Biology subjects

Borja, M.

Publications and source records attributed to Borja, M..

11 recordsLinked to original sources

bioRxiv2025

Comparative analysis of human and mouse ovaries across age

Mouse is a tractable model for human ovarian biology, however its utility is limited by incomplete understanding of how transcription and signaling differ interspecifically and with age. We compared ovaries between species using 3D-imaging, single-cell transcriptomics, and functional studies. In mice, we mapped declining follicle numbers and oocyte competence during aging; in human ovaries, we identified cortical follicle pockets and density changes. Oocytes had species-specific gene expression patterns during growth that converged toward maturity. Age-related transcriptional changes were greater in oocytes than granulosa cells across species, although mature oocytes change more in humans. We identified ovarian sympathetic nerves and glia; nerve density increased in aged human ovaries and, when ablated in mice, perturbed folliculogenesis. This comparative atlas defines shared and species-specific hallmarks of ovarian biology.

genomics↗

bioRxiv2024

Zebrahub-Multiome: Uncovering Gene Regulatory Network Dynamics During Zebrafish Embryogenesis

During embryonic development, gene regulatory networks (GRNs) drive molecular differentiation of cell types. However, the temporal dynamics of these networks remain poorly understood. Here, we present Zebrahub-Multiome, a single-cell multiomic atlas that captures chromatin accessibility and gene expression from 94,562 cells across six stages of zebrafish embryogenesis (10-24 hours post-fertilization), capturing key developmental stages from the end of gastrulation to the onset of organogenesis. By measuring regulatory element activity alongside transcriptional output from the same cells, we identify 640,000 cis-regulatory elements organized into 402 hierarchically structured modules corresponding to specific developmental pathways. Early embryonic stages employ broadly shared regulatory programs that progressively fragment into lineage-specific modules. Timeresolved gene regulatory network inference reveals that transcription factors undergo functional transitions - from multilineage regulators to specialized, lineage-committed factors. These quantitative measurements reveal the regulatory network rewiring that drives cell fate specification. Our interactive web portal (zebrahub.org/epigenomics) enables exploration of gene dynamics, regulatory networks, and perturbation predictions, providing a quantitative framework for understanding vertebrate developmental regulation.

developmental biology↗

bioRxiv2024

How Mycobacterium tuberculosis builds a home: Single-cell analysis reveals M. tuberculosis ESX-1-mediated accumulation of anti-inflammatory macrophages in infected mouse lungs.

Mycobacterium tuberculosis (MTB) infects and replicates in lung mononuclear phagocytes (MNPs) with astounding ability to evade elimination. ESX-1, a type VII secretion system, acts as a virulence determinant that contributes to MTBs ability to survive within MNPs, but its effect on MNP recruitment and/or differentiation remains unknown. Here, using single-cell RNA sequencing, we studied the role of ESX-1 in MNP heterogeneity and response in mice and murine bone marrow-derived macrophages (BMDM). We found that ESX-1 is required for MTB to recruit diverse MNP subsets with high MTB burden. Further, MTB induces an anti-inflammatory signature in MNPs and BMDM in an ESX-1 dependent manner. Similarly, spatial transcriptomics revealed an upregulation of anti-inflammatory signals in MTB lesions, where monocyte-derived macrophages concentrate near MTB-infected cells. Together, our findings suggest that MTB ESX-1 mediates the recruitment and differentiation of anti-inflammatory MNPs, which MTB can infect and manipulate for survival.

microbiology↗

bioRxiv2024

Spatio-temporal analysis of Vaccinia virus infection and host response dynamics using single-cell transcriptomics and proteomics

