Biology subjects

Mirzazadeh, R.

Publications and source records attributed to Mirzazadeh, R..

12 recordsLinked to original sources

bioRxiv2026

Spatial immune profiling reveals lymphocyte confinement to myeloid-mesenchymal niches and heterogeneous therapeutic T-cell opportunity in pediatric ependymoma

Pediatric posterior fossa group A (PFA) ependymoma is an aggressive, chemo-resistant brain tumor with a poor 10-year overall survival and no therapeutic options at relapse. Although conventionally classified as immune-cold, the spatial organization and therapeutic relevance of its rare immune infiltrates remain poorly characterized. Here, we present a spatially resolved immune analysis of 14 PFA ependymoma sections using published Visium spatial transcriptomics data analyzed through a multi-stage immune-focused computational framework combining reference-guided deconvolution, functional lymphocyte state scoring, ligand-receptor inference, and {beta}/{gamma}{delta} T cell immunotherapy opportunity scoring. Lymphocyte-associated hotspots were identified in 6 of 14 sections and, among confidently classified hotspots, were dominated by inflammatory-associated and retention-associated transcriptional states rather than cytotoxic or exhausted programs. These hotspots were preferentially confined to myeloid- and mesenchymal-rich tumor zones with near-complete exclusion from epithelial regions; ligand-receptor analysis identified four candidate restriction axes (SPP1-CD44, FN1-integrin, collagen VI-integrin, and APP-CD74). Immunotherapy opportunity scoring revealed heterogeneous and spatially compartmentalized {beta} and {gamma}{delta} T cell recognition landscapes across sections: {beta}T ligand availability and immunosuppressive tone both rose in the mesenchymal compartment, while the two components of {gamma}{delta} phosphoantigen-mediated recognition were spatially and transcriptionally dissociated from one another. Together, these findings reframe PFA ependymoma not as a monolithic immune desert but as a tumor type with spatially compartmentalized, mechanistically tractable immune niches, and provide a generalizable computational strategy for mapping immune architecture and T cell therapy susceptibility in low-infiltrated pediatric CNS tumors.

cancer biology↗

bioRxiv2026

Highly resolved tumor architecture via matched spatial and nucleus transcriptomics from a single tissue section

Spatial transcriptomics often relies on reference-based deconvolution to infer cell types in a tissue context; however, public single-cell datasets can miss patient-specific biology. Here we introduce SIMPlex, a method that generates matched spatial and single-nucleus gene-expression profiles from the same 5 um FFPE section. We demonstrate context-matched profiles across mouse brain, breast cancer and prostate cancer tissues, resolving fine-grained cell-states with distinct spatial signatures. By extracting both spatial and nuclear layers, SIMPlex maximises the information recovered from a single tissue section, an advantage for scarce archival and clinical specimens.

molecular biology↗

bioRxiv2026

Spatial mapping of pediatric brain tumors across diagnoses and relapses

We present a spatial transcriptomic atlas of 19 pediatric brain tumor patients spanning nine major and rare diagnoses, including seven relapses, revealing their spatial cellular and molecular organization. Each tumor section resolves into 2 - 4 recurrent spatial archetypes across 11 biological themes, with some mirroring developmental lineage patterns - for example, oligodendrocyte-lineage programs in pilocytic astrocytomas. Spatially inferred copy-number analysis identifies relapse-associated putative clones. In one rare embryonal tumor, spatial niches in the primary tumor harboring putative clones colocalized with an archetype enriched for nervous system development and glioblast-lineage programs. In one ependymoma and one pilocytic astrocytoma, relapse-associated putative clones preferentially localized to the vasculature, suggesting regrowth during relapse may be seeded by clonal selection of residual tumor cells within specialized microenvironmental niches. This resource provides an open-access spatially resolved map via an interactive viewer to inform research on pediatric brain tumor ecosystems, relapse biology, and therapeutic strategies.

cancer biology↗

bioRxiv2026

Pubertal maturation and chemotherapy-associated disruption of the pediatric ovary revealed by multimodal single-cell profiling

Ovarian tissue cryopreservation enables fertility preservation in females undergoing gonadotoxic therapies, restoring fertility in adults. Although offered even before puberty, the childhood ovary and its vulnerability to therapy remain poorly characterized. Here, ovarian tissue from 16 patients undergoing fertility preservation (aged 1-16 years) and 11 adult controls (aged 22-32 years) was analyzed using single-cell RNA sequencing, spatial transcriptomics, and multiplex immunostaining. In chemotherapy-naive samples, 13 somatic cell populations underwent extracellular matrix remodeling, vascular, neural, and stromal maturation during puberty, whereas changes in germline related to chromatin remodeling. Spatial transcriptomics resolved 23 clusters across, revealing distinct tissue organization and follicular niche composition between children and adults. Chemotherapy exposure depleted perifollicular and vascular cells, suppressed intercellular signaling, and dysregulated over half of puberty-associated genes, converging on stress responses and extracellular matrix remodeling, with SEPTIN7 as a potential biomarker. These findings uncover critical developmental vulnerabilities of the pediatric ovary relevant to fertility preservation.

