular chronology of mammary epithelial cell fate switching

The adult mammary gland is maintained by lineage-restricted progenitor cells through pregnancy, lactation, involution, and menopause. Injury resolution, transplantation-associated mammary gland reconstitution, and tumorigenesis are unique exceptions, wherein mammary basal cells gain the ability to reprogram to a luminal state. Here, we leverage newly developed cell-identity reporter mouse strains, and time-resolved single-cell epigenetic and transcriptomic analyses to decipher the molecular programs underlying basal-to-luminal fate switching in vivo. We demonstrate that basal cells rapidly reprogram toward plastic cycling intermediates that appear to hijack molecular programs we find in bipotent fetal mammary stem cells and puberty-associatiated cap cells. Loss of basal-cell specifiers early in dedifferentiation coincides with activation of Notch and BMP, among others. Pharmacologic blockade of each pathway disrupts basal-to-luminal transdifferentiation. Our studies provide a comprehensive map and resource for understanding the coordinated molecular changes enabling terminally differentiated epithelial cells to transition between cell lineages and highlights the stunning rapidity by which epigenetic reprogramming can occur in response to disruption of tissue structure.

cell biology↗

bioRxiv2021

Impaired T-cell and antibody immunity after COVID-19 infection in chronically immunosuppressed transplant recipients

Assessment of T-cell immunity to the COVID-19 coronavirus requires reliable assays and is of great interest, given the uncertain longevity of the antibody response. Some recent reports have used immunodominant spike (S) antigenic peptides and anti-CD28 co-stimulation in varying combinations to assess T-cell immunity to SARS-CoV-2. These assays may cause T-cell hyperstimulation and could overestimate antiviral immunity in chronically immunosuppressed transplant recipients, who are predisposed to infections and vaccination failures. Here, we evaluate CD154-expressing T-cells induced by unselected S antigenic peptides in 204 subjects-103 COVID-19 patients and 101 healthy unexposed subjects. Subjects included 72 transplanted and 130 non-transplanted subjects. S-reactive CD154+T-cells co-express and can thus substitute for IFN{gamma} (n=3). Assay reproducibility in a variety of conditions was acceptable with coefficient of variation of 2-10.6%. S-reactive CD154+T-cell frequencies were a) higher in 42 healthy unexposed transplant recipients who were sampled pre-pandemic, compared with 59 healthy non-transplanted subjects (p=0.02), b) lower in Tr COVID-19 patients compared with healthy transplant patients (p<0.0001), c) lower in Tr patients with severe COVID-19 (p<0.0001), or COVID-19 requiring hospitalization (p<0.05), compared with healthy Tr recipients. S-reactive T-cells were not significantly different between the various COVID-19 disease categories in NT recipients. Among transplant recipients with COVID-19, cytomegalovirus co-infection occurred in 34%; further, CMV-specific T-cells (p<0.001) and incidence of anti-receptor-binding-domain IgG (p=0.011) were lower compared with non-transplanted COVID-19 patients. Healthy unexposed transplant recipients exhibit pre-existing T-cell immunity to SARS-CoV-2. COVID-19 infection leads to impaired T-cell and antibody responses to SARS-CoV-2 and increased risk of CMV co-infection in transplant recipients.

immunology↗

bioRxiv2020

Plasmin cascade mediates thrombolytic events in SARS-CoV-2 infection via complement and platelet-activating systems

Recently emerged beta-coronavirus, SARS-CoV-2 has resulted in the current pandemic designated COVID-19. COVID-19 manifests as severe illness exhibiting systemic inflammatory response syndrome, acute respiratory distress syndrome (ARDS), thrombotic events, and shock, exacerbated further by co-morbidities and age1-3. Recent clinical reports suggested that the pulmonary failure seen in COVID-19 may not be solely driven by acute ARDS, but also microvascular thrombotic events, likely driven by complement activation4,5. However, it is not fully understood how the SARS-CoV-2 infection mechanisms mediate thrombotic events, and whether such mechanisms and responses are unique to SARS-CoV-2 infection, compared to other respiratory infections. We address these questions here, in the context of normal lung epithelia, in vitro and in vivo, using publicly available data. Our results indicate that plasmin is a crucial mediator which primes interactions between complement and platelet-activating systems in lung epithelia upon SARS-CoV-2 infection, with a potential for therapeutic intervention.

immunology↗