Molecular phenotyping of Parkinson's disease

Parkinson's disease is among the most prevalent neurodegenerative diseases, clinically characterized by motor symptoms resulting from progressive degeneration of dopaminergic neurons in the ventral midbrain. Pathologically, Parkinson's disease is defined by the accumulation of alpha-synuclein aggregates, forming Lewy bodies and Lewy neurites. However, the disease exhibits heterogeneous symptoms. Motor symptoms can vary substantially between patients, and non-motor symptoms often precede and accompany disease progression. Furthermore, Lewy pathology extends beyond the ventral midbrain to other brain regions, underscoring systematic cellular dysregulation in Parkinson's disease.

Current standard treatment with levodopa, a dopamine precursor, can provide symptomatic relief. However, its effectiveness varies between patients and diminishes over time, and it fails to reverse disease progression. Cell replacement therapy has since emerged as a promising alternative, supported by the pioneering transplantation of human fetal tissue showing long-term benefits in some patients. However, the variability in outcomes and ethical concerns have since shifted the research focus toward human pluripotent stem cells (hPSCs)- based strategies, requiring robust differentiation protocols for generating authentic midbrain dopaminergic neurons.

This thesis broadens our understanding of ventral midbrain cellular heterogeneity through (1) Developing an improved hPSCs differentiation protocol by recapitulating key spatiotemporal developmental signals and introducing a single- cell RNA-seq-based quality assessment framework (Paper I); (2) Characterizing ventral midbrain cellular diversity in both human development and adult brain (Paper Il and III); and (3) Multiomic profiling of Parkinson's disease midbrain and nearby regions, revealing disease-associated transcriptional dysregulation (Preliminary work).

This thesis begins with a literature review on ventral midbrain development, Parkinson's disease, and single-cell genomics to contextualize the work. Subsequent chapters then present and discuss the results from the studies included in this thesis.

List of scientific papers

I. Single-cell transcriptomics reveals correct developmental dynamics and high-quality midbrain cell types by improved hESC differentiation.

Nishimura, K., Yang, S., Lee, K.W., Ásgrímsdóttir, E.S., Nikouei, K., Paslawski, W., Gnodde, S., Lyu, G., Hu, L., Salto, C., Svenningsson, P., Hjerling-Leffler, J., Linnarsson, S. and Arenas. E.

Stem Cell Reports, 2022, 18(1), pp.337-353. https://doi.org/10.1016/j.stemcr.2022.10.016

II. Comprehensive cell atlas of the first-trimester developing human brain.

Braun, E., Danan-Gotthold, M., Borm, L.E., LEE, K.W., Vinsland, E., Lönnerberg, P., Hu, L., Li, X., He, X., Andrusivová, Ž., Lundeberg, J., Barker, R.A., Arenas, E., Sundström, E. and Linnarsson. S.

Science, 2023, 382(6667):eadf1226. https://doi.org/10.1126/science.adf1226

III. Transcriptomic diversity of cell types across the adult human brain.

Siletti, K., Hodge, R.D., Albiach, A.M., LEE, K.W., Ding, S.L., Hu, L., Lönnerberg, P., Bakken, T.E., Casper, T., Clark, M., Dee, N., Gloe, J., Hirschstein, D., Shapovalova, N.V., Keene, C.D., Nyhus, J., Tung, H., Yanny, A.M., Arenas, E., Lein, E.S. and Linnarsson, S.

Science, 2023, 382(6667):eadd7046. https://doi.org/10.1126/science.add7046