| 1. |
- hower, lee, et al.
(author)
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investigating cell type changes in schizophrenia with spatially-resolved transcriptomics
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Other publication (pop. science, debate, etc.)abstract
- Schizophrenia is a heritable and genetically complex disorder with poorly understood aetiology. Previous study from our lab has shown that this disorder could affect a limited number of cell types in the brain1. Here, we build on these findings and present the first spatially-resolved transcriptomics study of schizophrenia with a large number of samples (17 in total). By comparing spatial cell type distributions in diseased and healthy prefrontal cortices, we discover that certain non-neuronal cell types change their co-localization patterns
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| 2. |
- Lee, Hower, et al.
(author)
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Direct RNA targeted in situ sequencing for transcriptomic profiling in tissue
- 2022
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In: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 12:1
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Journal article (peer-reviewed)abstract
- Highly multiplexed spatial mapping of transcripts within tissues allows for investigation of the transcriptomic and cellular diversity of mammalian organs previously unseen. Here we explore a direct RNA (dRNA) detection approach incorporating the use of padlock probes and rolling circle amplification in combination with hybridization-based in situ sequencing chemistry. We benchmark a High Sensitivity Library Preparation Kit from CARTANA that circumvents the reverse transcription needed for cDNA-based in situ sequencing (ISS) via direct RNA detection. We found a fivefold increase in transcript detection efficiency when compared to cDNA-based ISS and also validated its multiplexing capability by targeting a curated panel of 50 genes from previous publications on mouse brain sections, leading to additional data interpretation such as de novo cell clustering. With this increased efficiency, we also found to maintain specificity, multiplexing capabilities and ease of implementation. Overall, the dRNA chemistry shows significant improvements in target detection efficiency, closing the gap to other fluorescent in situ hybridization-based technologies and opens up possibilities to explore new biological questions previously not possible with cDNA-based ISS.
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| 3. |
- lee, hower, et al.
(author)
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In-situ sequencing of expressed mutations via RNA-templated gap filling of padlock probes.
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Other publication (other academic/artistic)abstract
- Detecting complex mutations in-situ within fixed cells or tissues is challenging, because of low sensitivity or poor specificity. We developed an efficient and specific molecular tool based on the RNA-templated and controlled gap-filling of padlock probes. Our method enables the accurate in-situ sequencing of unknown RNA stretches surrounded by known flanking regions, allowing the in-situ detection of expressed mutations with higher sensitivity and specificity than currently available tools.
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| 4. |
- lee, hower, et al.
(author)
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KODFISH, a direct RNA targeted, single nucleotide sensitive in situ transcriptomics.
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Other publication (other academic/artistic)abstract
- In-situ detection of expressed point mutations within fixed cells or tissues is challenging due to the low sensitivity or poor specificity of available molecular tools. Here, we present KODFISH, an efficient and specific approach based on single nucleotide sensitive RNA-based in-situ sequencing (RNA-ISS) using padlock probes and rolling circle amplification. KODFISH enables the accurate in-situ discrimination of single nucleotide changes, allowing the spatial detection of expressed mutations with higher sensitivity and specificity than currently available methods.
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| 5. |
- lee, hower, et al.
(author)
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Open-source, high-throughput targeted in-situ transcriptomics for developmental and tissue biology
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Journal article (peer-reviewed)abstract
- Multiplexed spatial profiling of mRNAs has recently gained traction as a tool to explore the cellular diversity and the architecture of tissues. We propose a sensitive, open-source, simple and flexible method for the generation of in-situ expression maps of hundreds of genes. We exploit direct ligation of padlock probes on mRNAs, coupled with rolling circle amplification and hybridization-based in situ combinatorial barcoding, to achieve high detection efficiency, high throughput and large multiplexing. We validate the method across a number of species, and show its use in combination with orthogonal methods such as antibody staining, highlighting its potential value for developmental and tissue biology studies. Finally, we provide an end-to-end computational workflow that covers the steps of probe design, image processing, data extraction, cell segmentation, clustering and annotation of cell types. By enabling easier access to high-throughput spatially resolved transcriptomics, we hope to encourage a diversity of applications and the exploration of a wide range of biological questions.
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| 6. |
- Lee, Hower, et al.
(author)
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Open-source, high-throughput targeted in-situ transcriptomics for developmental biologists
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Other publication (other academic/artistic)abstract
- Multiplexed spatial profiling of mRNAs has recently gained traction as a tool to explore the cellular diversity and the architecture of tissues. We propose a sensitive, open-source, simple and flexible method for the generation of in-situ expression maps of hundreds of genes. We exploit direct ligation of padlock probes on mRNAs, coupled with rolling circle amplification and hybridization-based in situ combinatorial barcoding, to achieve high detection efficiency, high throughput, and large multiplexing. We validate the method across a number of species and show its use in combination with orthogonal methods such as antibody staining, highlighting its potential value for developmental biology studies. Finally, we provide an end-to-end computational workflow that covers the steps of probe design, image processing, data extraction, cell segmentation, clustering, and annotation of cell types. By enabling easier access to high throughput spatially resolved transcriptomics, we hope to encourage a diversity of applications and the exploration of a wide range of biological questions.
