Biology subjects

Miranda, A. M.

Publications and source records attributed to Miranda, A. M..

6 recordsLinked to original sources

bioRxiv2026

Nano- and microplastics in pediatric tonsil tissue: bioaccumulation, distribution, and immunomodulatory effects in human lymphoid aggregate organoids

Nano- and microplastics (NMPs), by-products of the fragmentation and degradation of plastic products, are ubiquitous environmental contaminants, yet their burden in pediatric immune tissues and functional consequences for developing immunity remain unknown. Here we report the first comprehensive characterization of NMPs in surgically excised pediatric tonsils (n = 30) using pyrolysis gas chromatography- mass spectrometry (Py-GC/MS), Nile Red fluorescence microscopy, and optical photothermal infrared (O-PTIR) spectroscopy. NMPs were detected in all specimens, with polystyrene, polyethylene, polyethylene terephthalate, and acrylonitrile butadiene styrene present in >90% of samples. To bridge clinical exposure data with mechanistic insight, we formulated a cryo-milled multi-polymer mixture reflecting the patient-derived polymer profile and challenged human lymphoid aggregate culture (HLAC) tonsil organoids at environmentally relevant concentrations. Multiplexed cytokine profiling of culture supernatants revealed a robust early inflammatory response at day 3, with significant upregulation of IL-6 (p = 0.011) and MIP-1{beta}/CCL4 (p = 0.011), followed by convergence toward control levels by day 14. Functional cytokine modules spanning immune, metabolic, structural, and growth factor pathways showed coordinated deviation from controls at day 3 post-exposure with subsequent normalization. Fluorescence-guided depth profiling demonstrated time-dependent penetration of 100 nm particles into organoid aggregates (70% tissue depth at day 3 versus 95% at day 14), and transmission electron microscopy revealed intracellular polyethylene within lymphocyte lysosomes. These findings establish pediatric tonsils as a sentinel tissue for NMP bioaccumulation and demonstrate that environmentally relevant polymer mixtures elicit transient but significant immunomodulatory responses in human lymphoid tissue, with implications for mucosal and systemic immune health in children. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=83 SRC="FIGDIR/small/728317v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@19395f4org.highwire.dtl.DTLVardef@5a0380org.highwire.dtl.DTLVardef@19c0741org.highwire.dtl.DTLVardef@a052c5_HPS_FORMAT_FIGEXP M_FIG Structure: Translational pipeline from clinical tissue characterization to patient-informed preclinical modeling of nano-microplastic (NMP) exposure in pediatric lymphoid tissue. Pediatric tonsil tissue collected from clinically indicated tonsillectomies underwent tissue digestion for NMP characterization to identify NMP type and size distributions. In parallel, tonsil tissue was used to generate human lymphoid aggregate culture (HLAC) organoids that recapitulate the cellular complexity of the native tissue. These patient-derived organoids were then exposed to environmentally relevant compositions and concentrations of NMPs over time-course experiments, with longitudinal assessment of immunomodulatory responses including cytokine profiling and functional readouts. This bedside-to-bench approach establishes a physiologically relevant human system for investigating NMP-immune interactions, bridging clinical tissue analysis with mechanistic preclinical modeling to inform understanding of pediatric environmental exposures and their potential health impacts. C_FIG

