Mapping of Brain Repair in Parkinson's Disease Using Spatial Transcriptomics

Abstract

Spatial transcriptomics is a recently developed method for analyzing the transcriptome while conserving the spatial information. Albeit not with single resolution as of now, it has a big potential for application in tissues in which the exact spatial information of gene expression is crucial. One of those cases are brain transplants aimed for replacing lost cell populations, e.g. in stroke or neurodegenerative disease. In the case of Parkinson's disease, human embryonic stem cells (hESC) derived dopaminergic neuron transplants can be used to alleviate the motor impairment associated with it. Spatial transcriptomics offers a way to assess the transcription profiles of the transplant and explore the functional identities of its cells to gain more information.
Native dopaminergic (DAergic) neurons of substantia nigra (A9 group) degenerate in Parkinson's disease, which is otherwise marked by α-synuclein self-aggregation and Lewy Bodies formation. The death of the A9 DAergic neurons causes lack of dopamine in the dorsolateral striatum involved in the motor functions, which causes Parkinson's disease most obvious motor symptoms, such as postural rigidity, bradykinesia, and tremor. Depletion of the same neurons in a rat model by DAergic-neuron specific neurotoxin causes the animals to attain Parkinson-like motor symptoms.
Through supplying dopamine-producing cells in the form of hESC derived DAergic transplant virtually identical to the missing population, motor functions can be significantly improved in the animal models. Translation of this research into clinical practice could mean a significant, if potentially temporary, symptomatic relief for patients suffering with Parkinson's disease.
By examining the transcriptomes of brain tissue of animals with hESC derived transplants, it is possible to compare the identities of cells within different morphological layers and asses the similarity of substantia nigra or other brain regions to the transplanted cells on the transcriptome level. Thus, detailed information about the transplant integration in the host and its interactions with its environment can be deduced based on the spatial transcriptome data and used to gain insight into the cell interactions and further improve methods used in cellular therapy for Parkinson's disease.

Popular Abstract

Parkinson's disease is a progressive neurodegenerative condition manifested with physical symptoms including slowness of movement, shaking and difficulty initiating movements as well as mental symptoms including dementia, pain, or loss of smell. Its physical symptoms can be largely attributed by the death of dopamine producing cells in the brain supplying the neurotransmitter into brain regions responsible for movement initiation and control.
Currently, this condition is managed by oral drugs, most common being oral supplementation with dopamine precursor L-dopa. Other options include deep brain stimulation or working therapy. However, none of these therapies manage to regenerate the brain to the original state, they only partially alleviate symptoms, often with noticeable side-effects. With efforts to regenerate damaged brain regions, cell therapy has entered pictures with the promise to replace the cells lost in the disease with functionally identical cells. These cells can have multiple sources, this thesis focuses on one of them, human embryonic stem cells, which are being used in many of the current transplantation clinical trials.
For the cells to have the desired therapeutic effect, the cells have to attain virtually the same identity as the population lost. A way to verify the cell identities is through analysis of their overall gene expression profile and through expression of genes unique to certain cell populations. Spatial transcriptomics is a method, which is able to extract information about genes expressed in a tissue and keep the information about the place of their expression. This information can then be connected to the tissue and identities of cells in throughout the tissue can be reconstructed. This allows among other things for visualization of patterns of gene expression within specific areas of the tissue, for example cell transplants or damaged or degenerated brain areas.
Within spatial transcriptomics method, tissue sections of interest are fixated on a slide containing feature 100 µm wide in diameter containing probes able of capturing mRNA and also featuring information about their position in a form of specific DNA sequence present prior to the mRNA binding site forming a spatial tag. When the tissue is disrupted, mRNA from inside the cells is released and immediately bound by the probes on the surface. These probes bind mRNA by featuring a sequence to the complementary to the polyadenylated end of released mRNA. Captured mRNA is then processed and sequenced. With the sequences of the genes and the spatial tags known, the expression of this gene can be shown throughout the whole tissue.
By combining spatial transcriptomics and cell therapy, it is possible to monitor the integration, development and environmental influences on the cellular transplant and gain information valuable for the therapy development not only in Parkinson's disease.
In this thesis, a tissue with transplant is analyzed through spatial transcriptomics with the goal of exploring expression of genes specific for dopamine producing neurons found in healthy population in substantia nigra. The overall gene expression of in the transplant area should be compared with that of substantia nigra as well as with the tissue the transplant is embedded in to assess the semblance of the expression profile of functionally varied areas. Similarities and differences found can provide valuable information, which can be used for improvement of the transplant injection site or cell preparation techniques and contribute to the optimization of cell therapy methods.

• author: Rajova, Jana
• supervisor: Tomas Björklund
• organization: Pure and Applied Biochemistry
• course: KBKM01 20181
• year: 2018
• type: H2 - Master's Degree (Two Years)
• subject: Biology and Life Sciences
• keywords: spatial transcriptomics, transcriptome, Parkinson's disease, cell therapy, hESC, transplant, molecular barcode, applied biochemistry
• language: English
• id: 8951089
• date added to LUP: 2022-08-01 12:27:05
• date last changed: 2022-08-01 12:27:05