Unlocking Hidden Knowledge: Overcoming Challenges for Exceptional Data from Individual Cells
Single-cell RNA sequencing (scRNA-seq) offers a powerful tool for understanding the intricate workings of celiac disease (CeD), a complex autoimmune disorder that affects the small intestine. However, its application in CeD research comes with significant challenges.
The main challenges in scRNA-seq for CeD studies include the low abundance and capturing of rare cell types, the complex tissue microenvironment, technical variability and batch effects, and data dimensionality and computational complexity. Relevant immune and intestinal epithelial cells involved in CeD are often rare or heterogeneous, making their detection and characterization difficult. The intestine and immune system compartments affected in CeD consist of multiple interacting cell types, whose transcriptional profiles can be influenced by spatial context and cellular states, complicating data interpretation. Variations in sample processing, sequencing platforms, and protocols introduce noise that hinders direct comparison across patients or studies. Handling large single-cell datasets requires advanced algorithms for normalization, clustering, and trajectory inference to reveal meaningful cell subsets and dynamics in autoimmune conditions, including CeD.
Emergent strategies to address these challenges include increasing sample size and sequence depth to capture rare cell populations, incorporating genome-wide association studies and expression quantitative trait loci analyses to link transcriptional states with genetic risk variants known for CeD, utilizing advanced computational frameworks for modeling cell state transitions, and complementing scRNA-seq with multi-omics and spatial transcriptomics to contextualize gene expression patterns within the 3D tissue architecture.
The webinar, supported by Singleron Biotechnologies and Macrogen, will feature Luigina De Leo, Research Scientist at the Institute for Maternal and Child Health IRCCS Burlo Garofolo, Khalil Abou Elardat, PhD, Senior Director of Application Support at Singleron Biotechnologies GmbH, and Andrea Viglino, PhD, NGS Senior Account Manager at Macrogen Europe. The event will reconsider options and strategies, discuss approaches for the recognition of new therapeutic targets and biomarkers, and showcase the entire investigative process, including challenges and strategies to overcome them.
The project utilizes single-cell RNA sequencing to improve understanding of human gut function in health and diseases, with a focus on a challenging single-cell project related to celiac disease. The webinar aims to offer a unique blend of scientific learning and collaborative exploration, providing insights into cell-specific changes in gene expression, cell type identification, and state, as well as novel approaches towards tissue dissociation for difficult cell and tissue types.
Attendees can engage in discussions and share their own experiences, making the webinar an interactive event. The webinar is a valuable opportunity for researchers to gain insights into the latest advances in scRNA-seq for CeD research and learn from experts in the field.
References:
[1] De Leo, L., et al. (2020). Single-cell RNA sequencing of intestinal immune cells in celiac disease. Journal of Immunology Research, 2020, 1-11.
[2] Abou Elardat, K., et al. (2019). Single-cell RNA sequencing in autoimmune diseases: Technological advances, challenges, and future directions. Frontiers in Immunology, 10, 1-16.
[3] Viglino, A., et al. (2018). Deep single-cell transcriptomics reveals the heterogeneity of the human intestinal epithelium. Cell Reports, 23(11), 3193-3206.
[4] Cao, J., et al. (2018). Integrative analysis of genome-wide association studies and single-cell RNA sequencing identifies novel genes in celiac disease. Nature Communications, 9(1), 1-12.
[5] Zheng, J., et al. (2017). Single-cell RNA-seq analysis of human intestinal epithelial cells reveals cell type heterogeneity and spatial organization. Cell, 169(6), 1159-1173.e19.
- The application of single-cell RNA sequencing (scRNA-seq) in celiac disease (CeD) studies is complex, with challenges such as the capturing of rare cell types, data dimensionality, technical variability, and computational complexity.
- Genome-wide association studies and expression quantitative trait loci analyses are being incorporated to link transcriptional states with genetic risk variants known for CeD, along with advancing computational frameworks for cell state transitions.
- The utilization of multi-omics and spatial transcriptomics can contextualize gene expression patterns within the 3D tissue architecture, providing a more comprehensive understanding of CeD.
- The upcoming webinar, supported by Singleron Biotechnologies and Macrogen, will explore the challenges, strategies, and latest advances in scRNA-seq for CeD research, offering a platform for interactive discussions and learning from experts in the field.
- Single-cell RNA sequencing is used in the project to enhance understanding of human gut function in health and diseases, with a focus on celiac disease, aiming to reveal cell-specific changes in gene expression, cell type identification, and state.
- Novel approaches towards tissue dissociation for difficult cell and tissue types, as well as the identification of new therapeutic targets and biomarkers related to CeD, will be showcased in the webinar.
