Biology subjects

Shirazi, S. P.

Publications and source records attributed to Shirazi, S. P..

5 recordsLinked to original sources

bioRxiv2025

AlveolEye: Rapid and precise lung morphometry guided by computer vision

Rigorous and reproducible evaluation of lung tissue under different conditions is necessary to interpret development, injury, and pharmacologic interventions. Common histological measurements in the distal lung include mean linear intercept (MLI) as a metric of alveolarization and airspace volume density (ASVD) as a metric of airspaces relative to tissue. Historically, these have been performed manually in a time-intensive process, with reproducible trends, but a high degree of variability between individuals. To improve the reproducibility and throughput of lung morphometry, we developed AlveolEye, an open source, semi-automated, computer vision-assisted tool that rapidly and reproducibly calculates MLI and ASVD from images of standard hematoxylin and eosin (H&E) stained tissue sections. AlveolEye-assisted MLI calculation closely aligns with manually-derived measurements for corresponding images, with preservation of trends in measurements between non-injured controls and neonatal mice subjected to two different injury models. Analyzing human tissue of varying ages suggests that the approach developed in AlveolEye is generalizable across species. Notably, AlveolEye markedly reduced the average variation across individual analyzers, with the greatest improvement in precision among individuals with the least experience in performing lung morphometry. The design of AlveolEye is intentionally semi-automated, preserving the investigators ability to assess and adjust parameters based on sample characteristics. AlveolEye facilitates efficient lung morphological measurements on larger sample sizes, allowing for greater statistical power for preclinical studies, and improves precision across individual observers, allowing for improved rigor in experimental design and execution.

developmental biology↗

bioRxiv2025

Infants who develop BPD have an airway endotype defined by vimentin expression and ciliary loss

RationaleBronchopulmonary Dysplasia (BPD) results from abnormal lung development after preterm birth, with structural deficits at every respiratory tree level. BPD with lower airway disease is emerging as a clinically significant phenotype with increased mortality, and there is a significant knowledge gap in the molecular mechanisms whereby preterm birth disrupts normal airway development. ObjectivesTo develop a human model of lower airway disease after preterm birth and to characterize a molecular endotype of evolving BPD (eBPD) at baseline and in response to injury. MethodsWe used a combination of an ex vivo organotypic Airway Epithelial Cell (AEC models) and well-characterized pathologic and transcriptomic patient samples for quantitative immunohistochemistry and RNA sequencing analyses. Measurements and Main ResultsCompared to AECs from healthy patients, eBPD- derived AECs have a molecular endotype of reduced proliferation, impaired differentiation to ciliated epithelium, and an expanded vimentin-positive population with a transcriptional shift toward stromal cell-associated genes. With hyperoxia exposure, eBPD-derived AECs exhibited a pronounced vimentin response ex vivo, which parallels the increased vimentin expression of airway cells observed in lung tissue from human infants with BPD. ConclusionsIn this organotypic model of neonatal airway differentiation, we find that infants with eBPD have impaired differentiation, increased expression of vimentin, and concomitant loss of cilia, with an exaggerated increase in vimentin expression after hyperoxia injury, findings that mimic the effects of prematurity in airway cells in human patients. These data provide a foundation for future mechanistic studies interrogating the role of intermediate filaments in epithelial differentiation and repair.

cell biology↗

bioRxiv2025

Natural killer cell TGF- signaling regulates senolytic activity and vascular patterning in the postnatal lung

