Biology subjects

Nieto, J. C.

Publications and source records attributed to Nieto, J. C..

9 recordsLinked to original sources

bioRxiv2026

MET inhibition exploits conserved regulatory dependencies in malignant rhabdoid tumors

Malignant rhabdoid tumors (MRTs) are lethal, yet genomically simple childhood cancers characterised by universal SWI/SNF dysregulation. Despite this shared molecular framework, the regulatory programs sustaining MRTs and how they wire actionable dependencies, remain poorly defined. Here, we integrated single-cell multi-omic profiling and spatial transcriptomics across anatomically and molecularly diverse MRTs, generating a comprehensive multimodal MRT dataset at single-cell resolution. We leveraged this resource to identify candidate tumor-specific dependencies, which were subsequently functionally validated in vitro and in vivo in matched patient-derived models. We found that distinct malignant subpopulations are spatially patterned in complex environmentally shaped topologies, consistent with reciprocal interactions with stromal and immune compartments contributing to intratumoral transcriptional diversity. We identified recurrent transcriptional metaprograms conserved across patients and molecular subtypes, including a previously undescribed shared core rhabdoid program, as well as a metaprogram characterized by extracellular matrix interactions, and preferentially localized in tumor-stroma intermixed neighborhoods, supporting identification of niche conditioning cues. Mechanistically, we identified regulatory wiring driving these metaprograms, with the core shared rhabdoid programme coordinated by a circuit centred on TCF12, ZNF148 and CHD2. Guided by target nominations from our integrated analyses, we performed a curated drug screen using patient-derived MRT models and validated HGF/MET signaling as a selective vulnerability in extrarenal rhabdoid tumors. Pharmacologic MET inhibition was cytotoxic in sensitive models and induced a complete response in vivo using a clinically approved compound. Importantly, MET expression in primary tumors correlated with response, supporting biomarker-guided patient stratification for immediate clinical translation. Collectively, our findings define the molecular architecture of MRTs, reveal conserved regulatory programs beyond anatomical and molecular subtypes, and highlight a targetable signaling axis with immediate translational potential, establishing a framework for precision therapy in this lethal pediatric malignancy.

cancer biology↗

bioRxiv2026

Multi-omic profiling of pleural effusions: a reservoir-incubator for non-invasive insights into tumor heterogeneity

Pleural effusions (PEs) are common in advanced cancer and are routinely sampled for cytological evaluation; however, their full potential as a source of tumor and immune information remains underexplored. Although malignant PEs (MPEs) are increasingly used for liquid biopsy, their cellular complex interactions have not been resolved at high resolution. Here, we present the first comprehensive single-cell and multi-omic atlas of PEs, integrating scRNA-seq, TCR-seq and whole-exome sequencing with lung, breast, or ovarian cancer, as well as non-malignant heart failure controls. We profiled over 200,000 cells and identified more than 30 immune, stromal, and tumor subpopulations across disease contexts. The tumor cell signature in MPEs recapitulates the genomic and transcriptomic features of matched primary tumors, supporting their use for non-invasive tumor profiling. In contrast, immune landscapes varied by disease: lung cancer MPEs were enriched in exhausted CD8 T cells, breast MPEs showed CD4 T helper cell dominance, and ovarian and heart failure PEs harbored tissue-resident myeloid cell populations. These data reveal that PEs are dynamic, disease-specific ecosystems shaped by tumor-driven immune remodeling. By leveraging their cellular diversity, we position MPEs as a powerful platform for studying metastatic adaptation and immune responses in vivo, with direct implications for diagnostics, immune monitoring, and precision oncology.

cancer biology↗

bioRxiv2025

Decoding the immune response in leptomeningeal disease through single-cell sequencing of cerebrospinal fluid

