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Kubis, J.

Publications and source records attributed to Kubis, J..

2 recordsLinked to original sources

Identification of neurodevelopmental organization of the cell populations of juvenile Huntington's disease using dorso-ventral HD organoids and HD mouse embryos

Huntingtons disease (HD), especially juvenile-onset HD (JOHD), involves early neurodevelopmental pathogenesis alongside the gradual breakdown of the corticostriatal neural axis. To better understand this mechanism, we created fused dorsal-ventral forebrain organoids from induced pluripotent stem cells (iPSCs) from JOHD to mimic early corticostriatal interactions in the disease. We observed characteristic growth phenotypes in HD organoids and found that these phenotypes were influenced by paracrine signals from opposite regions (dorsal-ventral and ventral-dorsal). These phenotypes were only partially rescued by conditioning with medium in HD compared to control organoids. We also investigated humanized HD embryonic mouse forebrains at E13.5 to validate the phenotypes. Using single-cell RNA sequencing (scRNAseq) and immunofluorescence of the internal structure of HD organoids, we observed early neurodevelopmental signs, including stalling during the phase of increased progenitor cell growth, delayed neuron maturation, and disrupted patterning between pallial and subpallial regions. A consistent feature across in vitro and in vivo models was an abnormal expansion of transthyretin (TTR)-positive cells resembling choroid plexus (ChP), along with ectopic expression of neuronal factors in ChP and a reduction in populations expressing intermediate progenitor and interneuron markers. In mosaic organoids that combined healthy and JOHD tissues, the healthy environment helped reduce ChP overgrowth and restore normal progenitor and neuronal development. This suggests that some developmental defects caused by mutant HTT are reversible and influenced by non-cell-autonomous factors. Overall, these findings point to early ChP-related abnormalities as a key aspect of JOHD neurodevelopmental disturbance and propose the ChP-CSF environment as an important area for future mechanistic studies and potential therapies.

developmental biology↗

The Cell Subtypes Selection by Genes (CSSG) algorithm for discovering cell populations in high resolution

The recent massive improvements in transcriptomics and single-cell technologies have led to a rising volume of data and demand for advances in bioinformatics processing. Existing methods are not fully capable of discovering genetic markers responsible for high-resolution cellular tissue heterogeneity, cell lineages during organism development, and cell differentiation with rare intermediate populations. In response to demand, we have generated a new Cell Subtypes Selection by Genes (CSSG) algorithm which is supported by a dedicated and fully automatic JSEQ(R) pipeline. The new CSSG algorithm is iterative, parallel, and able to make decisions for discovering cell populations in tissues based on transcript occurrence in cells. The CSSG/JSEQ is complemented by a new strategy and specialized algorithm for the naming of cell populations. Our approach allows for high-resolution tracing of cell populations, finding relations and hierarchy between them, particularly important for complex tissues such as the brain. The pipeline allows the establishment of developmental, differentiation, and pathogenic trajectory and takes a "snapshot" of a current physiological or pathological cellular stage of the investigated organ at the transcriptional level.

bioinformatics↗