immunology↗

bioRxiv2026

Endogenous mutational mechanisms and metabolic context shape endometrial cancer

Uterine corpus endometrial carcinoma (UCEC) is a common gynecologic malignancy with rising mortality, yet its genome-wide mutational architecture remains incompletely understood. Here we analyze deep whole-genome sequencing data from 440 UCEC tumors from The Cancer Genome Atlas, integrated with transcriptomic and clinical data, to define subtype-specific mutational processes and genomic architectures. We uncover pronounced molecular subtype-specific differences in endogenous mutational mechanisms, retrotransposition activity, structural variation, and chromosomal instability. LINE-1 retrotransposition emerges as a key contributor to genome instability in UCEC, acting as a prominent source of structural variation in copy-number stable tumors and associating with chromothripsis and ecDNA-mediated oncogene amplification in copy-number high tumors. Mutational signature SBS28 contributes significantly to mutations in POLE-deficient tumors and is strongly correlated with SBS10a and SBS10b. Mismatch repair-deficient tumors exhibit a previously unrecognized doublet base substitution signature and a defining imbalance between ID2 and ID1 indel processes, reflecting pervasive DNA template-strand replication slippage and associated with increased tumor immunogenicity. Copy-number low tumors follow a distinct low-mutagenesis evolutionary trajectory characterized by reduced replication stress, low proliferative activity, genomic stability and enrichment of SBS18 associated with oxidative damage. Notably, we identify a consistent inverse association between body mass index and tumor mutational burden in UCEC, suggesting that host metabolic state may influence fundamental cellular processes governing mutation accumulation, promoting tumor development through non-mutagenic mechanisms rather than elevated genomic instability. Together, these findings establish a mutagenesis-centric framework for UCEC that links endogenous mutational mechanisms to tumor architecture and host metabolic context, uncovering previously unrecognized subtype-specific genomic features with important implications for refined risk stratification and therapeutic strategies.

genomics↗

bioRxiv2025

A Thiopurine-like Mutagenic Process Defines TGCT Subtypes

Testicular germ cell tumors (TGCTs) are the most common malignancy in young men, exhibit a unique developmental origin and exceptional chemosensitivity. However, the molecular distinctions between TGCT subtypes remain poorly understood. Here we present a comprehensive genomic analysis of 252 treatment-naive primary TGCTs, integrating deep whole-genome sequencing with matched transcriptomic and epigenomic data. We identify new driver genes and uncover defining features of TGCTs, including pervasive chromosome X amplification with subtype-specific X chromosome inactivation, and a germ cell-like transcriptional program. Although previously reported, whole genome doubling (WGD) in TGCTs is further characterized here as ubiquitous, developmentally early, and associated with age at onset. Seminomas are enriched for early driver mutations, secondary WGD events, sustained XIST expression and replication stress-associated indel mutational signatures, while non-seminomas show greater structural complexity, subclonal diversity, relatively earlier-onset WGD, extended tumor latency, and telomere elongation. Moreover, we identify a mutational signature, SBS87, that is exceptionally rare across cancers with exception of thiopurine-treated leukemia, but strikingly prevalent in TGCT, especially non-seminomas. SBS87 is linked to extended tumor latency and telomere elongation, implicating possible environmental or endogenous processes that mimic thiopurine-induced DNA damage in TGCT pathogenesis. Collectively, our findings define TGCTs as molecularly distinct tumors shaped by early genomic instability and highlight SBS87 as a novel mutational footprint with potential etiologic and clinical relevance.

genomics↗

bioRxiv2024

Negative resilience trends to more frequent extreme droughts in Mediterranean oak species

Recent changes in climate have triggered widespread mortality events in oak forests worldwide. Despite the ecological importance of these ecosystems, limited information exists on the long-term resilience of oak forests in response to extreme climate events. Quercus canariensis, a semi-deciduous oak sensitive to summer drought characteristic of the Mediterranean climate, is currently showing defoliation and mortality episodes in the drier areas of its natural range. Here, we investigated the long-term impacts of climate on the radial growth of Q. canariensis and assessed changes in resilience to extreme droughts across eight populations in S Spain following an environmental gradient. We observed a clear latitudinal gradient in growth performance, as reflected by resilience indices across populations. Since 1970, Q. canariensis has shown a marked decline in resilience to extreme drought events at the wettest region, resulting in a diminished capacity to recover pre-drought growth levels. This trend has preceded growth declines in certain populations, suggesting increased vulnerability to the increasing frequency of extreme climatic events. Through growth analyses, we identified early-warning signals of forest decline in this Mediterranean oak species, highlighting the most sensitive populations and its high susceptibility to extreme droughts impacts.

ecology↗

bioRxiv2024

CD4+ T Cell Depletion Before Primary Dengue and/or Secondary Zika Infection Reveals Mechanistic Correlates of Antibody Functionality in Rhesus Macaques.