AbstractAssessing anti-tumor immune responses and immune microenvironments in central nervous system (CNS) neoplasms, such as brain tumors and leptomeningeal disease (LMD), provides prognostic insights and predictive biomarkers. Liquid biopsy of the cerebrospinal fluid (CSF) represents a promising minimally-invasive approach, but its ability to reflect immune responses against tumors remains unclear. Here, we used single-cell sequencing of CSF cells and spatial transcriptomics of CNS lesions to compare and contrast LMD patients with CNS lymphoma (CNSL), glioblastoma (GB) and brain metastases (BrM), to neuroinflammatory CNS disorders. We identified disease-specific CSF environments, reflecting parenchymal tumor microenvironment features. CNSL showed robust T cell responses, while BrM and GB were dominated by both blood-derived and tissue-resident myeloid cells. Longitudinal CSF sampling unveiled mechanisms of disease progression and therapy resistance, highlighting the potential of CSF liquid biopsies for uncovering disease biology, discovering cellular biomarkers and developing personalized therapies for CNS neoplasms.

immunology↗

bioRxiv2024

Spatio-temporal T cell tracking for personalized TCR-T designs in childhood cancer

Immune checkpoint inhibition (ICI) has revolutionized oncology, offering extended survival and long-term remission in previously incurable cancers. While highly effective in tumors with high mutational burden, lowly mutated cancers, including pediatric malignancies, present low response rate and limited predictive biomarkers. Here, we present a framework for the identification and validation of tumor-reactive T cells as a biomarker to quantify ICI efficacy and as candidates for a personalized TCR-T cell therapy. Therefore, we profiled a pediatric malignant rhabdoid tumor patient with complete remission after ICI therapy using deep single-cell T cell receptor (TCR) repertoire sequencing of the tumor microenvironment (TME) and the peripheral blood. Specifically, we tracked T cell dynamics longitudinally from the tumor to cells in circulating over a time course of 12 months, revealing a systemic response and durable clonal expansion of tumor-resident and ICI-induced TCR clonotypes. We functionally validated tumor reactivity of TCRs identified from the TME and the blood by co-culturing patient-derived tumor cells with TCR-engineered autologous T cells. Here, we observed unexpectedly high frequencies of tumor-reactive TCR clonotypes in the TME and confirmed T cell dynamics in the blood post-ICI to predict tumor-reactivity. These findings strongly support spatio-temporal tracking of T cell activity in response to ICI to inform therapy efficacy and to serve as a source of tumor-reactive TCRs for personalized TCR-T designs.

genomics↗

bioRxiv2024

STAMP: Single-Cell Transcriptomics Analysis and Multimodal Profiling through Imaging

We introduce Single-Cell Transcriptomics Analysis and Multimodal Profiling (STAMP), a scalable profiling approach of individual cells. Leveraging transcriptomics and proteomics imaging platforms, STAMP eliminates sequencing costs, to enable single-cell genomics from hundreds to millions of cells at an unprecedented low cost. Stamping cells in suspension onto imaging slides, STAMP supports single-modal (RNA or protein) and multimodal (RNA and protein) profiling and flexible, ultra-high-throughput formats. STAMP allows the analysis of a single or multiple samples within the same experiment, enhancing experimental flexibility, throughput and scale. We tested STAMP with diverse sample types, including peripheral blood mononuclear cells (PBMCs), dissociated cancer cells and differentiated embryonic stem cell cultures, as well as whole cells and nuclei. Combining RNA and protein profiling, we applied immuno-phenotyping of millions of blood cells simultaneously. We also used STAMP to identify ultra-rare cell populations, simulating clinical applications to identify circulating tumor cells (CTCs). Performing in vitro differentiation studies, we further showed its potential for large-scale perturbation studies. Together, STAMP establishes a new standard for cost-effective, scalable single-cell analysis. Without the need for sequencing, STAMP makes high-resolution profiling more affordable and accessible. Designed to meet the needs of research labs, diagnostic cores and pharmaceutical companies, STAMP holds the promise to transform our capacity to map human biology, diagnose diseases and drug discovery.

