Large-scale transcriptomics data studies revolutionised the fields of systems biology and medicine, allowing to generate deeper mechanistic insights into biological pathways and molecular functions. However, conventional bulk RNA-sequencing results in the analysis of an averaged signal of many input cells, which are homogenised during the experimental procedure.
Hence, those insights represent only a coarse-grained picture, potentially missing information from rare or unidentified cell types. Allowing for an unprecedented level of resolution, single-cell transcriptomics may help to identify and characterise new cell types, unravel developmental trajectories, and facilitate inference of cell type-specific networks. Besides all these tempting promises, there is one main limitation that currently hampers many downstream tasks: single-cell RNA-sequencing data is characterised by a high degree of sparsity.
Due to this limitation, no reliable network inference tools allowed to disentangle the hidden information in the single-cell data.
Single-cell correlation networks likely hold previously masked information and could allow inferring new insights into cell type-specific networks. To harness the potential of single-cell transcriptomics data, this dissertation sought to evaluate the influence of data dropout on network inference and how this might be alleviated. However, two premisses must be met to fulfil the promise of cell type-specific networks: (I) cell type annotation and (II) reliable network inference. Since any experimentally generated scRNA-seq data is associated with an unknown degree of dropout, a benchmarking framework was set up using a synthetic gold data set, which was subsequently affected with different defined degrees of dropout. Aiming to desparsify the dropout-afflicted data, the influence of various imputations tools on the network
structure was further evaluated. The results highlighted that for moderate dropout levels, a deep count autoencoder (DCA) was able to outperform the other tools and the unimputed data. To fulfil the premiss of cell type annotation, the impact of data imputation on cell-cell correlations was investigated using a human retina organoid data set. The results highlighted that no imputation tool intervened with cell cluster annotation.
Based on the encouraging results of the benchmarking analysis, a window of opportunity was identified, which allowed for meaningful network inference from imputed single-cell RNA-seq data. Therefore, the inference of cell type-specific networks subsequent to DCA-imputation was evaluated in a human retina organoid data set. To understand the differences and commonalities of cell type-specific networks, those were analysed for cones and rods, two closely related photoreceptor cell types of the retina. Comparing the importance of marker genes for rods and cones between their respective cell type-specific networks exhibited that these genes were of high importance, i.e. had hub-gene-like properties in one module of the corresponding network but were of less importance in the opposing network. Furthermore, it was analysed how many hub genes in general preserved their status across cell type-specific networks and whether they associate with similar or diverging sub-networks. While a set of preserved hub genes was identified, a few were linked to completely different network structures. One candidate was EIF4EBP1, a eukaryotic translation initiation factor binding protein, which is associated with a retinal pathology called age-related macular degeneration (AMD). These results suggest that given very defined prerequisites, data imputation via DCA can indeed facilitate cell type-specific network inference, delivering promising biological insights.
Referring back to AMD, a major cause for the loss of central vision in patients older than 65, neither the defined mechanisms of pathogenesis nor treatment options are at hand. However, light can be shed on this disease through the employment of organoid model systems since they resemble the in vivo organ composition while reducing its complexity and ethical concerns. Therefore, a recently developed human retina organoid system (HRO) was investigated using the single-cell toolbox to evaluate whether it provides a useful base to study the defined effects on the onset and progression of AMD in the future. In particular, different workflows for a robust and in-depth annotation of cell types were used, including literature-based and transfer learning approaches. These allowed to state that the organoid system may reproduce hallmarks of a more central retina, which is an important determinant of AMD pathogenesis. Also, using trajectory analysis, it could be detected that the organoids in part reproduce major developmental hallmarks of the retina, but that different HRO samples exhibited developmental differences that point at different degrees of maturation. Altogether, this analysis allowed to deeply characterise a human retinal organoid system, which revealed in vivo-like outcomes and features as pinpointing discrepancies. These results could be used to refine culture conditions during the organoid differentiation to optimise its utility as a disease model.
In summary, this dissertation describes a workflow that, in contrast to the current state of the art in the literature enables the inference of cell type-specific gene regulatory networks.
The thesis illustrated that such networks indeed differ even between closely related cells.
Thus, single-cell transcriptomics can yield unprecedented insights into so far not understood cell regulatory principles, particularly rare cell types that are so far hardly reflected in bulk-derived RNA-seq data.
| Identifer | oai:union.ndltd.org:DRESDEN/oai:qucosa:de:qucosa:78687 |
| Date | 04 April 2022 |
| Creators | Steinheuer, Lisa Maria |
| Contributors | Universität Leipzig |
| Source Sets | Hochschulschriftenserver (HSSS) der SLUB Dresden |
| Language | English |
| Detected Language | English |
| Type | info:eu-repo/semantics/publishedVersion, doc-type:doctoralThesis, info:eu-repo/semantics/doctoralThesis, doc-type:Text |
| Rights | info:eu-repo/semantics/openAccess |
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