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| 7. |
- Li, Xiaofei, et al.
(author)
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Profiling spatiotemporal gene expression of the developing human spinal cord and implications for ependymoma origin
- 2023
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In: Nature Neuroscience. - : Springer Nature. - 1097-6256 .- 1546-1726. ; 26:5, s. 891-901
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Journal article (peer-reviewed)abstract
- The authors created a comprehensive developmental cell atlas for spatiotemporal gene expression of the human spinal cord, revealed species-specific regulation during development and used the atlas to infer novel markers for pediatric ependymomas. The spatiotemporal regulation of cell fate specification in the human developing spinal cord remains largely unknown. In this study, by performing integrated analysis of single-cell and spatial multi-omics data, we used 16 prenatal human samples to create a comprehensive developmental cell atlas of the spinal cord during post-conceptional weeks 5-12. This revealed how the cell fate commitment of neural progenitor cells and their spatial positioning are spatiotemporally regulated by specific gene sets. We identified unique events in human spinal cord development relative to rodents, including earlier quiescence of active neural stem cells, differential regulation of cell differentiation and distinct spatiotemporal genetic regulation of cell fate choices. In addition, by integrating our atlas with pediatric ependymomas data, we identified specific molecular signatures and lineage-specific genes of cancer stem cells during progression. Thus, we delineate spatiotemporal genetic regulation of human spinal cord development and leverage these data to gain disease insight.
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| 8. |
- van Bruggen, David, et al.
(author)
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Developmental landscape of human forebrain at a single-cell level identifies early waves of oligodendrogenesis
- 2022
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In: Developmental Cell. - : Elsevier BV. - 1534-5807 .- 1878-1551. ; 57:11, s. 1421-1436, 1421-1436.e1-e5
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Journal article (peer-reviewed)abstract
- Oligodendrogenesis in the human central nervous system has been observed mainly at the second trimester of gestation, a much later developmental stage compared to oligodendrogenesis in mice. Here, we characterize the transcriptomic neural diversity in the human forebrain at post-conception weeks (PCW) 8–10. Using single-cell RNA sequencing, we find evidence of the emergence of a first wave of oligodendrocyte lineage cells as early as PCW 8, which we also confirm at the epigenomic level through the use of single-cell ATAC-seq. Using regulatory network inference, we predict key transcriptional events leading to the specification of oligodendrocyte precursor cells (OPCs). Moreover, by profiling the spatial expression of 50 key genes through the use of in situ sequencing (ISS), we identify regions in the human ventral fetal forebrain where oligodendrogenesis first occurs. Our results indicate evolutionary conservation of the first wave of oligodendrogenesis between mice and humans and describe regulatory mechanisms involved in human OPC specification.
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| 9. |
- Varela, João C., et al.
(author)
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Rolling circle amplification-on-a-chip towards portable isothermal detection of SARS-COV-2 RNA
- 2021
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In: Proceedings MicroTAS 2021 - 25th International Conference on Miniaturized Systems for Chemistry and Life Sciences. - : Chemical and Biological Microsystems Society. ; , s. 865-866
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Conference paper (peer-reviewed)abstract
- Rolling Circle Amplification (RCA) has shown significant potential for pathogen diagnostics providing high specificity and sensitivity combined with relatively low temperature (<37 °C) isothermal amplification. In the context of the ongoing COVID-19 pandemic, we report the development of an RCA-based method allowing direct detection of SARS-CoV-2 RNA in microfluidics. The viral RNA was hybridized to biotinylated oligos and L-probes in solution, enriched in a microchannel and subsequently amplified in situ using padlock probes against the L-probes. This method allowed the detection of 1x103 viral copies/μL within 90 minutes of amplification, demonstrating an alternative approach to current isothermal amplification methods.
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| 10. |
- Vicari, Marco, et al.
(author)
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Spatial multimodal analysis of transcriptomes and metabolomes in tissues
- 2023
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In: Nature Biotechnology. - 1087-0156 .- 1546-1696.
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Journal article (peer-reviewed)abstract
- We present a spatial omics approach that combines histology, mass spectrometry imaging and spatial transcriptomics to facilitate precise measurements of mRNA transcripts and low-molecular-weight metabolites across tissue regions. The workflow is compatible with commercially available Visium glass slides. We demonstrate the potential of our method using mouse and human brain samples in the context of dopamine and Parkinson’s disease.
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