bioRxiv Science⌕ Search

Biology subjects

Beckerman, P.

Publications and source records attributed to Beckerman, P..

2 recordsLinked to original sources

Amniotic Fluid Organoids As Personalized Tools For Real-Time Modeling Of The Developing Fetus

Despite biomedical advances, major knowledge gaps regarding human development remain, and many developmental disorders lack effective treatment, representing a huge clinical burden. This results from fetuses being largely inaccessible for analysis. Here, we employ fetal cells in human amniotic fluid (AF) to establish personalized fetal kidney and lung organoids (AFKO and AFLO, respectively), recapitulating fetal organs at single-cell resolution. AFKO harbor key fetal kidney cell populations, including nephrogenic, urothelial and stromal, endocytose albumin, and model PAX2-related anomalies. Strikingly, upon injection into the nephrogenic cortex of human fetal kidney explants, AFKO-derived progenitors integrate into the host progenitor niche and contribute to developing nephrons. AFLO comprise alveolar cells and most airway cell types in a typical pseudostratified structure, upregulate surfactant expression upon corticosteroid treatment, and show functional CFTR channels. Overall, this platform represents a new personalized tool that can be applied to virtually any fetus in real-time, affording unprecedented options in studying development, uncovering mechanisms of in utero pathologies (e.g., congenital anomalies, infections or chemical teratogens) deciphering the developmental origins of chronic diseases, and tailoring treatments for these pathologies, as well as for prematurity-related complications. Importantly, since AF contains cells from additional tissues (e.g., skin and gastrointestinal tract), and is derived in a procedure already performed in many patients, this platform may well become a broadly applicable tool in fetal medicine.

developmental biology↗

Kidney-specific methylation patterns correlate with kidney function and are lost upon kidney disease progression

Chronological and biological age correlate with DNA methylation levels at specific sites in the genome. Linear combinations of multiple methylation sites, termed epigenetic clocks, can inform us of the chronological age and predict multiple health-related outcomes. However, why some sites correlate with lifespan, healthspan, or specific medical conditions remains poorly understood. Kidney fibrosis is the common pathway for Chronic Kidney Disease, which affects 10% of Europe and USA population. Here we identify epigenetic clocks and methylation sites that correlate with kidney function. Moreover, we identify methylation sites that have a unique methylation signature in the kidney. Methylation levels in the majority of these sites correlates with kidney state and function. When kidney function deteriorates, all of these sites regress towards the common methylation pattern observed in other tissues. Interestingly, while the majority of sites are less methylated in the kidney and become more methylated with loss of function, a fraction of the sites are highly methylated in the kidney and become less methylated when kidney function declines. These methylation sites are enriched for specific transcription-factor binding sites. In a large subset of sites, changes in methylation pattern are accompanied by changes in gene expression in kidneys of chronic kidney disease patients. These results support the information theory of aging, and the hypothesis that the unique tissue identity, as captured by methylation patterns, is lost as tissue function declines. However, this information loss is not random, but guided towards a baseline that is dependent on the genomic loci.

bioinformatics↗