Poxviruses are a large group of DNA viruses with exclusively cytoplasmic life cycles and complex gene expression programs. A number of systems-level studies have analyzed bulk transcriptome and proteome changes upon poxvirus infection, but the cell-to-cell heterogeneity of the transcriptomic response, and the subcellular resolution of proteomic changes have remained unexplored. Here, we measured single-cell transcriptomes of Vaccinia virus-infected populations of HeLa cells and immortalized human fibroblasts, resolving the cell-to-cell heterogeneity of infection dynamics and host responses within those cell populations. We further integrated our transcriptomic data with changes in the levels and subcellular localization of the host and viral proteome throughout the course of Vaccinia virus infection. Our findings from single-cell RNA sequencing indicate conserved transcriptome changes independent of the cellular context, including widespread host shutoff, heightened expression of cellular transcripts implicated in stress responses, the rapid accumulation of viral transcripts, and the robust activation of antiviral pathways in bystander cells. While most host factors were co-regulated at the RNA and protein level, we identified a subset of factors where transcript and protein levels were discordant in infected cells; predominantly factors involved in transcriptional and post-transcriptional mRNA regulation. In addition, we detected the relocalization of several host proteins such as TENT4A, NLRC5, and TRIM5, to different cellular compartments in infected cells. Collectively, our comprehensive data provide spatial and temporal resolution of the cellular and viral transcriptomes and proteomes and offer a robust foundation for in-depth exploration of virus-host interactions in poxvirus-infected cells.

microbiology↗

bioRxiv2023

Single-nucleus RNA sequencing provides insights into the GL261-GSC syngeneic mouse model of glioblastoma

Glioblastoma (GBM) is an aggressive tumor with very bad prognosis. The urgent need to find new effective therapies is challenged by the unique characteristics of GBM, including high intra and intertumoral heterogeneity. Using single-nucleus transcriptomics (snRNA-seq), we characterized the panorama of a preclinical immunocompetent murine model based in the implantation of mouse glioblastoma stem cells (GL261-GSCs) into the brain parenchyma. Additionally, we performed Visium spatial transcriptomics in the in vivo model to confirm the location of annotated cells. To understand the technical bias of this approach, we performed two scRNA-seq methods in GBM cells. We thoroughly characterized the tumor microenvironment (TME) at early and late stages of tumor development and upon treatment with temozolomide (TMZ), the standard of care for patients with GBM, and with Tat-Cx43266-283, a promising experimental treatment. We identified prominent GBM targets that can be addressed using this preclinical model, such as Grik2, Nlgn3, Gap43 or Kcnn4, which are involved in electrical and synaptic integration of GBM cells into neural circuits, as well as the expression of Nt5e, Cd274 or Irf8, which indicates the development of immune evasive properties in these GBM cells. In agreement, snRNA-seq unveiled high expression of several immunosuppressive-associated molecules in immune cells, such as Csf1r, Arg1, Mrc1 and Tgfb1, suggesting the development of an immunosuppressive microenvironment. We also show the landscape of cytokines, cytokine receptors, checkpoint ligands and receptors in tumor and TME cells, which are crucial data for a rational design of immunotherapy studies. Thus, Mrc1, PD-L1, TIM-3 or B7-H3 are among the immunotherapy targets that can be addressed in this model. Finally, the comparison of the preclinical GL261-GSC GBM model with human GBM subtypes unveiled important similarities with the recently identified TMEmed human GBM, indicating that preclinical data obtained in GL261-GSC GBM model might be applied to TMEmed human GBM, improving patient stratification in clinical trials. In conclusion, this work provides crucial information for future preclinical studies in GBM improving their clinical application.

neuroscience↗

bioRxiv2023

Tutorial: guidelines for manual cell type annotation of single-cell multi-omics datasets using interactive software

