Biology subjects

Mittal, V.

Publications and source records attributed to Mittal, V..

11 recordsLinked to original sources

bioRxiv2026

Lipogenesis-driven EGFR palmitoylation enables metastatic immune evasion in triple-negative breast cancer.

Metastasis is the leading cause of death in triple-negative breast cancer (TNBC), yet how tumor cells evade immune recognition during dissemination remain unclear. Here, we show that de novo lipogenesis drives metastatic immune evasion through FASN-mediated palmitoylation of EGFR. This modification establishes a lipid-dependent membrane signaling scaffold that sustains PI3K-AKT-mTOR signaling independently of MAPK compensation, thereby suppressing MHC-I antigen presentation through post-translational regulation. As a result, metastatic-competent cells escape CD8+ T cell surveillance and colonize distant organs. Genetic or pharmacologic inhibition of fatty acid synthase (FASN), or expression of palmitoylation-deficient EGFR mutants restores MHC-I surface expression, unleashes robust CD8 T cell activation, and markedly impairs lung metastasis without affecting primary tumor growth. This lipid-dependent EGFR-PI3K-mTOR axis operates independently of MAPK signaling and is not rescued by exogenous lipids, revealing a non-redundant metabolic dependency. Our results identify FASN-driven EGFR palmitoylation as a tumor-intrinsic immunometabolic checkpoint that couples lipid metabolism to antigen-presentation and metastatic competence. Targeting this pathway with clinically advancing FASN inhibitors offers a promising strategy to suppress metastasis by restoring anti-tumor immunity in TNBC.

cancer biology↗

bioRxiv2025

User-friendly scheduler Using a hybrid architecture and supercomputing for big data processing

The exponential growth of omics data requires novel strategies for storage, transfer, and processing of said data. We present a scheduler based on the Temporal.io workflow framework which enables two key optimizations of bioinformatics workflows. Firstly, we enable users to transparently map workflow steps to diverse execution environments, including high-performance computing (HPC) resources managed by the SLURM resource manager through an easy-to-use graphical user interface. Secondly, we enable asynchronous execution of workflows, a feature which guarantees that workflows will achieve reasonable resource utilization even when the scheduler cannot make use of a systems full RAM and CPU resources. Thirdly, we propose a universal, platform agnostic JSON representation of workflows that allows platform-specific execution details to be abstracted away from the core scientific logic. Our work includes a custom executor plugin that supports translation of workflows from an external language, such as Nextflow, to our universal JSON format. Finally, we develop a graphical user interface to make our scheduler easy-to-use for non-technical users. When benchmarked on a bulk RNA sequencing workflow, these features reduced the cost and time requirements. We illustrated the merits of our cross-platform method using credit allocations from federally funded supercomputers.

bioinformatics↗

bioRxiv2025

Tumor-draining lymph node derived CD8⁺ T cells sustain durable systemic immunity after neoadjuvant IL-15 and PD-1 blockade.

The tumor-draining lymph node (tdLN) serves as a critical reservoir of tumor-reactive T cells, yet its contribution to preventing metastatic recurrence remains poorly understood. In this study, we investigate CD8 T cell clonal dynamics and memory responses induced by neoadjuvant anti-PD-1 therapy. We demonstrate that PD-1 blockade promotes the emergence of protective CD8 T cell memory, enriched with tumor-relevant clones that persist in the lymph nodes of long-term survivors. Furthermore, we show that combination of a neoadjuvant IL-15 superagonist with PD-1 blockade significantly increases clonal diversity, cytotoxicity, and clonal persistence in non-draining lymph nodes. These changes result in enhanced systemic antitumor immunity and durable memory that prevents tumor relapse. Our findings establish the tdLN as a critical immunologic hub that can be therapeutically targeted by IL-15 to augment PD-1 blockade efficacy and support a rationale for a phase II neoadjuvant combination immunotherapy trial in early-stage NSCLC. One sentence summaryNeoadjuvant IL-15 with PD-1 blockade expands lymph node clonal diversity and preserves stem-like CD8 T cell features, yielding superior antitumor efficacy, durable memory, and reduced metastatic recurrence.

immunology↗

bioRxiv2025

Simultaneous immunomodulation and epithelial-to-mesenchymal transition drives lung adenocarcinoma progression

Lung cancer remains the deadliest cancer in the United States, with lung adenocarcinoma (LUAD) as its most prevalent subtype. While computed tomography (CT)-based screening has improved early detection and enabled curative surgeries, the molecular and cellular dynamics driving early-stage LUAD progression remain poorly understood, limiting non-surgical treatment options. To address this gap, we profiled 2.24 million cells from 122 early-stage LUAD patients using multiplexed imaging mass cytometry (IMC). This analysis revealed the molecular, spatial, and temporal dynamics of LUAD development. Our findings uncover a binary progression model. LUAD advances through either inflammation, driven by a balance of cytotoxic and regulatory immune activity, or fibrosis, characterized by stromal activation. Surprisingly, tumor cell populations did not increase significantly. Instead, they displayed a mixed phenotypic profile consistent with epithelial-to-mesenchymal transition (EMT), effectively masking the expansion of malignant cells. Furthermore, we addressed discrepancies between CT-based and histology-based subtyping. CT scans, while non-invasive, often mischaracterize invasive fibrotic tumors--which account for 20.5% of LUAD cases--as mild, non-solid ground glass opacities (GGOs). Using high-content IMC imaging, we demonstrate that these tumors harbor significant risks and advocate for improved diagnostic strategies. These strategies should integrate molecular profiling to refine patient stratification and therapeutic decision-making. Altogether, our study provides a high-resolution, systems-level view of the tumor microenvironment in early-stage LUAD. We characterize key transitions in oncogenesis and propose a precision-driven framework to enhance the detection and management of aggressive disease subtypes.

