Asynchronous excitatory neuron development in an isogenic cortical spheroid model of Down syndrome

Abstract

The intellectual disability (ID) in Down syndrome (DS) is thought to result from a variety of developmental deficits such as alterations in neural progenitor division, neurogenesis, gliogenesis, cortical architecture, and reduced cortical volume. However, the molecular processes underlying these neurodevelopmental changes are still elusive, preventing an understanding of the mechanistic basis of ID in DS. In this study, we used a pair of isogenic (trisomic and euploid) induced pluripotent stem cell (iPSC) lines to generate cortical spheroids (CS) that model the impact of trisomy 21 on brain development. Cortical spheroids contain neurons, astrocytes, and oligodendrocytes and they are widely used to approximate early neurodevelopment. Using single cell RNA sequencing (scRNA-seq), we uncovered cell type-specific transcriptomic changes in the trisomic CS. In particular, we found that excitatory neuron populations were most affected and that a specific population of cells with a transcriptomic profile resembling layer IV cortical neurons displayed the most profound divergence in developmental trajectory between trisomic and euploid genotypes. We also identified candidate genes potentially driving the developmental asynchrony between trisomic and euploid excitatory neurons. Direct comparison between the current isogenic CS scRNA-seq data and previously published datasets revealed several recurring differentially expressed genes between DS and control samples. Altogether, our study highlights the power and importance of cell type-specific analyses within a defined genetic background, coupled with broader examination of mixed samples, to comprehensively evaluate cellular phenotypes in the context of DS.

Shaking up the silence: consequences of HMGN1 antagonizing PRC2 in the Down syndrome brain

“…Individuals with DS have an 18% reduction in brain volume as compared to those without DS, and this decrease can be detected as early as the second trimester [ 8 , 204 , 205 ]. This is recapitulated in the iPSC-based three-dimensional models (organoids and spheroids), which show a decrease in the size of DS-derived cortical organoids [ 206 ] and in our own work utilizing cortical spheroids [ 207 ] as well as in the Ts65Dn mouse model [ 208 ]. It is noteworthy that in the mouse and human cerebellum, there is also a decrease in the number of granule and Purkinje cells [ 10 , 200 , 209 , 210 ].…”

“…Similarly, HSA21 genes DSCAM and DYRK1A have been implicated in the dysregulated neuronal migration and cortical lamination in DS [ 206 , 219 ]. Deficient neuronal motility and the dysregulation of the “roundabout” signaling pathway have been widely observed in DS [ 176 , 207 , 237 ]. Importantly, genes, such as ROBO2, ROBO4, and SLIT2 , which mediate neuronal migration and axon guidance, appear to be targeted by EZH2 and SUZ-12 [ 68 , 235 , 236 ].…”

“…An enhanced rate of apoptosis has also been found in certain regions of the DS brain, including the hippocampus [ 9 ], cerebral cortex [ 14 , 244 ], cerebellum [ 244 ], as well as in the DS iPSC-derived NPCs [ 217 ], and cortical spheroids [ 207 ]. Increased neuronal cell death was detected in DS fetal brain [ 244 ] and the brains of middle-aged DS individuals [ 245 ].…”

Extracellular Vesicle Treatment Alleviates Neurodevelopmental and Neurodegenerative Pathology in Cortical Spheroid Model of Down Syndrome

“…These changes have been recapitulated recently in DS-derived three-dimensional cellular model organoids. Studies from our laboratory and others [ 33 , 35 ] demonstrated deficient detection of the neurons populating deep and superficial cortical layers in trisomic organoids. Furthermore, using single-cell transcriptomic studies, we found a particular vulnerability of trisomic excitatory neurons, transcriptomically corresponding to cortical layer IV [ 35 ], contributing further to the aberrant cortical development in DS.…”

“…In the current study, we used induced pluripotent stem cell (iPSC) isogenic lines derived from human patients with DS to generate cortical spheroids (CS) (or organoids) following a published protocol [ 58 ]. These CS contain several types of neural progenitor cells and excitatory neurons as well as inhibitory neurons, oligodendrocytes, and astrocytes [ 35 ] and recapitulate the developmental trajectory of an embryonic brain at mid-gestation [ 58 , 59 ].…”