Biology subjects

Al Alam, D.

Publications and source records attributed to Al Alam, D..

4 recordsLinked to original sources

bioRxiv2023

A Trisomy 21 Lung Cell Atlas

Trisomy 21 (T21), resulting in Down Syndrome (DS), is the most prevalent chromosomal abnormality worldwide. While pulmonary disease is a major cause of morbidity and mortality in DS, the ontogeny of pulmonary complications remains poorly understood. We recently demonstrated that T21 lung anomalies, including airway branching and vascular lymphatic abnormalities, are initiated in utero. Here, we aimed to describe molecular changes at the single cell level in prenatal T21 lungs. Our results demonstrate differences in the proportion of cell populations and detail changes in gene expression at the time of initiation of histopathological abnormalities. Notably, we identify shifts in the distribution of alveolar epithelial progenitors, widespread induction of key extracellular matrix molecules in mesenchymal cells and hyper-activation of IFN signaling in endothelial cells. This single cell atlas of T21 lungs greatly expands our understanding of antecedents to pulmonary complications and should facilitate efforts to mitigate respiratory disease in DS.

developmental biology↗

bioRxiv2022

Fgfr2b signaling is essential for the maintenance of the alveolar epithelial type 2 lineage during lung homeostasis in mice

Fibroblast growth factor receptor 2b (Fgfr2b) signaling is essential throughout lung development to form the alveolar epithelial lineage. However, its role in alveolar epithelial type 2 cells (AT2s) homeostasis was recently considered dispensable. SftpcCreERT2; tdTomatoflox/flox mice were used to delete Fgfr2b expression in cells belonging to the AT2 lineage, which contains mature AT2s and a novel SftpcLow lineage-traced population called "injury activated alveolar progenitors" or IAAPs. Upon continuous tamoxifen exposure for either one or two weeks to delete Fgfr2b, a shrinking of the AT2s is observed. Mature AT2s exit the cell cycle, undergo apoptosis and fail to form alveolospheres in vitro. However, the lung morphometry appears normal, suggesting the involvement of compensatory mechanisms. In mutant lungs, IAAPs which escaped Fgfr2b deletion expand, display enhanced alveolosphere formation in vitro and increase drastically their AT2 signature suggesting differentiation towards mature AT2s. Interestingly, a significant increase in AT2s and decrease in IAPPs occurs after a one-week tamoxifen exposure followed by an eight-week chase period. While mature AT2s partially recover their alveolosphere formation capabilities, the IAAPs no longer display this property. Single-cell RNA seq analysis confirms that AT2s and IAAPs represent stable and distinct cell populations and recapitulate some of their characteristics observed in vivo. Our results underscore the essential role played by Fgfr2b signaling in the maintenance of the AT2 lineage in the adult lung and suggest that the IAAPs could represent a new population of AT2 progenitors.

developmental biology↗

bioRxiv2020

Single cell transcriptomic profiling identifies molecular phenotypes of newborn human lung cells

RationaleWhile animal model studies have extensively defined mechanisms controlling cell diversity in the developing mammalian lung, the limited data available from late stage human lung development represents a significant knowledge gap. The NHLBI Molecular Atlas of Lung Development Program (LungMAP) seeks to fill this gap by creating a structural, cellular and molecular atlas of the human and mouse lung. MethodsSingle cell RNA sequencing generated transcriptional profiles of 5500 cells obtained from two one-day old human lungs (born at gestational ages of 39 and 31 weeks) from the LungMAP Human Tissue Core Biorepository at the University of Rochester. Frozen single cell isolates were captured, and library preparation was completed on the Chromium 10X system. Data was analyzed in Seurat, and cellular annotation was performed using the ToppGene functional analysis tool. Single cell sequence data from 32000 postnatal day 1, 3, 7 and 10 mouse lung (n = 2 at each time point) cells generated by the LungMAP Research Center at Cincinnati Childrens Hospital and Medical Center, using Dropseq platform, was integrated with the human data. In situ hybridization was used to confirm the spatial location of cellular phenotypes. ResultsTranscriptional interrogation of donor newborn human lung cells identified distinct clusters representing multiple populations of epithelial, endothelial, fibroblasts, pericytes, smooth muscle, and immune cells and signature genes for each of these populations were identified. Computational integration of newborn human and postnatal mouse lung development cellular transcriptomes facilitated the identification of distinct cellular lineages among all the major cell types. Integration of the human and mouse cellular transcriptomes also demonstrated cell type-specific differences in developmental states of the newborn human lung cells. In particular, matrix fibroblasts could be separated into those representative of younger cells (n=393), or older cells (n=158). This is the first comprehensive molecular map of the cellular landscape of neonatal human lung, including biomarkers for cells at distinct states of development. Our results indicate that integrated single cell RNA profiling of human and mouse lung will help identify common and species-specific mechanisms of lung development and respiratory disease.

genomics↗

bioRxiv2017

On growth and form of the distal air exchange surfaces within the lung.

Herein we show, using several novel imaging and computational approaches, how the air exchange units (AEUs) of the lung develop from the tips and sides of distinct families of tortuous ducts, that themselves ramify as distinct families distal to the bronchoalveolar duct junctions (BADJs), prenatally in humans but postnatally in mice. The mature AEUs thus consist of indented spheroids tightly packed between quite regularly spaced distal ducts. Since the diameter of the BADJs and the distal ducts increases rather than decreasing during the formation of AEUs, we further deduce that the AEUs must form by circular epithelial precursor buckling at their mouths with resulting extrusion of their lumen into the surrounding mesenchyme, stabilized firstly by interlocking rings of elastin and later by rings of elastin and collagen fibers surrounding the mouth of each of the prospective AEUs. Furthermore, we show that the surface of each of the AEUs is highly rugose, being indented by the capillary network that lies close beneath the AES membranes. We propose that, the kissing theorem proposed of Newton that expresses the number of times billiard balls may touch within their frame is a parsimonious solution to achieving optimum packing of the distal AES unit spaces, while allowing sufficient space between them to allow for conducting airways, closely applied pulsatile capillary blood vessels, lymphatics, nerves and other key components of the interstitial mesenchyme.\n\nSummary statementEmploying novel imaging and computational approaches we here deduce some new concepts as to how the distal shaping of airway lineage stem and progenitor cells may contribute to the growth and form of the air exchange surface (AES) of the lung, distal to the bronchoalveolar duct junction (BADJ). We then propose that the AES extrudes from the sides and tips of distinct families of small ducts, apparently by buckling of the thinning luminal epithelium into the surrounding mesenchyme, stabilized firstly by rings of elastin and later by rings of collagen and elastin fibers, that surround the mouth of each distal unit of the AES. We propose this mechanism as a parsimonious solution to achieving the optimum form, packing density and functional efficiency of the AES, while allowing sufficient space between for the plumbing of conducting airways, pulsatile capillary blood vessels, lymphatics, nerves and other key matrix and cellular components within the interstitial mesenchyme.

developmental biology↗