developmental biology↗

bioRxiv2025

Human growth plates house resting zone sub-populations with features of quiescent stem cells

Incomplete mapping of gene expression within human (epiphyseal) growth plates contributes to the challenges of diagnosing and treating patients with skeletal growth disorders. To address this issue, we applied spatially resolved transcriptomics to rare growth plate biopsies obtained from healthy adolescents. In addition to identifying novel markers of each zone of the human growth plate, spatial profiling revealed that the expression of genes associated with poorly understood growth disorders, including NKX3-2, SGMS2 and WNK4, is restricted to specific human growth plate zones. By elaborating on the low transcriptional activity of resting zone chondrocytes, we found that a subset of these cells exists in a functionally quiescent state in vivo, as determined by their predominantly nuclear mRNA, abundant heterochromatin, and ability to exit the G0 phase under specific conditions - features shared with skeletal stem cells in mouse growth plates. Additionally, we identified distinct and overlapping sub-populations of human resting zone chondrocytes; an exploration of their hierarchy determined that CHRDL2 and/or SFRP5-positive sub-populations are among the least quiescent resting zone cells. In summary, we generated the most comprehensive gene expression characterization of the human growth plate, which revealed novel zone-specific markers, new primary growth disorders, candidate pharmacological targets, and led us to uncover sub-populations of resting zone chondrocytes with features of quiescent stem cells. These results contribute to a better understanding of the cellular and molecular mechanisms governing human height and can facilitate improved diagnosis and treatment strategies of patients with skeletal growth disorders.

molecular biology↗

bioRxiv2023

Spatial Multimodal Analysis of Transcriptomes and Metabolomes in Tissues

We present a spatial omics approach that merges and expands the capabilities of independently performed in situ assays on a single tissue section. Our spatial multimodal analysis combines histology, mass spectrometry imaging, and spatial transcriptomics to facilitate precise measurements of mRNA transcripts and low-molecular weight metabolites across tissue regions. We demonstrate the potential of our method using murine and human brain samples in the context of dopamine and Parkinsons disease.

genomics↗

bioRxiv2022

Spatially resolved transcriptomic profiling of degraded and challenging fresh frozen samples

Spatially resolved transcriptomics (SRT) has enabled precise genome-wide mRNA expression profiling within tissue sections. The performance of unbiased SRT methods targeting the polyA tail of mRNA, relies on the availability of specimens with high RNA quality. Moreover, the high cost of currently available SRT assays requires a careful sample screening process to increase the chance of obtaining high-quality data. Indeed, the upfront analysis of RNA quality can show considerable variability due to sample handling, storage, and/or intrinsic factors. We present RNA-Rescue Spatial Transcriptomics (RRST), an SRT workflow designed to improve mRNA recovery from fresh frozen (FF) specimens with moderate to low RNA quality. First, we provide a benchmark of RRST against the standard Visium spatial gene expression protocol on high RNA quality samples represented by mouse brain and prostate cancer samples. Then, we demonstrate the RRST protocol on tissue sections collected from 5 challenging tissue types, including: human lung, colon, small intestine, pediatric brain tumor, and mouse bone/cartilage. In total, we analyzed 52 tissue sections and our results demonstrate that RRST is a versatile, powerful, and reproducible protocol for FF specimens of different qualities and origins.

genomics↗

bioRxiv2021

The spatial landscape of clonal somatic mutations in benign and malignant tissue

Defining the transition from benign to malignant tissue is fundamental to improve early diagnosis of cancer. Here, we provide an unsupervised approach to study spatial genome integrity in situ to gain molecular insight into clonal relationships. We employed spatially resolved transcriptomics to infer spatial copy number variations in >120 000 regions across multiple organs, in benign and malignant tissues. We demonstrate that genome-wide copy number variation reveals distinct clonal patterns within tumours and in nearby benign tissue. Our results suggest a model for how genomic instability arises in histologically benign tissue that may represent early events in cancer evolution. We highlight the power of an unsupervised approach to capture the molecular and spatial continuums in a tissue context and challenge the rationale for treatment paradigms, including focal therapy.

genomics↗

bioRxiv2020

Genomic instability is an early event driving chromatin reorganization and escape from oncogene-induced senescence