Dengue (DENV) virus and Zika virus (ZIKV) are two flaviviruses of major public health concern. One drawback designing effective vaccines is our limited understanding of the mechanisms ruling protection or harm among DENV serotypes, or between DENV and ZIKV. Here, we depleted rhesus macaques of CD4+ T cells in vivo before primary DENV infection and/or secondary ZIKV challenge to recreate a sub-optimal priming of the humoral immune response. Our results support that CD4+ T cells are needed to induce a quantitative and type-specific effective humoral immune response against primary DENV, but also against secondary ZIKV in DENV-experimented subjects. Our results also indicate a limited contribution of the DENV-Memory B cells to anti-ZIKV response. Furthermore, our results suggest that a suboptimal B cell priming during a primary DENV infection does differentially impact different antibody (Abs) properties. While binding or neutralization of ZIKV or DENV during a subsequent exposure to ZIKV is not affected by the lack of CD4+ T - B cells interaction during a primary DENV infection, that interaction is critical to guarantee the Abs specificity. Also, we found that depleting CD4+ T cells before DENV primary infection but not before ZIKV challenge significantly increases Abs cross-reactivity against DENV-EDIII domain and DENV-NS1 protein but not against ZIKV-EDIII domain or NS1 protein. Furthermore, there was more cross-reactivity among the DENV-NS1 proteins than against DENV-EDIII domains, suggesting that during a primary DENV infection CD4+ T cells have a different weight in the responses against EDIII domain and NS1 protein. The proper Abs binding and neutralization with increased cross-reactivity profile was associated with limited frequency of circulating peripheral T helper cells (pTfh) with T helper 1 phenotype (CD4+/CXCR5+/CXCR3+) and expressing markers related to B cell activation (CXCR5+/CXCR3+/PD-1+/ICOS+) in the group depleted of CD4+ T cells only before primary DENV infection. However, memory B cells - but not Antibody Secreting Cells (ASC) activation 7 days after the infection - positively correlate with those two populations of pTfh. Finally, when Abs cross-reactivity values were incorporated in a Principal Component Analysis (PCA), the DENV-CD4+ T depleted group separates from the other two groups with similar Abs binding and neutralization profiles. Our result strongly suggests that during a heterologous sequential DENV/ZIKV infections Abs binding, and neutralization, may be regulated by different factors than their specificity. Before, the induction of cross-neutralizing Abs has been described in the context of secondary DENV infection. Here, for the first time, we are reproducing the experimental conditions leading to the generation of such Abs population in vivo. In summary, we show that suboptimal immune priming during a primary flavivirus infection has functional consequences during a secondary heterologous infection. Finally, we shown that CD8+ T cells are essential to guarantee an optimal Abs neutralization activity. These results have huge implications understanding the immune response to DENV vaccines (and maybe ZIKV), including why an optimal vaccine or natural-induced neutralizing response not necessarily protects or enhances pathogenesis during a subsequent natural heterologous exposure.

immunology↗

bioRxiv2021

SorCS2 deletion leads to altered neuronal lysosome activity

Vps10p domain receptors are important for regulating intracellular protein sorting within the central nervous system and as such constitute risk factors for different brain pathologies. Here, we show that removal of SorCS2 leads to altered lysosomal activity in mouse primary neurons. SorCS2-/- neurons show elevated lysosomal markers such as LAMP1 and acidic hydrolases including cathepsin B and D. Despite increased levels, SorCS2-/- neurons fail to degrade cathepsin specific substrates in a live context. SorCS2-deficient mice present an increase in lysolipids, which may contribute to membrane permeabilization and increased susceptibility to lysosomal stress. Our findings highlight SorCS2 as an important factor for a balanced neuronal lysosome milieu.

cell biology↗