Assigning cell identity to clusters of single cells is an essential step towards extracting biological insights from many genomics datasets. Although annotation workflows for datasets built with a single modality are well established, limitations exist in annotating cell types in datasets with multiple modalities due to the need for a framework to exploit them jointly. While, in principle, different modalities could convey complementary information about cell identity, it is unclear to what extent they can be combined to improve the accuracy and resolution of cell type annotations. Here, we present a conceptual framework to examine and jointly interrogate distinct modalities to identify cell types. We integrated our framework into a series of vignettes, using immune cells as a well-studied example, and demonstrate cell type annotation workflows ranging from using single-cell RNA-seq datasets alone, to using multiple modalities such as single-cell Multiome (RNA and chromatin accessibility), CITE-seq (RNA and surface proteins). In some cases, one or other single modality is superior to the other for identification of specific cell types, in others combining the two modalities improves resolution and the ability to identify finer subpopulations. Finally, we use interactive software from CZ CELLxGENE community tools to visualize and integrate histological and spatial transcriptomic data.

bioinformatics↗

bioRxiv2023

Zebrahub - Multimodal Zebrafish Developmental Atlas Reveals the State Transition Dynamics of Late Vertebrate Pluripotent Axial Progenitors

Elucidating the developmental processes of organisms requires a comprehensive understanding of cellular lineages in the spatial, temporal, and molecular domains. In this study, we introduce Zebrahub, a dynamic atlas of zebrafish embryonic development that integrates single-cell sequencing time course data with lineage reconstructions facilitated by light-sheet microscopy. This atlas offers high-resolution and in-depth molecular insights into zebrafish development, achieved through the sequencing of individual embryos across ten developmental stages, complemented by trajectory reconstructions. Zebrahub also incorporates an interactive tool to navigate the complex cellular flows and lineages derived from light-sheet microscopy data, enabling in silico fate mapping experiments. To demonstrate the versatility of our multi-modal resource, we utilize Zebrahub to provide fresh insights into the pluripotency of Neuro-Mesodermal Progenitors (NMPs). Our publicly accessible web-based platform, Zebrahub, is a foundational resource for studying developmental processes at both transcriptional and spatiotemporal levels, providing researchers with an integrated approach to exploring and analyzing the complexities of cellular lineages during zebrafish embryogenesis.

developmental biology↗

bioRxiv2022

Dissecting the contributions of tumor heterogeneity on metastasis at single-cell resolution

Metastasis is the leading cause of cancer-related deaths, but metastasis research is challenged by limited access to patient material and a lack of experimental models that appropriately recapitulate tumor heterogeneity. Here, we analyzed single-cell transcriptomes of matched primary tumor and metastasis from patient-derived xenograft models of breast cancer, demonstrating that primary tumor and metastatic cells show profound transcriptional differences across heterogeneous tumors. While primary tumor cells upregulated several metabolic genes, metastatic cells displayed a motility phenotype in micrometastatic lesions and increased stress response signaling during metastatic progression. Additionally, we identified gene signatures that are associated with the metastatic potential and correlated with patient outcomes. Poorly metastatic primary tumors showed increased immune-regulatory control that may prevent metastasis, whereas highly metastatic primary tumors upregulated markers of epithelial-mesenchymal transition (EMT). We found that intra-tumor heterogeneity is dominated by epithelial-mesenchymal plasticity (EMP) which presented as a dynamic continuum with intermediate cell states that were characterized by novel, specific markers. These intermediate EMP markers correlated with worse patient outcomes and could serve as potential new therapeutic targets to block metastatic development.

cancer biology↗

bioRxiv2022

Comparative analysis of MERFISH spatial transcriptomics with bulk and single-cell RNA sequencing

Spatial transcriptomics extends single cell RNA sequencing (scRNA-seq) by providing spatial context for cell type identification and analysis. Imaging-based spatial technologies such as Multiplexed Error-Robust Fluorescence In Situ Hybridization (MERFISH) can achieve single-cell resolution, directly mapping single cell identities to spatial positions. MERFISH produces an intrinsically different data type than scRNA-seq and a technical comparison between the two modalities is necessary to ascertain how to best integrate them. We performed MERFISH on mouse liver and kidney and compared the resulting bulk and single-cell RNA statistics with those from the Tabula Muris Senis cell atlas as well as from two Visium datasets. MERFISH quantitatively reproduced the bulk RNA-seq and scRNA-seq results with improvements in overall dropout rates and sensitivity. Finally, we found that MERFISH independently resolved distinct cell types and spatial structure in both liver and kidney. Computational integration with the Tabula Muris Senis atlas did not enhance these results. We conclude that compared to scRNA-seq, MERFISH provides a quantitatively comparable method for measuring single-cell gene expression and can robustly identify cell types without the need for computational integration with scRNA-seq reference atlases.