Oncogene-induced senescence (OIS) is an inherent and important tumor suppressor mechanism. However, if not timely removed via immune surveillance, senescent cells will also present a detrimental side. Although this has mostly been attributed to the senescence-associated-secretory-phenotype (SASP) of these cells, we recently proposed that "escape" from the senescent state represents another unfavorable outcome. Here, we exploit genomic and functional data from a prototypical human epithelial cell model carrying an inducible CDC6 oncogene to identify an early-acquired recurrent chromosomal inversion, which harbors a locus encoding the circadian transcription factor BHLHE40. This inversion alone suffices for BHLHE40 activation upon CDC6 induction and for driving cell cycle re-entry and malignant transformation. In summary, we now provide strong evidence in support of genomic instability underlying "escape" from oncogene-induced senescence. HIGHLIGHTSO_LIOncogene driven error-prone repair produces early genetic lesions allowing escape from senescence C_LIO_LICells escaping oncogene-induced senescence display mutational signatures observed in cancer patients C_LIO_LIA single recurrent inversion harboring a circadian TF gene suffices for bypassing oncogene-induced senescence C_LIO_LIChromatin loop and compartment remodeling support the "escape" transcriptional program C_LI

cell biology↗

bioRxiv2018

Modelling double strand break susceptibility to interrogate structural variation in cancer

BackgroundStructural variants (SVs) are known to play important roles in a variety of cancers, but their origins and functional consequences are still poorly understood. Many SVs are thought to emerge via errors in the repair processes following DNA double strand breaks (DSBs) and previous studies have experimentally measured DSB frequencies across the genome in cell lines.\n\nResultsUsing these data we derive the first quantitative genome-wide models of DSB susceptibility, based upon underlying chromatin and sequence features. These models are accurate and provide novel insights into the mutational mechanisms generating DSBs. Models trained in one cell type can be successfully applied to others, but a substantial proportion of DSBs appear to reflect cell type specific processes. Using model predictions as a proxy for susceptibility to DSBs in tumours, many SV enriched regions appear to be poorly explained by selectively neutral mutational bias alone. A substantial number of these regions show unexpectedly high SV breakpoint frequencies given their predicted susceptibility to mutation, and are therefore credible targets of positive selection in tumours. These putatively positively selected SV hotspots are enriched for genes previously shown to be oncogenic. In contrast, several hundred regions across the genome show unexpectedly low levels of SVs, given their relatively high susceptibility to mutation. These novel coldspot regions appear to be subject to purifying selection in tumours and are enriched for active promoters and enhancers.\n\nConclusionsWe conclude that models of DSB susceptibility offer a rigorous approach to the inference of SVs putatively subject to selection in tumours.

bioinformatics↗

bioRxiv2018

In situ quantification of individual mRNA transcripts in melanocytes discloses gene regulation of relevance to speciation

Functional validation of candidate genes for adaptation and speciation remains challenging. We here exemplify the utility of a method quantifying individual mRNA transcripts in revealing the molecular basis of divergence in feather pigment synthesis during early-stage speciation in crows. Using a padlock probe assay combined with rolling circle amplification we quantified cell-type specific gene expression in the native, histological context of growing feather follicles. Expression of Tyrosinase related protein 1 (TYRP1), Solute carrier family 45 member 2 (SLC45A2) and Hematopoietic prostaglandin D synthase (HPGDS) was melanocyte-limited and significantly reduced in follicles from hooded crow explaining the substantially lower melanin content in grey vs. black feathers. The central upstream transcription factor Microphthalmia-associated transcription factor (MITF) only showed differential expression specific to melanocytes - a feature not captured by bulk RNA-seq. Overall, this study provides insight into the molecular basis of an evolutionary young transition in pigment synthesis, and demonstrates the power of histologically explicit, statistically substantiated single-cell gene expression quantification for functional genetic inference in natural populations.

evolutionary biology↗

bioRxiv2016

BLISS: quantitative and versatile genome-wide profiling of DNA breaks in situ

We present a method for genome-wide DNA double-strand Breaks (DSBs) Labeling In Situ and Sequencing (BLISS) which, compared to existing methods, introduces several key features: 1) high efficiency and low input requirement by in situ DSB labeling in cells or tissue sections directly on a solid surface; 2) easy scalability by performing in situ reactions in multi-well plates; 3) high sensitivity by linearly amplifying tagged DSBs using in vitro transcription; and 4) accurate DSB quantification and control of PCR biases by using unique molecular identifiers. We demonstrate the ability to use BLISS to quantify natural and drug-induced DSBs in low-input samples of cancer cells, primary mouse embryonic stem cells, and mouse liver tissue sections. Finally, we applied BLISS to compare the specificity of CRISPR-associated RNA-guided endonucleases Cas9 and Cpf1, and found that Cpf1 has higher specificity than Cas9. These results establish BLISS as a versatile, sensitive, and efficient method for genome-wide DSB mapping in many applications.

molecular biology↗