cancer biology↗

bioRxiv2025

Acquisition of discrete immune suppressive barriers contributes to the initiation and progression of preinvasive to invasive human lung cancer.

Computerized chest tomography (CT)-guided screening in populations at risk for lung cancer has increased the detection of preinvasive subsolid nodules, which progress to solid invasive adenocarcinoma. Despite the clinical significance, there is a lack of effective therapies for intercepting the progression of preinvasive to invasive adenocarcinoma. To uncover determinants of early disease emergence and progression, we used integrated single-cell approaches, including scRNA-seq, multiplexed imaging mass cytometry and spatial transcriptomics, to construct the first high-resolution map of the composition, lineage/functional states, developmental trajectories and multicellular crosstalk networks from microdissected non-solid (preinvasive) and solid compartments (invasive) of individual part-solid nodules. We found that early disease initiation and subsequent progression are associated with the evolution of immune-suppressive cellular phenotypes characterized by decreased cytotoxic CD8 T and NK cells, increased T cell exhaustion and accumulation of immunosuppressive regulatory T cells (Tregs) and M2-like macrophages expressing TREM2. Within Tregs, we identified a unique population of 4-1BB+ Treg subset enriched for the IL2-STAT5 suppressive pathway with transcription profiles supporting discrete metabolic alterations. Spatial analysis showed increased density of suppressive immune cells around tumor cells, increased exhaustion phenotype of both CD4 and CD8 T cells expressing chemokine CXCL13, and spatial micro-complex of endothelial and lymphocyte interactions within tertiary lymphoid structures. The single-cell architecture identifies determinants of early disease emergence and progression, which may be developed not only as diagnostic/prognostic biomarkers but also as targets for disease interception. Additionally, our dataset constitutes a valuable resource for the preinvasive lung cancer research community.

cancer biology↗

bioRxiv2023

Novel co-culture strategies of tumor organoids with autologous T-cells reveal clinically relevant combinations of immune-checkpoint and targeted therapies

Patient derived tumor organoids (PDTOs) have become relevant pre-clinical models for therapeutic modelling since they highly recapitulate patients response to treatment. Nevertheless, their value for immunotherapy modelling has not been fully explored. We developed a tumor processing protocol that enable the establishment of PDTOs and tumor infiltrating lymphocytes (TILs) isolation. By the optimization of functional assays, we compared the T-cells effector functions of matching PBMCs and TILs, demonstrating that PBMCs after co-culture and TILs after initial expansion display similar responses. In addition, the evaluation of cytokine production by fluorospot in combination with an image-based killing assay enable the screening of different immune-checkpoint inhibitors as well as its combination with target inhibitors. Our proof-of-concept functional assays showed the potential and versatility of PDTOs and T-cells co-culture systems for immunotherapy screening. The optimization of scalable functional assays downstream co-culture represents a significant step forward to increase the value of PDTOs as pre-clinical models for immunotherapeutic screens.

immunology↗

bioRxiv2022

Epigenetic dysregulation from chromosomal transit in micronuclei

Chromosomal instability (CIN) and epigenetic alterations are characteristics of advanced and metastatic cancers [1-4], yet whether they are mechanistically linked is unknown. Here we show that missegregation of mitotic chromosomes, their sequestration in micronuclei [5, 6], and subsequent micronuclear envelope rupture [7] profoundly disrupt normal histone post-translational modifications (PTMs), a phenomenon conserved across humans and mice as well as cancer and non-transformed cells. Some of the changes to histone PTMs occur due to micronuclear envelope rupture whereas others are inherited from mitotic abnormalities prior to micronucleus formation. Using orthogonal techniques, we show that micronuclei exhibit extensive differences in chromatin accessibility with a strong positional bias between promoters and distal or intergenic regions. Finally, we show that inducing CIN engenders widespread epigenetic dysregulation and that chromosomes which transit in micronuclei experience durable abnormalities in their accessibility long after they have been reincorporated into the primary nucleus. Thus, in addition to genomic copy number alterations, CIN can serve as a vehicle for epigenetic reprogramming and heterogeneity in cancer.

cancer biology↗

bioRxiv2022

EchinoDB: An update to the web-based application for genomic and transcriptomic data on Echinoderms.