bioinformatics↗

bioRxiv2020

Molecular hallmarks of heterochronic parabiosis at single cell resolution

Slowing or reversing biological ageing would have major implications for mitigating disease risk and maintaining vitality. While an increasing number of interventions show promise for rejuvenation, the effectiveness on disparate cell types across the body and the molecular pathways susceptible to rejuvenation remain largely unexplored. We performed single-cell RNA-sequencing on 13 organs to reveal cell type specific responses to young or aged blood in heterochronic parabiosis. Adipose mesenchymal stromal cells, hematopoietic stem cells, hepatocytes, and endothelial cells from multiple tissues appear especially responsive. On the pathway level, young blood invokes novel gene sets in addition to reversing established ageing patterns, with the global rescue of genes encoding electron transport chain subunits pinpointing a prominent role of mitochondrial function in parabiosis-mediated rejuvenation. Intriguingly, we observed an almost universal loss of gene expression with age that is largely mimicked by parabiosis: aged blood reduces global gene expression, and young blood restores it. Altogether, these data lay the groundwork for a systemic understanding of the interplay between blood-borne factors and cellular integrity.

genomics↗

bioRxiv2019

Reactive Dicarbonyl Scavenging Effectively Reduces MPO-Mediated Oxidation of HDL and Preserves HDL Atheroprotective Functions

High-density lipoprotein (HDL) is atheroprotective by mediating cholesterol efflux, anti-inflammatory, and anti-oxidation functions. Atheroprotective functions of HDL are related to the activity of HDL-associated enzymes such as paraoxonase 1 (PON1). We examined the impact of inhibition of myeloperoxidase (MPO)-mediated HDL oxidation by PON1 on HDL malondialdehyde (MDA) content and HDL function. In the presence of PON1, crosslinking of apoAI in response to MPO-mediated oxidation of HDL was abolished and MDA-HDL adduct levels were decreased. In addition, PON1 prevented the impaired cholesterol efflux capacity of MPO-oxidized HDL from Apoe-/- macrophages. Direct modification of HDL with MDA increased apoAI crosslinking and reduced the cholesterol efflux capacity in a dose dependent manner. In addition, MDA modification of HDL reduced its anti-inflammatory function compared to native HDL as the expression of IL-1{beta} and IL6 increased by 3-(p<0.05) and 1.8-fold (p<0.05) in Apoe-/- macrophages in response to LPS. MDA-HDL also had impaired ability to increase PON1 activity. Importantly, HDL from subjects with familial hypercholesterolemia (FH-HDL) versus controls had increased MDA-apoAI adducts, and normalization of the PON1 activity to PON1 mass revealed a 24 % (p<0.05) decrease in specific activity indicating that PON1 activity is also impaired in FH. Consistent with the impaired PON1 activity and increased MDA-apoAI, FH-HDL induced a pro-inflammatory response in Apoe-/- macrophages compared to incubation with LPS alone. FH-HDL versus control HDL also had an impaired ability to promote cholesterol efflux from Apoe-/- macrophages. Interestingly, reactive dicarbonyl scavengers effectively abolished MPO-mediated apoAI crosslinking, MDA adduct formation, and improved cholesterol efflux capacity. Importantly, in vivo treatment of hypercholesterolemic mice with reactive dicarbonyl scavengers effectively reduced MDA-HDL adduct formation and increased PON1 activity and HDL cholesterol efflux capacity, supporting a therapeutic potential of reactive carbonyl scavenging in maintaining HDL function.

pharmacology and toxicology↗