Schwiening, A. | bioRxiv Science

bioRxiv2024

10x GENOMICS GENE EXPRESSION FLEX IS A POWERFUL TOOL FOR SINGLE-CELL TRANSCRIPTOMICS OF XENOGRAFT MODELS

The 10x Genomics Gene Expression Flex protocol allows profiling of fixed or frozen material, greatly simplifying the logistics of sample collection, storage and transfer prior to single -cell sequencing. The method makes single-cell transcriptomics possible for existing fresh-frozen or FFPE tissue samples, but also facilitates the logistics of the sampling process, allowing instant preservation of samples. The technology relies on species-specific probes available for human and mouse. Nevertheless, processing of patient-derived (PDX) or cell line (CDX) xenografts, which contain mixed human and mouse cells, is currently not supported by this protocol due to the high degree of homology between the probe sets. Here we show that it is feasible to simultaneously profile populations containing both human and mouse cells by mixing the transcriptome probe sets of both species. Cellranger outputs a count table for each of the species allowing evaluation of the performance of the different probe sets. Cross-reactive probes are greatly outperformed by the specific probe hybridizations leading to a clear difference in the recovery of UMIs and unique genes per cell. Furthermore, we developed a pipeline that removes cross-reactive signal from the data and provides species-specific count tables for further downstream analysis. Hence, the 10x Genomics Gene Expression Flex protocol can be used to process xenograft samples without the need for separation of human and mouse cells by flow sorting and allows analysis of the human and mouse single-cell transcriptome from each sample. We anticipate it will be increasingly used for single-cell sequencing of cancer cell line and patient-derived xenografts, facilitating the preservation of the samples and allowing the interrogation of both the (human) xenograft and the (mouse) tumor microenvironment at single-cell resolution.

genomics↗

bioRxiv2023

Metformin may reduce dementia risk through neuroprotection not mitigation of diabetes

Dementia is a largely untreatable syndrome that is epidemiologically associated with metabolic diseases such as type 2 diabetes (T2D) and obesity. Drugs used to treat T2D such as metformin are inexpensive, safely given to millions of people, and have also been reported to slow neurodegeneration. We hypothesised that the neuroprotective benefits of metformin might extend to metabolically healthy individuals and tested this hypothesis in a mouse prion model that recapitulates key features of human neurodegenerative disease, including synaptic loss and motor impairment. These features and the time course of this model (24 weeks) allows the effects of metabolic risk factors and metformin to be tested and potentially generalised to other forms of neurodegenerative disease. Mice fed a high fat diet (HFD) developed high adiposity with impaired glucose and insulin homeostasis, similar to the effects of chronic obesity seen in humans whereas mice on matched control diet (CD) remain metabolically healthy. Chronic treatment with metformin in HFD-fed mice significantly increased survival and health span relative to vehicle-treated mice. Mice fed a HFD also had a modestly extended health span relative to mice fed CD, as measured by development of motor signs of prion disease. Metformin also significantly extended health span in metabolically healthy CD-fed mice. Using targeted mass spectrometry, we found that metformin reached deep brain structures at functional concentrations, driving a reduction in pPERK and changing the activity of microglia in vivo. Metformin was able to alter ER stress pathways at the same concentrations in healthy animals and using human iPSC-derived microglia and mouse organotypic slices we show that the action of metformin at these concentrations does not require a systemic mechanism, necessary for the treatment of diabetes, and is likely a result of direct secondary pharmacology in the brain. Together, these data broadly support the premise of repurposing metformin for neuroprotection, even in metabolically healthy individuals.

neuroscience↗