| 1. |
- Eisfeldt, Jesper, et al.
(författare)
-
Multi-Omic Investigations of a 17-19 Translocation Links MINK1 Disruption to Autism, Epilepsy and Osteoporosis
- 2022
-
Ingår i: International Journal of Molecular Sciences. - : MDPI. - 1661-6596 .- 1422-0067. ; 23:16
-
Tidskriftsartikel (refereegranskat)abstract
- Balanced structural variants, such as reciprocal translocations, are sometimes hard to detect with sequencing, especially when the breakpoints are located in repetitive or insufficiently mapped regions of the genome. In such cases, long-range information is required to resolve the rearrangement, identify disrupted genes and, in symptomatic carriers, pinpoint the disease-causing mechanisms. Here, we report an individual with autism, epilepsy and osteoporosis and a de novo balanced reciprocal translocation: t(17;19) (p13;p11). The genomic DNA was analyzed by short-, linked- and long-read genome sequencing, as well as optical mapping. Transcriptional consequences were assessed by transcriptome sequencing of patient-specific neuroepithelial stem cells derived from induced pluripotent stem cells (iPSC). The translocation breakpoints were only detected by long-read sequencing, the first on 17p13, located between exon 1 and exon 2 of MINK1 (Misshapen-like kinase 1), and the second in the chromosome 19 centromere. Functional validation in induced neural cells showed that MINK1 expression was reduced by >50% in the patient's cells compared to healthy control cells. Furthermore, pathway analysis revealed an enrichment of changed neural pathways in the patient's cells. Altogether, our multi-omics experiments highlight MINK1 as a candidate monogenic disease gene and show the advantages of long-read genome sequencing in capturing centromeric translocations.
|
|
| 2. |
- Schuy, Jakob
(författare)
-
Complex genomic rearrangements in rare brain disorders : genetic architecture and molecular consequences
- 2023
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Structural variants (SVs) within the genome, such as deletions, duplications, inversions, and translocations, are common but underappreciated causes of rare diseases. Complex genomic rearrangements involving two or more SVs in cis are incredibly challenging to detect. The genome is analyzed using sequencing technologies to understand such events and their underlying mechanisms. Patient-specific cell models help deepen the understanding of the mechanism causing disease. Paper I investigated patient-derived neural cells from an individual with a ring chromosome 21 and partial monosomy 21, and with two individuals with trisomy 21. RNA-Seq revealed 13.7% differential expression genome-wide in the ring 21 cells. When comparing the ring 21 cells to trisomy 21 lines, approximately 8.8% of all genes showed contrasting expression patterns, with some genes being upregulated in cells with trisomy 21 while downregulated in ring 21 cells and vice versa. Paper II utilized Nanopore long-read genome sequencing to map a challenging balanced translocation between the short arm of chromosome 17 and the centromere of chromosome 19. The event had occurred de novo in an individual with autism, congenital cataract, epilepsy, and osteoporosis. A candidate gene, MINK1, was disrupted, leading to reduced RNA levels of MINK1 in patient-derived neural cells shown with RNA-Seq and qPCR. Paper III focused on three individuals with developmental delay and complex chromosomal rearrangements spanning chromosome 21. Following short-read and longread genome sequencing and optical genome mapping, we identified 15, 8, and 26 breakpoints in each patient. Using the T2T-CHM13 assembly, we showed that the satellite region of 21p was involved in all three events. Paper IV examined three individuals with CTNND2 disruptions. Using patient-derived neural cells and brain organoids, we demonstrated that CTNND2 plays a crucial role in neurogenesis and cell proliferation, mainly through the WNT signaling pathway. When this pathway was not externally stimulated, it partially rescued the cellular and transcriptional abnormalities.
|
|
| 3. |
- Schuy, Jakob, et al.
(författare)
-
Partial Monosomy 21 Mirrors Gene Expression of Trisomy 21 in a Patient-Derived Neuroepithelial Stem Cell Model
- 2022
-
Ingår i: Frontiers in Genetics. - : Frontiers Media SA. - 1664-8021. ; 12
-
Tidskriftsartikel (refereegranskat)abstract
- Induced pluripotent stem cells (iPSCs) from patients are an attractive disease model to study tissues with poor accessibility such as the brain. Using this approach, we and others have shown that trisomy 21 results in genome-wide transcriptional dysregulations. The effects of loss of genes on chromosome 21 is much less characterized. Here, we use patient-derived neural cells from an individual with neurodevelopmental delay and a ring chromosome 21 with two deletions spanning 3.8 Mb at the terminal end of 21q22.3, containing 60 protein-coding genes. To investigate the molecular perturbations of the partial monosomy on neural cells, we established patient-derived iPSCs from fibroblasts retaining the ring chromosome 21, and we then induced iPSCs into neuroepithelial stem cells. RNA-Seq analysis of NESCs with the ring chromosome revealed downregulation of 18 genes within the deleted region together with global transcriptomic dysregulations when compared to euploid NESCs. Since the deletions on chromosome 21 represent a genetic “contrary” to trisomy of the corresponding region, we further compared the dysregulated transcriptomic profile in with that of two NESC lines with trisomy 21. The analysis revealed opposed expression changes for 23 genes on chromosome 21 as well as 149 non-chromosome 21 genes. Taken together, our results bring insights into the effects on the global and chromosome 21 specific gene expression from a partial monosomy of chromosome 21qter during early neuronal differentiation.
|
|