Here we release a new version of EchinoDB (https://echinodb.uncc.edu). EchinoDB is a database of genomic and transcriptomic data on echinoderms. The initial database consisted of groups of 749,397 orthologous and paralogous transcripts arranged in orthoclusters by sequence similarity. The new version of EchinoDB includes RNA-seq data of the brittle star Ophioderma brevispinum and high-quality genomic assembly data of the green sea urchin Lytechinus variegatus. In addition, we enabled keyword searches for annotated data and installed an updated version of Sequenceserver to allow BLAST searches. The data are downloadable in FASTA format. The first version of EchinoDB appeared in 2016 and was implemented in GO on a local server. The new version has been updated using R Shiny to include new features and improvements in the application. Furthermore, EchinoDB now runs entirely in the cloud for increased reliability and scaling. EchinoDB enjoys a user base drawn from the fields of phylogenetics, developmental biology, genomics, physiology, neurobiology, and regeneration. As use cases, we illustrate how EchinoDB is used in discovering pathways and gene regulatory networks involved in the tissue regeneration process.

bioinformatics↗

bioRxiv2020

Evolution of immune escape mechanisms in the progression from preinvasive to invasive human lung adenocarcinoma.

The tumor microenvironment (TME) of lung adenocarcinoma (LUAD) precursor lesions has not been described. We interrogated by multiplex immunofluorescence the TME of preinvasive and invasive Stage 1A LUADs selected by computer tomography (CT) scan-density. Pure non-solid (p-NS) CT density nodules are preinvasive/minimally invasive, whereas solid CT density nodules are frankly invasive cancers. Our data reveal an intensely immune-suppressive immune TME in p-NS tumors characterized by an increase in Treg cells and a decrease in cytotoxic T cells relative to normal lung. The TME of the solid tumor group, more advanced lesions than the p-NS yet still early in disease development, were increasingly more immune-suppressive. Provocatively, there was a further increase in both Treg cells and cytotoxic T cells, establishing a nascent albeit ineffective anti-tumor immune response in transition from preinvasive p-NS to invasive solid tumors. Regulatory T cells play a dominant role throughout progression, while additional immune evasive mechanisms are employed at different stages of disease progression, including T cell exclusion from cancer cell nests early and activation of immune checkpoints later. Our study establishes that different immune-targeted strategies are required to intercept disease progression at these two distinct early points of lung cancer development. Statement of SignificanceUsing multiplexed IF, we compared the cellular composition and activation state of the tumor immune microenvironment between pre/minimally invasive and frankly invasive adenocarcinoma. We found a progressive increase in immunosuppressive mechanisms in association with disease progression suggesting that Interception strategies should be specifically tailored based on underlying immune escape mechanisms

cancer biology↗

bioRxiv2020

Unacylated ghrelin and AZP531 suppress the 3D growth of breast cancers

Breast cancer is the most common type of cancer in women and notwithstanding important therapeutic advances, it remains the second leading cause of cancer-related death in the US. Despite extensive research relating to the hormone ghrelin, responsible for the stimulation of growth hormone release and appetite, little is known of the effects of its unacylated form, especially in cancer. One major area of research relates to its reported effects to increase insulin sensitivity in diabetics, this being the basis for the development of unacylated ghrelin analog, AZP531 or livoletide, now in clinical trials for the treatment of Prader-Willi Syndrome. The mechanism of action of unacylated ghrelin is largely uncharacterized, in any system, because it does not bind to or activate the cognate ghrelin receptor, GHSR1a. The present study aimed to characterize effects of unacylated ghrelin on breast cancer cells, define its mechanism of action, and explore the therapeutic potential of unacylated ghrelin or analog AZP531. We report potent effects of unacylated ghrelin, at picomolar doses, on the growth of breast cancer cells, dependent on 3D culture and activation of Gi. Suppression of MAPK signaling by unacylated ghrelin leads to cell cycle arrest and apoptosis. AZP531 also suppresses the growth of breast cancer cells in vitro and in xenografts, and may be a novel approach for the safe and effective treatment of breast cancer.

cancer biology↗

bioRxiv2019

Classification models for Invasive Ductal Carcinoma Progression, based on gene expression data-trained supervised machine learning

Early detection of breast cancer and its correct stage determination are important for prognosis and rendering appropriate personalized clinical treatment to breast cancer patients. However, despite considerable efforts and progress, there is a need to identify the specific genomic factors responsible for, or accompanying Invasive Ductal Carcinoma (IDC) progression stages, which can aid the determination of the correct cancer stages. We have developed two-class machine-learning classification models to differentiate the early and late stages of invasive ductal carcinoma. The prediction models are trained with RNA-seq gene expression profiles representing different IDC stages of 610 patients, obtained from The Cancer Genome Atlas (TCGA). Different supervised learning algorithms were trained and evaluated with an enriched model learning, facilitated by different feature selection methods. We also developed a machine-learning classifier trained on the same datasets with training sets reduced data corresponding to IDC driver genes. Based on these two classifiers, we have developed a web-server Duct-BRCA-CSP to predict early stage from late stages of IDC based on input RNA-seq gene expression profiles. The analysis conducted by us also enables deeper insights into the stage-dependent molecular events accompanying breast ductal carcinoma progression. The server is publicly available at http://bioinfo.icgeb.res.in/duct-BRCA-CSP.

bioinformatics↗