BackgroundBronchopulmonary dysplasia (BPD) is a disease of neonatal lung development that is linked to impaired pulmonary vascularization, dysregulated transforming growth factor-{beta} (TGF-{beta}) signaling and the accumulation of senescent cells. Despite the established role for TGF-{beta} signaling in promoting vascular remodeling and suppressing the senolytic activity of natural killer (NK) cells, the contribution of NK cell TGF-{beta} signaling to postnatal lung patterning and the pathogenesis of BPD remains unclear. MethodsMice bearing an NK cell-selective deletion of the type-II TGF-{beta} receptor (Tgfbr2NK-/-) were analyzed for vascular and alveolar structure, lung NK cell infiltration, senescence markers and lung function testing across neonatal and adult timepoints. Single-cell RNA sequencing of lung tissue from both neonatal mice and human infants with BPD was performed. The effect of enhanced NK cell activity in a hyperoxia-induced model of BPD was assessed in Tgfbr2NK-/-neonates, as well as pharmacologically, using the TGF-{beta} ligand trap/IL-15 superagonist, HCW9218. ResultsNeonatal Tgfbr2NK-/- mice exhibited a baseline reduction in distal arteriolar density, impaired alveolarization, and sex-specific deficits in long-term lung function. Single-cell RNA sequencing identified the excessive clearance of senescent endothelial cells by TGF-{beta} insensitive NK cells in the lungs of Tgfbr2NK-/- neonates, which served as a contributor of the BPD-like phenotype observed in naive animals. Tgfbr2NK-/- mice were protected from impaired lung development in the hyperoxia model. Sequencing from lung tissue from infants with BPD confirmed excessive TGF-{beta} signaling and cytotoxic impairment in NK cells. Treatment with HCW9218 prevented senescent cell accumulation and rescued lung development in the hyperoxia mouse model. ConclusionsThese findings identify TGF-{beta} as a tunable regulator of NK cell senolytic activity that is essential to normal postnatal lung development. Excessive NK cell TGF-{beta} signaling contributes to impaired lung development following exposure to neonatal hyperoxia and may serve as a viable therapeutic target for human BPD.

developmental biology↗

bioRxiv2025

A spatial transcriptomic atlas of acute neonatal lung injury across development and disease severity

A molecular understanding of lung organogenesis requires delineation of the timing and regulation of the cellular transitions that ultimately form and support a surface capable of gas exchange. While the advent of single-cell transcriptomics has allowed for the discovery and identification of transcriptionally distinct cell populations present during lung development, the spatiotemporal dynamics of these transcriptional shifts remain undefined. With imaging-based spatial transcriptomics, we analyzed the gene expression patterns in 17 human infant lungs at varying stages of development and injury, creating a spatial transcriptomic atlas of [~]1.2 million cells. We applied computational clustering approaches to identify shared molecular patterns among this cohort, informing how tissue architecture and molecular spatial relationships are coordinated during development and disrupted in disease. Recognizing that all preterm birth represents an injury to the developing lung, we created a simplified classification scheme that relies upon the routinely collected objective measures of gestational age and life span. Within this framework, we have identified cell type patterns across gestational age and life span variables that would likely be overlooked when using the conventional "disease vs. control" binary comparison. Together, these data represent an open resource for the lung research community, supporting discovery-based inquiry and identification of targetable molecular mechanisms in both normal and arrested human lung development.

genomics↗

bioRxiv2024

Bronchopulmonary Dysplasia with Pulmonary Hypertension Associates with Loss of Semaphorin Signaling and Functional Decrease in FOXF1 Expression

Lung injury in preterm infants leads to structural and functional respiratory deficits, with a risk for bronchopulmonary dysplasia (BPD) that in its most severe form is accompanied by pulmonary hypertension (PH). To examine cellular and molecular dynamics driving evolving BPD in humans, we performed single-cell RNA sequencing of preterm infant lungs in early stages of BPD and BPD+PH compared to term infants. Analysis of the endothelium revealed a unique aberrant capillary cell-state primarily in BPD+PH marked by ANKRD1 expression. Predictive signaling analysis identified deficits in the semaphorin guidance-cue signaling pathway and decreased expression of pro-angiogenic transcription factor FOXF1 within the alveolar parenchyma in neonatal lung samples with BPD/BPD+PH. Loss of semaphorin signaling was replicated in a murine BPD model and in humans with alveolar capillary dysplasia (ACDMPV), suggesting a mechanistic link between the developmental programs underlying BPD and ACDMPV and a critical role for semaphorin signaling in normal lung development.

genomics↗