Transcriptome analysis of genetically matched human induced pluripotent stem cells disomic or trisomic for chromosome 21
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Abstract
Trisomy of chromosome 21, the genetic cause of Down syndrome, has the potential to alter expression of genes on chromosome 21, as well as other locations throughout the genome. These transcriptome changes are likely to underlie the Down syndrome clinical phenotypes. We have employed RNA-seq to undertake an in-depth analysis of transcriptome changes resulting from trisomy of chromosome 21, using induced pluripotent stem cells (iPSCs) derived from a single individual with Down syndrome. These cells were originally derived by Li et al, who genetically targeted chromosome 21 in trisomic iPSCs, allowing selection of disomic sibling iPSC clones. Analyses were conducted on trisomic/disomic cell pairs maintained as iPSCs or differentiated into cortical neuronal cultures. In addition to characterization of gene expression levels, we have also investigated patterns of RNA adenosine-to-inosine editing, alternative splicing, and repetitive element expression, aspects of the transcriptome that have not been significantly characterized in the context of Down syndrome. We identified significant changes in transcript accumulation associated with chromosome 21 trisomy, as well as changes in alternative splicing and repetitive element transcripts. Unexpectedly, the trisomic iPSCs we characterized expressed higher levels of neuronal transcripts than control disomic iPSCs, and readily differentiated into cortical neurons, in contrast to another reported study. Comparison of our transcriptome data with similar studies of trisomic iPSCs suggests that trisomy of chromosome 21 may not intrinsically limit neuronal differentiation, but instead may interfere with the maintenance of pluripotency.
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Genome-wide dysregulation of gene expression in neurons likely leads to over-expression and/or under-expression of key genes that regulate synaptogenesis.
“Genome-wide dysregulation of gene expression (Box 3) in neurons likely leads to over-expression and/or under-expression of key genes that regulate synaptogenesis, but specific candidates have yet to be identified74,77,81,143.”
From Consequences of trisomy 21 for brain development in Down syndrome (2024) · cites this paper as [143]
The Results (‘Gene expression in trisomic cells’; page unavailable) report 1,377 transcripts differentially expressed between trisomic and disomic neuronal cultures, including changes in synaptic-signaling categories. They do not establish that these changes affect genes regulating synaptogenesis or lead to altered synapse formation; the paper also cautions that the neuronal cultures may not have differentiated equivalently. (LLM, conf=0.84)
Experimental — accuracy not yet measuredT21 impacts gene expression across the genome.
“However, unbiased analyses using omics technology have recently revealed that T21 impacts gene expression across the genome39,74,143,156–159.”
From Consequences of trisomy 21 for brain development in Down syndrome (2024) · cites this paper as [143]
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Additional file 3 of Restoration of keratinocytic phenotypes in autonomous trisomy-rescued cells
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Additional file 4 of Restoration of keratinocytic phenotypes in autonomous trisomy-rescued cells
Tanuma‐Takahashi, A., Inoue, M., Kajiwara, K., Takagi, R., Yamaguchi, A., Samura, O., Akutsu, H., Sago, H., Kiyono, T., Okamoto, A., et al. (2021) · Figshare · doi:10.6084/m9.figshare.16442118
Additional file 5 of Restoration of keratinocytic phenotypes in autonomous trisomy-rescued cells
Tanuma‐Takahashi, A., Inoue, M., Kajiwara, K., Takagi, R., Yamaguchi, A., Samura, O., Akutsu, H., Sago, H., Kiyono, T., Okamoto, A., et al. (2021) · Figshare · doi:10.6084/m9.figshare.16442124
Larsen, E. C., Moon, J. E., King, O. D., & Lawrence, J. B. (2026) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2026.02.014
Trisomy 21 Drives ADARB1 Overexpression and Premature RNA Recoding in the Developing Fetal Brain
Breen, M. S., Yang, A., Wang, X., Santos, M. R. D. L., Ran, T. A. O., Weinberger, D. R., Kleinman, J. E., Mihova, K. Y., Stancheva, G. S., Savova, S., et al. (2026) · Nature Communications · doi:10.1038/s41467-026-70217-5
- Authors
- Gonzales, P. K., Roberts, C. M., Fonte, V., Jacobsen, C., Stein, G. H., & Link, C. D.
- Affiliations
- University of Colorado Boulder (US)
- Corresponding author
- Gonzales, Patrick K.
- Roberts, Christine M.
- Jacobsen, Connor
- Stein, Gretchen H.
- Link, Christopher D.
- Venue
- PLOS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2018-03-27
- Volume
- 13
- Issue
- 3
- Pages
- e0194581
- ISSN
- 1932-6203 (ISSN-L)
- PMC
- PMC5870938
- OpenAlex
- W2949064102
- Cited by
- 45
- References
- 45
- Citations by year
- 2026: 2 · 2025: 1 · 2024: 7 · 2023: 4 · 2022: 9 · 2021: 12 · 2020: 8 · 2019: 2
- FWCI
- 5.24
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- PLoS ONE (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- CU Scholar (University of Colorado Boulder) (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Figshare (submittedVersion, cc-by)
- Funders
- Linda Crnic Institute for Down Syndrome (pilot grant)
- Topics
- Health Sciences › Medicine › Public Health, Environmental and Occupational Health › Down syndrome and intellectual disability research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Pluripotent Stem Cells Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Keywords
- Down syndrome, induced pluripotent stem cells, transcriptome, alternative splicing, RNA editing, repetitive elements, cortical neuron differentiation, pluripotency, gene expression changes
- MeSH terms
- Cell Differentiation, Cell Line, Chromosomes, Human, Pair 21, Down Syndrome, Humans, Neurons, Trisomy, RNA Editing, Alternative Splicing, Sequence Analysis, RNA, Gene Expression Profiling, Induced Pluripotent Stem Cells, Transcriptome
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