genomics↗

bioRxiv2023

Quantifying Adaptive Evolution of the Human Immune Cell Landscape

The human immune system is under constant evolutionary pressure, primarily through its role as first line of defence against pathogens. Accordingly, population genomics studies have shown that immune-related genes have a high rate of adaptive evolution. These studies, however, are mainly based on protein-coding genes without cellular context, leaving the adaptive role of cell types and states uncharted. Inferring the rate of protein-coding genes adaptation in developing and adult immune cells at cellular resolution, we found cell types from both the lymphoid and myeloid compartments to harbour significantly increased adaptation rates. Specific cell states, such as foetal Pre-Pro B cells and adult T resident memory CD8+ cells show highly elevated rates of adaptation. We further analysed activated cell states, specifically, iPSC-derived macrophages responding to various challenges, including pro- and anti-inflammatory cytokines or bacterial and viral infections, the latter simulating the evolutionary arms race between humans and pathogens. Here, we found positive selection to be concentrated in early immune responses, suggesting benefits for the host to adapt to early stages of infection to control pathogen numbers and spread. Together, our study reveals spatio-temporal and functional biases in human immune populations with evidence of rapid adaptive evolution and provides a retrospect of forces that shaped the complexity, architecture, and function of the human body.

immunology↗

bioRxiv2023

FixNCut: Single-cell genomics through reversible tissue fixation and dissociation

The use of single-cell technologies for clinical applications requires disconnecting sampling from downstream processing steps. Early sample preservation can further increase robustness and reproducibility by avoiding artifacts introduced during specimen handling. We present FixNCut, a methodology for the reversible fixation of tissue followed by dissociation that overcomes current limitations. We applied FixNCut to human and mouse tissues to demonstrate the preservation of RNA integrity, sequencing library complexity, and cellular composition, while diminishing stress-related artifacts. Besides single-cell RNA sequencing, FixNCut is compatible with multiple single-cell and spatial technologies, making it a versatile tool for robust and flexible study designs.

bioinformatics↗

bioRxiv2023

Multi-organ single-cell transcriptomics of immune cells uncovered organ-specific gene expression and functions

Despite the large number of publicly available single-cell datasets, there is a limited understanding of the distinct resident immune cells and their concomitant features in diverse human organs. To address this, we compiled a dataset of 114,275 CD45+ immune cells from 14 organs from healthy donors. Although the transcriptome of immune cells is constant across organs, organ-specific gene expression changes were detected revealing unique expression in certain organs (GTPX3 in kidney, DNTT and ACVR2B in thymus). These alterations are associated with different transcriptional factor activities and pathways including metabolism. TNF- signaling through the NFkB pathway was found in various organs and immune compartments including distinct expression profiles of NFkB family genes and their target genes such as cytokines indicating their role in cell positioning. Taken together, immune cells not only protect the organs but also adapt to the host organ environment and contribute to its function and homeostasis.

immunology↗

bioRxiv2022

An Atlas of Cells in the Human Tonsil

Palatine tonsils are secondary lymphoid organs representing the first line of immunological defense against inhaled or ingested pathogens. Here, we present a comprehensive census of cell types forming the human tonsil by applying single-cell transcriptome, epigenome, proteome and adaptive immune repertoire sequencing as well as spatial transcriptomics, resulting in an atlas of >357,000 cells. We provide a glossary of 121 annotated cell types and states, and disentangle gene regulatory mechanisms that drive cells through specialized lineage trajectories. Exemplarily, we stratify multiple tonsil-resident myeloid slancyte subtypes, establish a distant BCL6 superenhancer as locally active in both follicle-associated T and B cells, and describe SIX5 as a potentially novel transcriptional regulator of plasma cell maturation. Further, our atlas is a reference map to understand alterations observed in disease. Here, we discover immune-phenotype plasticity in tumoral cells and microenvironment shifts of mantle cell lymphomas (MCL). To facilitate such reference-based analysis, we develop HCATonsilData and SLOcatoR, a computational framework that provides programmatic and modular access to our dataset; and allows the straightforward annotation of future single-cell profiles from secondary lymphoid organs.

immunology↗